28 research outputs found

    The Implementation of Analytical Hierarchy Process Method for Determining Livestock Alabio Duck Development Strategy in Rawa Hulu Sungai Utara

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    The cultivation of Alabio ducks (Anas Platyrynchos Borneo) so far is still natural and only involves one parameter; furthermore, each location has different characteristics. The hierarchical structure constructed has a ranking of importance as an alternative option for ducks' development in peatland ecosystems. This research aims to formulate a strategy for duck production in the Hulu Sungai Utara Regency. AHP (Analytical Hierarchy Process) method in this study is used to structure the decision-making flow from goals and alternatives and weigh the variables. Data collection was carried out with duck farming experts from academia, farmer groups, and policymakers. This study found that the availability of feed, both sago (0.254) and bran (0.218), is a significant component from an ecological perspective. Distance to market (0.307) and hatchery location (0.287) is an economic variable. The social part consists of distance from the settlement (0.443) and labor availability (0.247). Meanwhile, the availability of feed (0.282), hatchery technology (0.269), and Mina ducks (0.251) are the development strategies for duck cultivation in swamp areas, and economic stimulus (0.93) is the final contributor.The cultivation of Alabio ducks (Anas Platyrynchos Borneo) so far is still natural and only involves one parameter; furthermore, each location has different characteristics. The hierarchical structure constructed has a ranking of importance as an alternative option for ducks' development in peatland ecosystems. This research aims to formulate a strategy for duck production in the Hulu Sungai Utara Regency. AHP (Analytical Hierarchy Process) method in this study is used to structure the decision-making flow from goals and alternatives and weigh the variables. Data collection was carried out with duck farming experts from academia, farmer groups, and policymakers. This study found that the availability of feed, both sago (0.254) and bran (0.218), is a significant component from an ecological perspective. Distance to market (0.307) and hatchery location (0.287) is an economic variable. The social part consists of distance from the settlement (0.443) and labor availability (0.247). Meanwhile, the availability of feed (0.282), hatchery technology (0.269), and Mina ducks (0.251) are the development strategies for duck cultivation in swamp areas, and economic stimulus (0.93) is the final contributor

    Modélisation, simulation et analyse des dynamiques spatiales des zones humides urbaines par automate cellulaire : une étude de cas à la ville de Bogota, Colombie

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    Les zones humides sont Ă©cosystĂšmes reconnus de vitale importance pour la conservation de la biodiversitĂ© et pour un dĂ©veloppement soutenable. En Colombie, 26 % du territoire continental national est couvert de ces Ă©cosystĂšmes. Le complexe de zones humides urbaines de Bogota, en fait partie, avec 15 Ă©cosystĂšmes, dont la Convention Ramsar reconnaĂźt 11. Ils sont uniques et jouent un rĂŽle important dans l’approvisionnement des services Ă©cosystĂšmes Ă  la zone urbaine. Cependant, ces Ă©cosystĂšmes urbains font face Ă  de nombreux dĂ©fis en raison de leur emplacement. Les causes et les consĂ©quences de leur transformation sont trĂšs complexes. En appliquant des approches des systĂšmes complexes, sa dynamique de changement peut ĂȘtre Ă©tudiĂ©e. Les automates cellulaires sont l’une des techniques largement utilisĂ©es dans la modĂ©lisation de la dynamique spatiotemporelle des changements de l’usage et de l’occupation des sols. Cette Ă©tude propose l’analyse et la simulation des zones humides urbaines en appliquant une approche hybride par un modĂšle couplĂ© de chaĂźne de Markov, de rĂ©seaux de neurones artificiels et d’automates cellulaires, afin d’estimer leurs changements d’étendue pour les annĂ©es 2016, 2022, 2028 et 2034 dans la ville de Bogota, en Colombie. Pour extraire le changement d’occupation et d’utilisation du sol, trois images analogues des annĂ©es 1998, 2004 et 2010 ont Ă©tĂ© a utilisĂ©es. Les rĂ©sultats ont montrĂ© une diminution de 0,30 % de la couverture des zones humides en douze ans. De plus, les rĂ©sultats suggĂšrent que la couverture des zones humides reprĂ©sentera 1,97 % de la zone d’étude totale en 2034, reprĂ©sentant une probabilitĂ© de diminution de 14 % en 24 ans. D’ailleurs, en appliquant l’analyse d’intensitĂ©, il a Ă©tĂ© constatĂ© que le gain de cultures et de pĂąturages cible la perte de zones humides. Bien dont ces Ă©cosystĂšmes soient protĂ©gĂ©s et d’utilisation restreinte, leur patron de rĂ©duction se poursuivra en 2034. La pertinence de ce projet rĂ©side dans sa contribution potentielle au processus dĂ©cisionnel au sein de la ville et en tant qu’instrument de gestion des ressources naturelles. En outre, les rĂ©sultats de cette Ă©tude pourraient aider Ă  atteindre l’objectif de dĂ©veloppement durable 6 « Eau propre et assainissement » et l’attĂ©nuation du changement climatique.Wetlands are ecosystems recognized as being of vital importance for the conservation of biodiversity and for sustainable development. In Colombia, 26% of the national continental territory is covered by these ecosystems. The complex of urban wetlands of Bogota is one of them, with 15 ecosystems, of which the Ramsar Convention recognizes 11. They are unique and play an important role in providing ecosystem services to the urban area. However, these urban ecosystems face many challenges due to their location. The causes and consequences of their transformation are very complex. By applying complex systems approaches, the dynamics of change can be studied. Cellular automata is one of the widely used techniques in modeling the spatiotemporal dynamics of land use and land cover changes. This study proposes the analysis and simulation of urban wetlands by applying a hybrid approach through a coupled model of the Markov chain, artificial neural networks, and cellular automata, in order to estimate the extent of changes for the years 2016, 2022, 2028, and 2034 in the city of Bogota, Colombia. To extract the change in land cover and land use, three analogous images from the years 1998, 2004, and 2010 were used. The results showed a 0.30% decrease in wetland coverage in twelve years. Furthermore, the results suggest that wetland cover will be 1.97% of the total study area in 2034, representing a 14% probability of a decrease in 24 years. Moreover, by applying the intensity analysis, it was found that the gain of crop and pastureland targets the loss of wetlands. Although these ecosystems are protected and of limited use, their pattern of reduction will continue in 2034. The relevance of this project lies in its potential contribution to decision-making within the city and as a natural resource management tool. In addition, the results of this study could help achieve Sustainable Development Goal 6 “Clean Water and Sanitation” and climate change mitigation

    Integrating host population contact structure and pathogen whole-genome sequence data to understand the epidemiology of infectious diseases : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy, Massey University, Manawatƫ, New Zealand

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    With advances in high-throughput sequencing technologies, computational biology, and evolutionary modelling, pathogen sequence data is increasingly being used to inform infectious disease outbreak investigations; supporting inferences on the timing and directionality of transmission as well as providing insights into pathogen evolutionary dynamics and the development of antimicrobial resistance. This thesis focuses on the application of pathogen whole-genome sequence data in conjunction with social network analysis to investigate the transmission dynamics of two important pathogens; Campylobacter jejuni and Staphylococcus aureus. The first four studies centre around the recent emergence of an antimicrobial-resistant C. jejuni strain that was found to have rapidly spread throughout the New Zealand commercial poultry industry. All four studies build on the results of an industry survey that were not only used to determine the basic farm demographics and biosecurity practices of all poultry producers, but also to construct five contact networks representing the on- and off-farm movement patterns of goods and services. Contact networks were used in study one to investigate the relationship between farm-level contact risk pathways and the reported level of biosecurity. However, despite many farms having a number of contact risk pathways, no relationship was found due to the high level of variability in biosecurity practices between producers. In study two the contact risk between commercial poultry, backyard poultry, and wild birds was investigated by examining the spatial overlap between the commercial contact networks and (i) all poultry transactions made through the online auction website TradeMeÂź and, (ii) all wild bird observations made through the online citizen science bird monitoring project, eBird, with study results suggesting that the greatest risk is due to the growing number of online trades made over increasingly long distances and shorter timespans. Study three further uses the commercial contact networks to investigate the role of multiple transmission pathways on the genetic relatedness of 167 C. jejuni isolates sampled from across 30 commercial poultry farms. Permutational multivariate analysis of variance and distance-based linear models were used to explore the relative importance of network distances as potential determinants of the pairwise genetic relatedness between the C. jejuni isolates, with study results highlighting the importance of transporting feed vehicles in addition to the geographical proximity of farms and the parent company in the spread of disease. In the last of the four C. jejuni studies, a compartmental disease transmission model was developed to simulate both the spread and sequence mutations across an outbreak within the commercial poultry industry. Simulated sequences were used in an analysis mirroring the methods used in study three in order to validate the approaches examining the contribution of local contacts and network contacts towards disease transmission. An additional analysis is also performed in which the simulated sequence data is used to infer a transmission tree and explore the use of pathogen phylogenies in determining who-infected-whom across different model systems. A further study, motivated by the application of whole-genome sequence data to infer transmission, investigated the spread of S. aureus within the New Zealand dairy industry. This study demonstrated how whole-genome sequence data can be used to investigate pathogen population and evolutionary dynamics at multiple scales: from local to national and international. For this study, the genetic relatedness between 57 bovine-derived S. aureus isolates sampled from across 17 New Zealand dairy herds were compared with 59 S. aureus isolates that had been previously sampled and characterised from humans and domestic pets from across New Zealand and 103 S. aureus isolates extracted from GenBank that included both human and livestock isolates sampled from across 19 countries. Results from this study not only support evidence showing that the movement of live animals is an important risk factor for the spread of S. aureus, but also show that using cattle-tracing data alone may not be enough to fully capture the between farm transmission dynamics of S. aureus. Overall, by using these two pathogen examples, this thesis demonstrates the potential use of pathogen whole-genome sequence data alongside contact network data in an epidemiological investigation, whilst highlighting the limitations and future challenges that must be considered in order to continue to develop robust methods that can be used to reliably infer the transmission and evolutionary dynamics across a range of infectious diseases

    Strategies for efficient foraging in a deep-diving bird; the imperial shag (Phalacrocorax atriceps).

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    Predators are frequently involved in an arms race with their prey, with improved abilities on one side demanding compensatory improvements on the other. Those that breathe air but forage underwater are faced with the additional challenge of capturing prey in a medium where their own capacity to remain is limited. This thesis examines some of the strategies used by my model organism, the imperial shag (Phalacrocorax atriceps) to enhance its foraging efficiency. I did this by using recent developments in animal-attached technology to measure the patterns and costs of bird behaviour during foraging at a fine-scale. Time appeared to be of the essence for these birds, as their movements were consistent with a strategy to maximise the rate of energy gain. Male and female shags were found to forage at depths where their foraging efficiency was maximised, which manifested itself in the horizontal segregation of male and female foraging areas. Analysis of the mechanical power used underwater suggested that these birds may be limited in the burst speeds they can produce at shallow depths; as the greater the power required to counteract their buoyancy the less is available for prey pursuit. Finally, analysis of the fine-scale tortuosity in the foraging movements of imperial shags revealed that the distribution of their prey was not aggregated at the scales over which they forage. Nevertheless, tortuosity was a good indicator of prey ingestion rates and revealed that shags adjusted their movements to recent prey encounter within both prey-searching and resting phases. This work indicates that imperial shags have an extensive armoury of strategies by which they may increase their efficiency as underwater predators, and methods used and refined in this thesis mean that users are now well-equipped to investigate them

    Transmission dynamics of Avian Influenza A virus

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    Influenza A virus (AIV) has an extremely high rate of mutation. Frequent exchanges of gene segments between different AIV (reassortment) have been responsible for major pandemics in recent human history. The presence of a wild bird reservoir maintains the threat of incursion of AIV into domestic birds, humans and other animals. In this thesis, I addressed unanswered questions of how diverse AIV subtypes (classified according to antigenicity of the two surface proteins, haemagglutinin and neuraminidase) evolve and interact among different bird populations in different parts of the world, using Bayesian phylogenetic methods with large datasets of full genome sequences. Firstly, I explored the reassortment patterns of AIV internal segments among different subtypes by quantifying evolutionary parameters including reassortment rate, evolutionary rate and selective constraint in time-resolved Bayesian tree phylogenies. A major conclusion was that reassortment rate is negatively associated with selective constraint and that infection of wild rather than domestic birds was associated with a higher reassortment rate. Secondly, I described the spatial transmission pattern of AIV in China. Clustering of related viruses in particular geographic areas and economic zones was identified from the viral phylogeographic diffusion networks. The results indicated that Central China and the Pearl River Delta are two main sources of viral out flow; while the East Coast, especially the Yangtze River delta, is the major recipient area. Simultaneously, by applying a general linear model, the predictors that have the strongest impact on viral spatial diffusion were identified, including economic (agricultural) activity, climate, and ecology. Thirdly, I determined the genetic and phylogeographic origin of a recent H7N3 highly pathogenic avian influenza outbreak in Mexico. Location, subtype, avian host species and pathogenicity were modelled as discrete traits and jointly analysed using all eight viral gene segments. The results indicated that the outbreak AIV is a novel reassortant carried by wild waterfowl from different migration flyways in North America during the time period studied. Importantly, I concluded that Mexico, and Central America in general, might be a potential hotspot for AIV reassortment events, a possibility which to date has not attracted widespread attention. Overall, the work carried out in this thesis described the evolutionary dynamics of AIV from which important conclusions regarding its epidemiological impact in both Eurasia and North America can be drawn
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