Made available in DSpace on 2014-06-11T19:32:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-04-27Bitstream added on 2014-06-13T19:22:36Z : No. of bitstreams: 1 rabelo_rn_dr_jabo.pdf: 419029 bytes, checksum: 56edeae338cf6c261ac2c73378a0f5ac (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A contagem de células somáticas (CCS) do leite de tanques de expansão está relacionada com os índices de mastite no rebanho, enquanto a contagem bacteriana total (CBT) demonstra a higiene de ordenha e do ambiente em que os animais são alojados, além dos procedimentos de limpeza dos equipamentos de ordenha. Partindo dessa premissa, foram caracterizadas as qualidades celulares, microbiológicas, físicas e químicas de leites procedentes de tanques de expansão individuais no período de 2007 a 2011. Os resultados mostraram que para o ano de 2007, das 850 amostras analisadas, as CCS variaram de 5,3x105 céls.mL-1 (maio) a 1,1x106 céls.mL-1 (novembro) e para CBT variaram de 5,2x105 UFC.mL-1 (abril) a 1.,6x106 UFC.mL-1. Para 2008, das 892 amostras analisadas, as CCS variaram de 7,0x105 céls.mL-1 (abril) a 1,1x106 céls.mL-1 (outubro) e, para CBT variaram de 9,0x105 UFC.mL-1 (junho) a 1,8x106 UFC.mL-1 (abril). No ano de 2009 as CCS variaram de 6,7x105 céls.mL-1 (março) a 1,0x106 céls.mL-1 (fevereiro) e, para CBT variaram de 3,8x105 UFC.mL-1 (abril) a 1,7x106 UFC.mL-1 (janeiro). Para o ano de 2010, as CCS variaram de 5,6x105 céls.mL-1 (setembro) a 8,8x105 céls.mL-1 (novembro) e para CBT, variaram de 5,0x105 UFC.mL-1 (agosto) a 1,4x106 UFC.mL-1 (fevereiro). No ano de 2011, as variações foram de 5,1x105 céls.mL-1 (agosto) a 8,7x105 céls.mL-1 (janeiro) para CCS e para CBT essas variações foram de 4,6x105 UFC.mL-1 (maio) a 1,2x106 UFC.mL-1 (fevereiro). As CCS e CBT variaram na série histórica, com tendência à redução; o período de chuvas influenciou a incidência de CCS e CBT fora dos padrões da IN 51 e o período de chuvas e seca não interferiu nos parâmetros físicos e químicos em todos os anos pesquisados, com variações mínimas, mas dentro dos padrões estabelecidos pela legislação... / Bulk tank somatic cell count (SCC), milk tanks expansion is related to the indices of mastitis in the herd, while the total bacterial count (CBT) demonstrates the hygiene of milking and the environment in which animals are housed, in addition to procedures for cleaning of the equipment of milking. From this premise, we characterized the cellular, microbiological and physical-chemical quality properties of milk coming from individual bulk tanks in the period 2008 to 2010. The results showed that for the year 2007, the 850 samples analyzed, the CCS ranged from 526x10³ cels.mL-1 (May) to 1,065x10³ cels.mL-1 (November) and CBT varied from 517x10³ UFC.mL-1 (April) to 1,643x10³ UFC.mL-1. The results showed that for the year 2008, of 892 samples analyzed, SCC ranged from 696x10³ cells.mL-1 (April) to 1,102x10³ cells.mL-1 (october), and for TBC varied from 896x10³ CUF.mL-1 (June) to 1,781x10³ CUF.mL-1 (april). In 2009 the SCC ranged from 667x10³ cells.mL-1 (march) the 1,026x10³ cells.mL-1 (February) and for TBC ranging from 377x10³ CUF/ mL (april) to 1,746x10³ CUF.mL-1 (january). For the year 2010, the SCC ranged from 561x10³ cells.mL-1 (september) to 883x10³ cells.mL-1 (november) and TBC, ranged from 503x10³ UFC.mL-1 (august) 1,395x10³ CUF.mL-1 (february). In the year 2011, the variations were 5.1 x105 cels.mL-1 (August) the 8.7x105 cels.mL-1 (January) to SCC and for TBC these variations were 4.6x105 CFU.ml-1 (may) the 1.2x106 CFU.ml-1 (February). The SCC and TBC varied in historical series, with a tendency toward reduction; the rainy period influenced the incidence of SCC and TBC outside of the patterns of IN 51, and rain and dry period did not interfere with physical and chemical parameters in all the years surveyed, with minimal changes, but within the standards established by current legislation. The individual results... (Complete abstract click electronic access below)

Magister Scientiae (Biodiversity and Conservation Biology) / Homopus areolatus is an endemic terrestrial tortoise that resides in a Mediterranean type of climate, which is characterised by winter rainfall and mild winter temperatures. Within ectotherms, such as H. areolatus, physiological changes are elicited by changes in the ambient temperature. These physiological changes are evident in the blood profile of reptiles. I described the morphology of immature and mature erythrocytes, leukocytes as well as thrombocytes of H. areolatus. Additionally, I evaluated erythrocytes, leukocytes and thrombocytes to assess the effects of season and cohort on these cells. Blood samples were collected in 2000 and 2001 at Elandsberg Nature Reserve in the Western Cape from H. areolatus cohorts (female, male, juvenile) in all seasons (spring, summer, autumn, winter). Blood smears were made and stained with modified Giemsa stain. SigmaStat was used for all statistical analysis. Immature erythrocyte types within H. areolatus included basophilic rubricytes, polychromatophilic rubricytes and polychromatophilic erythrocytes. Upon my evaluation, I encountered evidence to suggest that small and large immature erythrocytes possibly developed from two distinctive lineages. Further research is required to discern which lineage gave rise to which immature erythrocyte type. Cohort had no effect upon immature erythrocytes. Erythropoiesis was most prevalent during winter and spring within H. areolatus. Aberrant features of erythrocytes appeared to be more prevalent during autumn, which signified the driest season with limited food and water. Mature erythrocytes play a huge role in oxygen transport and metabolism in individuals. Factors such as size and shape are relevant since small, mature, ellipsoidal erythrocytes transport oxygen more efficiently than large, spherical erythrocytes. In H. areolatus small, mature, ellipsoidal erythrocytes appeared to be most prevalent during spring and summer. During winter however, large, spherical erythrocytes appeared to be most prevalent. Thrombocytes and seven types of leukocytes were observed within H. areolatus, namely heterophils, lymphocytes, eosinophils, basophils, monocytes, plasma cells and azurophils. Among cohort and season heterophils were most prevalent overall, followed by lymphocytes and eosinophils respectively. Basophils, monocytes, plasma cells and azurophils were present but overall, were relatively few. H. areolatus appeared to be healthy, and leukocyte counts as well as its dimensions appeared to be in accordance with other reptilian studies. This study serves as the first baseline haematological reference forH. areolatus. The study forms the second of its kind on South African tortoises, only one other haematological study has been done namely, P. geometricus which is a sympatric species to H. areolatus.

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<p> Statistical analysis of panel count data is an important topic to a number of applied fields including biology, engineering, econometrics, medicine, and public health. Panel count data include observations on subjects over multiple time points where the response variable is a count or recurrent event process when only the numbers of events occurring between observation time points are available. The choice of method for analyzing panel count data usually depends on the relationship between the observation times and the response variable and questions of interest. Most of the previous research was done when the observation times are fixed. If the observation times are random, the data structure becomes more challenging since the observation times for individual subjects vary in addition to the incompleteness of observations. The model-based approach was used to deal with such data. However, this method relies on extra assumptions on the observation scheme and thus is restrictive in practice. In this dissertation, we discuss the problem of multi-sample nonparametric comparison of counting processes with panel count data, which arise naturally when recurrent events are considered. For the problem considered, we develop some new nonparametric tests.</p> <p> First, we construct a class of nonparametric test statistics based on the integrated weighted differences between the estimated mean functions of the count processes, where the isotonic regression estimate is used for the mean functions. The asymptotic distributions of the proposed statistics are derived and their finite-sample properties are examined through Monte Carlo simulations. A panel count data from a cancer study is analyzed and presented as an illustrative example.</p> <p>As shown through Monte Carlo simulations, the nonparametric maximum likelihood estimator (NPMLE) of the mean function is more efficient than the nonparametric maximum pseudo-likelihood estimator (NPMPLE). However, no nonparametric tests have been discussed in the literature for panel count data based on the NPMLE since the NPMLE is more complicated both theoretically and computationally. It is, therefore, particularly important to develop nonparametric tests based on the NPMLE for panel count data.</p> <p> In the second part of the dissertation, we focus on the situation when treatment indicators can be regarded as independent and identically distributed random variables and propose a nonparametric test in this case using the maximum likelihood estimator. The asymptotic property of the test statistic is derived. Simulation studies are carried out which suggest that the proposed method works well for practical situations, and is more powerful than the existing tests based on the NPMPLEs of the mean functions.</p> <p>In the third part of the dissertation, we consider more general situations. We construct a class of nonparametric tests based on the accumulated weighted differences between the rates of increase of the estimated mean functions of the counting processes over observation times, where the nonparametric maximum likelihood approach is used to estimate the mean functions instead of the nonparametric maximum pseudolikelihood. The asymptotic distributions of the proposed statistics are derived and their finite-sample properties are evaluated by means of Monte Carlo simulations. The simulation results show that the proposed methods work quite well and the tests based on NPMLE are more powerful than those based on NPMPLE. Two real data sets are analyzed and presented as illustrative examples.</p> <p>The last part of the dissertation discusses a special type of panel count data, namely, current status or case 1 interval-censored data. Such data often occur in tumorigenicity experiments. For nonparametric two-sample comparison based on censored or interval-censored data, most of the existing methods have focused on testing the hypothesis that specifies the two population distributions to be identical under the assumption that observation or censoring times have the same distribution. We consider the nonparametric Behrens-Fisher hypothesis (NBFH) under this settings. For this purpose, we study the asymptotic property of the nonparametric maximum likelihood estimator of the probability that an observation from the first distribution exceeds an observation from the second distribution. A nonparametric test for the NBFH is proposed and the asymptotic normality of the proposed test is established. The method is evaluated using simulation studies and illustrated by a set of real data from a tumorigenicity experiment.</p> / Thesis / Doctor of Philosophy (PhD)

In recent actuarial literature, the bivariate Poisson regression model has been found to be useful for modeling paired count data. However, the basic assumption of marginal equi-dispersion may be quite restrictive in practice. To overcome this limitation, we consider here the recently developed bivariate Conway–Maxwell–Poisson (CMP) distribution. As a distribution that allows data dispersion, the bivariate CMP distribution is a flexible distribution which includes the bivariate Poisson, bivariate Bernoulli and bivariate Geometric distributions all as special cases. We discuss inferential methods for this CMP distribution. An application to automobile insurance data demonstrates its usefulness as an alternative framework to the commonly used bivariate Poisson model. / Thesis / Master of Science (MSc)

Master of Science / Statistics / Nora M. Bello / Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Sand bluestem exhibits phenotypic divergence related to epicuticular properties and enhanced drought tolerance relative to big bluestem. Understanding the mechanisms underlying differential drought tolerance is relevant in the face of climate change. For bluestem subspecies, presence or absence of these phenotypes may be associated with RNA transcripts characterized by low number of read counts. So called low-count transcripts pose particular inferential challenges and are thus usually filtered out at early steps of data management protocols and ignored for analyses. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on low-count transcripts as motivated by differential bluestem phenotypes. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60% of which are classified as low-count) collected from leaf tissue of 4 individual plants of big bluestem and 4 of sand bluestem. We also compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the performance of recently developed statistical methods for differential expression (DE) analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively. Our results indicate that proper specification of DE methods can remove the need for ad- hoc data filtering at arbitrary expression threshold, thus allowing for inference on low-count transcripts. Practical recommendations for inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications also focused on transcripts of low expression levels.

En säker bakteriediagnostik kräver en korrekt provtagningsteknik, ett lämpligt transportsätt och rätt odlingsteknik. På grund av centralisering av verksamheter och ekonomiska begräsningar, är transport av prover till mikrobiologilaboratorium mycket vanligt. Detta medför behov av ett transportmedium som håller känsliga bakterier vid liv under långa transport- och förvaringstider. Dessutom skall transportrören klara av maskinell utodling som kräver ett vätskebaserat provtagningsmedium. Denna övergång minskar även arbetsbelastning och förbättra ergonomin hos personalen. I denna studie utvärderades viabilitet av Propionibacterium acnes (n=3), Bacteroides fragilis (n=2) och Neisseria gonorrhoeae (n=3) i transportmediet från COPAN E-swab™. Alla tre bakterier förvarades i transportrören i 24, 48 och 72 timmar (h) och dessutom i 120h för P. acnes och B. fragilis. Den ursprungliga koncentrationen samt den procentuella viabilitetsförlusten över tid beräknades med hjälp av viable count. Efter 120h förvaring i transportmediet hade viabiliteten minskat till 47 – 80 % för P. acnes, 18 % för B. fragilis 1 och 73 % för B. fragilis 2. N. gonorrhoeae visade en minskad viabilitet med 96 – 99,97 % efter 24h förvaring i 4°C och rumstemperatur. P. acnes och B. fragilis kunde förvaras i transportmediet i upp till 5 dygn utan att diagnostiken äventyrades. N. gonorrhoeae kunde förvaras i transportmediet i 24h för att diagnostik genom odling ska vara möjlig. / Safe bacterial diagnostics requires proper sampling techniques, suitable specimen transport and correct inoculation techniques. As a result of centralization of operations and economic restraints, transportation of samples to microbiology laboratories is very common. This entails the need for a transport medium that keeps sensitive bacteria alive under the long transport and storage time. Additionally, the transport tube should be convenient for automatic inoculation that requires a liquid based medium. This transition also reduces workload and improves ergonomics of the staff. In this study the survival of Propionibacterium acnes (n = 3), Bacteroides fragilis (n = 2) and Neisseria gonorrheae (n = 3) in the transport medium Copan E-swab™   was evaluated. All the species were inoculated in the tubes for 24, 48, 72h and also 120h for B. fragilis and P. acnes.  Initial concentration at start time and the percentage survival over time was calculated with the help of viable count. Viability decreased to 47 – 80 % for P. acnes, 18 % for B. fragilis 1 and 73% for B. fragilis 2 after 120 h storage in the transportmedium. N. gonorrhoeae showed a reduction in viability of 96 – 99,97 % after 24h storage in the medium at 4°C and in room temperature. P. acnes and B. fragilis can be stored in the medium for up to 5 days, without endangering a diagnosis. N. gonorrhoeae can be stored in the transport medium for up to 24h to secure a diagnosis through culturing.

We will propose a random changepoint model for the analysis of longitudinal CD4 and CD8 T-cell counts, as well as viral RNA loads, for HIV infected subjects following highly active antiretroviral treatment. The data was taken from two studies, one of the Aids Clinical Group Trial 398 and one performed by the Terry Beirn Community Programs for Clinical Research on AIDS. Models were created with the changepoint following both exponential and truncated normal distributions. The estimation of the changepoints was performed in a Bayesian analysis, with implementation in the WinBUGS software using Markov Chain Monte Carlo methods. For model selection, we used the deviance information criterion (DIC), a two term measure of model adequacy and complexity. DIC indicates that the data support a random changepoint model with the changepoint following an exponential distribution. Visual analyses of the posterior densities of the parameters also support these conclusions.

CoordenaÃÃo de AperfeÃoamento de Pessoal de NÃvel Superior / Neste trabalho apresentamos o PrincÃpio Fundamental da Contagem (PFC) como uma consequÃncia do PrincÃpio de InduÃÃo Finita (PIF) e, como aplicaÃÃo do (PFC), apresentamos a soluÃÃo de vÃrios problemas envolvendo contagem, arranjos, permutaÃÃes e combinaÃÃes. O principal objetivo do trabalho à apresentar o raciocÃnio lÃgico-matemÃtico que envolve a noÃÃo de contagem evitando dar o protagonismo que costumeiramente à dado as fÃrmulas matemÃticas no ensino bÃsico. Neste intuito, resolvemos vÃrios problemas sem fazer uso de fÃrmulas matemÃticas, priorizando a aplicaÃÃo direta do PFC. / We presented The Fundamental Principle Count (PFC) as a consequence of the Principle Finite Induction (PIF) and as the application (PFC), we presented the resolution of various problems involving count, arrangements, combinations and permutations. The main objective of this work is to present the logical-mathematical reasoning that involves counting notion avoiding to give the leadership that is customarily given to mathematical formulas. To this end, we solve various problems without using mathematical formulas, giving priority to direct application of the PFC.

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