Spectral characteristics and thermal evolution of long-period gratings in photonic crystal fibers fabricated with a near-IR radiation femtosecond laser using point-by-point inscription

The spectral properties of long-period gratings (LPGs) fabricated in photonic crystal fibers using femtosecond laser pulses by the point-by-point technique, without oil-immersion of the fiber, are investigated in detail. Postfabrication spectral monitoring at room temperature showed significant long-term instability of the gratings and stable spectra only after 600 h. The stabilized spectral properties of the gratings improved with increasing annealing temperature. The observed changes in resonant wavelength, optical strength, and grating birefringence were correlated to the laser inscription energy and were further used to study the mechanism of femtosecond inscription. Furthermore, the femtosecond-laser inscribed LPGs were compared to electric-arc fabricated LPGs. Comparison of experimental results with theoretical models of LPGs and laser propagation during inscription indicate that the major processes responsible for the index change are permanent compaction and thermally induced strain, the latter can be significantly changed through annealing. © 2011 Optical Society of America.

Real-time high-resolution heterodyne-based measurements of spectral dynamics in fibre lasers

Conventional tools for measurement of laser spectra (e.g. optical spectrum analysers) capture data averaged over a considerable time period. However, the generation spectrum of many laser types may involve spectral dynamics whose relatively fast time scale is determined by their cavity round trip period, calling for instrumentation featuring both high temporal and spectral resolution. Such real-time spectral characterisation becomes particularly challenging if the laser pulses are long, or they have continuous or quasi-continuous wave radiation components. Here we combine optical heterodyning with a technique of spatiooral intensity measurements that allows the characterisation of such complex sources. Fast, round-trip-resolved spectral dynamics of cavity-based systems in real-time are obtained, with temporal resolution of one cavity round trip and frequency resolution defined by its inverse (85 ns and 24 MHz respectively are demonstrated). We also show how under certain conditions for quasi-continuous wave sources, the spectral resolution could be further increased by a factor of 100 by direct extraction of phase information from the heterodyned dynamics or by using double time scales within the spectrogram approach.

A fresh look at decision making in international investment choices: Firm international coherence and home-host country relatedness

Understanding how decisions for international investments are made and how this affects the overall pattern of investments and firm’s performance is of particular importance both in strategy and international business research. This dissertation introduced first home-host country relatedness (HHCR) as the degree to which countries are efficiently combined within the investment portfolios of firms. It theorized and demonstrated that HHCR will vary with the motivation for investments along at least two key dimensions: the nature of foreign investments and the connectedness of potential host countries to the rest of the world. Drawing on cognitive psychology and decision-making research, it developed a theory of strategic decision making proposing that strategic solutions are chosen close to a convenient anchor. Building on research on memory imprinting, it also proposed that managers tend to rely on older knowledge representation. In the context of international investment decisions, managers use their home countries as an anchor and are more likely to choose as a site for foreign investments host countries that are ‘close’ to the home country. These decisions are also likely to rely more strongly on closeness to time invariant country factors of historic and geographic nature rather than time-variant institutions. Empirical tests using comprehensive investments data by all public multinational companies (MNC) worldwide, or over 15,000 MNCs with over half a million subsidiaries, support the claims. Finally, the dissertation introduced the concept of International Coherence (IC) defined as the degree to which an MNE’s network comprises countries that are related. It was hypothesized that maintaining a high level of coherence is important for firm performance and will enhance it. Also, the presence of international coherence mitigates some of the negative effects of unrelated product diversification. Empirical tests using data on foreign investments of over 20,000 public firms, while also developing a home-host country relatedness index for up to 24,300 home-host pairs, provided support for the theory advanced.

Examining argumentative coherence in essays by undergraduate students of English as a foreign language in Mainland China and their English speaking peers in the United States

I conducted this study to provide insights toward deepening understanding of association between culture and writing by building, assessing, and refining a conceptual model of second language writing. To do this, I examined culture and coherence as well as the relationship between them through a mixed methods research design. Coherence has been an important and complex concept in ESL/EFL writing. I intended to study the concept of coherence in the research context of contrastive rhetoric, comparing the coherence quality in argumentative essays written by undergraduates in Mainland China and their U.S. peers. In order to analyze the complex concept of coherence, I synthesized five linguistic theories of coherence: Halliday and Hasan's cohesion theory, Carroll's theory of coherence, Enkvist's theory of coherence, Topical Structure Analysis, and Toulmin's Model. Based upon the synthesis, 16 variables were generated. Across these 16 variables, Hotelling t-test statistical analysis was conducted to predict differences in argumentative coherence between essays written by two groups of participants. In order to complement the statistical analysis, I conducted 30 interviews of the writers in the studies. Participants' responses were analyzed with open and axial coding. By analyzing the empirical data, I refined the conceptual model by adding more categories and establishing associations among them. The study found that U.S. students made use of more pronominal reference. Chinese students adopted more lexical devices of reiteration and extended paralleling progression. The interview data implied that the difference may be associated with the difference in linguistic features and rhetorical conventions in Chinese and English. As far as Toulmin's Model is concerned, Chinese students scored higher on data than their U.S. peers. According to the interview data, this may be due to the fact that Toulmin's Model, modified as three elements of arguments, have been widely and long taught in Chinese writing instruction while U.S. interview participants said that they were not taught to write essays according to Toulmin's Model. Implications were generated from the process of textual data analysis and the formulation of structural model defining coherence. These implications were aimed at informing writing instruction, assessment, peer-review, and self-revision.

In vivo characterization of epileptic tissue with optical spectroscopy

For children with intractable seizures, surgical removal of epileptic foci, if identifiable and feasible, can be an effective way to reduce or eliminate seizures. The success of this type of surgery strongly hinges upon the ability to identify and demarcate those epileptic foci. The ultimate goal of this research project is to develop an effective technology for detection of unique in vivo pathophysiological characteristics of epileptic cortex and, subsequently, to use this technology to guide epilepsy surgery intraoperatively. In this PhD dissertation the feasibility of using optical spectroscopy to identify uniquein vivo pathophysiological characteristics of epileptic cortex was evaluated and proven using the data collected from children undergoing epilepsy surgery. ^ In this first in vivo human study, static diffuse reflectance and fluorescence spectra were measured from the epileptic cortex, defined by intraoperative ECoG, and its surrounding tissue from pediatric patients undergoing epilepsy surgery. When feasible, biopsy samples were taken from the investigated sites for the subsequent histological analysis. Using the histological data as the gold standard, spectral data was analyzed with statistical tools. The results of the analysis show that static diffuse reflectance spectroscopy and its combination with static fluorescence spectroscopy can be used to effectively differentiate between epileptic cortex with histopathological abnormalities and normal cortex in vivo with a high degree of accuracy. ^ To maximize the efficiency of optical spectroscopy in detecting and localizing epileptic cortex intraoperatively, the static system was upgraded to investigate histopathological abnormalities deep within the epileptic cortex, as well as to detect unique temporal pathophysiological characteristics of epileptic cortex. Detection of deep abnormalities within the epileptic cortex prompted a redesign of the fiberoptic probe. A mechanical probe holder was also designed and constructed to maintain the probe contact pressure and contact point during the time dependent measurements. The dynamic diffuse reflectance spectroscopy system was used to characterize in vivo pediatric epileptic cortex. The results of the study show that some unique wavelength dependent temporal characteristics (e.g., multiple horizontal bands in the correlation coefficient map γ(λref = 800 nm, λcomp ,t)) can be found in the time dependent recordings of diffuse reflectance spectra from epileptic cortex defined by ECoG.^

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The work embodied in this thesis was carried out by the author in the Department of Applied Chemistry, CUSAT, Kochi, during the period 2009-2012. The thesis is an introduction to our attempts to evaluate the coordination behavior of some compounds of our interest. The biological activities of semicarbazones and their metal complexes have been an active area of research during the past years because of their significant role in naturally occurring biological systems. Tridentate NNO and ONO semicarbazone systems formed from heterocyclic and aromatic carbonyl compounds and their transition metal complexes are wellauthenticated compounds in this field and their synthesis, crystal structures and spectral studies are well desirable. Hence, we decided to develop a research program aimed at the syntheses, crystal structures and spectral studies of new N4- phenylsemicarbazones derived from 2-formylpyridine and 3-ethoxysalicylaldehyde and their transition metal complexes and new transition metal complexes of 2- benzoylpyridine-N4-phenylsemicarbazone. In addition to various physicochemical methods of analysis, single crystal X-ray diffraction studies were also used for the characterization of the complexes.

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Ocular manifestations of microcephaly with or without chorioretinopathy, lymphedema or intellectual disability (MCLID) syndrome associated with mutations in KIF11

Purpose Microcephaly with or without chorioretinopathy, lymphedema or intellectual disability (MCLID) is an autosomal dominant condition. Mutations in KIF11 have been found to be causative in approximately 75% of cases. This study describes the ocular phenotype in patients with confirmed KIF11 mutations. Methods Standard ophthalmic examination and investigation including visual acuity, refraction and fundus examination was carried out in all patients. Fundus autofluorescence imaging (FAF) was performed in three patients, and four patients underwent spectral domain optical coherence tomography (OCT). Flash electroretinography (ERG) was performed in seven patients, and five underwent additional pattern electroretinography (PERG). Results The patients ranged in age from 2 to 10 years. Most presented with visual acuity loss. Fundus examination revealed lacunae of chorioretinal atrophy. Pigmentary macular changes and optic disc pallor were present in three of seven patients. Fundus autofluorescence demonstrated hypoautofluorescence at the macula in two of three patients. The lacunae of chorioretinal atrophy were hypoautofluorescent. The OCT showed atrophic maculae in three of four patients. Follow-up in one patient showed no deterioration of the vision over a 9-year period. The lesions appear not to be progressive on the follow-up imaging. Electrophysiology showed generalized rod and cone dysfunction and severe macular dysfunction. Inner retinal dysfunction was evident in three of seven patients. Conclusions Patients with KIF11 mutations show a specific ocular phenotype with variable expressivity and intrafamilial variability. Macular atrophy and dysfunction have not been consistently documented before. The fundus lesions appear non-progressive. The findings assist in providing an accurate diagnosis and thus improving the management and follow-up of patients with this syndrome.

Ionization in atmospheres of brown dwarfs and extrasolar planets. V. Alfvén Ionization

Observations of continuous radio and sporadic X-ray emission from low-mass objects suggest they harbor localized plasmas in their atmospheric environments. For low-mass objects, the degree of thermal ionization is insufficient to qualify the ionized component as a plasma, posing the question: what ionization processes can efficiently produce the required plasma that is the source of the radiation? We propose Alfv´en ionization as a mechanism for producing localized pockets of ionized gas in the atmosphere, having sufficient degrees of ionization ( 10−7) that they constitute plasmas. We outline the criteria required for Alfv´en ionization and demonstrate its applicability in the atmospheres of low-mass objects such as giant gas planets, brown dwarfs, and M dwarfs with both solar and sub-solar metallicities. We find that Alfv´en ionization is most efficient at mid to low atmospheric pressures where a seed plasma is easier to magnetize and the pressure gradients needed to drive the required neutral flows are the smallest. For the model atmospheres considered, our results show that degrees of ionization of 10−6–1 can be obtained as a result of Alfv´en ionization. Observable consequences include continuum bremsstrahlung emission, superimposed with spectral lines from the plasma ion species (e.g., He, Mg, H2, or CO lines). Forbidden lines are also expected from the metastable population. The presence of an atmospheric plasma opens the door to a multitude of plasma and chemical processes not yet considered in current atmospheric models. The occurrence of Alfv´en ionization may also be applicable to other astrophysical environments such as protoplanetary disks.

Thermomechanical sensitivity of microcantilever in the mid-infrared spectral region

This paper reports the thermomechanical sensitivity of bimaterial cantilevers over a mid-infrared (IR) spectral range (5-10 µm) that is critical both for chemical analysis via vibrational spectroscopy and for direct thermal detection in the 300-700 K range. Mechanical bending sensitivity and noise were measured and modeled for six commercially available microcantilevers, which consist of either an aluminum film on a silicon cantilever or a gold film on a silicon nitride cantilever. The spectral sensitivity of each cantilever was determined by recording cantilever deflection when illuminated with IR light from a monochromator. Rigorous modeling and systematic characterization of the optical system allowed for a quantitative estimate of IR energy incident upon the cantilever. Separately, spectral absorptance of the cantilever was measured using Fourier transform infrared (FT-IR) microscopy, which was compared with analytical models of radiation onto the cantilever and heat flow within the cantilever. The predictions of microcantilever thermomechanical bending sensitivity and noise agree well with measurements, resulting in a ranking of these cantilevers for their potential use in IR measurements.

Phase noise and spur reduction in an array of direct digital synthesizers

Many applications, including communications, test and measurement, and radar, require the generation of signals with a high degree of spectral purity. One method for producing tunable, low-noise source signals is to combine the outputs of multiple direct digital synthesizers (DDSs) arranged in a parallel configuration. In such an approach, if all noise is uncorrelated across channels, the noise will decrease relative to the combined signal power, resulting in a reduction of sideband noise and an increase in SNR. However, in any real array, the broadband noise and spurious components will be correlated to some degree, limiting the gains achieved by parallelization. This thesis examines the potential performance benefits that may arise from using an array of DDSs, with a focus on several types of common DDS errors, including phase noise, phase truncation spurs, quantization noise spurs, and quantizer nonlinearity spurs. Measurements to determine the level of correlation among DDS channels were made on a custom 14-channel DDS testbed. The investigation of the phase noise of a DDS array indicates that the contribution to the phase noise from the DACs can be decreased to a desired level by using a large enough number of channels. In such a system, the phase noise qualities of the source clock and the system cost and complexity will be the main limitations on the phase noise of the DDS array. The study of phase truncation spurs suggests that, at least in our system, the phase truncation spurs are uncorrelated, contrary to the theoretical prediction. We believe this decorrelation is due to the existence of an unidentified mechanism in our DDS array that is unaccounted for in our current operational DDS model. This mechanism, likely due to some timing element in the FPGA, causes some randomness in the relative phases of the truncation spurs from channel to channel each time the DDS array is powered up. This randomness decorrelates the phase truncation spurs, opening the potential for SFDR gain from using a DDS array. The analysis of the correlation of quantization noise spurs in an array of DDSs shows that the total quantization noise power of each DDS channel is uncorrelated for nearly all values of DAC output bits. This suggests that a near N gain in SQNR is possible for an N-channel array of DDSs. This gain will be most apparent for low-bit DACs in which quantization noise is notably higher than the thermal noise contribution. Lastly, the measurements of the correlation of quantizer nonlinearity spurs demonstrate that the second and third harmonics are highly correlated across channels for all frequencies tested. This means that there is no benefit to using an array of DDSs for the problems of in-band quantizer nonlinearities. As a result, alternate methods of harmonic spur management must be employed.

Spectral self-action of THz emission from ionizing two-color laser pulses in gases

The spectrum of terahertz (THz) emission in gases via ionizing two-color femtosecond pulses is analyzed by means of a semi-analytic model and numerical simulations in 1D, 2D and 3D geometries taking into account propagation effects of both pump and THz fields. We show that produced THz signals interact with free electron trajectories and thus significantly influence further THz generation upon propagation, i.e., make the process inherently nonlocal. This self-action contributes to the observed strong spectral broadening of the generated THz field. Weshow that diffraction of the generated THz radiation is the limiting factor for the co-propagating low frequency amplitudes and thus for the self-action mechanism in 2D and 3D geometries.

Insights into the emission of the blazar 1ES 1011+496 through unprecedented broadband observations during 2011 and 2012

Context. 1ES 1011+496 (z = 0.212) was discovered in very high-energy (VHE, E >100 GeV) γ rays with MAGIC in 2007. The absence of simultaneous data at lower energies led to an incomplete characterization of the broadband spectral energy distribution (SED). Aims. We study the source properties and the emission mechanisms, probing whether a simple one-zone synchrotron self-Compton (SSC) scenario is able to explain the observed broadband spectrum. Methods. We analyzed data in the range from VHE to radio data from 2011 and 2012 collected by MAGIC, Fermi-LAT, Swift, KVA, OVRO, and Metsähovi in addition to optical polarimetry data and radio maps from the Liverpool Telescope and MOJAVE. Results. The VHE spectrum was fit with a simple power law with a photon index of 3.69 ± 0.22 and a flux above 150 GeV of (1.46±0.16)×10^(−11) ph cm^(−2) s^(−1) . The source 1ES 1011+496 was found to be in a generally quiescent state at all observed wavelengths, showing only moderate variability from radio to X-rays. A low degree of polarization of less than 10% was measured in optical, while some bright features polarized up to 60% were observed in the radio jet. A similar trend in the rotation of the electric vector position angle was found in optical and radio. The radio maps indicated a superluminal motion of 1.8 ± 0.4 c, which is the highest speed statistically significant measured so far in a high-frequency-peaked BL Lac. Conclusions. For the first time, the high-energy bump in the broadband SED of 1ES 1011+496 could be fully characterized from 0.1 GeV to 1 TeV, which permitted a more reliable interpretation within the one-zone SSC scenario. The polarimetry data suggest that at least part of the optical emission has its origin in some of the bright radio features, while the low polarization in optical might be due to the contribution of parts of the radio jet with different orientations of the magnetic field with respect to the optical emission.

Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil

Many efforts are currently oriented toward extracting more information from ocean color than the chlorophyll a concentration. Among biological parameters potentially accessible from space, estimates of phytoplankton cell size and light absorption by colored detrital matter (CDM) would lead to an indirect assessment of major components of the organic carbon pool in the ocean, which would benefit oceanic carbon budget models. We present here 2 procedures to retrieve simultaneously from ocean color measurements in a limited number of bands, magnitudes, and spectral shapes for both light absorption by CDM and phytoplankton, along with a size parameter for phytoplankton. The performance of the 2 procedures was evaluated using different data sets that correspond to increasing uncertainties: ( 1) measured absorption coefficients of phytoplankton, particulate detritus, and colored dissolved organic matter ( CDOM) and measured chlorophyll a concentrations and ( 2) SeaWiFS upwelling radiance measurements and chlorophyll a concentrations estimated from global algorithms. In situ data were acquired during 3 cruises, differing by their relative proportions in CDM and phytoplankton, over a continental shelf off Brazil. No local information was introduced in either procedure, to make them more generally applicable. Over the study area, the absorption coefficient of CDM at 443 nm was retrieved from SeaWiFS radiances with a relative root mean square error (RMSE) of 33%, and phytoplankton light absorption coefficients in SeaWiFS bands ( from 412 to 510 nm) were retrieved with RMSEs between 28% and 33%. These results are comparable to or better than those obtained by 3 published models. In addition, a size parameter of phytoplankton and the spectral slope of CDM absorption were retrieved with RMSEs of 17% and 22%, respectively. If these methods are applied at a regional scale, the performances could be substantially improved by locally tuning some empirical relationships.