No description available.

This thesis explores a new way to analyze spatiotemporal data. By combining topology, the path signature and machine learning a robust model to analyze swarming behavior over time is created. Using persistent homology a representation of spatial data is obtained and the path signature gives us a representation for how this changes over time. This representation allows us to compare samples even if they have different amounts of time steps and different length of the sequence. It is also resistant to noise in the spatial representation. Using this data is then used to train a gaussian process regressor to extract parameters that govern the movement of swarms. Our analysis shows that the tested method is a good candidate for analyzing spatiotemporal data and that it warrants further studies. / Detta examensarbete utforskar ett nytt sätt att analysera spatiotemporal data. Genom att kombinera topologi, vägsignaturer och maskininlärning skapas en robust modell för att analysera svärmar beter sig över tid. Genom persistent homology erhålls en representation av spatial data och dess vägsignatur ger oss en representation för hur detta förändras över tiden. Denna representation gör det möjligt för oss att jämföra data även om de har olika antal tidssteg och sekvenserna är olika långa. Den är också motståndskraftig mot brus i den spatiala representationen. Denna data används sedan för att träna en gaussisk process-regressor för att extrahera parametrar som styr svärmarnas rörelse. Vår analys visar att den testade metoden är en bra kandidat för att analysera spatiotemporal data och att den är värd att studera ytterligare.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Daniel U. Thomson / Bovine viral diarrhea virus (BVDV) has emerged as one of the most important infectious diseases in cattle. One particular important manifestation, after successfully establishing an in utero infection of the fetus during the first trimester, is the development of a persistently-infected BVDV (PI-BVDV) calf. Persistently infected BVDV animals are a continuous source of virus and can shed the virus in virtually all secretions and excretions, including nasal discharges, saliva, semen, urine, tears, milk, and, to a lesser extent, feces. The objectives of this research were to determine: 1) the effects of short term exposure (13 – 18 days on feed (DOF)) to PI-BVDV feeder cattle; 2) the outcome of testing and removing PI-BVDV feeder calves at time of feedlot arrival on health, performance, and carcass characteristics; 3) the survival of BVDV on materials associated with livestock production; and 4) characterization of testing and longitudinal prevalences for PI-BVDV beef cattle. Testing and removing PI-BVDV calves at 13 to 18 DOF was too late to remove a morbidity effect due to PI-BVDV exposure. However, mortality, performance, and carcass characteristics were not different in cattle exposed to PI-BVDV cattle. Additionally, there were no harmful outcomes when newly arrived feeder cattle were exposed to a PI-BVDV animal for one to two days following feedlot entry. A non-cytopathic, Type 1b, BVDV was capable of surviving after application to various materials used in livestock production. BVDV tended to survive longer on non-porous materials than porous materials. When in the presence of mucus, BVDV was protected from degradation for longer periods of time than when not in the presence of mucus. There was no difference in overall PI-BVDV prevalence within cattle sampled in 2006 and 2007. Cattle that weighed less than 300 lbs. had a greater likelihood of being PI-positive than cattle with increased weights. Several months of the year had a greater likelihood of having PI-positive animals. Based on operation, cow-calf and stocker operations had a greater likelihood of having PI-positive animals than did feedlot operations.

No description available.

In the UK there has been growing concern about the relationship between levels of alcohol consumption and offending behaviour. The Alcohol Treatment Requirement (ATR) was introduced to the UK in 2007 and was piloted in a District in the north of England in July 2007. The ATR is a coercive form of treatment delivered jointly by the probation service and the National Health Service (NHS) and was funded by the NHS. The ATR centres on supporting offenders to cease their offending behaviour and reduce or end their alcohol misuse. Two female alcohol treatment workers have been appointed to specifically deliver the ATR. Therefore this study aimed to investigate the delivery of the ATR, and more specifically, aimed to explore what impact the ATR might have in relation to positive behaviour change and rehabilitation for offenders with alcohol problems. In order to meet the expectations of producing 'outcome' data for the NHS funders, and indepth theoretical data worthy of an academic PhD, this research took a pragmatic methodological approach which enabled different social realities of the ATR to be explored. To this end, a mixed methods design was employed involving quantitative and qualitative data collection methods. The data for this research was generated in three phases with Phase One aiming to explore quantitatively the characteristics, impacts and outcomes of those sentenced to the ATR. This phase revealed that the ATR is being delivered to predominantly young, male, alcohol dependent, violent, persistent offenders. This analysis further revealed that the ATR was effective in bringing about positive treatment outcomes and in reducing reoffending. In order to explore further how this positive change was occurring, Phase Two consisted of qualitative participant observations of the treatment interaction involving the female alcohol treatment workers and the male offenders. By drawing on positioning theory, the analysis considered the complexity of the gendered interactions that occurred during these encounters. It was found that the two female alcohol treatment workers resisted positions of 'feminine carer' offered up by these young men in order to occupy positions of control. Indeed this analysis provided great insight into the constant flow of negotiations and manoeuvring of positions that occurred between the alcohol treatment worker and the offender, argued to be vitally important in working towards positive behaviour change. During Phase Three ten offenders were interviewed in order to explore through a dialogical lens (Bakhtin, 1982) how they constructed and experienced treatment on the ATR. In exploring the offenders' stories dialogically, the analysis highlighted how the ATR was enabling, in that it offered a 'space' for these offenders to engage and internalise a dialogue that draws on the authoritative voice of therapy. Therefore it was revealed that through dialogue with the 'other', offenders were able to re-author a more 'moral' and 'worthy' self. Moreover, the ATR has been found to be successful in enabling the offenders' hegemonic masculine identities to be both challenged and protected as a result of the multilayered interactions that occurred during these treatment encounters. This research therefore concludes that coercive treatment, rather than being a concern, should be embraced as a way of enabling change for offenders with alcohol problems. Furthermore, this research has highlighted the value of the relational aspect of treatment in bringing about positive behaviour changes. Finally this research has shown that community sentences offer a more constructive way of engaging with offenders than those who receive a custodial sentence.

<p>Persistent organic pollutants (POPs) is a group of chemicals that are toxic, undergo long-range transport and accumulate in biota. Due to their persistency the distribution and recirculation in the environment often continues for a long period of time. Thereby they appear virtually everywhere within the biosphere, and poses a toxic stress to living organisms. In this thesis, attempts are made to contribute to the understanding of factors that influence the distribution of POPs with focus on processes in the marine environment. The bioavailability and the spatial distribution are central topics for the environmental risk management of POPs. In order to study these topics, various field studies were undertaken. To determine the bioavailable fraction of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated naphthalenes (PCNs), and polychlorinated biphenyls (PCBs) the aqueous dissolved phase were sampled and analysed. In the same samples, we also measured how much of these POPs were associated with suspended particles. Different models, which predicted the phase distribution of these POPs, were then evaluated. It was found that important water characteristics, which influenced the solid-water phase distribution of POPs, were particulate organic matter (POM), particulate soot (PSC), and dissolved organic matter (DOM). The bioavailable dissolved POP-phase in the water was lower when these sorbing phases were present. Furthermore, sediments were sampled and the spatial distribution of the POPs was examined. The results showed that the concentration of PCDD/Fs, and PCNs were better described using PSC- than using POM-content of the sediment. In parallel with these field studies, we synthesized knowledge of the processes affecting the distribution of POPs in a multimedia mass balance model. This model predicted concentrations of PCDD/Fs throughout our study area, the Grenlandsfjords in Norway, within factors of ten. This makes the model capable to validate the effect of suitable remedial actions in order to decrease the exposure of these POPs to biota in the Grenlandsfjords which was the aim of the project. Also, to evaluate the influence of eutrophication on the marine occurrence PCB data from the US Musselwatch and Benthic Surveillance Programs are examined in this thesis. The dry weight based concentrations of PCB in bivalves were found to correlate positively to the organic matter content of nearby sediments, and organic matter based concentrations of PCB in sediments were negatively correlated to the organic matter content of the sediment.</p>

While motor neuron activity has been studied for many decades, the relative contribution of synaptic and non-synaptic mechanisms underlying this activity during natural behaviors is not well understood. Thus, the goal of this dissertation was to further understand the role of non-synaptic properties of motor neurons during voluntary activity. In particular, I considered three non-synaptic properties: persistent inward currents (PICs) that boost synaptic inputs, spike-threshold accommodation that affects recruitment threshold as excitation rates of rise slow, and spike-frequency adaptation that leads to a decrease in firing rate despite constant excitation levels. Computer simulations were employed to understand the potential effect that these properties could have on firing rate behavior. In particular, the focus was on paired motor unit recordings where a lower threshold motor unit’s firing rate served as a proxy for synaptic drive, and differences in firing rate (ΔF) were compared at a higher threshold unit’s recruitment and derecruitment. While ΔF has been used by others to estimate PIC activation, the simulation results indicated that each of these non-synaptic mechanisms could lead to positive ΔF. Furthermore, by varying contraction speed and duration it seemed possible to determine which property contributes to ΔF in vivo. The results from human experiments indicated that adaptation is most likely the predominant contributor to ΔF during natural behaviors. Additionally, positive ΔF was even observed in the genioglossus muscle of the tongue, where the role of PICs has been debated. These results suggested that ΔF may not the best method to detect PICs during natural behaviors. As such, I also considered whether there might be another metric to infer PIC activation during natural behaviors. Motor unit firing rates tend to plateau, or saturate, despite continued force increase, and one hypothesis is that PICs contribute to this behavior. Indeed, motor unit firing rate saturation was diminished by the addition of inhibition, which should have limited PIC activation. Therefore, this final study provided possible evidence for PIC activation during natural behaviors. Overall, this dissertation highlights that non-synaptic properties of motor neurons are activated during natural behaviors and that they contribute significantly to firing rate output.

The main purpose of this research was to evaluate use of Last Observation Carried Forward (LOCF) as an imputation method when persistent binary outcomes are missing in a Randomized Controlled Trial. A simulation study was performed to see the effect of dropout rate and type of dropout (random or associated with treatment arm) on Type I error and power. Properties of estimated event rates, treatment effect, and bias were also assessed. LOCF was also compared to two versions of complete case analysis - Complete1 (excluding all observations with missing data), and Complete2 (only carrying forward observations if the event is observed to occur). LOCF was not recommended because of the bias. Type I error was increased, and power was decreased. The other two analyses also had poor properties. LOCF analysis was applied to a mammogram dataset, with results similar to the simulation study.

O acúmulo de poluentes orgânicos persistentes é um dos principais problemas de contaminação do meio ambiente em todo o mundo. As atividades industriais e os avanços tecnológicos na maioria dos setores de produção contribuem com a crescente liberação de compostos poluentes, altamente tóxicos, biocumulativos e resistentes à degradação física, química, fotolítica e biológica. Esses poluentes são o resultado do uso indevido de pesticidas de um modo geral, da subprodução não planejada de sintéticos tóxicos como dioxinas policloradas e de uma lista enorme de atividades que promovem a combustão incompleta da matéria orgânica e despejam no ambiente uma vasta quantidade de hidrocarbonetos aromáticos persistentes. A biorremediação é uma estratégia biotecnológica que vem lançar luz sobre as técnicas de revitalização de sítios contaminados. É baseada na utilização de microorganismos, ou suas enzimas, para reduzir ou eliminar perigos ambientais contaminantes em substâncias inertes, CO2 e água. As oxigenases são uma classe de enzimas amplamente estudadas por suas propriedades catalíticas únicas, sendo a clorocatecol 1,2- dioxigenase de Pseudomonas putida um interessante alvo biotecnológico para a biorremediação devido a sua ampla especificidade a substratos aromáticos, aromáticos halogenados e dialogenados altamente poluentes, biocumulativos e carcinogênicos. Nesse trabalho, o protocolo de expressão heteróloga em E. coli foi implementado em nosso laboratório e a purificação realizada em coluna de afinidade através do uso de resina de quitina. Os cristais de cor marrom avermelhado da enzima clorocatecol 1,2-dioxigenase Pseudomonas putida foram obtidos na presença de polietilenogligol e acetato de magnésio durante o período de 10 dias, utilizando-se a técnica de difusão de vapor em gota sentada. A estrutura cristalográfica da enzima Pp 1,2-CCD foi determinada através da utilização da técnica MR-SAD, utilizando átomos de ferro, cofator da proteína, como agentes espalhadores e as coordenadas da enzima 3-clorocatecol 1,2-dioxigenase de Rhodococcus opacus como modelo de busca. O modelo final, contendo 3 moléculas na unidade assimétrica foi refinado a 3.4 Å de resolução. A enzima se enovela na forma dimérica (Fe3+)2, e apresenta de um modo geral, dois domínios catalíticos compostos de fitas-beta e uma região de loops e um domínio de ligação composto por hélices formando um túnel hidrofóbico. Como a primeira clorocatecol de bactérias gram-negativa a ser descrita para essa classe de enzimas, será possível investigar as diferenças conformacionais que levam aos mecanismos de catálise, amplo a diversos substratos, e avaliar características de seu funcionamento e ativação, como uma importante ferramenta para validação do papel desta proteína dentro do processo de biorremediação. / Accumulation of persistent organic pollutants is one of the most important environmental problems worldwide. Industrial activities and technological advances contribute to the spread of pollutants, highly toxic, bioaccumulative, and resistant to physical, chemical, photolytic and biological degradation. The persistent organic pollutants are consequence of the inappropriate use of pesticides, the production of toxic synthetic compounds such as polychlorinated biphenyls and a large list of activities promote incomplete combustion of which organic matter and release a large amount of persistent aromatic hydrocarbons to the environment. Bioremediation is a biotechnogical strategy that has shed light on revitalization techniques of contaminated sites. It is based on the application of microorganisms, or their enzymes, to eliminate or reduce environmental contaminants into inert substances, CO2 and water. The oxygenases are a class of largely studied enzymes due to their catalytic properties, being chlorocatechol 1,2-dioxygenase from Pseudomonas putida an interesting biotechnological target for bioremediation due to its specificity to a broad spectrum of highly polluted aromatic substrates. In the present work, heterologous expression protocol has been implemented in our laboratory and purification was performed by using affinity column in chitin resin. Brown-reddish crystals of chlorocatechol 1,2-dioxygenase from Pseudomonas putida were obtained in presence of polyethylene glycol (PEG) and magnesium acetate after 10 days, by utilizing vapor diffusion techniques in sitting drops. The crystallographic structure of Pp 1,2-CCD has been solved by MR-SAD technique, using iron atoms, the enzyme cofactor, as scattering centers and the coordinates of 3- chlorocatechol 1,2-dioxygenase of Rhodococcus opacus as the search model. The final model, containing three molecules in the asymmetric unit, has been refined up to 3.4 Å resolution. The enzyme folds in the dimeric form (Fe3+)2, and shows two catalytic domains composed of -strands and a loop region, and a helical domain that pack together forming a hydrophobic channel. As being the first member of the chlorocatechol dioxygenase family of enzymes from a gram-negative bacteria to be solved, it will be possible to explore the crystallographic structure of chlorocatechol 1,2- dioxygenase from Pseudomonas putida in order to investigate the conformational differences that explain its mechanism of action, on a broad spectrum of substrates, and evaluate the functional features, as an important tool to validate the role of this enzyme in the bioremediation process.

Atualmente, os materiais luminescentes que apresentam a luminescência persistente tem ganhando um destaque devido a capacidade de emitir luz por um período de tempo que pode variar de minutos à horas depois de cessada a excitação. Todavia, não há um grande número de estudos quantitativos a respeito dos fatores que influenciam esse fenômeno. Dessa forma, para o estudar do efeito do band gap na luminescência persistente comparou-se as propriedades de duas matrizes similares. A matriz ortossilicato de cádmio, Cd2SiO4, foi comparada com a matriz metassilicato de cádmio, CdSiO3, já descrita na literatura. A matriz ortossilicato de cádmio não dopada e dopada com íons terra rara foi sintetizada via síntese de estado sólido pelo método cerâmico a 1050 °C. A caracterização e o estudo da pureza se deram através das técnicas difração de raios X (DRX) usando radiação Síncrotron e CuK&#945;. O estado de oxidação foi estudado usando espectroscopia de absorção de raios X próximo a borda (XANES) com radiação Síncrotron. As propriedades luminescentes foram compreendidas pelos experimentos de fotoluminescência no UV-Vis e espectroscopia com radiação Síncrotron na região do UV vácuo. Os difratogramas mostraram a presença de pequenas porcentagens de impurezas e a obtenção da fase pura para o Cd2SiO4:Pr3+. O espectro de XANES mostrou a presença apenas de íons terras raras trivalentes. O valor do band gap para a matriz ortossilicato de cádmio em 4,1 eV foi determinado utilizando espectros de excitação e emissão em 77 K dos materiais Cd2SiO4 e Cd2SiO4:Gd3+. Os espectros de excitação e emissão dos materiais Cd2SiO4:Pr3+ e Cd2SiO4:Tb3+ permitiram a comparação das propriedades luminescentes entre a fase ortossilicato e metassilicato, além de indicar a posição de alguns níveis 5d dentro da banda de condução. Com os dados obtidos foi proposto um mecanismo de luminescência persistente para o íon Pr3+ que mostrou-se muito mais eficiente nessa matriz em relação ao metassilicato de cádmio, comportamento oposto ao observado com os íons Tb3+, devido às suas posições dentro do band gap da matriz / Persistent luminescence materials have gained special attention lately due to their special property of emitting light for long time after ceased irradiation. However, hitherto, there is no deep quantitative analysis on the factors that affects this phenomenon. On this way, we compared the persistent luminescence properties on two similar inorganic hosts differing only in their band gap energies. The cadmium orthosilicate (Cd2SiO4) was compared to the cadmium metasilicate (CdSiO3) already well described in literature. The non-doped and rare earth doped cadmium orthosilicate were prepared with solid state synthesis at 1050 °C. The characterization and phase purity study were made with X-ray diffraction techniques using both Synchrotron and Cu&#945;K radiation. The oxidation state was studied with Synchrotron radiation X-ray absorption Near Edge structure measurements (XANES). The photoluminescence study was done with UV-Vis and VUV-UV emission and excitation spectroscopies. The XRD patterns allowed the determination of the phase purity and confirmed the preparation of pure Cd2SiO4:Pr3+. XANES data confirmed the presence of only trivalent rare earths. The band gap was determined as 4.1 eV with the 77 K excitation spectra of Cd2SiO4 and Cd2SiO4:Gd3+. The excitation spectra of Cd2SiO4:Pr3+ and Cd2SiO4:Tb3+ allowed the comparation between the optical properties of meta- and orthosilicate crystal phases like the position of 5d levels which are inside Cd2SiO4 conduction band. The obtained data allowed the proposition of a persistent luminescence mechanism for Pr3+ ion, considerably more efficient on orthosilicate when compared to metasilicate. This behavior is on the opposite way to the one observed for Tb3+ ions, due to their position in the band gap.