2,334 research outputs found

    Advanced sequencing technologies applied to human cytomegalovirus

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    The betaherpesvirus human cytomegalovirus (HCMV) is a ubiquitous viral pathogen. It is the most common cause of congenital infection in infants and of opportunistic infections in immunocompromised patients worldwide. The large double-stranded DNA genome of HCMV (236 kb) contains several genes that exhibit a high degree of variation among strains within an otherwise highly conserved sequence. These hypervariable genes encode immune escape, tropism or regulatory factors that may affect virulence. Variation arising from these genes and from an evolutionary history of recombination between strains has been hypothesised to be linked to disease severity. To investigate this, the HCMV genome has been scrutinised in detail over the years using a variety of molecular techniques, most looking only at one or a few of these genes at a time. The advent of high-throughput sequencing (HTS) technology 20 years ago then started to enable more in-depth whole-genome analyses. My study extends this field by using both HTS and the more recently developed long-read nanopore technology to determine HCMV genome sequences directly from clinical samples. Firstly, I used an Illumina HTS pipeline to sequence HCMV strains directly from formalin-fixed, paraffin-embedded (FFPE) tissues. FFPE samples are a valuable repository for the study of relatively rare diseases, such as congenital HCMV (cCMV). However, formalin fixation induces DNA fragmentation and cross-linking, making this a challenging sample type for DNA sequencing. I successfully sequenced five whole HCMV genomes from FFPE tissues. Next, I developed a pipeline utilising the single-molecule, long-read sequencer from Oxford Nanopore Technologies (ONT) to sequence HCMV initially from high-titre cellcultured laboratory strains and then from clinical samples with high HCMV loads. Finally, I utilised a direct RNA sequencing protocol with the ONT sequencer to characterise novel HCMV transcripts produced during infection in cell culture, demonstrating the existence of transcript isoforms with multiple splice sites. Overall, my findings demonstrate how advanced sequencing technologies can be used to characterise the genome and transcriptome of a large DNA virus, and will facilitate future studies on HCMV prognostic factors, novel antiviral targets and vaccine development

    Secure storage systems for untrusted cloud environments

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    The cloud has become established for applications that need to be scalable and highly available. However, moving data to data centers owned and operated by a third party, i.e., the cloud provider, raises security concerns because a cloud provider could easily access and manipulate the data or program flow, preventing the cloud from being used for certain applications, like medical or financial. Hardware vendors are addressing these concerns by developing Trusted Execution Environments (TEEs) that make the CPU state and parts of memory inaccessible from the host software. While TEEs protect the current execution state, they do not provide security guarantees for data which does not fit nor reside in the protected memory area, like network and persistent storage. In this work, we aim to address TEEs’ limitations in three different ways, first we provide the trust of TEEs to persistent storage, second we extend the trust to multiple nodes in a network, and third we propose a compiler-based solution for accessing heterogeneous memory regions. More specifically, • SPEICHER extends the trust provided by TEEs to persistent storage. SPEICHER implements a key-value interface. Its design is based on LSM data structures, but extends them to provide confidentiality, integrity, and freshness for the stored data. Thus, SPEICHER can prove to the client that the data has not been tampered with by an attacker. • AVOCADO is a distributed in-memory key-value store (KVS) that extends the trust that TEEs provide across the network to multiple nodes, allowing KVSs to scale beyond the boundaries of a single node. On each node, AVOCADO carefully divides data between trusted memory and untrusted host memory, to maximize the amount of data that can be stored on each node. AVOCADO leverages the fact that we can model network attacks as crash-faults to trust other nodes with a hardened ABD replication protocol. • TOAST is based on the observation that modern high-performance systems often use several different heterogeneous memory regions that are not easily distinguishable by the programmer. The number of regions is increased by the fact that TEEs divide memory into trusted and untrusted regions. TOAST is a compiler-based approach to unify access to different heterogeneous memory regions and provides programmability and portability. TOAST uses a load/store interface to abstract most library interfaces for different memory regions

    WasmWalker: Path-based Code Representations for Improved WebAssembly Program Analysis

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    WebAssembly, or Wasm, is a low-level binary language that enables execution of near-native-performance code in web browsers. Wasm has proven to be useful in applications including gaming, audio and video processing, and cloud computing, providing a high-performance, low-overhead alternative to JavaScript in web development. The fast and widespread adoption of WebAssembly by all major browsers has created an opportunity for analysis tools that support this new technology. In this study, we performed an empirical analysis on the root-to-leaf paths of the abstract syntax trees in the WebAssembly Text format of a large dataset of WebAssembly binary files compiled from over 4,000 source packages in the Ubuntu 18.04 repositories. After refining the collected paths, the initial number of over 800,000 paths was reduced to only 3,352 unique paths that appeared across all of the binary files. With this insight, we propose two novel code representations for WebAssembly binaries. These novel representations serve not only to generate fixed-size code embeddings but also to supply additional information to sequence-to-sequence models. Ultimately, our approach seeks to help program analysis models uncover new properties from Wasm binaries, expanding our understanding of their potential. We evaluated our new code representation on two applications: (i) method name prediction and (ii) recovering precise return types. Our results demonstrate the superiority of our novel technique over previous methods. More specifically, our new method resulted in 5.36% (11.31%) improvement in Top-1 (Top-5) accuracy in method name prediction and 8.02% (7.92%) improvement in recovering precise return types, compared to the previous state-of-the-art technique, SnowWhite

    Modernising European Legal Education (MELE) : Innovative Strategies to Address Urgent Cross-Cutting Challenges

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    This open access book presents innovative strategies to address cross-cutting topics and foster transversal competences. The modernization of European legal education presents a compelling challenge that calls for enhanced interdisciplinary collaboration among academic disciplines and innovative teaching methods. The volume introduces venues towards education innovation and engages with complex and emerging topics such as datafication, climate change, gender, and the aftermath of the COVID-19 pandemic. The insights presented not only emphasize the importance of preserving traditional approaches to legal disciplines and passing them on to future generations, but also underscore the need to critically reassess and revolutionize existing structures. As our societies become more diverse and our understanding of legitimacy, justice, and values undergoes transformations, it is imperative to reconsider the role of traditional values while exploring promising alternative approaches

    Space Oddity: Space Cybersecurity Lessons from a Simulated OPS-SAT Attack

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    The space industry is currently experiencing a rapid transformation, driven by innovations both in space and on the ground. Lower access barriers to orbit and the widespread use of commercial off-the-shelf components have facilitated the rise of CubeSats. These small satellites, with their modular design and cost-effectiveness, enable smaller teams to engage in space operations and larger players to conduct groundbreaking technological demonstrations. Furthermore, decreasing launch costs and on-demand access to ground station services have encouraged more players to join the space industry, fostering an agile and diverse environment for experimentation. However, this growth is accompanied by significant cybersecurity challenges that demand urgent attention. Historically, the space industry has relied on security-through-obscurity, but this approach can no longer be tolerated as the industry opens up to new players and technologies. This work aims to address the often-dismissed matter of securing space vehicles, using OPS-SAT, one of the most advanced CubeSat missions, as a case study. Despite its remarkable capabilities, OPS-SAT is not immune to the general dismissal of cybersecurity that plagues the industry. This work will employ a demonstrative approach, devising and implementing an attack scenario against OPS-SAT. The chosen attacker model for this scenario is that of a malicious user with limited to no cybersecurity knowledge, reflecting the reality that attackers with varying degrees of expertise can pose a threat. While keeping the attack as simple as possible, the goal is to demonstrate the potential damage that could be caused. The findings of this work illustrate that the rapid pace of development in the space industry should be accompanied by an equally enthusiastic and vigilant security force. The importance of addressing cybersecurity concerns becomes evident as the industry evolves and attracts more players, emphasizing the need for a proactive and robust security posture to safeguard space missions and future infrastructures

    Academic writing for IT students

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    This textbook is intended for Master and PhD Information Technology students (B1-C1 level of English proficiency). The instructions of how to write a research paper in English and the relevant exercises are given. The peculiarities of each section of a paper are presented. The exercises are based on real science materials taken from peer-reviewed journals. The subject area covers a wide scope of different Information Technology domains

    Evaluation Methodologies in Software Protection Research

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    Man-at-the-end (MATE) attackers have full control over the system on which the attacked software runs, and try to break the confidentiality or integrity of assets embedded in the software. Both companies and malware authors want to prevent such attacks. This has driven an arms race between attackers and defenders, resulting in a plethora of different protection and analysis methods. However, it remains difficult to measure the strength of protections because MATE attackers can reach their goals in many different ways and a universally accepted evaluation methodology does not exist. This survey systematically reviews the evaluation methodologies of papers on obfuscation, a major class of protections against MATE attacks. For 572 papers, we collected 113 aspects of their evaluation methodologies, ranging from sample set types and sizes, over sample treatment, to performed measurements. We provide detailed insights into how the academic state of the art evaluates both the protections and analyses thereon. In summary, there is a clear need for better evaluation methodologies. We identify nine challenges for software protection evaluations, which represent threats to the validity, reproducibility, and interpretation of research results in the context of MATE attacks

    Majority Voting Approach to Ransomware Detection

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    Crypto-ransomware remains a significant threat to governments and companies alike, with high-profile cyber security incidents regularly making headlines. Many different detection systems have been proposed as solutions to the ever-changing dynamic landscape of ransomware detection. In the majority of cases, these described systems propose a method based on the result of a single test performed on either the executable code, the process under investigation, its behaviour, or its output. In a small subset of ransomware detection systems, the concept of a scorecard is employed where multiple tests are performed on various aspects of a process under investigation and their results are then analysed using machine learning. The purpose of this paper is to propose a new majority voting approach to ransomware detection by developing a method that uses a cumulative score derived from discrete tests based on calculations using algorithmic rather than heuristic techniques. The paper describes 23 candidate tests, as well as 9 Windows API tests which are validated to determine both their accuracy and viability for use within a ransomware detection system. Using a cumulative score calculation approach to ransomware detection has several benefits, such as the immunity to the occasional inaccuracy of individual tests when making its final classification. The system can also leverage multiple tests that can be both comprehensive and complimentary in an attempt to achieve a broader, deeper, and more robust analysis of the program under investigation. Additionally, the use of multiple collaborative tests also significantly hinders ransomware from masking or modifying its behaviour in an attempt to bypass detection.Comment: 17 page

    Chatbots for Modelling, Modelling of Chatbots

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    Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Ingeniería Informática. Fecha de Lectura: 28-03-202

    Cybersecurity applications of Blockchain technologies

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    With the increase in connectivity, the popularization of cloud services, and the rise of the Internet of Things (IoT), decentralized approaches for trust management are gaining momentum. Since blockchain technologies provide a distributed ledger, they are receiving massive attention from the research community in different application fields. However, this technology does not provide cybersecurity by itself. Thus, this thesis first aims to provide a comprehensive review of techniques and elements that have been proposed to achieve cybersecurity in blockchain-based systems. The analysis is intended to target area researchers, cybersecurity specialists and blockchain developers. We present a series of lessons learned as well. One of them is the rise of Ethereum as one of the most used technologies. Furthermore, some intrinsic characteristics of the blockchain, like permanent availability and immutability made it interesting for other ends, namely as covert channels and malicious purposes. On the one hand, the use of blockchains by malwares has not been characterized yet. Therefore, this thesis also analyzes the current state of the art in this area. One of the lessons learned is that covert communications have received little attention. On the other hand, although previous works have analyzed the feasibility of covert channels in a particular blockchain technology called Bitcoin, no previous work has explored the use of Ethereum to establish a covert channel considering all transaction fields and smart contracts. To foster further defence-oriented research, two novel mechanisms are presented on this thesis. First, Zephyrus takes advantage of all Ethereum fields and smartcontract bytecode. Second, Smart-Zephyrus is built to complement Zephyrus by leveraging smart contracts written in Solidity. We also assess the mechanisms feasibility and cost. Our experiments show that Zephyrus, in the best case, can embed 40 Kbits in 0.57 s. for US1.64,andretrievethemin2.8s.SmartZephyrus,however,isabletohidea4Kbsecretin41s.Whilebeingexpensive(aroundUS 1.64, and retrieve them in 2.8 s. Smart-Zephyrus, however, is able to hide a 4 Kb secret in 41 s. While being expensive (around US 1.82 per bit), the provided stealthiness might be worth the price for attackers. Furthermore, these two mechanisms can be combined to increase capacity and reduce costs.Debido al aumento de la conectividad, la popularización de los servicios en la nube y el auge del Internet de las cosas (IoT), los enfoques descentralizados para la gestión de la confianza están cobrando impulso. Dado que las tecnologías de cadena de bloques (blockchain) proporcionan un archivo distribuido, están recibiendo una atención masiva por parte de la comunidad investigadora en diferentes campos de aplicación. Sin embargo, esta tecnología no proporciona ciberseguridad por sí misma. Por lo tanto, esta tesis tiene como primer objetivo proporcionar una revisión exhaustiva de las técnicas y elementos que se han propuesto para lograr la ciberseguridad en los sistemas basados en blockchain. Este análisis está dirigido a investigadores del área, especialistas en ciberseguridad y desarrolladores de blockchain. A su vez, se presentan una serie de lecciones aprendidas, siendo una de ellas el auge de Ethereum como una de las tecnologías más utilizadas. Asimismo, algunas características intrínsecas de la blockchain, como la disponibilidad permanente y la inmutabilidad, la hacen interesante para otros fines, concretamente como canal encubierto y con fines maliciosos. Por una parte, aún no se ha caracterizado el uso de la blockchain por parte de malwares. Por ello, esta tesis también analiza el actual estado del arte en este ámbito. Una de las lecciones aprendidas al analizar los datos es que las comunicaciones encubiertas han recibido poca atención. Por otro lado, aunque trabajos anteriores han analizado la viabilidad de los canales encubiertos en una tecnología blockchain concreta llamada Bitcoin, ningún trabajo anterior ha explorado el uso de Ethereum para establecer un canal encubierto considerando todos los campos de transacción y contratos inteligentes. Con el objetivo de fomentar una mayor investigación orientada a la defensa, en esta tesis se presentan dos mecanismos novedosos. En primer lugar, Zephyrus aprovecha todos los campos de Ethereum y el bytecode de los contratos inteligentes. En segundo lugar, Smart-Zephyrus complementa Zephyrus aprovechando los contratos inteligentes escritos en Solidity. Se evalúa, también, la viabilidad y el coste de ambos mecanismos. Los resultados muestran que Zephyrus, en el mejor de los casos, puede ocultar 40 Kbits en 0,57 s. por 1,64 US$, y recuperarlos en 2,8 s. Smart-Zephyrus, por su parte, es capaz de ocultar un secreto de 4 Kb en 41 s. Si bien es cierto que es caro (alrededor de 1,82 dólares por bit), el sigilo proporcionado podría valer la pena para los atacantes. Además, estos dos mecanismos pueden combinarse para aumentar la capacidad y reducir los costesPrograma de Doctorado en Ciencia y Tecnología Informática por la Universidad Carlos III de MadridPresidente: José Manuel Estévez Tapiador.- Secretario: Jorge Blasco Alís.- Vocal: Luis Hernández Encina
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