Deciphering Taxa-function Relationships in Population-level Studies of Human Gut Microbiomes

The human gut microbiome is a complex and dynamic ecosystem, featuring a multitude of microbes all interacting with their hosts in an elaborate manner. Even though this exchange is often mediated through microbial metabolic and functional outputs, such as the production of certain metabolites, environmental exposures, and host lifestyle are highly influential in shaping the presence of microbial species irrespective of their individual roles. As such, a comprehensive understanding of the microbiome requires researchers to examine the relationship between taxonomic abundance and function simultaneously. Assessing microbial contributions to important ecosystem services can enable identification of robust functions supported by a variety of species, or to identify important keystone taxa that are associated with a disease-causing biochemical pathway. The primary objective of this thesis is to assess different approaches for investigating the taxa-function relationship and evaluate its value in providing unique biological insights. First, we leveraged densely collected multi-omics data from the New Hampshire Birth Cohort Study to identify genus-metabolite pairs that are core to infant gut microbiomes. Second, we developed a novel statistical method that enables integrating taxa-function relationships in epidemiological studies. Third, we assessed microbial phenotypic traits as a potential source for defining interpretable and human-centric microbiome function

Exploiting cloud utility models for profit and ruin

A key characteristic that has led to the early adoption of public cloud computing is the utility pricing model that governs the cost of compute resources consumed. Similar to public utilities like gas and electricity, cloud consumers only pay for the resources they consume and only for the time they are utilized. As a result and pursuant to a Cloud Service Provider\u27s (CSP) Terms of Agreement, cloud consumers are responsible for all computational costs incurred within and in support of their rented computing environments whether these resources were consumed in good faith or not. While initial threat modeling and security research on the public cloud model has primarily focused on the confidentiality and integrity of data transferred, processed, and stored in the cloud, little attention has been paid to the external threat sources that have the capability to affect the financial viability of cloud-hosted services. Bounded by a utility pricing model, Internet-facing web resources hosted in the cloud are vulnerable to Fraudulent Resource Consumption (FRC) attacks. Unlike an application-layer DDoS attack that consumes resources with the goal of disrupting short-term availability, a FRC attack is a considerably more subtle attack that instead targets the utility model over an extended time period. By fraudulently consuming web resources in sufficient volume (i.e. data transferred out of the cloud), an attacker is able to inflict significant fraudulent charges to the victim. This work introduces and thoroughly describes the FRC attack and discusses why current application-layer DDoS mitigation schemes are not applicable to a more subtle attack. The work goes on to propose three detection metrics that together form the criteria for detecting a FRC attack from that of normal web activity and an attribution methodology capable of accurately identifying FRC attack clients. Experimental results based on plausible and challenging attack scenarios show that an attacker, without knowledge of the training web log, has a difficult time mimicking the self-similar and consistent request semantics of normal web activity necessary to carryout a successful FRC attack

A simulation approach for increased safety in advanced C-ITS scenarios

Com os recentes desenvolvimentos em diferentes áreas de conhecimento, como redes de comunicação sem fio e sensores, bem como a evolução recente em vários tópicos na área da Computação, os Sistemas Inteligentes e Cooperativos de Transporte (CITSs) tornaram-se um tema muito importante, e espera-se que comecem a ser cada vez mais implementados num futuro próximo. Nesta tese, é feita uma análise sobre estes sistemas e diferentes possiveis cenários focando no cenário de Platooning, assim como sobre comunicações Veículo-a-Tudo (V2X) com foco no ETSI ITS-G5, o standard europeu mais amplamente aceite na indústria automóvel para este tipo de comunicações. O desenvolvimento de duas ferramentas de co-simulação para análise de cenários C-ITS usando comunicações veículo para veículo (V2V), foi feito no contexto desta tese. COPADRIVe é uma ferramenta de co-simulação que junta um simulador de rede e um simulador robótico. A outra ferramenta de co-simulação, é uma ferramenta hardware-in-the-loop que úne um simulador robótico com comunicações feitas através de hardware real, On-Board units (OBUs). Ambas as ferramentas foram desenvolvidas e usadas como forma de análise e teste de situações de Platooning e componentes de software para implementação neste tipo de cenários. Este desenvolvimento teve origem na necessidade de existência deste tipo de ferramentas para suporte dos desenvolvimentos feitos no contexto dos Projetos europeus de I&D SafeCOP e ENABLE-S3, onde o CISTER participava ativamente.With the developments in different areas like Wireless Communication Networks and sensors, as well as, the recent evolution on various topics on Computing, Cooperative Intelligent Transportation Systems(C-ITSs) became a hot topic for research, and are expected to be increasingly deployed in the future. From the different possible scenarios, in this thesis, we focus in analyzing Cooperative Platooning and particularly, in enabling a set of simulation tools capable of encompassing the supporting Vehicle-to-Everything(V2X) communications guaranteed by the ETSI ITS-G5, the most widely accepted European standard on the automotive industry for these kind of communications. Therefore this thesis presents the development of two co-simulation tools for analysis of C-ITS scenarios using Vehicle-to-Vehicle(V2V) communications. First, COPADRIVe is a co-simulation tool joining together a network simulator and a robotic simulator. The other co-simulation tool, uses a a hardware-in-theloop approach one bridging a robotic simulator with real communications via OnBoard-Units (OBUs). Both tools were developed and used as the means to test and analyze Platooning scenarios and software components relevant in such applications, importantly. These tools’ were developed in line with the R&D European Projects SafeCOP and ENABLE-S3, where CISTER was and active participant