367 research outputs found

    Ecological and evolutionary drivers of microbial community structure in termite guts

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    Presumably descending from subsocial cockroaches 150 million years ago, termites are an order of social insects that gained the ability to digest wood through the acquisition of cellulolytic flagellates. These eukaryotic protists fill up the bulk of the hindgut volume and are the major habitat of the prokaryotic community present in the digestive tract of lower termites. The complete loss of gut flagellates in the youngest termite family Termitidae, also called higher termites, led to an entirely prokaryotic gut microbiota as well as a substantial dietary diversification and enormous ecological success. While the subfamily Macrotermitinae established a symbiosis with wood-degrading fungi of the genus Termitomyces, other higher termites exploit diets with a higher degree of humification. Previous studies on the gut communities of termites have observed that while the gut microbiota of closely related hosts is very similar, those of more distantly related hosts are characterized by considerable differences in gut communities. Since these observations are based on highly limited samplings of hosts, it is uncertain if these differences reflect important evolutionary patterns. This dissertation includes studies examining the archaeal and bacterial diversity of the gut microbiota over a wide range of termites using high-throughput sequencing of the 16S rRNA genes. In comparison to the rather simple archaeal communities, which were mainly composed of methanogens, the bacterial gut microbiota were characterized by considerably higher diversity. At the phylum-level, Bacteroidetes, Firmicutes, Proteobacteria and Spirochaetes were ubiquitously distributed among the termites, albeit with differences in relative abundance. Other phyla, however, such as Elusimicrobia, Fibrobacteres and the candidate division TG3, occured only in certain host groups of termites. The distribution pattern of archaeal and bacterial lineages reflects both host phylogeny and differences in the digestive strategy of the host. Although several genus-level bacterial lineages showed a certain degree of host-specificity, phylogenetic analyses of the amplified rRNA genes showed that these bacterial lineages do not appear to be cospeciating with their hosts. The findings of studies included in this dissertation and other published studies were evaluated to identify potential drivers of community structure and other shaping mechanisms. Thus, gut community structure in termites is primarily shaped by habitat and niche selection. The stochastic element of these mechanisms, however, is strongly attenuated by proctodeal trophallaxis, which facilitates coevolution and might ultimately lead to cospeciation. While coevolution is likely true for many lineages and documented by host-specific microbial lineages, there is only little evidence of cospeciation in the gut microbiota of termites. If present, it is restricted almost exclusively to flagellates and their symbionts in lower termites. The higher wood-feeding termites have long been associated with a marked abundance of the phyla Fibrobacteres and cand. div. TG3. Although these phyla have been shown to be members of a specific cellulolytic community associated with wood particles in the hindguts of higher termites, their full functional potential still remains unknown. In order to elucidate the role of these organisms, a study in this dissertation carries out metagenomic analyses of various higher termites. In wood-feeding representatives, Fibrobacteres and cand. div. TG3 were in fact highly abundant, but only a few or no genes could be assigned to both groups by the usual database-dependent classification programs due to the lack of suitable genomes in these databases. In response, a new study was conceived to compensate this discrepancy. By further development of a new reference-independent method, over 30 population genomes of Fibrobacteres and cand. div. TG3 could be reconstructed from the metagenomic data sets. Subsequent comparative analysis revealed that organisms of both groups differ in their potential of wood degradation, but likely complement each other. Further analyses indicate that representatives of both groups might be able to fix nitrogen and respire under hypoxic conditions — two favourable adaptations to the unique termite gut environment

    Abstracts of Papers, 88th Annual Meeting of the Virginia Academy of Science

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    Full list of Abstracts from the 88th Annual Meeting of the Virginia Academy of Science, May 20 - 21, 2010, James Madison University Harrisonburg, V

    Vulnerability detection in device drivers

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    Tese de doutoramento, Informática (Ciência da Computação), Universidade de Lisboa, Faculdade de Ciências, 2017The constant evolution in electronics lets new equipment/devices to be regularly made available on the market, which has led to the situation where common operating systems (OS) include many device drivers(DD) produced by very diverse manufactures. Experience has shown that the development of DD is error prone, as a majority of the OS crashes can be attributed to flaws in their implementation. This thesis addresses the challenge of designing methodologies and tools to facilitate the detection of flaws in DD, contributing to decrease the errors in this kind of software, their impact in the OS stability, and the security threats caused by them. This is especially relevant because it can help developers to improve the quality of drivers during their implementation or when they are integrated into a system. The thesis work started by assessing how DD flaws can impact the correct execution of the Windows OS. The employed approach used a statistical analysis to obtain the list of kernel functions most used by the DD, and then automatically generated synthetic drivers that introduce parameter errors when calling a kernel function, thus mimicking a faulty interaction. The experimental results showed that most targeted functions were ineffective in the defence of the incorrect parameters. A reasonable number of crashes and a small number of hangs were observed suggesting a poor error containment capability of these OS functions. Then, we produced an architecture and a tool that supported the automatic injection of network attacks in mobile equipment (e.g., phone), with the objective of finding security flaws (or vulnerabilities) in Wi-Fi drivers. These DD were selected because they are of easy access to an external adversary, which simply needs to create malicious traffic to exploit them, and therefore the flaws in their implementation could have an important impact. Experiments with the tool uncovered a previously unknown vulnerability that causes OS hangs, when a specific value was assigned to the TIM element in the Beacon frame. The experiments also revealed a potential implementation problem of the TCP-IP stack by the use of disassociation frames when the target device was associated and authenticated with a Wi-Fi access point. Next, we developed a tool capable of registering and instrumenting the interactions between a DD and the OS. The solution used a wrapper DD around the binary of the driver under test, enabling full control over the function calls and parameters involved in the OS-DD interface. This tool can support very diverse testing operations, including the log of system activity and to reverse engineer the driver behaviour. Some experiments were performed with the tool, allowing to record the insights of the behaviour of the interactions between the DD and the OS, the parameter values and return values. Results also showed the ability to identify bugs in drivers, by executing tests based on the knowledge obtained from the driver’s dynamics. Our final contribution is a methodology and framework for the discovery of errors and vulnerabilities in Windows DD by resorting to the execution of the drivers in a fully emulated environment. This approach is capable of testing the drivers without requiring access to the associated hardware or the DD source code, and has a granular control over each machine instruction. Experiments performed with Off the Shelf DD confirmed a high dependency of the correctness of the parameters passed by the OS, identified the precise location and the motive of memory leaks, the existence of dormant and vulnerable code.A constante evolução da eletrónica tem como consequência a disponibilização regular no mercado de novos equipamentos/dispositivos, levando a uma situação em que os sistemas operativos (SO) mais comuns incluem uma grande quantidade de gestores de dispositivos (GD) produzidos por diversos fabricantes. A experiência tem mostrado que o desenvolvimento dos GD é sujeito a erros uma vez que a causa da maioria das paragens do SO pode ser atribuída a falhas na sua implementação. Esta tese centra-se no desafio da criação de metodologias e ferramentas que facilitam a deteção de falhas nos GD, contribuindo para uma diminuição nos erros neste tipo de software, o seu impacto na estabilidade do SO, e as ameaças de segurança por eles causadas. Isto é especialmente relevante porque pode ajudar a melhorar a qualidade dos GD tanto na sua implementação como quando estes são integrados em sistemas. Este trabalho inicia-se com uma avaliação de como as falhas nos GD podem levar a um funcionamento incorreto do SO Windows. A metodologia empregue usa uma análise estatística para obter a lista das funções do SO que são mais utilizadas pelos GD, e posteriormente constrói GD sintéticos que introduzem erros nos parâmetros passados durante a chamada às funções do SO, e desta forma, imita a integração duma falta. Os resultados das experiências mostraram que a maioria das funções testadas não se protege eficazmente dos parâmetros incorretos. Observou-se a ocorrência de um número razoável de paragens e um pequeno número de bloqueios, o que sugere uma pobre capacidade das funções do SO na contenção de erros. Posteriormente, produzimos uma arquitetura e uma ferramenta que suporta a injeção automática de ataques em equipamentos móveis (e.g., telemóveis), com o objetivo de encontrar falhas de segurança (ou vulnerabilidades) em GD de placas de rede Wi-Fi. Estes GD foram selecionados porque são de fácil acesso a um atacante remoto, o qual apenas necessita de criar tráfego malicioso para explorar falhas na sua implementação podendo ter um impacto importante. As experiências realizadas com a ferramenta revelaram uma vulnerabilidade anteriormente desconhecida que provoca um bloqueio no SO quando é atribuído um valor específico ao campo TIM da mensagem de Beacon. As experiências também revelaram um potencial problema na implementação do protocolo TCP-IP no uso das mensagens de desassociação quando o dispositivo alvo estava associado e autenticado com o ponto de acesso Wi-Fi. A seguir, desenvolvemos uma ferramenta com a capacidade de registar e instrumentar as interações entre os GD e o SO. A solução usa um GD que envolve o código binário do GD em teste, permitindo um controlo total sobre as chamadas a funções e aos parâmetros envolvidos na interface SO-GD. Esta ferramenta suporta diversas operações de teste, incluindo o registo da atividade do sistema e compreensão do comportamento do GD. Foram realizadas algumas experiências com esta ferramenta, permitindo o registo das interações entre o GD e o SO, os valores dos parâmetros e os valores de retorno das funções. Os resultados mostraram a capacidade de identificação de erros nos GD, através da execução de testes baseados no conhecimento da dinâmica do GD. A nossa contribuição final é uma metodologia e uma ferramenta para a descoberta de erros e vulnerabilidades em GD Windows recorrendo à execução do GD num ambiente totalmente emulado. Esta abordagem permite testar GD sem a necessidade do respetivo hardware ou o código fonte, e possuí controlo granular sobre a execução de cada instrução máquina. As experiências realizadas com GD disponíveis comercialmente confirmaram a grande dependência que os GD têm nos parâmetros das funções do SO, e identificaram o motivo e a localização precisa de fugas de memória, a existência de código não usado e vulnerável

    J. EDGAR HOOVER AND THE RHETORICAL RISE OF THE FBI: THE PUBLIC CAMPAIGNS AGAINST VERMIN, THE FIFTH COLUMN, AND RED FASCISM.

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    This project examines J. Edgar Hoover's rhetorical leadership of the Federal Bureau of Investigation during the Franklin D. Roosevelt and Harry S Truman administrations (1933-1953). Hoover launched and sustained a concerted domestic propaganda program that helped enhance his own political power and invented the FBI as a central force in domestic and international matters. In the process, he re-envisioned conceptions of U.S. citizenship by promoting notions of idealized citizenship. Hoover entered law enforcement and U.S. politics during the early decades of the twentieth century--a time of increased use of public campaigns sponsored by the U.S. government and presidential administrations to alter public opinion on important policy matters. This period witnessed, for example, the country's experimentation with domestic propaganda during World War I. While the Soviet Union and Germany used disease, vermin, parasite, and body metaphors to organize their own domestic propaganda campaigns in the following decades, Hoover used these same metaphors to advance the need to purify America and exterminate its social pariah. Through his public campaigns against vermin (1933-1939), the Fifth Column (1939-1945), and Red Fascism (1945-1953), Hoover constructed a reality in which corruption and subversion were immutable elements of democratic life. Increasingly, Hoover's tactics of threat and intimidation began to mimic the tactics of threat practiced by America's enemies, moving the country closer to what many at the time called a police state. Hoover's coupling of propaganda and coercive tactics ultimately helped him to rapidly expand the FBI and undermine his superiors and counterparts in the executive, legislative, and judicial branches of government. Whereas Roosevelt benefited politically from building up a secret police force, Truman inherited a cunning FBI director eager to use his power to expand and exploit the rhetorical presidency during the Red Scare

    Text miner's little helper: scalable self-tuning methodologies for knowledge exploration

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    L'abstract è presente nell'allegato / the abstract is in the attachmen

    Assessing the success and evaluating the benefits of government-sponsored regional internet-trading platforms for small and medium enterprises: A Western Australian perspective

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    The Internet has been viewed as an opportunity for small and medium enterprises (SMEs) to efficiently compete in the global arena with their larger counterparts by overcoming distance and size. However, research has shown that actual uptake of Internet e-commerce by SMEs has been lagging behind that of larger companies. Fearing a growing digital divide between large companies and SMEs, some governments have taken specific measures to encourage SME participation in ecommerce. One of the more direct government initiatives to hasten the progression of SMEs on the e-commerce adoption curve is the creation, sponsorship and management of regional Internet trading platforms for these enterprises. Such a move is predicated on the belief that these platforms will offer SMEs a low-cost introduction to participation in Internet trading platforms without the need for significant technology investments, allowing them to reap benefits like lower costs, improved customer service and new levels of innovation through knowledge-sharing

    EduVentures WebExpedition

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    This project, sponsored by EduVentures and the National Museum of Namibia, sought to increase Namibian secondary students\u27 awareness of biodiversity by creating and deploying a computer game called WebExpedition. We received input from teachers and students to optimize the game\u27s usefulness and effectiveness, and performed trial runs with Namibian students. The game teaches students about scientific classification of organisms, and allows students to connect animals and plants to their habitats in Namibia

    Qualitive and quantitive mass spectrometric analysis of neuroactive substances from single insect neurons

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    Organisms need to constantly adapt their behavior to the changing environment as well as react towards changes in their internal state. The nervous system perceives and processes such stimuli and coordinates the corresponding reactions of the body. This system is based on regulated cell-cell communication, utilizing a wide range of different chemical signaling molecules and receptors. If one wants to fully grasp how neural circuits process, modulate and relay incoming information, then the involved neuroactive substances, their cellular distribution, temporal and quantitative dynamics have to be analyzed on single cell resolution. Single cell mass spectrometry (SCMS) allows the interrogation of chemical profiles from individual cells, including neuroactive substances such as neuropeptides and biogenic amines. Matrix assisted laser desorption/ionization – time-of-flight mass spectrometry (MALDI-TOF MS) has established itself as a fast and reliable tool for the analysis of neuropeptides from single neurons of invertebrates and vertebrates alike. However, the detection of small signaling molecules, such as biogenic monoamines, by MALDI-TOF SCMS has been challenging. Biogenic monoamines play key roles in orchestrating and modulating neural circuits, therefore a MALDI-TOF SCMS based method for their detection and quantification is highly desirable. Additionally, biogenic monoamines can be co-localized with neuropeptides. Therefore the development of a MALDI-TOF SCMS based method capable of detecting both neuroactive substances would help to reveal such overlapping expression profiles. In the current thesis, I focused on the development of a MALDI-TOF SCMS based method that allows the detection and quantification of biogenic monoamines from single somata of insect neurons. The study focused on the insect octopaminergic/tyraminergic system, with an emphasis on octopamine (OA), which is considered to be homologous to the vertebrate noradrenalin/adrenalin system. By using chemical derivatization of amine moieties of OA and tyramine (TA) and an optimized sample preparation, I was able to lower the respective detection limits to single cell concentrations. Additionally, I could show that the chemical derivatization does not interfere with the detection of neuropeptides from the same sample, hence allowing the simultaneous detection of both substance classes. Further, I could show that absolute quantification of OA and TA is possible from single cell sample volumes using isotopically labeled synthetic standards. I used the developed protocol for the qualitative and quantitative analysis of OA/TA from genetically labeled and manually microdissected somata of interneurons from the fruit fly Drosophila melanogaster. Using the newly developed approach, I analyzed intracellular OA/TA ratios, compared somatic OA titers between sexes and two different OAergic cell clusters and revealed that prolonged cooling of animals has an increasing effect on detectable OA titers in the analyzed neurons. Furthermore, I used the developed protocol to analyze changes in somatic OA titers of aggression modulating OAergic neurons from the gnathal ganglion in socially naive and experienced adult male D. melanogaster. I could show that the somatic OA titer increases in these neurons when flies had social contact with the same sex compared to naive flies, which is possibly mediated by an input from pheromone detecting gustatory receptor neurons. To my knowledge, this is the first study to report a quantified increase of a somatic biogenic monoamine titer detected directly from individual isolated neurons of intact insect brains between two behavioral states by mass spectrometric analysis. In a collaborative study, I employed the developed protocol to intracellular recorded descending dorsal unpaired median neurons from the Indian stick insect Carausius morosus and was able to confirm that these neurons contain OA and TA and thus could be OAergic. Finally, as a starting point in an effort to create a map of neuropeptidergic neurons and their repertoire of neuroactive substances in adult D. melanogaster, I was involved in the analysis of single genetically labeled neuropeptidergic neuron somata using MALDI-TOF SCMS. In summary, we could describe a total of 10 different cell types characterized by their expressed neuropeptides and their location in the CNS. Future studies will focus on analyzing these cell types towards potential co-localized aminergic transmitters using the developed protocol
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