Understanding the formation conditions of seep carbonate is crucial to better constrain the dynamic fluid flow and chemical fluxes associate with cold seeps on the seafloor. Rare earth element (REE) in seep carbonates collected from modern cold seeps of Gulf of Mexico, Black Sea, Congo Fan, ancient seeps of Beauvoisin (Oxfordian, J3, Southeastern France) and Marmorito (Miocene, Northern Italy) were studied. Our focus has been on 5% HNO3-treated solution (authigenic carbonate minerals) of carbonates. Several crystalline forms of carbonate minerals have been selected for analysis. Total REE (ΣREE) contents in seep carbonates varies widely, from 0.068 to 43.655 ppm, but the common trend is that the ΣREE in microcrystalline phases is highest and lowest of in sparite, suggesting that the ΣREE of seep carbonates may be a function of diagenesis. The shale-normalized REE patterns of the seep carbonates show varied Ce anomalies across several seep sites and even within one site, suggesting that the formation condition of seep carbonate is variable and complex. Overall, our results show that apart from anoxic, oxic formation condition is also common at hydrocarbon seep environments.

Over a decade after the completion of the human genome, researchers around the world are still wondering what information is hidden in the genome. Although the sequences of all human genes are known, it is still almost impossible to determine much more than the primary protein structure from the coding sequence of a gene. As a result of that, the need for recombinantly produced proteins to study protein structure and function is greater than ever. The main objective of this thesis has been to improve protein production, particularly using Escherichia coli. To improve protein production in Escherichia coli there are a number of different parameters to consider. Two very important parameters in the process of protein production are transcription and translation. To study the influence of differences in transcription rate, target proteins with different characteristics were produced under control of three promoters of different strength (lacUV5, trc and T7). Analyzing the total amount of target protein as well as the amount of soluble protein demonstrated the benefits of using a strong promoter such as T7. However, protein production is also highly dependent on translational efficiency, and a drawback associated with the use of Escherichia coli as host strain is that codons rarely used in this host can have a negative effect on the translation. The influence of using a strain supplied with genes for rare codon tRNAs, such as Rosetta(DE3), instead of the standard host strain BL21(DE3), was therefore evaluated. By using Rosetta(DE3) an improved protein yield for many of the poorly produced proteins was achieved, but more importantly the protein purity was significantly increased for a majority of the proteins. For further understanding of the underlying causes of the positive effects of Rosetta(DE3), the improved purity was thoroughly studied. The cause of this improvement was explained by the fact that Rosetta(DE3) has a significantly better read through of the full sequence during translation and thereby less truncated versions of the full-length protein is formed.  Moreover, the effect of supplementation of rare tRNAs was shown to be highly dependent on the target gene sequence. Surprisingly, it was not the total number of rare codons that determined the benefit of using Rosetta(DE3), instead it was shown that rare arginine codons and to some extent also rare codon clusters had a much bigger impact on the final outcome. As a result of the increased interest in large-scale studies in the field of proteomics, the need for high-throughput protein production pipelines is greater than ever. For that purpose, a protein production pipeline that allows handling of nearly 300 different proteins per week was set up within the Swedish Human Protein Atlas project. This was achieved by major and minor changes to the original protocol including protein production, purification and analysis. By using this standard setup almost 300 different proteins can be produced weekly, with an overall success rate of 81%. To further improve the success rate it has been shown that by adding an initial screening step, prior high-throughput protein production, unnecessary protein production can be avoided. A plate based micro-scale screening protocol for parallel production and verification of 96 proteins was developed. In that, protein production was performed using the EnBase® cultivation technology followed by purification based on immobilized metal ion affinity chromatography. The protein products were finally verified using matrix-assisted laser desorption ionization time-of-flight MS. By using this method, proteins that will be poorly produced can be sorted out prior high-throughput protein production. / <p>QC 20131120</p>

The present study analyzed the evolutionary history of Erigeron trifidus Hook. by addressing two main questions: 1) Is the current hypothesis of the origin of the species by hybridization between E.compositus and E.lanatus supported by molecular data? and 2)Is the species monophyletic? An analysis of uni-and-biparentally inherited molecular markers from three species throughout the range of E.trifidus yielded data that supports the hybridization hypothesis. First, a restriction site analysis of cpDNA revealed 4 haplotypes. In most cases, cpDNA haplotypes were the same as in E.lanatus, suggesting E.lanatus as the maternal parent. Sequencing and cloning the nuclear ETS region revealed the presence of multiple repeat types in most individuals sampled. This further supports the hybrid origin hypothesis in that E.trifidus contained only repeat types present in one or the other of the putative parents. In addition, E.trifidus displayed the highest percentage of intrainidividual repeat type polymorphism, a common trait of hybrid species. Erigeron trifidus populations collected in the northern region appear to be monophyletic as they all exhibited a particular pattern of repeat type variation, a pattern absent in Ram Mountain and Waterton Lakes National Park populations. As E.lanatus has never been recorded from Ram Mountain, it is likely that the populations identified as E.trifidus are instead a different agamospermous variant of E.compositus. In Waterton Lakes National Park, populations of E.trifidus are thought to be the product of local hybridization but the identity of the putative parents remains uncertain. Therefore, E.trifidus is concluded to be polyphyletic. / viii, 66 leaves : ill. (some col.) ; 28 cm.

Impurity trapped excitons (ITEs) occurring in divalent ytterbium doped calcium and strontium fluoride crystals have been investigated by exploiting the radically different radiative decay rates of the lowest exciton state and higher excited states, utilizing a novel two-colour transient photoluminescence enhancement experiment. The ITE energy levels have been directly measured with the observation of sharp transitions occurring from the changes of states of the localized hole and broad bands associated with changes of state of the delocalized electrons. The dynamic behaviour under excitation by time delayed ultra-violet (UV) and infrared (IR) pulses has been observed allowing for the identification of excitation and decay pathways between the ITE states. The position and transition intensities of the sharp lines within the IR excitation spectrum have been successfully matched using a semi-empirical effective Hamiltonian crystal field model. In CaCaF₂:Yb²⁺ the lines occurring at 249 and 1145 cm⁻¹ were matched with the crystal field parameter B4 = 800 cm⁻¹ and the exchange parameter G3(fs) = 5900 cm⁻¹. In SrCaF₂:Yb²⁺ these lines were observed at 178 and 1284 cm⁻¹ and matched with B4 = 600 cm⁻¹ and G3(fs) = 7278 cm⁻¹. Local heating and direct absorption by intra-excitonic transitions are found to be the causes of the broad band observed in the spectrum and have been deconvolved by studying the dynamic behaviour of the monitored emission at different IR excitation frequencies. Through this modeling, higher lying ITE states have been identified occurring at 785 cm⁻¹ in SrCaF₂:Yb²⁺ and in between 740 - 820 cm⁻¹ in CaCaF₂:Yb²⁺. The dynamic model developed successfully simulates the temporal behaviour of the emission under IR excitation under a variety of parameters including IR fluence, excitation frequency, sample temperature and UV - IR pulse delay. Examination of the SrCaF₂:Yb²⁺ dynamic behaviour over a time scale of 100 ms shows UV driven trap population at a rate of approximately 3% per pulse, which are liberated and recycled to the Yb²⁺ ground state by the IR pulse. The two-colour technique is applied to MgCaF₂:Yb²⁺, a candidate for possible ITE emission. Temperature dependent emission spectra obtained under UV excitation indicates the possibility of an ITE state, independently populated from the 5d level of the Yb²⁺. Typical 5d emission is also observed from this system. Under IR excitation, liberation of shallow traps and possible local heating is observed. No ITE emission is conclusively found with IR probing.

A comparative study is done on the Mini Drift Chamber (MDC) and the Scintillating Electromagnetic Calorimeter (SEC), two main components of the WASA detector. The purpose of the study is to determine the most effective way to calculate the mass of the η−meson by determining the invariant mass of the final products in the η → e+e− decay. When calculating the invariant mass of the lepton pair the distribution from the MDC had a standard deviation of σMDC = (4.212 ± 0.080) · 10−2 GeV/c2 and from the SEC σSEC = (3.563±0.011)·10−2 GeV/c2. To get a precise measurement, events with a lepton scattering at a polar angle below 30◦ have to be rejected, and to achieve highest precision, it is favorable to use the SEC for momenta above 0.28 GeV/c and the MDC below, respectively. In this study, a combined method is developed which results in an invariant mass resolution of σMix = (3.341±0.012)·10−2 GeV/c2. Thus, the combined method gives a small improvement compared to using the SEC alone, but a considerable improvement compared to using only the MDC.

Ce travail de thèse s'inscrit dans le cadre de la recherche de nouvelles formulations verrières pour le conditionnement des produits de fission et actinides mineurs (PFA). Il s'agit d'étudier une composition de verre dans le domaine peralumineux (défaut de compensateurs de charge en alcalins et alcalino-terreux par rapport à l'aluminium) présentant un taux de charge au moins équivalent à celui du verre R7T7 (18,5 % mass. PFA) et de statuer sur la potentialité de ces matrices vitreuses comme matrice de conditionnement. La première partie de cette étude évalue les propriétés physico-chimiques de verres peralumineux complexes en fonction de la teneur en PFA (de 18,5 à 32 % mass.) afin de vérifier leur adéquation avec le cahier des charges prédéfini. La très faible tendance à la cristallisation de ces matrices pour des teneurs en PFA allant jusqu'à 22,5 % massiques ainsi que l'excellente durabilité chimique observée jusqu'à présent sont des atouts indéniables. La seconde partie de l'étude apporte des informations sur l'incorporation des terres rares dans des verres de composition simplifiée du système SiO2-B2O3-Al2O3-Na2O-CaO-TR2O3 (TR=Nd ou La). L'homogénéité et la tendance à la dévitrification des verres sont étudiés à l'échelle micrométrique (DRX, MEB) et nanométrique (MET) et la spectroscopie RMN (MAS, MQMAS, REDOR, HMQC, DHMQC), combinée à la spectroscopie d'absorption optique du néodyme, se révèle un outil puissant pour mettre en évidence le rôle structural de la terre rare vis-à-vis de l'aluminium et décrire de façon précise l'organisation du réseau vitreux peralumineux. L'homogénéité des matrices sur une large gamme de composition et des données structurales inédites sur l'organisation du réseau vitreux à fortes teneurs en terres ont ainsi pu être mis en évidence.

Im frühen Sonnensystem fanden während der Kondensation der chemischen Elemente volatilitätskontrollierte Fraktionierungsprozesse statt. Gegenstand dieser Doktorarbeit sind Fraktionierungen refraktär-lithophiler Elemente in einzelnen Chondritkomponenten sowie zwischen Bulk-Chondriten, Achondriten und Planeten. Mittels laser ablation inductively coupled plasma mass spectrometry wurden die Gehalte der Seltenen Erden (REE) sowie von Nb, Ta, Zr und Hf analysiert. Einzelne Chondritkomponenten wurden in-situ an dem CV-Chondrit Leoville untersucht. Von den Bulk-Chondriten, Achondriten und terrestrischen Proben wurden Gesamtgesteinsproben durch Laserschmelzen unter aerodynamischer Levitation angefertigt. Die Untersuchung der verschiedenen Bestandteile des Leoville-Chondrits ergab, dass die refraktären Einschlüsse volatilitätskontrollierte fraktionierte REE group-II-Muster und subchondritische Nb/Ta-Verhältnisse aufweisen. Sie sind demzufolge aus einem residualen Gas entstanden, von dem zuvor eine ultrarefraktäre Komponente isoliert worden war. Chondren haben zumeist relativ unfraktionierte REE-Muster sowie unfraktionierte Zr/Hf- und Nb/Ta-Verhältnisse. Einige Typ-1-Chondren, die Al-reichen Chondren und die Chondritmatrix weisen jedoch fraktionierte REE-Muster auf. Dies ist ein Hinweis auf Beimengungen refraktären Materials mit REE group-II-Muster. Die Analysen an Bulk-Chondriten zeigen, dass kohlige Chondrite im Vergleich zu dem CI-Chondrit Orgueil charakteristische volatilitätskontrollierte REE-Muster (ultrarefraktär oder group-II) besitzen, was auf den Einbau refraktärer Komponenten mit fraktionierten Seltenen Erden zurückgeführt wurde. Die Mehrheit der gewöhnlichen, Rumuruti- und Enstatit-Chondrite hat dagegen relativ unfraktionierte REE-Muster. Es konnte gezeigt werden, dass sowohl gewöhnliche, Enstatit- und Rumuruti-Chondrite als auch Proben von Achondriten, Mars, Mond und Erde geringe negative Tm-Anomalien gegenüber dem CI-Chondrit Orgueil aufweisen. Die Objekte des inneren Sonnensystems wurden daher anhand ihrer relativen Gehalte an schweren Seltenen Erden (HREE) in zwei Gruppen eingeteilt: Ein kohliges und ein nichtkohliges Chondrit-Reservoir, dem auch die Achondrite, Mars, Erde und Mond angehören. Es wurde angenommen, dass die Objekte des nichtkohligen Chondrit-Reservoirs die HREE-Verhältnisse des Sonnensystems widerspiegeln; kohlige Chondrite haben dagegen variable Tm-Anomalien, welche durch den Eintrag fraktionierter refraktärer Komponenten in ihre Entstehungsregion zu erklären sind. CI-Chondrite, welche allgemein als die chemisch primitivste Chondritgruppe angesehen werden, hätten in diesem Fall eine positive Tm-Anomalie von 4,8 ± 0,9 % und stimmten somit chemisch nicht mit dem Sonnensystem überein. Durch eine Beimengung von nur 0,2 Gewichtsprozent einer refraktären Komponente mit REE group-II-Muster zu den CI-Chondriten konnte diese Tm-Anomalie erklärt werden.

Kernel methods are a popular choice in solving a number of problems in statistical machine learning. In this thesis, we propose new methods for two important kernel based classification problems: 1) learning from highly unbalanced large-scale datasets and 2) selecting a relevant subset of input features for a given kernel specification. The first problem is known as the rare class problem, which is characterized by a highly skewed or unbalanced class distribution. Unbalanced datasets can introduce significant bias in standard classification methods. In addition, due to the increase of data in recent years, large datasets with millions of observations have become commonplace. We propose an approach to address both the problem of bias and computational complexity in rare class problems by optimizing area under the receiver operating characteristic curve and by using a rare class only kernel representation, respectively. We justify the proposed approach theoretically and computationally. Theoretically, we establish an upper bound on the difference between selecting a hypothesis from a reproducing kernel Hilbert space and a hypothesis space which can be represented using a subset of kernel functions. This bound shows that for a fixed number of kernel functions, it is optimal to first include functions corresponding to rare class samples. We also discuss the connection of a subset kernel representation with the Nystrom method for a general class of regularized loss minimization methods. Computationally, we illustrate that the rare class representation produces statistically equivalent test error results on highly unbalanced datasets compared to using the full kernel representation, but with significantly better time and space complexity. Finally, we extend the method to rare class ordinal ranking, and apply it to a recent public competition problem in health informatics. The second problem studied in the thesis is known as the feature selection problem in literature. Embedding feature selection in kernel classification leads to a non-convex optimization problem. We specify a primal formulation and solve the problem using a second-order trust region algorithm. To improve efficiency, we use the two-block Gauss-Seidel method, breaking the problem into a convex support vector machine subproblem and a non-convex feature selection subproblem. We reduce possibility of saddle point convergence and improve solution quality by sharing an explicit functional margin variable between block iterates. We illustrate how our algorithm improves upon state-of-the-art methods.

La région de l'Abitibi renferme d'abondants dépôts fluvioglaciaires de sables et de graviers, notamment des eskers, reconnus comme des aquifères exceptionnels étant donné leurs caractéristiques hydrogéologiques intrinsèques et la faible perméabilité du roc sous-jacent. Une meilleure compréhension des régimes hydrauliques relatifs à ces systèmes est nécessaire afin d'établir une gestion adaptée de la ressource hydrique. Ainsi, une étude ayant recours aux isotopes des gaz rares fut initiée dans les eskers de la région d'Amos. Douze échantillons d'eaux furent prélevés dans l'esker Saint-Mathieu-Berry (SMB), la moraine d'Harricana, l'esker de Barraute et dans la plaine argileuse située entre ces formations. Spécifiquement, des analyses sur les concentrations en gaz rares ont été effectuées. Les résultats des rapports 20Ne/4He contre 3He/4He indiquent un mélange entre une composante radiogénique enrichie en 4He, tritiogénique enrichie en 3He et atmosphérique. Le rapport mesuré 3He/4He normalisé à celui de l'atmosphère (R/Ra), où Ra=1,386*10-6, varie entre 0.224±0.012 pour l'eau d'un puits privé prélevée dans le roc (P1) et 1.849±0.036 pour le puits d'Amos. Les âges 3H-3He, obtenus grâce aux contenus en tritium et en 3He mesurés, dévoilent la présence d'eaux modernes (≤32 ans) situées principalement dans les formations fluvioglaciaires. La moraine d'Harricana, marquée par une signature atmosphérique, présente les eaux les plus jeunes variant entre 6.44±1.30 et 9.80±1.29 ans. Les âges 3H-3He montrent une relation linéaire avec la profondeur des puits pour l'esker Saint-Mathieu-Berry (SMB) et la moraine d'Harricana. Cette relation, appuyant l'utilisation du modèle d'écoulement piston pour la plupart des puits, permet de calculer des gradients verticaux d'infiltration variant entre 0.9 et 7 m/an. Elle permet d'identifier un phénomène de dispersion/diffusion dans les puits du secteur sud de l'esker de SMB appuyé par la comparaison entre les concentrations en tritium et la courbe des précipitations à Ottawa. De ce fait, la datation 3H-3He ne semble pas valide pour les puits du secteur sud. La calibration du taux de production en 4He permet l'estimation des temps de séjour (U-Th)/4He des eaux dans les aquifères. Ces derniers montrent l'occurrence de masses d'eaux intermédiaires (50 à 6000 ans) et fossiles (≥6000 ans). Quatre échantillons de l'esker de SMB montrent des eaux possiblement d'âge intermédiaire (50 à 738 ans) selon les analyses (U-Th)/4He, mais modernes selon les analyses 3H/3He. Ces puits, en grande partie situés dans une zone de faille de type indéterminé, montre une signature d'un mélange entre une eau ancienne circulant dans les zones fragilisées du socle granitiques sous-jacent l'esker et de l'eau jeune. Les eaux de l'esker ne présentent pas de signature typique des eaux profondes circulant dans la plaine argileuse. D'autre part, l'âge apparent (U-Th)/4He le plus élevé de la zone d'étude est d'environ 8000 ans. Cet âge correspond à celui d'un puits situé dans le socle fracturé de la plaine argileuse. La salinité et le rapport 3He/4He mis en fonction de la profondeur des puits suggèrent un mélange entre de l'eau minéralisée riche en 4He radiogénique et de l'eau douce moderne plus superficielle dans l'aquifère du socle rocheux de la plaine. Cela peut également indiquer une augmentation graduelle de la salinité engendrée lors du transport de l'eau puisque le temps de séjour augmente aussi avec la distance longitudinale par rapport à la moraine d'Harricana. Ainsi, la moraine semble représenter une zone de recharge importante à la fois pour l'esker de Barraute et pour le socle de la plaine argileuse. Notons que les eaux les plus minéralisées et riches en 4He radiogénique sont celles provenant du socle fracturé Archéen de la plaine argileuse. Les températures de recharge obtenues varient entre -0.10±0.61°C et 11.64±0.73°C. Pour la plupart des puits, elles diminuent avec l'augmentation de l'élévation estimée pour la recharge. Les échantillons situés dans la plaine montrent les températures de recharge les plus basses (entre -0.10 et 2.91°C), alors que celles de l'esker SMB se situent entre 6.19 et 11.6°C. La paléotempérature pour la moraine d'Harricana est plus faible en surface (3.87°C) qu'en profondeur (9.52°C). ______________________________________________________________________________

Increased demand for rare earth elements (REEs) for applications in modern technologies has led to an increase in REE exploration. Several deposits are expected to begin mining within a decade, but few studies have examined the possible environmental effects created by these mines. Metal toxicity is thought to be greater in aqueous environments when metals occur as free ions rather than complexes, and the speciation can also impact the treatment technologies utilized to reduce metal concentrations. This research investigates the mineralogical source of REEs and the mechanism of REE mobility in low-temperature waters that have interacted with pilot plant tailings from the Nechalacho deposit, Northwest Territories. The Nechalacho deposit is owned by Avalon Rare Metals Inc. and located approximately 100 km east of Yellowknife. The deposit is hosted within a hydrothermally altered layered nepheline-sodalite syenite in the peralkaline Blatchford Lake complex. The main REE ore minerals are zircon, fergusonite, allanite, monazite, bastnäsite, and synchisite-parasite. Characterization of the tailings using mineral liberation analyzer (MLA) show that the ore minerals are fine grained and well liberated. Bastnäsite and synchisite-parasite are the only potentially soluble ore minerals at low temperature and near-neutral pH. Shake flask experiments were designed to simulate the interaction of tailings with three different leach waters to identify soluble phases and mobile elements. Decanted solutions from the shake flasks were filtered to 0.45µm and 0.01µm. Speciation modelling of the 0.01µm filtrate suggests that carbonate ligands will form the dominant complexes with the REEs, and <2% occur as free metal ions. Higher proportions of LREEs (1-6%) occur as free metal ions than HREEs (<1%) and LREEs occur in higher concentrations (2 to 8 times greater) than the HREE. REEs were found in the colloidal fraction ([REEcolloid] = [REE0.45µm] – [REE0.01µm]). Ionic strength is the dominant control on distribution of REEs between colloidal and dissolved fraction. Colloids captured on filters from ultrafiltration analyzed using scanning electron microscopy and synchrotron microanalysis show REEs are hosted in colloidal rare earth minerals (e.g. zircon) and also show colloidal humic acid, Fe-oxides and Mn-oxides. Speciation modeling shows that REE sorption to these phases is probable. / Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2014-05-28 11:06:41.351