BIG DATA и анализ высокого уровня : материалы конференции

В сборнике опубликованы результаты научных исследований и разработок в области BIG DATA and Advanced Analytics для оптимизации IT-решений и бизнес-решений, а также тематических исследований в области медицины, образования и экологии

A new computational framework for the classification and function prediction of long non-coding RNAs

Long non-coding RNAs (lncRNAs) are known to play a significant role in several biological processes. These RNAs possess sequence length greater than 200 base pairs (bp), and so are often misclassified as protein-coding genes. Most Coding Potential Computation (CPC) tools fail to accurately identify, classify and predict the biological functions of lncRNAs in plant genomes, due to previous research being limited to mammalian genomes. In this thesis, an investigation and extraction of various sequence and codon-bias features for identification of lncRNA sequences has been carried out, to develop a new CPC Framework. For identification of essential features, the framework implements regularisation-based selection. A novel classification algorithm is implemented, which removes the dependency on experimental datasets and provides a coordinate-based solution for sub-classification of lncRNAs. For imputing the lncRNA functions, lncRNA-protein interactions have been first determined through co-expression of genes which were re-analysed by a sequence similaritybased approach for identification of novel interactions and prediction of lncRNA functions in the genome. This integrates a D3-based application for visualisation of lncRNA sequences and their associated functions in the genome. Standard evaluation metrics such as accuracy, sensitivity, and specificity have been used for benchmarking the performance of the framework against leading CPC tools. Case study analyses were conducted with plant RNA-seq datasets for evaluating the effectiveness of the framework using a cross-validation approach. The tests show the framework can provide significant improvements on existing CPC models for plant genomes: 20-40% greater accuracy. Function prediction analysis demonstrates results are consistent with the experimentally-published findings

The Arab Archive: Mediated Memories and Digital Flows

As the revolutions across the Arab world that came to a head in 2011 devolved into civil war and military coup, representation and history acquired a renewed and contested urgency. The capacities of the internet have enabled sharing and archiving in an unprecedented fashion. Yet, at the same time, these facilities institute a globally dispersed reinforcement and recalibration of power, turning memory and knowledge into commodified and copyrighted goods. In The Arab Archive: Mediated Memories and Digital Flows, activists, artists, filmmakers, producers, and scholars examine which images of struggle have been created, bought, sold, repurposed, denounced, and expunged. As a whole, these cultural productions constitute an archive whose formats are as diverse as digital repositories looked after by activists, found footage art documentaries, Facebook archive pages, art exhibits, doctoral research projects, and ‘controversial’ or ‘violent’ protest videos that are abruptly removed from YouTube at the click of a mouse by sub-contracted employees thousands of kilometers from where they were uploaded. The Arab Archive investigates the local, regional, and international forces that determine what materials, and therefore which pasts, we can access and remember, and, conversely, which pasts get erased and forgotten

Identificação e caracterização de pequenos RNAs não codificantes e genes alvos envolvidos em estresse abiótico (seca e salinidade) em Eugenia uniflora L. (Myrtaceae)

As plantas, por serem organismos sésseis, enfrentam persistentemente perturbações ambientais adversas denominadas estresses abióticos, sendo as mais importantes, a seca, a salinidade do solo, as temperaturas extremas e a presença de metais pesados. Em resposta, as plantas desenvolveram mecanismos de tolerância, resistência e prevenção para minimizar a influência do estresse, utilizando estratégias de curto prazo para readaptar rápida e eficientemente seu metabolismo. Neste sentido, os pequenos RNAs não codificantes (sncRNAs) são fortes candidatos para realizar este tipo de regulação. Através do sequenciamento de nova geração revelou-se o papel dos sncRNAs na regulação da expressão gênica em nível transcricional e póstranscricional. Dentre os sncRNAs, os microRNAs (miRNAs) são os mais conhecidos e os fragmentos derivados dos RNAs transportadores (tRFs) são os mais novos e com maiores perspectivas de descobertas futuras. Os miRNAs desempenham papéis regulatórios essenciais tanto no crescimento das plantas quanto no desenvolvimento e resposta ao estresse, enquanto os tRFs, em sua maioria, têm sido associados a respostas de estresse. Eugenia uniflora L., “pitanga” ou a cereja brasileira é uma árvore frutífera nativa da América do Sul que pertence à família Myrtaceae. Ela cresce em diferentes ambientes; florestas, restingas e ambientes áridos e semi-áridos no nordeste brasileiro, sendo uma espécie versátil em termos de adaptabilidade e que desempenha um papel fundamental na manutenção da vegetação costeira arbustiva. Além disso, é muito conhecida por suas propriedades medicinais que são atribuídas aos metabólitos especializados presentes nas folhas e frutos. E. uniflora representa uma fonte fascinante da biodiversidade do germoplasma e tem um grande potencial como fonte de genes para o melhoramento genético. Portanto, a compreensão dos mecanismos que conferem tolerância ao estresse nesta planta é de particular importância. Nesse contexto, o objetivo do presente trabalho é a identificação de sncRNAs (miRNAs e tRFs) por ferramentas de bioinformática e análise do padrão de expressão destes sob condições de estresse abiótico (seca e salinidade), bem como avaliação dos genes envolvidos nesta resposta. No capítulo 1, bibliotecas de DNA, pequenos RNAs (sRNAs) e RNAseq de folhas foram usadas para identificar pre-miRNAs, miRNAs maduros e potenciais alvos destes miRNAs, respectivamente. A montagem de novo do genoma permitiu identificar 38 miRNAs conservados e 28 novos miRNAs. Após a avaliação da expressão destes, 11 conservados, entre eles miR156 e miR170, mostraram variação significativa nas condições de restinga e de estresse induzido por PEG. A maioria deles foram previamente descritos em processos de estresse em outras espécies. 14 novos miRNAs foram avaliados em diferentes tecidos de pitanga mostrando variação significativa no padrão de expressão. Os alvos destes últimos miRNAs foram preditos e validados por RTqPCR. Eles correspondem a genes de fatores de transcrição e outros genes como transferases ou ATPases e demonstraram o padrão esperado oposto à expressão dos miRNAs. No capítulo 2, as mesmas bibliotecas foram usadas para identificar tRFs conservados na família das Myrtaceae. Para isso, os tRNAs de Eucalyptus grandis e E. uniflora foram anotados e os tRNAs comuns foram utilizados para o ancoramento dos sRNAs. 479 tRFs foram identificados em pitanga, na maioria com 18 nucleotídeos (nt). Um conjunto de 11 tRFs conservados em ambas espécies, assim como seus alvos, foram avaliados em condições de estresse salino e seca demonstrando diferenças significativas dependendo do tipo de estresse. Os alvos identificados correspondem a genes previamente descritos como envolvidos em estresse salino e seca para outras espécies. O presente trabalho apresenta fortes evidências do envolvimento dos miRNAs em processos de desenvolvimento e estresse, assim como dos tRFs na resposta à seca e estresse salino presente em E. uniflora. Além disso, os dados produzidos poderão ser utilizados em estudos funcionais mais aprofundados que servirão para melhor compreensão dos mecanismos de tolerância presentes nesta importante planta.Plants being sessile organisms, persistently face adverse environmental perturbations termed as abiotic stresses, most important being drought, soil salinity, extreme temperatures, and heavy metals. They developed several strategies such as tolerance, resistance, and avoidance to minimize stress influence, thus require short-term strategies to quickly and efficiently readapt their metabolism. In this sense, small non coding RNAs are strong candidates to do this kind of fine tune regulation. Next generation sequencing technologies have revealed the key role of these sncRNAs in the transcriptional and posttranscriptional gene-expression regulation. Among the myriad of new sncRNAs, miRNAs are the most known ones and the fragments derived from tRNAs (tRFs) are the newest but with high perspective ones. The miRNAs are endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. In the case of tRFs, they are mainly involved in stress response. Eugenia uniflora L., ‘pitanga’ or Brazilian cherry is a fruit tree native to South America that belongs to Myrtaceae family. It grows in several different harsh environments, including forests, restingas, near the beach, and arid and semiarid environments in the Brazilian northeast. This species is very versatile in terms of adaptability and plays a fundamental role in the maintenance of the shrubby coastal vegetation. However, this species is best-known because its medicinal properties that are attributed to specialized metabolites with known biological activities present in their leaves and fruits. E. uniflora is a fascinating reservoir of germplasm biodiversity and has great potential as a source of genes for plant breeding. Therefore, understanding the mechanisms conferring stress tolerance will be very useful. In this sense, the objective of this work is to identify sncRNAs (miRNAs and tRFs) by bioinformatic tools and to analyze their expression pattern under stress conditions as well as the genes involved in that response. In chapter 1, DNA, small RNA (sRNA) and RNAseq libraries from leaves were used to identify pre-miRNAs, mature miRNAs and potential targets of these miRNAs, respectively. De novo assembly of the genome identified 38 conserved miRNAs and 28 novel miRNAs. After evaluating their expression pattern, 11 11 conserved miRNAs, including miR156 and miR170, showed significant variation in the natural (restinga habitat) and PEG induced stress. Most of them were previously reported in stress processes. 14 novel miRNAs were evaluated in different tissues of pitanga showing significant variation in the expression pattern. The targets of the last miRNAs were predicted and validated by RT-qPCR. They were transcription factor genes and other genes such as transferases or ATPases and showed the expected opposite pattern to miRNA expression. In Chapter 2, the same libraries were used to identify conserved tRFs in the Myrtaceae family. To do this, the tRNAs of Eucalyptus grandis and E. uniflora were annotated and sRNAs mapped into them. 479 tRFs were identified in pitanga with predominance of those with 18 nucleotide length. 11 conserved tRFs in both species, as well as their targets, were evaluated under saline and drought stress conditions showing significant differences depending on the stress type. The targets were genes previously involved in saline and drought stress for other species. The present work shows strong evidences of the involvement of the miRNAs in the development and stress, as well as the tRFs in the tolerance to drought and saline stress of E. uniflora. In addition, the data could be used in more detailed functional studies that will serve to corroborate and better understand the mechanism of tolerance present in this important plant

More than meets the eye: the conceptual essence of intrinsic memorability

In a world where sensory threads weave an endless tapestry of multi-modal data, the human brain stands as the masterful weaver of meaning. As we wade through this tempest of input, our brain spins these threads into an intelligible internal representation and holds on tight to what it deems important. But what, exactly, makes certain threads more important than others? And how can we predict their significance? Memorability is the tensile strength of the threads that tie us to the world. It is a proxy for human importance, indicating which threads the human brain will curate and retain with exceptional fidelity. This research investigates these multisensory threads by exploring the influence of audio, visual, and textual modalities on predicting video memorability, and how the interplay between them can influence the overall memorability of a given piece of content. The findings suggest that, while visual data may dominate our sensory experience, it is the underlying conceptual essence that truly holds the key to memorability. This thesis leverages state-of-the-art image synthesis techniques to distill and examine this essence, creating surrogate dreams of video scenes to facilitate the disentanglement of conceptual and perceptual elements of memorability. The work also leverages human EEG data to explore the possibility of a moment of memorability—a moment of encoding that corresponds to a remembering moment—which we expect to exist due to the temporal nature of the world and the natural encoding limits of our brains. The previously murky relationship between the two core means of remembrance---recognition and recall---are reconciled by conducting a novel video memorability drawing task. The research sheds new light on the nature of multi-modal memorability, providing a deeper understanding of how our brain processes and retains information in a complex sensory world. By uncovering the conceptual essence that lies at the heart of memorability, it opens up new avenues for predicting and curating more meaningful media content, and ultimately deepen our connection to the world around us

NEW APPROACHES IN UNDERSTANDING DRUG METABOLISM

Limitations in technology, such as DNA sequencing and appropriate model systems, have made it difficult to understand the genetic and non-genetic factors that influence the liver's role in metabolizing drugs. New approaches are required to overcome these limitations. In this Dissertation, we evaluate 3 such new approaches. Our first new approach relates to the field of pharmacogenetics: using genetics to predict how a patient will respond to medication based on their genetic code. We looked for polymorphisms in a novel target gene, Cytochrome P450 Oxidoreductase (POR). Our results show a mutation in P450 reductase (L577P) that associates with decreased metabolism for 8 of 10 major drug metabolizing enzymes. However, even though we found a statistical association between POR polymorphism and drug metabolism, a wide range of variation in POR activity was still observed among the samples with the L577/ P577 genotype, making predicting POR activity solely on the basis of L577P genotype difficult. POR represents only a single gene amongst the tens of thousands present in the human genome. To investigate the relationship between how genes and their products interact, a systems approach is necessary. Therefore, in our second new approach, we will characterize the transcriptome of our model system, the HepaRG cell line. We found that HepaRG cells globally transcribe genes at the levels more similar to human primary hepatocytes and human liver than HepG2 cells, particularly in genes encoding drug processing proteins. Finally, I describe the third new approach: the use of next-generation DNA sequencing to understand hepatic drug response. This section contains two parts. First, we introduce methods that significantly decrease the false discovery rate of genotyping from RNA-Seq data. With these high fidelity SNPs, we were able to perform a genome-wide pharmacogenomic analysis on HepaRG cells. Second, we introduce a new program, called PRUNE, to more accurately quantify gene expression, and compare its performance to that of established programs

Jornadas Nacionales de Investigación en Ciberseguridad: actas de las VIII Jornadas Nacionales de Investigación en ciberseguridad: Vigo, 21 a 23 de junio de 2023

Jornadas Nacionales de Investigación en Ciberseguridad (8ª. 2023. Vigo)atlanTTicAMTEGA: Axencia para a modernización tecnolóxica de GaliciaINCIBE: Instituto Nacional de Cibersegurida

A User Centric Security Model for Tamper-Resistant Devices

In this thesis we propose a design for a ubiquitous and interoperable device based on the smart card architecture to meet the challenges of privacy, trust, and security for traditional and emerging technologies like personal computers, smart phones and tablets. Such a de- vice is referred a User Centric Tamper-Resistant Device (UCTD). To support the smart card architecture for the UCTD initiative, we propose the delegation of smart card owner- ship from a centralised authority (i.e. the card issuer) to users. This delegation mandated a review of existing smart card mechanisms and their proposals for modifications/improve- ments to their operation. Since the inception of smart card technology, the dominant ownership model in the smart card industry has been refer to as the Issuer Centric Smart Card Ownership Model (ICOM). The ICOM has no doubt played a pivotal role in the proliferation of the technology into various segments of modern life. However, it has been a barrier to the convergence of different services on a smart card. In addition, it might be considered as a hurdle to the adaption of smart card technology into a general-purpose security device. To avoid these issues, we propose citizen ownership of smart cards, referred as the User Centric Smart Card Ownership Model (UCOM). Contrary to the ICOM, it gives the power of decision to install or delete an application on a smart card to its user. The ownership of corresponding applications remains with their respective application providers along with the choice to lease their application to a card or not. In addition, based on the UCOM framework, we also proposed the Coopetitive Architecture for Smart Cards (CASC) that merges the centralised control of card issuers with the provision of application choice to the card user. In the core of the thesis, we analyse the suitability of the existing smart card architectures for the UCOM. This leads to the proposal of three major contributions spanning the smart card architecture, the application management framework, and the execution environment. Furthermore, we propose protocols for the application installation mechanism and the application sharing mechanism (i.e. smart card firewall). In addition to this, we propose a framework for backing-up, migrating, and restoring the smart card contents. Finally, we provide the test implementation results of the proposed protocols along with their performance measures. The protocols are then compared in terms of features and performance with existing smart cards and internet protocols. In order to provide a more detailed analysis of proposed protocols and for the sake of completeness, we performed mechanical formal analysis using the CasperFDR.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Philosophical and Historical Foundations of the Concept of Innovation: Some Implications for Contemporary Higher Education as a Service Sector

The Australian higher education services sector has significantly increased its economic contribution to Gross Domestic Product in the twenty-first century. Innovation is highly prized in an increasingly competitive global knowledge economy. However, there is currently no theory of innovation in the higher education services sector. This factor is framed as the thesis research problem. The hypothesis of this thesis is that: based on an examination of the implications of the philosophical and historical foundations of the concept of innovation, contemporary higher education sector innovation can be meaningfully interpreted through a framework based on service sector innovation theory. Based on the findings of an extended investigation of the philosophical and historical foundations of the concept of innovation, implications are explored by ‘field-testing’ a potential theoretical framework for its ability to identify innovative trends in the higher education sector. Case studies of the finance service sub-sector are constructed and are used as a template to compare current practices in the ‘lagging’ higher education services sector. The thesis concludes that the hypothesis is supported and confirmed. That is, based on an examination of the implications of the philosophical and historical foundations of the concept of innovation, contemporary higher education sector innovation can be meaningfully interpreted through a framework based on service sector innovation theory