Equine herpesvirus type 1 (EHV-1) is a common pathogen of horses that typically causes upper respiratory disease, however is also associated with late-term abortion, neonatal foal death and neurologic disease. Once a horse is infected, the virus concentrates to local lymphoid tissue, where it becomes latent. The virus can recrudesce during times of stress, which can lead to the initiation of devastating outbreaks. Some variants of EHV-1 have been associated with more severe disease outcomes. Appropriate outbreak management focuses on minimizing the movement of potentially exposed horses. This approach lacks a strategy for prevention at the level of latency largely due to a knowledge paucity in regards to carriage rate of latent EHV-1. Biosecurity decisions are also dependent on awaiting currently-available diagnostic testing that often take several days for results. Thus, our work has been focused on understanding the carriage rate of the latent virus in different geographic regions as well as improving diagnostic efficiency, both of which are essential for improving the management of EHV-1 disease. Loop mediated isothermal amplification (LAMP) is a method that amplifies nucleic acid rapidly at a constant temperature and is minimally affected by inhibitors that are often found in clinical samples. This procedure can be followed by multiple detection methods. A new, efficient sequencing method, called nanopore sequencing, has been developed in a handheld device, called MinION, that provides thorough output in a timely manner. When combined with LAMP, it has been referred to as LAMPore. The first objective of our work was to estimate the prevalence of latent EHV-1 and compare the frequency of each variant in the submandibular lymph nodes from horses in Virginia. Our second objective was to perform direct DNA sequencing of EHV-1 using the mobile MinION sequencer in combination with LAMP viral enrichment. Our findings demonstrated a low apparent prevalence of latent EHV-1 DNA in submandibular lymph nodes in this population of horses in Virginia as well as successful detection and identification of EHV-1 in equine nasal swab samples using LAMPore sequencing. / Doctor of Philosophy / Horses can develop disease from a virus called equine herpesvirus type 1 (EHV-1). Symptoms can vary from mild respiratory signs to the inability to rise leading to death or euthanasia. Horses transmit this virus to other nearby horses; however, the virus also becomes dormant once a horse is infected, meaning the virus is not infectious but is present within the animal. When the horse undergoes stress, such as during travel or competition, the virus can become active again, leading to the spread to other horses. This results in outbreaks, many of which are devastating to the equine industry. In order to minimize the risks of this virus spreading and causing disease, management is currently focused on minimizing the movement of horses that may have been exposed to the virus. There is little information regarding the number of horses that harbor the dormant virus and the current methods to detect the infectious virus can take multiple days for results. These limit decision-making during the management of an outbreak. Our work seeks to determine the number of horses in a region that harbor EHV-1 and also to test a new, efficient diagnostic method to identify the virus in samples from horses. Our findings showed a low number of horses in Virginia harbor dormant EHV-1 in the lymph nodes under their mandible, a common site of dormancy. Further, we found that our new method of detection was effective in identifying the virus in samples from nasal secretions from horse.

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Can we find people infected with the flu virus even though they did not visit a doctor? Can the temporal features of a trending hashtag or a keyword indicate which topic it belongs to without any textual information? Given a history of interactions between blogs and news websites, can we predict blogs posts/news websites that are not in the sample but talk about the "the state of the economy" in 2008? These questions have two things in common: a network (social networks or human contact networks) and a virus (meme, keyword or the flu virus) diffusing over the network. We can think of interactions like memes, hashtags, influenza infections, computer viruses etc., as viruses spreading in a network. This treatment allows for the usage of epidemiologically inspired models to study or model these interactions. Understanding the complex propagation dynamics involved in information diffusion with the help of these models uncovers various non-trivial and interesting results. In this thesis we propose (a) A fast and efficient algorithm NetFill, which can be used to find quantitatively and qualitatively correct infected nodes, not in the sample and finding the culprits and (b) A method, SansText that can be used to find out which topic a keyword/hashtag belongs to just by looking at the popularity graph of the keyword without textual analysis. The results derived in this thesis can be used in various areas like epidemiology, news and protest detection, viral marketing and it can also be used to reduce sampling errors in graphs. / Master of Science

Para analisar o número e tamanho dos linfonodos mediastinais, cinqüenta cadáveres de brasileiros adultos foram dissecados de acordo com o mapa de Naruke/ATS-LCSG (1997). Foram retirados 1742 linfonodos, com 2,58±1,89 linfonodos por região, e realizadas suas medidas por processo digital. O tamanho médio da área, eixo maior e menor foi maior na cadeia 7 (195mm2, 18,75mm e 10,92mm) e 4R (115mm2, 13,72mm e 8,30mm), apresentando média de 49,41mm2, 9,40mm e 5,76mm para as demais regiões, respectivamente. A distribuição, número e tamanho dos linfonodos não mudou de acordo com a idade, sexo, raça, peso ou altura, contudo o tamanho aumentou em função da coalescência por processos granulomatosos prévios, com diminuição do número total de linfonodos / To analyze the number and sizes of the lymph nodes in the mediastinum, fifth human adult cadavers were dissected according to the Naruke/ATS-LCSG map (1997). It were removed 1742 lymph nodes, with 2,58±1,89 nodes for each region, and measured by a digital process. The mean area, long and minor axis were larger in regions 7 (195mm2, 18,75mm and 10,92mm) and 4R (115mm2, 13,72mm and 8,30mm), with a mean of 49,41mm2, 9,40mm and 5,76mm in the other regions, respectively. The distribution, number and size of the lymph nodes did not showed changes according age, sex, race, weight or high, however the size increases as function of coalescence by previous granulomatous processes, with decrease of the total number of lymph nodes

Para analisar o número e tamanho dos linfonodos mediastinais, cinqüenta cadáveres de brasileiros adultos foram dissecados de acordo com o mapa de Naruke/ATS-LCSG (1997). Foram retirados 1742 linfonodos, com 2,58±1,89 linfonodos por região, e realizadas suas medidas por processo digital. O tamanho médio da área, eixo maior e menor foi maior na cadeia 7 (195mm2, 18,75mm e 10,92mm) e 4R (115mm2, 13,72mm e 8,30mm), apresentando média de 49,41mm2, 9,40mm e 5,76mm para as demais regiões, respectivamente. A distribuição, número e tamanho dos linfonodos não mudou de acordo com a idade, sexo, raça, peso ou altura, contudo o tamanho aumentou em função da coalescência por processos granulomatosos prévios, com diminuição do número total de linfonodos / To analyze the number and sizes of the lymph nodes in the mediastinum, fifth human adult cadavers were dissected according to the Naruke/ATS-LCSG map (1997). It were removed 1742 lymph nodes, with 2,58±1,89 nodes for each region, and measured by a digital process. The mean area, long and minor axis were larger in regions 7 (195mm2, 18,75mm and 10,92mm) and 4R (115mm2, 13,72mm and 8,30mm), with a mean of 49,41mm2, 9,40mm and 5,76mm in the other regions, respectively. The distribution, number and size of the lymph nodes did not showed changes according age, sex, race, weight or high, however the size increases as function of coalescence by previous granulomatous processes, with decrease of the total number of lymph nodes

Wireless sensor networks(WSNs) have a diverse set of applications such as military surveillance, health and environmental monitoring, and home automation. Sensor nodes are equipped with pre-charged batteries, which drain out when the nodes sense, process, and communicate data. Eventually, the nodes of the WSN die and the network dies. Energy harvesting(EH) is a green alternative to solve the limited lifetime problem in WSNs. EH nodes recharge their batteries by harvesting ambient energy such as solar, wind, and radio energy. However, due to the randomness in the EH process and the limited amounts of energy that can be harvested, the EH nodes are often intermittently available. Therefore, even though EH nodes live perpetually, they do not cater to the network continuously. We focus on the energy-efficient design of WSNs that incorporate EH, and investigate the new design trade-offs that arise in exploiting the potentially scarce and random energy arrivals and channel fading encountered by the network. To this end, firstly, we compare the performance of conventional, all-EH, and hybrid WSNs, which consist of both conventional and EH nodes. We then study max function computation, which aims at energy-efficient data aggregation, in EH WSNs. We first argue that the conventional performance criteria used for evaluating WSNs, which are motivated by lifetime, and for evaluating EH networks are at odds with each other and are unsuitable for evaluating hybrid WSNs. We propose two new and insightful performance criteria called the k-outage and n-transmission durations to evaluate and compare different WSNs. These criteria capture the effect of the battery energies of the nodes and the channel fading conditions on the network operations. We prove two computationally-efficient bounds for evaluating these criteria, and show their use in a cost-constrained deployment of a WSN involving EH nodes. Next, we study the estimation of maximum of sensor readings in an all-EH WSN. We analyze the mean absolute error(MAE) in estimating the maximum reading when a random subset of the EH nodes periodically transmit their readings to the fusion node. We determine the optimal transmit power and the number of scheduled nodes that minimize the MAE. We weigh the benefits of the availability of channel information at the nodes against the cost of acquiring it. The results are first developed assuming that the readings are transmitted with infinite resolution. The new trade-offs that arise when quantized readings are instead transmitted are then characterized.Our results hold for any distribution of sensor readings, and for any stationary and ergodic EH process.

Over the last decade, biological sequence repositories have been growing at an exponential rate. Sophisticated indexing techniques are required to facilitate efficient searching through these humongous genetic repositories. A particularly attractive index structure for such sequence processing is the classical suffix-tree, a vertically compressed trie structure built over the set of all suffixes of a sequence. Its attractiveness stems from its linearity properties -- suffix-tree construction times are linear in the size of the indexed sequences, while search times are linear in the size of the query strings. In practice, however, the promise of suffix-trees is not realized for extremely long sequences, such as the human genome, that run into the billions of characters. This is because suffix-trees, which are typically an order of magnitude larger than the indexed sequence, necessarily have to be disk-resident for such elongated sequences, and their traditional construction and traversal algorithms result in random disk accesses. We investigate, in this thesis, post-construction techniques for disk-based suffix-tree storage optimization, with the objective of maximizing disk-reference locality during query processing. We begin by focusing on the layout reorganization in which the node-to-block assignments and sequence of blocks are reworked. Our proposed algorithm is based on combining the breadth-first layout approach advocated in the recent literature with probabilistic techniques for minimizing the physical distance between successive block accesses, based on an analysis of node traversal patterns. In our next step, we consider techniques for reducing the space overheads incurred by suffix-trees. In particular, we propose an embedding strategy whereby leaf nodes can be completely represented within their parent internal nodes, without requiring any space extension of the parent node's structure. To quantitatively evaluate the benefits of our reorganized and restructured layouts, we have conducted extensive experiments on complete human genome sequences, with complex and computationally expensive user queries that involve finding the maximal common substring matches of the query strings. We show, for the first time, that the layout reorganization approach can be scaled to entire genomes, including the human genome. In the layout reorganization, with careful choice of node-to-block assignment condition and optimized sequence of blocks, search-time improvements ranging from 25% to 75% can be achieved with respect to the construction layouts on such genomes. While the layout reorganization does take considerable time, it is a one-time process whereas searches will be repeatedly invoked on this index. The internalization of leaf nodes results in a 25% reduction in the suffix-tree space occupancy. More importantly, when applied to the construction layout, it provides search-time improvements ranging from 25% to 85%, and in conjunction with the reorganized layout, searches are speeded up by 50% to 90%. Overall, our study and experimental results indicate that through careful choice of node implementations and layouts, the disk access locality of suffix-trees can be improved to the extent that upto an order-of-magnitude improvements in search-times may result relative to the classical implementations.