Numerous wastewater treatment processes are currently available for nitrogen removal or ammonia conversion to nitrate. Those that are economically feasible rely mostly on microbiological processes, which are only effective when the microorganisms remain in a healthy state. If a biological process upset was to occur, due to a toxic shock load or cold weather, it may result in a discharge of ammonia or total nitrogen into the receiving water body. The impact of such a discharge could have deleterious effects on aquatic life or human health. The main objective of the breakpoint pilot study was to define optimum breakpoint pilot plant operating conditions which could then be applied to the design of a full scale breakpoint facility and serve as an emergency backup to biological nitrification. A pilot study was built on site at the Upper Occoquan Sewage Authority's Regional Water Reclamation Facility in Centreville Virginia. Testing was conducted in two phases (I and II) over a two year period in order to determine the operating conditions at which the breakpoint reaction performed best. Tests were performed during Phase I to determine the optimum operating pH, Cl₂:NH₃-N dose ratio, S0₂:Cl₂ dose ratio, and the minimum detention time for completion of the breakpoint reaction. Other testing done during Phase I included several special studies; including examination of appropriate analytical methods for monitoring breakpoint reactions, and investigation of the breakpoint reaction by-product nitrogen trichloride. Phase II testing examined how varying breakpoint operating temperatures, varying influent ammonia concentrations, higher influent organic nitrogen concentrations, and higher influent nitrite concentrations influenced the performance of the breakpoint pilot operation. Averages of data from operation at three different rapid mix pHs (7.0, 7.5, and 8.0) showed that pilot performance (i.e., ammonia oxidation) improved and the reaction was more stable at the higher operating pHs 7.5 and 8.0. Examination of dose ratios used during the study showed that the ideal operating ratios for this particular water was around 8:1 Cl₂:NH₃-N for the breakpoint reaction and 1.3:1 S0₂:Cl₂ for the dechlorination reaction. Although detention times for completion of the breakpoint reaction varied with pilot influent temperature, it generally required around 30-35 minutes to reach ammonia concentrations of < 0.2 mg/L NH₃-N at 8-12°C. Completion of the breakpoint reaction was found to be quickest at 20°C (the highest water temperature tested at the pilot). The tests of varying influent ammonia concentrations showed that although higher influent ammonia concentrations (11.0 mg/L) resulted in faster ammonia oxidation rates initially, the pilot operated better and had the same final performance results when the influent ammonia was lowered. Increasing the organic nitrogen concentrations (~ 1.0 mg/L) in the pilot influent resulted in a slightly higher Cl₂:NH₃-N dose ratio needed to reach breakpoint, a higher S0₂:Cl₂ dose needed to dechlorinate, and resulted in the formation of numerous disinfection byproducts. Increasing the nitrite concentration in the pilot influent increased the chlorination dose requirement. / Master of Science

La compréhension de la dynamique des réarrangements génomiques est une problématique importante en phylogénie.La phylogénie est l'étude de l'évolution des espèces. Un but majeur est d'établir les relations d'évolution au sein d'un groupe d'espèces, pour déterminer la topologie de l'arbre d'évolution formé par ce groupe et des ancêtres communs à certains sous-ensembles.Pour ce faire, il est naturellement très utile de disposer d'un moyen d'évaluer les distances évolutionnaires relatives entre des espèces, ou encore d'être capable d'inférer à un groupe d'espèces le génome d'un ancêtre commun à celles-ci.Ce travail de thèse, dans la lignée d'autres travaux, consiste à élaborer de tels moyens, ici dans des cas particuliers où les génomes possèdent des gènes en multiples copies, ce qui complique les choses.Plusieurs hypothèse explicatives de la présence de duplications ont été considérées, des formules de distance ainsi que des algorithmes de calcul de scénarios ont été élaborés, accompagnés de preuves de complexité. / Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order to infer the topology of an evolutionary tree formed by this group and common ancestors to some of these species. In this context, having means to evaluate relative evolutionary distances between species, or to infer common ancestor genomes to a group of species would be of great help.This work, in the vein of other studies from the past, aims at designing such means, here in the particular case where genomes present multiple occurrencies of genes, which makes things more complex. Several hypotheses accounting for the presence of duplications were considered. Distances formulae as well as scenario computing algorithms were established, along with their complexity proofs.

The goal of this thesis was to design the support for output breakpoints in the Java language and implement the designed solution including integration into the Eclipse IDE. An output breakpoint represents a location in an output media (e.g. file, standard output or socket) where the execution of program should stop. The location in the output media is generalized as a stop condition - it can be in the form of absolute position, a particular line and a character or an occurrence of a text string. The designed solution is based on observing the classes responsible for output using entry method breakpoints that are a standard part of the Java language. This solution is dependent on a particular version and implementation of JRE because some of observed methods are not a part of public Java API.

Deletion of the long arm of chromosome 6 is one of the most common genetic alterations in human malignant melanoma. Recently, a reciprocal translocation between chromosomes 6q and 17p was detected in a melanoma cell line, UACC-930, using arm painting probes of 6p and 6q. Reciprocal translocation is seldom observed in solid tumors. Upon further characterization of the translocation marker using techniques such as Southern blotting, genomic library screening and DNA sequencing, a complex rearrangement including two inversions of 6q and a translocation between the inverted 6q and 17p, [der(6)inv(6)(q21q22)(q22q27)t(6;17)(q27;p13)], was detected. An NCBI blast search revealed 3 genes being interrupted by the breakpoints: prenyl diphosphate synthase subunit 2 (PDSS2) at 6q21, Parkin at 6q27 and p53 at 17p13. Down-regulation of PDSS2 was commonly observed in 59/87 (67.8%) primary melanomas, which was significantly higher than that in benign nevi (7/66, 10.6%, p<0.001), indicating the tumor-suppressive potential of PDSS2 in melanoma development. To characterize the function of PDSS2 in tumorigenesis, PDSS2 was stably transfected into a highly tumorigenic melanoma cell line, UACC-903. The tumor-suppressive function of PDSS2 was demonstrated by both in vitro and in vivo assays. The results showed that PDSS2 could inhibit tumor cell growth, decrease the colony-forming ability in soft agar, and totally abrogate the tumorigenicity of UACC-903 in nude mice. PDSS2 is the first enzyme involved in the CoQ10 biosynthesis pathway. Other studies have demonstrated PDSS2 mutations can cause severe CoQ10 deficiency and markedly reduced ATP production because of respiratory chain dysfunction. Interestingly, proteomics analysis revealed 7 out of 11 identified proteins (HSPA8, GAPDHS, TPI1, HSPA5, PGK1, ENO1, and ATP5B) differentially expressed in PDSS2-overexpressing cells were related to energy metabolism. Further studies are required to determine how PDSS2 could alter the energy supply in tumor cells. Taken together, these results support the proposal that PDSS2 is a novel tumor suppressor gene which may play an important role in the development of malignant melanoma via altering tumor metabolism.

We assume pairs of random variables (X_i, Y_i), whereby the real variable X_i measures the creditworthiness of individual i with i = 1, . . . , n. The Bernoulli variable Y_i represents the default indicator of individual i. Our main target is a division of the creditworthiness into a given number of groups with a homogeneous default risk, i.e. to estimate rating classes. The framework of change point analysis provides a nonparametric method to estimate the breakpoints between the rating classes under quite weak assumptions. Up to now, the theory of breakpoint estimation is developed under the assumption of exactly one breakpoint. The contribution at hand, basically implements this theory, but extends it into a multi-stage heuristic. That means, we sequentially apply the theory for only one breakpoint as a multi-stage procedure. With this article we transfer the interesting theoretical issue of breakpoint estimation into an applicable form. Thereby, all the results are checked and obtained by simulation. The main results are as follows. Applying a sequential breakpoint estimation basically works and leads to outcomes of practical purpose. Thereby, the multistage heuristic reveals some weakness esp. in the case of quite huge differences between default probabilities that can be resolved by some interventions.

Constructing the genomic median of several given genomes is crucial in developing evolutionary trees, since the genomic median provides an estimate for the ordering of the genes in a common ancestor of the given genomes. This is due to the fact that the content of DNA molecules is often similar, but the difference is mainly in the order in which the genes appear in various genomes. The mutations that affect this ordering are called genome rearrangements, and many structural differences between genomes can be studied using genome rearrangements. In this thesis our main focus is on applying combinatorial optimization techniques to genomic median problems, with particular emphasis on the breakpoint distance as a measure of the difference between two genomes. We will study different variations of the breakpoint median problem from signed to unsigned, unichromosomal to multichromosomal, and linear to circular to mixed. We show how these median problems can be formulated in terms of problems in combinatorial optimization, and take advantage of well-known combinatorial optimization techniques and apply these powerful methods to study various median problems. Some of these median problems are polynomial and many are NP-hard. We find efficient algorithms and approximation methods for median problems based on well-known combinatorial optimization structures. The focus is on algorithmic and combinatorial aspects of genomic medians, and how they can be utilized to obtain optimal median solutions.

Constructing the genomic median of several given genomes is crucial in developing evolutionary trees, since the genomic median provides an estimate for the ordering of the genes in a common ancestor of the given genomes. This is due to the fact that the content of DNA molecules is often similar, but the difference is mainly in the order in which the genes appear in various genomes. The mutations that affect this ordering are called genome rearrangements, and many structural differences between genomes can be studied using genome rearrangements. In this thesis our main focus is on applying combinatorial optimization techniques to genomic median problems, with particular emphasis on the breakpoint distance as a measure of the difference between two genomes. We will study different variations of the breakpoint median problem from signed to unsigned, unichromosomal to multichromosomal, and linear to circular to mixed. We show how these median problems can be formulated in terms of problems in combinatorial optimization, and take advantage of well-known combinatorial optimization techniques and apply these powerful methods to study various median problems. Some of these median problems are polynomial and many are NP-hard. We find efficient algorithms and approximation methods for median problems based on well-known combinatorial optimization structures. The focus is on algorithmic and combinatorial aspects of genomic medians, and how they can be utilized to obtain optimal median solutions.

Studien syftar till att undersöka vilka faktorer som haft betydelse för sex elitidrottares nya karriärval efter avslutad idrottskarriär. Den metod som användes var kvalitativ med inslag av både hermeneutiken och det narrativa synsättet för att få fram respondenternas egna beskrivningar av brytpunkten. Resultatet visar att upplevelsen av karriäravslutet skiljer sig mellan elitidrottare som slutat frivilligt och elitidrottare som slutat ofrivilligt, på grund av mättnad respektive skada. Processen mot att välja en ny karriär beskrevs av samtliga respondenter som svår samtidigt som alla kände sig motiverade inför det nya valet och i efterhand upplevde sin nya roll samt det nya karriärvalet som tillfredsställande. Respondenterna fattade ett praktiskt rationellt beslut utifrån tidigare erfarenheter av yrket, värderingar och känslor vid valet av ny karriär. Före detta elitidrottares karriärval är ett outforskat område inom vägledningsområdet vilket gör studien intressant för vidare forskning inom studie- och yrkesvägledningen. / This study will aim to explore the major important factors that influenced six elite athletes in their new career choices after retirement. The method used was predominantly qualitative, with hermeneutics and narratives added in order to encapsulate the respondents own descriptions of point break. The result shows that the experience of retirement differs between those whom retired wilfully, and those who were forced to; because of injury or lack of motivation. The process to choose a new career was described by all respondents as difficult. However, they all felt motivated in their new choices, and were, ultimately, satisfied. The respondents made a practical rational choice based on earlier experiences of the particular line of work, values and emotional content. The post-retirement careers of elite athletes is a field relatively unexplored within vocational guidance counselling, which makes this study interesting for further development of this field.

A two-part paleolimnological study was conducted to: i) understand the important factors that are related to the present-day distribution of scaled-chrysophytes; ii) investigate changes in the scaled-chrysophyte assemblages in the Experimental Lakes Area northwestern Ontario, in response to recent climate warming. Scaled-chrysophyte assemblages were analyzed in the modern sediments of 40 ELA lakes to determine their relationship to measured environmental variables. The sediment record from 210Pb dated cores from six ELA lakes were analyzed at a sub-decadal resolution to evaluate if chrysophytes were changing in a consistent fashion and if these changes could be accounted for by measured climatic factors. Ordination analysis of the modern chrysophyte flora was significantly related to pH, lake depth, and the degree of thermal stratification, as well as water temperature. Mallomonas punctifera ‘small’ and Mallomonas acaroides were indicators of warm surface-waters. High-resolution analysis of six ELA lakes revealed pronounced shifts in the chrysophyte assemblages over the last ca. 150 years. The most notable shift in the chrysophyte assemblage was characterized by an overall shift towards higher relative abundances of colonial taxa. In several lakes increases in unicellular warm-water taxa were also observed. Breakpoint Analysis identified significant changes in the chrysophyte assemblages beginning in the late-1800s to mid-1900s in most lakes. An interclass correlation coefficient (ri) was used to assess the temporal coherency of the chrysophyte assemblages over the past ca. 100 years. All lakes displayed a similar directional change which was significantly coherent (p<0.05). A Brien’s Test identified sub-sets of lakes that were temporally coherent and homogenous. The high coherency of two groups, (Group A, grand mean=0.89, p-value=5.3x10-15; Group B, grand mean=0.38, p-value=0.038), suggests the dominance in extrinsic factors in governing the lake responses. The average PCA axis-1 scores of Group A (r-value=0.62, p=0.03) and Group B (r-value=0.60, p=0.038) were significantly correlated to regional mean annual temperature. Collectively, the results of this study suggest that changes observed in the scaled-chrysophyte assemblages in the ELA region are consistent with recent climate warming. / Thesis (Master, Biology) -- Queen's University, 2011-09-29 16:42:06.753

Constructing the genomic median of several given genomes is crucial in developing evolutionary trees, since the genomic median provides an estimate for the ordering of the genes in a common ancestor of the given genomes. This is due to the fact that the content of DNA molecules is often similar, but the difference is mainly in the order in which the genes appear in various genomes. The mutations that affect this ordering are called genome rearrangements, and many structural differences between genomes can be studied using genome rearrangements. In this thesis our main focus is on applying combinatorial optimization techniques to genomic median problems, with particular emphasis on the breakpoint distance as a measure of the difference between two genomes. We will study different variations of the breakpoint median problem from signed to unsigned, unichromosomal to multichromosomal, and linear to circular to mixed. We show how these median problems can be formulated in terms of problems in combinatorial optimization, and take advantage of well-known combinatorial optimization techniques and apply these powerful methods to study various median problems. Some of these median problems are polynomial and many are NP-hard. We find efficient algorithms and approximation methods for median problems based on well-known combinatorial optimization structures. The focus is on algorithmic and combinatorial aspects of genomic medians, and how they can be utilized to obtain optimal median solutions.