An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Runaway Greenhouse Effect in a Semigray Radiative-Convective Model

The effects of the nongray absorption (i.e., atmospheric opacity varying with wavelength) on the possible upper bound of the outgoing longwave radiation (OLR) emitted by a planetary atmosphere have been examined. This analysis is based on the semigray approach, which appears to be a reasonable compromise between the complexity of nongray models and the simplicity of the gray assumption (i.e., atmospheric absorption independent of wavelength). Atmospheric gases in semigray atmospheres make use of constant absorption coefficients in finite-width spectral bands. Here, such a semigray absorption is introduced in a one-dimensional (1D) radiative– convective model with a stratosphere in radiative equilibrium and a troposphere fully saturated with water vapor, which is the semigray gas. A single atmospheric window in the infrared spectrum has been assumed. In contrast to the single absolute limit of OLR found in gray atmospheres, semigray ones may also show a relative limit. This means that both finite and infinite runaway effects may arise in some semigray cases. Of particular importance is the finding of an entirely new branch of stable steady states that does not appear in gray atmospheres. This new multiple equilibrium is a consequence of the nongray absorption only. It is suspected that this new set of stable solutions has not been previously revealed in analyses of radiative–convective models since it does not appear for an atmosphere with nongray parameters similar to those for the earth’s current state

The effect of atmospheric absorption of sunlight on the runaway greenhouse point

The longwave emission of planetary atmospheres that contain a condensable absorbing gas in the infrared (i.e., longwave), which is in equilibrium with its liquid phase at the surface, may exhibit an upper bound. Here we analyze the effect of the atmospheric absorption of sunlight on this radiation limit. We assume that the atmospheric absorption of infrared radiation is independent of wavelength except within the spectral width of the atmospheric window, where it is zero. The temperature profile in radiative equilibrium is obtained analytically as a function of the longwave optical thickness. For illustrative purposes, numerical values for the infrared atmospheric absorption (i.e., greenhouse effect) and the liquid vapor equilibrium curve of the condensable absorbing gas refer to water. Values for the atmospheric absorption of sunlight (i.e., antigreenhouse effect) take a wide range since our aim is to provide a qualitative view of their effects. We find that atmospheres with a transparent region in the infrared spectrum do not present an absolute upper bound on the infrared emission. This result may be also found in atmospheres opaque at all infrared wavelengths if the fraction of absorbed sunlight in the atmosphere increases with the longwave opacity

Influence of average size and interface passivation on the spectral emission of Si nanocrystals embedded in SiO2

The correlation between the structural (average size and density) and optoelectronic properties [band gap and photoluminescence (PL)] of Si nanocrystals embedded in SiO2 is among the essential factors in understanding their emission mechanism. This correlation has been difficult to establish in the past due to the lack of reliable methods for measuring the size distribution of nanocrystals from electron microscopy, mainly because of the insufficient contrast between Si and SiO2. With this aim, we have recently developed a successful method for imaging Si nanocrystals in SiO2 matrices. This is done by using high-resolution electron microscopy in conjunction with conventional electron microscopy in dark field conditions. Then, by varying the time of annealing in a large time scale we have been able to track the nucleation, pure growth, and ripening stages of the nanocrystal population. The nucleation and pure growth stages are almost completed after a few minutes of annealing time at 1100°C in N2 and afterward the ensemble undergoes an asymptotic ripening process. In contrast, the PL intensity steadily increases and reaches saturation after 3-4 h of annealing at 1100°C. Forming gas postannealing considerably enhances the PL intensity but only for samples annealed previously in less time than that needed for PL saturation. The effects of forming gas are reversible and do not modify the spectral shape of the PL emission. The PL intensity shows at all times an inverse correlation with the amount of Pb paramagnetic centers at the Si-SiO2 nanocrystal-matrix interfaces, which have been measured by electron spin resonance. Consequently, the Pb centers or other centers associated with them are interfacial nonradiative channels for recombination and the emission yield largely depends on the interface passivation. We have correlated as well the average size of the nanocrystals with their optical band gap and PL emission energy. The band gap and emission energy shift to the blue as the nanocrystal size shrinks, in agreement with models based on quantum confinement. As a main result, we have found that the Stokes shift is independent of the average size of nanocrystals and has a constant value of 0.26±0.03 eV, which is almost twice the energy of the Si¿O vibration. This finding suggests that among the possible channels for radiative recombination, the dominant one for Si nanocrystals embedded in SiO2 is a fundamental transition spatially located at the Si¿SiO2 interface with the assistance of a local Si-O vibration.

Sensitivity of yellow passion fruit to ultraviolet-B radiation

The objective of this work was to evaluate the effects of UV-B radiation on the vegetative growth and on the gas exchange characteristics of passion fruit plants (Passiflora edulis) grown in greenhouse. The average unweighted UV-B radiation near the apex of the plants was 8 W m-2 for the UV-B treatment (high UV-B), and 0.8 W m-2 for the control plants (low UV-B). Plants were irradiated with UV-B for 7 hours per day, centered on solar noon, during 16 days. High UV-B radiation resulted in lower shoot dry matter accumulation per plant. The content of UV-B absorbing compounds and anthocyanins was increased in the plants exposed to high UV-B radiation, when compared with the control. UV-B radiation did not affect stomatal conductance or transpiration rate, but reduced photosynthesis and instantaneous water-use efficiency, and increased intercellular CO2 concentration. The accumulation of UV-B-absorbing compounds and anthocyanins did not effectively shield plants from supplementary UV-B radiation, since the growth and photosynthetic processes were significantly reduced.

Identification of acetates in elasmopalpulus lignosellus pheromone glands using a newly created mass spectral database and kóvats retention indices

Based on a specially created mass spectral database utilizing 23 tetradecenyl and 22 hexadecenyl acetate standards along with Kóvats retention indices obtained on a very polar stationary phase [poly (biscyanopropyl siloxane)] (SP 2340), (Z)-9-hexadecenyl acetate, (Z)-11-hexadecenyl acetate and (E)-8-hexadecenyl acetate were identified in active pheromone extracts of Elasmopalpus lignosellus. This identification was more efficient than our previous study using gas chromatography/mass spectrometry with a dimethyl disulfide derivative where we could only identify the first two acetates. The acetate composition of the pheromone gland differed from region to region in Brazil and from that from the Tifton (GA, USA) population, suggesting polymorphism or a different sub-species.

Initial development and gas exchange of Talisia subalbens (Mart.) Radlk. under different shading conditions

Ecophysiological studies under semi-controlled conditions in nurseries and greenhouses are essential to enable the use of native species to recover degraded areas and for commercial planting. Talisia subalbens (Mart) Radlk, 'cascudo', is a native fruiting species of the Cerrado on the verge of extinction. The ecophysiological performance of this species was evaluated in nursery conditions under different levels of shading (full sunshine, 30%, 50% and 70%). Initial growth, biomass allocation, gas exchange and chlorophyll content of the plants were analyzed. Full sunshine cultivated plants showed a higher accumulation of total, shoot, and root dry biomass. There was no significant difference in the root/shoot ratio among the treatments. Seedlings cultivated under full sunshine and 30% shading showed higher values for height, basal diameter, and leaf area. Differences in stomata conductance and photosynthesis rate were not observed among the different shading levels. Plants cultivated under 70% of shading had higher contents of chlorophyll a, b, and total. During the initial phase with higher levels of radiation were fundamental for the development of T. subalbens seedlings.

Porous silicon optical filters in gas sensing applications

In this thesis, the gas sensing properties of porous silicon-based thin-film optical filters are explored. The effects of surface chemistry on the adsorption and desorption of various gases are studied in detail. Special emphasis is placed on investigating thermal carbonization as a stabilization method for optical sensing applications. Moreover, the possibility of utilizing the increased electrical conductivity of thermally carbonized porous silicon for implementing a multiparametric gas sensor, which would enable simultaneous monitoring of electrical and optical parameters, is investigated. In addition, different porous silicon-based optical filter-structures are prepared, and their properties in sensing applications are evaluated and compared. First and foremost, thermal carbonization is established as a viable method to stabilize porous silicon optical filters for chemical sensing applications. Furthermore, a multiparametric sensor, which can be used for increasing selectivity in gas sensing, is also demonstrated. Methods to improve spectral quality in multistopband mesoporous silicon rugate filters are studied, and structural effects to gas sorption kinetics are evaluated. Finally, the stability of thermally carbonized optical filters in basic environments is found to be superior in comparison to other surface chemistries currently available for porous silicon. The results presented in this thesis are of particular interest for developing novel reliable sensing systems based on porous silicon, e.g., label-free optical biosensors.

Readout Electronics for Gas Electron Multiplier Detectors

The European Organization for Nuclear Research (CERN) operates the largest particle collider in the world. This particle collider is called the Large Hadron Collider (LHC) and it will undergo a maintenance break sometime in 2017 or 2018. During the break, the particle detectors, which operate around the particle collider, will be serviced and upgraded. Following the improvement in performance of the particle collider, the requirements for the detector electronics will be more demanding. In particular, the high amount of radiation during the operation of the particle collider sets requirements for the electronics that are uncommon in commercial electronics. Electronics that are built to function in the challenging environment of the collider have been designed at CERN. In order to meet the future challenges of data transmission, a GigaBit Transceiver data transmission module and an E-Link data bus have been developed. The next generation of readout electronics is designed to benefit from these technologies. However, the current readout electronics chips are not compatible with these technologies. As a result, in addition to new Gas Electron Multiplier (GEM) detectors and other technology, a new compatible chip is developed to function within the GEMs for the Compact Muon Solenoid (CMS) project. In this thesis, the objective was to study a data transmission interface that will be located on the readout chip between the E-Link bus and the control logic of the chip. The function of the module is to handle data transmission between the chip and the E-Link. In the study, a model of the interface was implemented with the Verilog hardware description language. This process was simulated by using chip design software by Cadence. State machines and operating principles with alternative possibilities for implementation are introduced in the E-Link interface design procedure. The functionality of the designed logic is demonstrated in simulation results, in which the implemented model is proven to be suitable for its task. Finally, suggestions that should be considered for improving the design have been presented.

Kr-Ar laser Raman spectrometer for low temperature measurements /

A Czerny Mount double monochromator is used to measure Raman scattered radiation near 90" from a crystalline, Silicon sample. Incident light is provided by a mixed gas Kr-Ar laser, operating at 5145 A. The double monochromator is calibrated to true wavelength by comparison of Kr and Ar emission Une positions (A) to grating position (A) display [1]. The relationship was found to be hnear and can be described by, y = 1.219873a; - 1209.32, (1) where y is true wavelength (A) and xis grating position display (A). The Raman emission spectra are collected via C"*""*" encoded software, which displays a mV signal from a Photodetector and allows stepping control of the gratings via an A/D interface. [2] The software collection parameters, detector temperature and optics are optimised to yield the best quality spectra. The inclusion of a cryostat allows for temperatmre dependent capabihty ranging from 4 K to w 350 K. Silicon Stokes temperatm-e dependent Raman spectra, generally show agreement with Uterature results [3] in their frequency haxdening, FWHM reduction and intensity increase as temperature is reduced. Tests reveal that a re-alignment of the double monochromator is necessary before spectral resolution can approach literature standard. This has not yet been carried out due to time constraints.

REFLECT : logiciel de restitution des réflectances au sol pour l’amélioration de la qualité de l'information extraite des images satellitales à haute résolution spatiale

RÉSUMÉ - Les images satellitales multispectrales, notamment celles à haute résolution spatiale (plus fine que 30 m au sol), représentent une source d’information inestimable pour la prise de décision dans divers domaines liés à la gestion des ressources naturelles, à la préservation de l’environnement ou à l’aménagement et la gestion des centres urbains. Les échelles d’étude peuvent aller du local (résolutions plus fines que 5 m) à des échelles régionales (résolutions plus grossières que 5 m). Ces images caractérisent la variation de la réflectance des objets dans le spectre qui est l’information clé pour un grand nombre d’applications de ces données. Or, les mesures des capteurs satellitaux sont aussi affectées par des facteurs « parasites » liés aux conditions d’éclairement et d’observation, à l’atmosphère, à la topographie et aux propriétés des capteurs. Deux questions nous ont préoccupé dans cette recherche. Quelle est la meilleure approche pour restituer les réflectances au sol à partir des valeurs numériques enregistrées par les capteurs tenant compte des ces facteurs parasites ? Cette restitution est-elle la condition sine qua non pour extraire une information fiable des images en fonction des problématiques propres aux différents domaines d’application des images (cartographie du territoire, monitoring de l’environnement, suivi des changements du paysage, inventaires des ressources, etc.) ? Les recherches effectuées les 30 dernières années ont abouti à une série de techniques de correction des données des effets des facteurs parasites dont certaines permettent de restituer les réflectances au sol. Plusieurs questions sont cependant encore en suspens et d’autres nécessitent des approfondissements afin, d’une part d’améliorer la précision des résultats et d’autre part, de rendre ces techniques plus versatiles en les adaptant à un plus large éventail de conditions d’acquisition des données. Nous pouvons en mentionner quelques unes : - Comment prendre en compte des caractéristiques atmosphériques (notamment des particules d’aérosol) adaptées à des conditions locales et régionales et ne pas se fier à des modèles par défaut qui indiquent des tendances spatiotemporelles à long terme mais s’ajustent mal à des observations instantanées et restreintes spatialement ? - Comment tenir compte des effets de « contamination » du signal provenant de l’objet visé par le capteur par les signaux provenant des objets environnant (effet d’adjacence) ? ce phénomène devient très important pour des images de résolution plus fine que 5 m; - Quels sont les effets des angles de visée des capteurs hors nadir qui sont de plus en plus présents puisqu’ils offrent une meilleure résolution temporelle et la possibilité d’obtenir des couples d’images stéréoscopiques ? - Comment augmenter l’efficacité des techniques de traitement et d’analyse automatique des images multispectrales à des terrains accidentés et montagneux tenant compte des effets multiples du relief topographique sur le signal capté à distance ? D’autre part, malgré les nombreuses démonstrations par des chercheurs que l’information extraite des images satellitales peut être altérée à cause des tous ces facteurs parasites, force est de constater aujourd’hui que les corrections radiométriques demeurent peu utilisées sur une base routinière tel qu’est le cas pour les corrections géométriques. Pour ces dernières, les logiciels commerciaux de télédétection possèdent des algorithmes versatiles, puissants et à la portée des utilisateurs. Les algorithmes des corrections radiométriques, lorsqu’ils sont proposés, demeurent des boîtes noires peu flexibles nécessitant la plupart de temps des utilisateurs experts en la matière. Les objectifs que nous nous sommes fixés dans cette recherche sont les suivants : 1) Développer un logiciel de restitution des réflectances au sol tenant compte des questions posées ci-haut. Ce logiciel devait être suffisamment modulaire pour pouvoir le bonifier, l’améliorer et l’adapter à diverses problématiques d’application d’images satellitales; et 2) Appliquer ce logiciel dans différents contextes (urbain, agricole, forestier) et analyser les résultats obtenus afin d’évaluer le gain en précision de l’information extraite par des images satellitales transformées en images des réflectances au sol et par conséquent la nécessité d’opérer ainsi peu importe la problématique de l’application. Ainsi, à travers cette recherche, nous avons réalisé un outil de restitution de la réflectance au sol (la nouvelle version du logiciel REFLECT). Ce logiciel est basé sur la formulation (et les routines) du code 6S (Seconde Simulation du Signal Satellitaire dans le Spectre Solaire) et sur la méthode des cibles obscures pour l’estimation de l’épaisseur optique des aérosols (aerosol optical depth, AOD), qui est le facteur le plus difficile à corriger. Des améliorations substantielles ont été apportées aux modèles existants. Ces améliorations concernent essentiellement les propriétés des aérosols (intégration d’un modèle plus récent, amélioration de la recherche des cibles obscures pour l’estimation de l’AOD), la prise en compte de l’effet d’adjacence à l’aide d’un modèle de réflexion spéculaire, la prise en compte de la majorité des capteurs multispectraux à haute résolution (Landsat TM et ETM+, tous les HR de SPOT 1 à 5, EO-1 ALI et ASTER) et à très haute résolution (QuickBird et Ikonos) utilisés actuellement et la correction des effets topographiques l’aide d’un modèle qui sépare les composantes directe et diffuse du rayonnement solaire et qui s’adapte également à la canopée forestière. Les travaux de validation ont montré que la restitution de la réflectance au sol par REFLECT se fait avec une précision de l’ordre de ±0.01 unités de réflectance (pour les bandes spectrales du visible, PIR et MIR), même dans le cas d’une surface à topographie variable. Ce logiciel a permis de montrer, à travers des simulations de réflectances apparentes à quel point les facteurs parasites influant les valeurs numériques des images pouvaient modifier le signal utile qui est la réflectance au sol (erreurs de 10 à plus de 50%). REFLECT a également été utilisé pour voir l’importance de l’utilisation des réflectances au sol plutôt que les valeurs numériques brutes pour diverses applications courantes de la télédétection dans les domaines des classifications, du suivi des changements, de l’agriculture et de la foresterie. Dans la majorité des applications (suivi des changements par images multi-dates, utilisation d’indices de végétation, estimation de paramètres biophysiques, …), la correction des images est une opération cruciale pour obtenir des résultats fiables. D’un point de vue informatique, le logiciel REFLECT se présente comme une série de menus simples d’utilisation correspondant aux différentes étapes de saisie des intrants de la scène, calcul des transmittances gazeuses, estimation de l’AOD par la méthode des cibles obscures et enfin, l’application des corrections radiométriques à l’image, notamment par l’option rapide qui permet de traiter une image de 5000 par 5000 pixels en 15 minutes environ. Cette recherche ouvre une série de pistes pour d’autres améliorations des modèles et méthodes liés au domaine des corrections radiométriques, notamment en ce qui concerne l’intégration de la FDRB (fonction de distribution de la réflectance bidirectionnelle) dans la formulation, la prise en compte des nuages translucides à l’aide de la modélisation de la diffusion non sélective et l’automatisation de la méthode des pentes équivalentes proposée pour les corrections topographiques.

Influence of ambient gas on the temperature and density of laser produced carbon plasma

The effect of ambient gas on the dynamics of the plasma generated by laser ablation of a carbon target using 1.06 μm radiation from a Q-switched Nd:YAG laser has been investigated using a spectroscopic technique. The emission characteristics of the carbon plasma produced in argon, helium and air atmospheres are found to depend strongly on the nature and pressure of the surrounding gas. It has been observed that hotter and denser plasmas are formed in an argon atmosphere rather than in helium or air as an ambient.

Spectral features of laser induced plasma from YBa2Cu3O7 and GdBa2Cu3O7 highTc superconductors

Laser induced plasma emission spectra from highT c superconducting samples of YBa2Cu3O7 and GdBa2Cu3O7 obtained with 1.06µm radiation from a Q switched Nd:YAG laser beam has been analysed. The results clearly show the presence of diatomic oxides in addition to ionized species of the constituent metals in the plasma thus produced.

Modelling of Ultraviolet and Vissible Emissions in Comets

Comets are the spectacular objects in the night sky since the dawn of mankind. Due to their giant apparitions and enigmatic behavior, followed by coincidental calamities, they were termed as notorious and called as `bad omens'. With a systematic study of these objects modern scienti c community understood that these objects are part of our solar system. Comets are believed to be remnant bodies of at the end of evolution of solar system and possess the material of solar nebula. Hence, these are considered as most pristine objects which can provide the information about the conditions of solar nebula. These are small bodies of our solar system, with a typical size of about a kilometer to a few tens of kilometers orbiting the Sun in highly elliptical orbits. The solid body of a comet is nucleus which is a conglomerated mixture of water ice, dust and some other gases. When the cometary nucleus advances towards the Sun in its orbit the ices sublimates and produces the gaseous envelope around the nucleus which is called coma. The gravity of cometary nucleus is very small and hence can not in uence the motion of gases in the cometary coma. Though the cometary nucleus is a few kilometers in size they can produce a transient, extensive, and expanding atmosphere with size several orders of magnitude larger in space. By ejecting gas and dust into space comets became the most active members of the solar system. The solar radiation and the solar wind in uences the motion of dust and ions and produces dust and ion tails, respectively. Comets have been observed in di erent spectral regions from rocket, ground and space borne optical instruments. The observed emission intensities are used to quantify the chemical abundances of di erent species in the comets. The study of various physical and chemical processes that govern these emissions is essential before estimating chemical abundances in the coma. Cameron band emission of CO molecule has been used to derive CO2 abundance in the comets based on the assumption that photodissociation of CO2 mainly produces these emissions. Similarly, the atomic oxygen visible emissions have been used to probe H2O in the cometary coma. The observed green ([OI] 5577 A) to red-doublet emission ([OI] 6300 and 6364 A) ratio has been used to con rm H2O as the parent species of these emissions. In this thesis a model is developed to understand the photochemistry of these emissions and applied to several comets. The model calculated emission intensities are compared with the observations done by space borne instruments like International Ultraviolet Explorer (IUE) and Hubble Space Telescope (HST) and also by various ground based telescopes.

Studies on laser induced optogalvanic effect in certain gas discharges

Electrical gas discharges have been the subject of numerous investigations from the last century due to their growing interest in technological and fundamental applications. Absorption of electromagnetic radiation by a gas discharge result into a change in electrical impedance due to a significant perturbations in the steady state population of excited levels and the degree of ionization. This change in impedance produced by resonant absorption of radiation is known as optogalvanic COG) effect. where as that is produced by injecting electrons in to the discharge by photoelectric emission is usually known as photoemission optogalvanic (FOG) effect. With the development of lasers and sophisticated electronic equipment. these effects have established their importance in analytical and spectroscopic measurements. The present thesis deals with the work carried out by the author in the field optogalvanic effect during the past few years at the Department of Physics in Cochin University of Science| and "Fechnology. The results and the observation are summarized in nine chapters and the references to the literature is made at the end of each chapter