The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on November 17, 2009). Thesis advisor: Dr. Patrick Westhoff. Includes bibliographical references.

This thesis documents the contribution of my bioinformatics research activities, including novel software development, to a range of research projects aimed at investigating the interactions between bacterial and viral pathogens and their hosts. The focus is largely on farm animal species and their pathogens, although some of the research has a wider scientific impact. RNA interference (RNAi) refers to a variety of related regulatory pathways present in animals, plants and insects. The major pathways are microRNAs (miRNAs), small-interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). Marek’s disease virus is an important pathogen of poultry, causing T-cell lymphoma. We identified the presence and expression patterns of several MDV-encoded microRNAs, including the identification of 5 novel microRNAs. We also showed that not only do virus-encoded microRNAs dominate the mirNome within chicken cells, but also that specific host-microRNAs are down-regulated. We also identify novel virus-encoded microRNAs in other Herpesviridae and provide the first evidence of miRNA evolution by duplication in viruses. In related work, we present a novel microRNA generated by the canonical miRNA biogenesis pathway in Avian Leukosis Virus, another avian oncogenic virus, and publish data showing the expression pattern of known chicken microRNAs across a range of important avian cells. Two of the other RNAi pathways (siRNA and piRNA) form an important part of the antiviral response in arthropods. We have published work demonstrating an siRNA antiviral response to bluetongue virus and Schmallenberg virus in cells from the Culicoides midge, an important insect vector, as well as work demonstrating the importance of the piRNA pathway in the antiviral response to Semliki forest virus (SFV). Further work on flaviviruses in ticks demonstrates the active suppression of the siRNA response by Langat Virus, as well as a key difference between the siRNA responses in Mosquitos compared to ticks. Salmonella is one of the most important zoonoses, with an estimated 1.4 million cases of human salmonellosis per annum in the USA alone. Salmonella infections of farm animals are an important route into the human food chain. This thesis presents work on the comparative structure and function of 13 fimbrial operons within Salmonella enterica serovar Enteritidis as well as a genomic comparison of that serovar with Salmonella enterica serovar Gallinarum, a chicken-specific serovar. We characterised the global expression profile of Salmonella enterica serovar Typhimurium during colonization of the chicken intestine, and we have published the genomes of four strains of Salmonella eneterica serovars of well-defined virulence in food-producing animals. Our work in this area led to us publishing an important and comprehensive review of the automatic annotation of bacterial genomes. Finally, I present work on novel software development. ProGenExpress, a software tool that allows the easy and accurate integration and visualisation of quantitative data with the genome annotation of bacteria; Meta4 is a web application that allows data sharing of bacterial genome annotations from metagenomes; CORNA, a software tool that allows scientists to link together microRNA targets, gene expression and functional annotation; viRome, a software tool for the analysis of siRNA and piRNA responses in virus-infection studies; DetectiV, a software tool for the analysis of pathogen-detection microarray data; and poRe, a software tool that enables users to organise and analyse nanopore sequencing data.

Doctor of Philosophy / Department of Economics / Jason S. Bergtold / Benjamin B. Schwab / Agricultural development is an essential factor in the economic development of much of the developing world and comprises a significant element of foreign assistance portfolios. Over the last decade, there has seen a renewed interest in more credible estimates of the economic impacts of development programs, such as assistance to extension programs. We compare the estimation of technical efficiency to farm output and income as an outcome variable to evaluate the impact of development programs such as farm education and extension programs. We develop a simple theoretical model which shows that using technical efficiency as an outcome variable could be a viable alternative to more traditionally used outcome variables such as farm output and farm profit. We note that when farmers are capital constrained, extension programs can theoretically have a large efficiency effect despite a small or zero change in farm profits. If farm technical efficiency is used as an outcome variable, then it must be estimated correctly. Mismeasurement of farm technical efficiency leads to misleading extension program evaluations. Farm households face heterogeneous infrastructural constraints (Suri 2011; Ojiem et al. 2006), credit constraints, information barriers and other input market constraints (Duflo, Kremer and Robinson 2011; Jack 201; Suri 2011and Stifel and Minten 2008), labor markets constraints (Henning and Henningsen 2007), socio-economical (Ojiem et al. 2006) and non-farm income opportunities (Chang et al. 2012) and thus have different access to agricultural inputs and outputs. These constraints have a substantial impact on agricultural production decisions of farm households. A key production decision of farm households is the allocation of resource to cash and food crops. Production of cash crops requires relatively higher market involvement in both the purchase of inputs and the selling of output than home-consumed food crops. The heterogeneous constraints across farm households leads to a substantial imbalance in the transaction costs associated with the production of each crop. Moreover, home-consumed crops may have quality attributes (e.g. color, taste, softness of dough, and suitability for certain dishes) not reflected in market prices. Factors such as transaction costs, crop quality attributes, and other factors such as household characteristics are farmer specific and drive a heterogeneous price wedge between the market prices for household’s crop production and the economic value of these crops for the household. These distinctions have important implication for farm productivity analysis, such as technical efficiency measurement. The standard approach to productivity analysis, such as efficiency estimation, assume that farm households face homogenous price wedges that leads to homogenous set of production and profit functions. However, the price gap created by transaction costs, crop quality attributes, and other factors such as household characteristics generally vary among subsistence, semi-subsistence and commercial farmers and leads to a heterogeneous set of profit and production frontiers. Subsistence and semi-subsistence farmers who produce largely home consumed crops have potentially greater price wedges than commercial farmers. Failing to account for the heterogeneity in price wedges that drive heterogeneity profit and production frontiers is likely to lead to underestimation of the efficiency of subsistence and semi-subsistence farmers. We test if traditional productivity analysis indeed underestimates the efficiency of subsistence and semi-subsistence farmers by employing a conditional Data Envelopment Analysis (DEA) model for household survey data in Uganda. Results confirm that naïve estimates of efficiency understate the efficiency scores of subsistence and semi-subsistence farmers. The results cast doubt on policies, such as extension programs or other information treatments, that interpret low efficiency scores for subsistence and semi-subsistence farmers as a management shortfall. We demonstrate the use of farm technical efficiency as an outcome measure by analyzing data from 2008-2012 for farm training program in Armenia. In this program, farmers received technical guidance on modern farm techniques. Two previous evaluations (Schwab and Shanoyan 2016; Fortson et al. 2012) find ambiguous evidence that farm profits increased. The measurement or potential gain from an extension program is captured using farm technical efficiency measures. We find evidence that the program in Armenia increased farm technical efficiency from 2008 to 2012.

Thesis (M.A.)--Boston University / A quantitative study of the dentition of the Thomas Farm fossil horses indicates that Anchitherium clarencei Simpson, Miohippus sp. (?), Parahippus blackbergi Hay and P. leonensis Sellards occurred at this locality during the Early Miocene. The amount of cement on the teeth as a diagnostic character of Thomas Farm fossil horses is held to be invalid and in this case its importance as an indication of evolutionary grade is questioned.

Made available in DSpace on 2014-06-11T19:31:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2001-02-05Bitstream added on 2014-06-13T20:22:38Z : No. of bitstreams: 1 nagaoka_ak_dr_botfca.pdf: 2279820 bytes, checksum: 149eef5c845342281d3c5d15503e3456 (MD5) / O principal objetivo deste trabalho foi desenvolver, instrumentar e avaliar o desempenho de um equipamento para ensaio de pneus agrícolas acoplado a um trator, acionado pela sua tomada de potência, com a finalidade de ensaiar dinâmica e individualmente pneus em condição de campo e avaliar o efeito da passagem do pneu no solo. O equipamento foi desenvolvido no Núcleo de Ensaios de Máquinas e Pneus Agrícolas (NEMPA), pertencente ao Departamento de Engenharia Rural da Faculdade de Ciências Agronômicas da Universidade Estadual Paulista (UNESP), situado no município de Botucatu. Os dados obtidos nas calibrações e nos ensaios foram ajustados pelo método de regressão e os dados do experimento foram analisados considerando-se o delineamento experimental em blocos, no esquema de parcelas subdivididas, tendo nas parcelas os pneus e nas subparcelas as cargas, com cinco repetições. Os valores de índice de cone do solo foram analisados considerando-se o delineamento experimental em blocos, no esquema de parcelas subsubdivididas, e tendo na parcela os pneus, na subparcela as cargas e na subsubparcela as camadas, com cinco repetições. Os resultados do experimento foram interpretados estatisticamente, por meio da análise de variância, adotando-se o nível de significância de 5% e pelo teste de comparação de médias de Tukey. Foram realizados ensaios com variações de velocidades de 0 a 14 km/h, patinagens de 3% a 34%, diâmetros de pneus de 1250 mm a 1722 mm, larguras de pneus de 500 mm a 602 mm e cargas verticais de 5.000 N a 24.000 N. Para estes valores não foram observados danos ao equipamento. O comprimento mais adequado da parcela para os ensaios de campo foi de 20m com freqüência de aquisição de 1Hz. O equipamento permitiu avaliar o desempenho dinâmico de pneus, em condições de solo agrícola, pista asfáltica e comparar diferentes tipos de pneus... / The main objective of this research was to develop, to instrument and to evaluate the performance of a Single Wheel Testing Equipment, linked to a tractor and motioned by the power take off (PTO) with the purpose of dynamically testing individual tires in field and laboratory conditions. The equipment was developed in Agricultural Machinery and Tire Testing Center (NEMPA), Rural Engineering Department of Agronomic Science College, São Paulo State University (UNESP), Botucatu County. The obtained calibration and test data were adjusted using regression method and the experiment data were analyzed considering an experimental design in split plot blocks, with the tire in the parcels and the load tire in the subparcels, with five repetitions. The cone index values were analyzed considering the same experimental design, with the tire in the parcels, the tire load in the subparcels, and the soil layers in the subsubparcels, with five repetitions. The experiment results were statistically interpreted by means of variance analysis, adopting 5% of significance level and using Tukey average test comparison. The tests were realized varying the forward speed from 0 to 14 km/h, the slip from 3% to 34 %, the tire diameter from 1,250 mm to 1,722 mm, the tire width from 500 mm to 602 mm, and the tire loads from 5,000 to 24,000 N. The device worked very well and it was not observed damages or failures for all tested situations. The most adequate parcel length obtained on the field tests was 20 m, using the acquisition frequency of 1 Hz. The equipment permitted to evaluate tire dynamic performance on agricultural field conditions, asphalt track and to compare different tire types as a function of inflation pressure, slip, rolling radius, and tire load. The equipment evaluated individuality the tested tire and have an eletronic date colect system, providing agility and practicity in the tests...(Complete abstract, click electronic access below)

Made available in DSpace on 2014-12-02T11:16:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-07-22Bitstream added on 2014-12-02T11:21:39Z : No. of bitstreams: 1 000800224.pdf: 1677677 bytes, checksum: 16eb46fbdef5f226b52052759a028b0b (MD5) / O cultivo da cana - de - açúcar é uma das mais imp ortantes atividades econômicas d a história brasileira. A colheita mecanizada da cana - de - açúcar foi implantada devido a questões econômicas , operacionais e ambientais. Desta forma o material remanescente das operações de colheita mecanizada pode causar problemas como a incidência de pragas de difícil controle e incêndios acidentais e criminosos . A utilização do resíduo disponível no campo, através do recolhimento e enfardamento des se material, proporciona novas fontes de energia para a indústria. Esse trabalho teve como objetivo estudar o desempenho operacional de duas máquinas de enfardamento prismático no palhiço de cana - de - açúcar em uma usina canavieira no município de São Miguel dos Campos – AL. A s máquinas foram avaliada s em três volumes diferentes de recolhimento do palhiço, regulando - se o aleirador para o aleiramento de cada volume de palhiço definido . Foram avaliadas, consumo de combustível, peso dos fardos, impureza mineral agregada ao palhiço e umidade dos fardos, distância altura e largura das leiras, tempo e distância que se refere à produção de cada fardo, capacidade operacional no enfardamento . Os resultados obtidos mostram que a M áquina 2 obteve maior massa específica d o s fa rdos em relação a M áquina 1 . A Máquina 1 apresentou menor consumo horário de combustível . No entanto, a Máquina 2 obteve ma ior produção de fardos por hora . Não ho uve diferenças significativas com relação à impureza mineral nos fardos nos três diferentes volumes a leirados . A capacidade de campo operacional em todos os tratamentos ... / The cultivation of sugar cane is one of the most important economic activities in Brazilian history. Mechanized harvesting of sugar cane was implanted due to economic, operational and environmental issues. Thus the remaining material of mechanized harvest oper ations can cause problems as the incidence of pests and difficult to control accidental and criminal. The use of available waste in the field by the gathering and bundling of this material provides new energy sources for industry. This work aimed to study the operational performance of two prismatic baling machines in the straw of sugarcane in company agricultural in São Miguel dos Campos - AL. The machines were evaluated in three different volumes of straw pickup, by regulating the accumulator of straw for each defined volume of straw. Were evaluated, fuel consumption, weight of bales, mineral impurities and moisture from the bales, distance height and width of the windrows, time and distance refers to the production of each bale, baling operational capabil ity. The results show that the Machine 2 has obtained higher density bales compared to Machine 1. The M achine 1 presented less fuel consumption. However, the Machine 2 produced the highest quantity of bales per hour. There were no significant differences w ith respect to mineral impurities in bales in three different volumes accumulation of straw. The operational field capacity in all treatments analyzed, was better for Machine ...

Orientador: Sérgio Hugo Benez / Coorientador: Paulo Roberto Arbex Silva / Banca: André Satoshi Seki / Banca: Marcelo de Almeida Silva / Resumo: O cultivo da cana - de - açúcar é uma das mais imp ortantes atividades econômicas d a história brasileira. A colheita mecanizada da cana - de - açúcar foi implantada devido a questões econômicas , operacionais e ambientais. Desta forma o material remanescente das operações de colheita mecanizada pode causar problemas como a incidência de pragas de difícil controle e incêndios acidentais e criminosos . A utilização do resíduo disponível no campo, através do recolhimento e enfardamento des se material, proporciona novas fontes de energia para a indústria. Esse trabalho teve como objetivo estudar o desempenho operacional de duas máquinas de enfardamento prismático no palhiço de cana - de - açúcar em uma usina canavieira no município de São Miguel dos Campos - AL. A s máquinas foram avaliada s em três volumes diferentes de recolhimento do palhiço, regulando - se o aleirador para o aleiramento de cada volume de palhiço definido . Foram avaliadas, consumo de combustível, peso dos fardos, impureza mineral agregada ao palhiço e umidade dos fardos, distância altura e largura das leiras, tempo e distância que se refere à produção de cada fardo, capacidade operacional no enfardamento . Os resultados obtidos mostram que a M áquina 2 obteve maior massa específica d o s fa rdos em relação a M áquina 1 . A Máquina 1 apresentou menor consumo horário de combustível . No entanto, a Máquina 2 obteve ma ior produção de fardos por hora . Não ho uve diferenças significativas com relação à impureza mineral nos fardos nos três diferentes volumes a leirados . A capacidade de campo operacional em todos os tratamentos ... / Abstract: The cultivation of sugar cane is one of the most important economic activities in Brazilian history. Mechanized harvesting of sugar cane was implanted due to economic, operational and environmental issues. Thus the remaining material of mechanized harvest oper ations can cause problems as the incidence of pests and difficult to control accidental and criminal. The use of available waste in the field by the gathering and bundling of this material provides new energy sources for industry. This work aimed to study the operational performance of two prismatic baling machines in the straw of sugarcane in company agricultural in São Miguel dos Campos - AL. The machines were evaluated in three different volumes of straw pickup, by regulating the accumulator of straw for each defined volume of straw. Were evaluated, fuel consumption, weight of bales, mineral impurities and moisture from the bales, distance height and width of the windrows, time and distance refers to the production of each bale, baling operational capabil ity. The results show that the Machine 2 has obtained higher density bales compared to Machine 1. The M achine 1 presented less fuel consumption. However, the Machine 2 produced the highest quantity of bales per hour. There were no significant differences w ith respect to mineral impurities in bales in three different volumes accumulation of straw. The operational field capacity in all treatments analyzed, was better for Machine ... / Mestre

This study estimates the value of farmers stated succession plans in predicting revealed succession decisions. The stated succession plan exists when a farmer answers in a survey questionnaire that the farm is going to be transferred to a new entrant within a five year period. The succession is revealed when the farm is transferred to a successor. The stated and revealed behaviour is estimated as a recursive Binomial-Probit- Model, which accounts for censoring of the decision variables and controls for a potential correlation between the estimating equations. The results suggest that the succession plans, as stated by elderly farmers in the questionnaires, do not provide information that is significant and valuable in predicting the true, revealed successions, once certain farm and farmer characteristics are controlled for.

No description available.

The present thesis is a study compiling farm management information to be used as the basis for extensive literature for distribution to British Columbia farmers. The phases of farm management which are presented here are farm accounting, the use of farm accounts in making production plans for the farm business, and the methods of acquiring and financing farm businesses in British Columbia. An introductory chapter containing data with respect to the position of the agricultural industry in British Columbia precedes the chapters on farm management practises. A system of farm accounting, which is particularly adapted to the filing of the Federal Income Tax returns is described in the second chapter. In addition, a description of other useful farm records is given there. The third chapter is concerned with the use of the farm records in the analysis of the present farm business operation and in the formulation of future farm production plans. The final chapter is devoted to a description of the methods used in appraising a farm for purchase or lease the procedure followed in acquiring Crown land in British Columbia; the sources of loan funds available to British Columbia farmers. A sample accounting and physical records form together with a suggested lease form is appended to the thesis. / Land and Food Systems, Faculty of / Graduate