<p>Despite high vaccination rates and effective adaptive immune responses from the part of infected individuals, influenza A viruses cause significant morbidity and mortality annually. This is due to influenza's rapid antigenic evolution, whereby continual mutations occurring in epitope regions of the virus's hemagglutinin protein result in the diminishment of long-term antibody recognition, in a process that has been termed `antigenic drift'. Although it is clear that antigenic drift enables previously infected individuals to become reinfected, the mechanism that is responsible for influenza's antigenic drift is still under debate. As recently as 2009, a new hypothesis of antigenic drift was put forward that argues that binding avidity changes in the viral hemagglutinin result in antigenic drift as a side effect. This hypothesis stands in contrast to the traditionally accepted hypothesis that mutations in epitope regions are positively selected for their ability to evade immune recognition. This thesis focuses on the use of epidemiological models and empirical data analysis to explore different hypotheses of antigenic drift. </p><p>In the first chapter, I am asking what effects on antigenic drift rate would be produced under the new hypothesis. I mathematically formulate the hypothesis that antigenic drift is simply a side effect of cellular receptor binding avidity changes that occur as the virus is transmitted between individuals of different immune status levels. I then use this formulation to explore how influenza's rate of antigenic drift depends on different epidemiological factors, including host contact rate, host lifespan, and the duration of infection. Finally, I use the model to assess alternative vaccination strategies by the impact they have on rates of antigenic drift and therewith rates of disease incidence/</p><p>In the second chapter, I critically evaluate the binding avidity hypothesis by comparing predictions of the hypothesis against empirical data. I first use a `phylodynamic' extension of the model presented in the first chapter to determine whether the hypothesis is consistent with the ladderlike phylogeny of influenza's hemagglutinin protein. I then use viral sequence data and metadata to determine whether older aged individuals (with a higher number of previous infections) harbor viruses with higher binding avidity than younger aged individuals (with a lower number of previous infections), a prediction made by the binding avidity hypothesis. Finally, I perform a phylogenetic analysis to determine how rapidly binding avidity changes occur. From these analyses, I conclude that the binding avidity hypothesis is not well supported by empirical data.</p><p>In the third chapter, I develop an integrated viral life cycle model, in which viral replication depends on three viral phenotypes: receptor binding avidity, neuraminidase activity, and antigenicity. This integrated model recognizes that receptor binding avidity changes will influence viral replication, but also allows for antigenic evolution to be brought about directly by epitope changes. I first use this model to show how the evolutionary dynamics of these phenotypes are dependent on one another and how antigenic drift can be interpreted within this framework. I then return to some of the questions addressed in the first chapter to ask how different epidemiological factors impact influenza's rate of antigenic drift.</p><p>Together, these three chapters highlight the importance of viral phenotypes other than antigenicity in contributing to influenza's antigenic evolution, and, more generally, the importance of computational and mathematical research in understanding constraints on viral adaptation.</p> / Dissertation

Soil organic matter (SOM) is a dynamic soil property, sensitive and responsive to many factors. The possibility of increasing soil carbon (C) sequestration by changing land use and management practices has been of great interest recently due to concerns with global changes in the atmospheric carbon dioxide (CO2) balance. Nonetheless, as a result of the complex dynamics of SOM, there is still the need for SOM characterization procedures capable of monitoring SOM stabilization, taking into account all the factors involved. This study characterized SOM stabilization as affected by management practices in three long-term field experiments, considering physical, chemical and biological components. The field experiments are located near Lexington, Kentucky, on a Maury silt loam (fine, mixed, mesic Typic Paleudalfs). The first experiment evaluates tillage and nitrogen (N) rate effects. The second experiment studies manure and N rate effects. The third experiment evaluates the five corn components of three crop rotations [continuous (monoculture) corn, corn-wheat/double crop soybean, and hay-hay-corn-corn-corn]. Soil organic matter content, stability, and composition, for physically separated fractions, were assessed using δ13C natural abundance and diffuse reflectance Fourier transformed infrared (DRIFT) spectroscopy. In addition, management effects on microbial biomass and microbial function as indicated by phenol oxidase enzyme activity were evaluated. The results indicate that management practices affect SOM content, stability, and composition, and these effects differ by the soil aggregate fraction. No-tillage (NT), N fertilization, manure application and increased corn in crop rotations enhanced SOM levels. However, the effect of NT was observed mainly at the soil surface. Soil organic matter storage was determined by the aggregate size distribution. The proportion of recently deposited C was generally positively related to aggregate size, especially for the first and third experiments. Most of the recently deposited C was stabilized in microaggregates within macroaggregates, across the management treatments and field experiments. In addition, this fraction consistently exhibited low to medium SOM reactivity. These results suggest that SOM stabilization, as influenced by management practices, required achieving a specific composition and location within the soil matrix. This implies that soil C forms and aggregate size and stability are closely interrelated.

Det här examensarbetet har utförts på uppdrag åt Trollhättan Energi AB (TEAB). Examensarbetet är en utredning beträffande förutsättningar för sammankoppling av TEAB:s och Hjärtum Elförenings elnät. De nuvarande ledningsnäten har radialnät och det innebär att det endast har inmatning från ena ledningsänden. En sammankoppling skulle ge möjlighet till sektionerad drift vilket innebär inmatningsmöjligheter från båda ledningsändar. Det gör att ledningsnätet blir mer säkert, tillförlitligt och effektivt. Ett förslag på ett nytt ledningsnät där delar av TEAB:s och Hjärtum Elförenings ledningsnät är sammankopplade har tagits fram. Med det nya förslaget blir ledningsnätet mer driftsäkert och uppfyller lag- och myndighetskrav. Beräkningarna som ligger till grund för arbetet är teoretiskt utförda. Därför bör en fortsatt planering och undersökning inom ämnet utföras innan ledningsnäten sammankopplas. Budgetpriset för ombyggnationen i ledningsnätet har beräknats till cirka 700 000 kronor och investeringen anses nödvändig för att kunna utföra en sammankoppling utav elnäten. / This bachelor´s thesis is conducted on behalf of Trollhättan Energi AB (TEAB). The bachelor´s thesis is an investigation of conditions for interconnection of TEAB and Hjärtum Elförenings electrical grids. The current electrical grids are radial electrical grids and means that it can only be fed from one cable end. An interconnection would allow for sectional operation of the electrical grid. This means input opportunities from both cable ends and that the electrical grid becomes more safely, reliably and efficiently. Suggestion for new electrical grids which parts of TEAB and Hjärtum Elförenings electrical grids are interconnected has been developed. With the new suggestions becomes the electrical grid more reliable and complies with legal and regulatory requirements. The calculations that are underpinning the work is theoretical. Therefore, a continued planning and research in the subject should be performed before the electrical grids are interconnected. Budget price for the reconstruction of the electrical grids have been estimated to be about 700 000 SEK and the investment is considered essential for the interconnection.

No description available.

Flodpärlmusslan (Margaritifera margaritifera. L) har en obligatorisk fas i sin komplexa livcykel där den lever som parasit på antingen öringens (Salmo trutta, L) eller laxens (Salmo salar, L) gälar. För värdfisken skulle detta kunna innebära en ökad energikostnad när den födosöker i rinnande vatten. Öringens furagering består i att den finner en utgångspunkt (eng. focal point) i strömmen utifrån vilken den fångar sina byten. I denna studie undersöks det om en infektion av flodpärlmusslans glochidielarver på öring påverkar öringens födointag och hantering av födan. Sextio årsungar av öring infekterades med glochidielarver av känd koncentration, och deras födosökning mättes över en 10-veckors period för att bedöma effekten av den växande mussellarven i jämförelse med en icke-infekterad (kontrollgrupp) grupp fiskar. Individuella födoförsök, tio försök per mätningstillfällena, utfördes i ett strömakvarium där en enskild öring matades med drivande föda i fem minuter. Bytet släpptes ned i strömmen med två sekunders intervall, antalet byten räknades och furageringsbeteendet observerades. Födoförsöken genomfördes med två veckors intervall. Vid försöken hittades inga signifikanta skillnader med avseende på: 1) antalet fångade byten, 2) proportionen av fångade byten av försökets första tre minuter, eller 3) de rumsliga aspekterna av öringens utgångspunkt. Vidare uppmättes ingen signifikant effekt av tid på furageringsframgången på den infekterade gruppen jämfört med kontrollgruppen. Däremot var det ett högre antal infekterade individer som spottade ut byten jämfört med kontrollgruppen. Skillnaden i utspottade byten pekar på att infektionen har en negativ påverkan på fiskarnas furageringsförmåga. Dock visade försöken inga resultat som stödjer tidigare studier där signifikant skillnad erhållits med avseende på födointag. Förklaring till detta kan finnas i metodskillnader mellan denna och tidigare studier, inklusive skillnad i typ av byte, strömakvarier, ursprungsström för musslorna och öringen och infektionsgrad hos de infekterade fiskarna samt kontrollgruppen. / The freshwater pearl mussel (Margaritifera margaritifera, L) has a mandatory phase of its complex life cycle where it lives as a parasite on the gills of either trout (Salmo trutta, L) or salmon (Salmo salar, L). For the host fish this could mean an increased cost when it forages in running water. The trout´s foraging consists of finding a focal point in the stream from where it catches its prey. This study examines whether an infection of the freshwater pearl mussel´s glochidium larva on the gills of brown trout affect trout foraging. Sixty juvenile (0+) brown trout were infected with glochidium larva of a known concentration, and trout foraging behaviour was measured over a 10-week period to assess the effects of the growing mussel larvae of the fish compared to non-infected (control) fish.  Individual feeding trials, ten replicates for each session, were conducted in a stream aquarium where a single trout was fed drifting prey for five minutes. The prey were released into the stream every two seconds, the number of prey captured was counted, and the foraging behavior was characterized. Feeding trials were conducted at two-week intervals. No significant differences between the infected and control groups were found for: 1) the number of prey eaten, 2) the proportion of prey eaten during the first three minutes of the trial, or 3) location of the focal points. Furthermore, there was no significant effect of time on foraging success of the infected group compared to the control group. However, there was a higher number of infected individuals who spat out the prey compared with the control group. The difference in rejected prey suggests that the infection has a negative impact on the fish’s foraging ability. However, the results of this experiment do not support previous studies, where a significant difference was obtained with respect to food intake. This might be explained by differences in experimental protocol between this and previous studies, including differences in prey type, stream aquaria, stream origins of mussels and trout, and the infection status of infected and control fish.

Aktiebolag ska enligt lag upprätta finansiella rapporter enligt rådande redovisningsstandards, vilka sedan ska granskas av en revisor. Revisorn avger sedan ett yttrande om företagets finansiella ställning, där ett företags förmåga att fortleva som en going concern, med normalt en tidshorisont på tolv månader framåt i tiden, ska tas i beaktande. Om revisorn bedömer ett företags förmåga att fortleva som en going concern som osäker, ska det återges i revisionsberättelsen. Tidigare studier har påvisat att en majoritet av de företag som tilldelas en Going Concern-varning, tenderar att avvika från att upphöra sin existens och således, fortleva. Anledningen till att företag som tilldelas en GC-varning inte upphör sin existens, har vidare förklarats av att det föreligger låg kvalitet i revisorernas granskningar. Aktuell studie tar en annan utgångspunkt och fokuserar på företagen i fråga och inkluderar ett företags kapacitet som en förklaring till att en GC-varning utfaller differentierat. Studien omfattar ett urval av 149 stycken företag som år 2008 har tilldelats en GC-varning. Aktuell studie har kunnat påvisa att det finns indikationer för att en förklaring till att en GC-varning utfaller differentierat är på grund av att revisorer inte tar hänsyn till subjektiva aspekter, det vill säga ett företags kapacitet, utan utgår från objektivt synbara företeelser i företagens finansiella ställning. Kapacitet har i aktuell studie visat sig bidra med en bra förklaring till varför vissa företag tenderar att fortleva, medan andra upphör att existera. Det går med hänsyn till det att diskutera tidigare forskning som talar i termer av revisionskvalitet och snarare förklara differentierade utfall av en GC-varning med att företag har varierad företagskvalitet.

Thesis (M.Sc. (Physics))--North-West University, Potchefstroom Campus, 2008.

Although higher correlation between gauge and radar at hourly or daily accumulations are reported, it is rarely observed at higher time resolution (e.g. 10 -minute). This study investigates six major rainfall events in year 2000 in the greater Winnipeg area with durations varying from four to nine hours. The correlation between gauge and radar measurements of precipitation is found to be only 0.3 at 10-minute resolution and 0.55 at hourly resolution using Marshall-Palmer’s Z-R relationship (Z=200R1.6). The rainfalls are classified into convective and stratiform regions using Steiner et al. (1995)’s algorithm and two different Z-R relationships are tested to minimize the error associated with the variability of drop-size-distribution, however no improvement is observed. The performance of the artificial neural network is explored as a reflectivity-rainfall mapping function. Three different types of neural networks are explored: the back propagation network, the radial basis function network, and the generalized regression neural network. It is observed that the neural network’s performance is better than the Z-R relationship to estimate the rainfall events which was used for training and validation (correlation 0.67). When this network is tested on a new rainfall its performance is found quite similar to that obtained from the Z-R relationship (correlation 0.33). Based on this observation neural network may be recommended as a post-processing tool but may not be very useful for operational purposes - at least as used in this study. Variability in weather and precipitation scenarios affects the radar measurements which apparently makes it impossible for the neural network or the Z-R relationship to show consistent performance at every rainfall event. To account for variability in weather and rainfall scenarios conventional correction schemes for attenuation and hail contamination are applied and a trajectory model is developed to account for rainfall advection due to wind drift. The trajectory model uses velocity obtained from the single-doppler observation. A space-time interpolation technique is applied to generate reflectivity maps at one-minute resolution based on the direction obtained from the correlation based tracking algorithm. The trajectory model uses the generated reflectivity maps having one-minute resolution which help to account for the travel time by the rainfall mass to reach to the ground. It was found that the attenuation correction algorithm adversely increases the reflectivity. This study assumes that the higher reflectivity caused by hail contaminated regions is one reason for the overestimation in the attenuation correction process. It was observed that the hail capping method applied prior to the attenuation correction algorithm helps to improve the situation. A statistical expression to account for radome attenuation is also developed. It is observed that the correlation between the gauge and the radar measurement is 0.81 after applying the various algorithms. Although Marshall-Palmer’s relationship is recommended for stratiform precipitation only, this study found it suitable for both convective and stratiform precipitation when attenuation is properly taken into account. The precipitation processing model developed in this study generates more accurate rainfall estimates at the surface from radar observations and may be a better choice for rainfall-runoff modellers.

Thesis (M.Sc. (Physics))--North-West University, Potchefstroom Campus, 2008.

Initial results are presented for two analyses using data from the recently completed laser calibration system of the time projection chambers for the Tokai-to- Kamioka long baseline neutrino oscillation experiment. Data taken with the first two production time projection chambers, while tested at TRIUMF, has been used to investigate the signal arrival time and subsequently the ionization drift speed and the relative gain of the micromegas and electronics systems. It has been found that an analytic Gaussian t produces the best overall results for establishing an arrival time, having both the lowest standard deviation, of 11 ns, and good amplitude dependence while remaining fast. Using the analytic fit technique the drift speeds of ionization has been found to be in agreement with the expected values at the 2% level. The largest of the contributing errors were found to be due to systematics involved in the calculation of the ionization production time and will be reduced in future. Relative gain analysis results have shown that the gain can be calculated based on a simple model relating the mean signal size of data channels to the variance. Further gain results have shown that an offset found in the laser data can be corrected for by sampling signal amplitudes from channels that do not detect ionization or can remain uncorrected if the fitting for the relative gain includes a correction parameter. Preliminary results of the gain's dependence on the gas temperature and pressure have shown a positive nonzero slope. However, systematic errors were found be large relative to the temperature and pressure ranges. This dependence and its use as a correction for such changes will need to be investigated further at the experiment site in Japan.