1,088 research outputs found
The role of the oral microbiome in the immunobullous diseases pemphigus vulgaris and mucous membrane pemphigoid and oral lichen planus
Saliva is formed from contributions of salivary glands and the serum exudates principally from gingival margins or damaged mucosa combined with components derived from the environment, including a community of microorganisms - the microbiome. I postulate that changes in microbial diversity and population structure play key roles in the modulation of host- microbial interactions which influence both the hypersensitive autoimmune responses and inflammation seen in these inflammatory mucocutaneous disorders. For my research, a total of 186 participants were recruited: 48 mucous membrane pemphigoid (MMP), 48 pemphigus vulgaris (PV), 50 oral lichen planus (OLP) patients, and 40 healthy controls. Unstimulated whole saliva, subgingival plaque, serum, and plasma samples were collected from 186 participants. In addition, metadata were collected on the following covariates: age, gender, ethnicity, type of the diet, disease history and therapeutic intervention in the preceding six months. Oral disease severity scores (ODSS) were assessed, and periodontal status was examined using a periodontal six pocket chart. To characterise microbiome profiles, saliva and subgingival plaque were processed for sequencing genomic DNA using the NGS Shotgun metagenomics sequencing technique. Inflammatory cytokines and proteases were investigated in saliva and serum using Human Magnetic Luminex Screening Assay (R&D Systems). Selected cytokines were analysed by enzyme-linked immunosorbent assay (ELISA) technique (R&D Systems) to determine host inflammatory responses in saliva and serum samples. Additionally, saliva and plasma samples were analysed for metabolites by nuclear magnetic resonance (NMR). Significant increases in periodontal score (PISA) in all three groups of disease were identified compared to healthy control group with significant positive correlation between oral disease severity (ODSS) and PISA in OLP and PV groups. All three groups of diseases had significantly higher levels of inflammatory Th2/Th17 cytokines (IL-6, IL-13 and IL-17 in saliva samples), as well as higher levels of MMP-3 matrixins in saliva. In addition, there were positive correlations between ODSS and salivary IL-6, IL-13 and MMP-3 in saliva of OLP, salivary and serum levels of IL-6 and MMP-3 in MMP group, and significant association of salivary IL-6, IL-1β and MMP-3 in PV group. Metabolomic data showed that saliva is a better biofluid for correlation of the metabolomic profile with oral disease severity than plasma. Salivary ethanol was corelated with disease severity in the OLP group, whereas in PV was a strong correlation of ODSS with choline. Finally, a unique microbial community was found in each group of diseases. In the MMP group, ODSS was significantly correlated with L. hofstadii, C. sputigena, N. meningitidis, N. cinerea and P. sacchar0lytica. In PV, a positive correlation was found with F. nucleatum, G. morbillorum, and E. corrodens, G. elegans, H. sapiens and T. vincentii. In OLP, the disease tends to worsen when there was reduced abundance of X. cellulosilytica, Actinomyces ICM 47, S. parasanguinis, S. salivarius, L. mirabilis and O. sinus. Lower microbial diversity was correlated with ODSS in saliva and plaque of the OLP group. In conclusion, this study provides strong evidence of the complex interplay between the oral microbiome, immunological factors, and metabolites in the context of immunobullous diseases and OLP. The findings highlight the integral role of oral bacteria in disease progression, the significance of immune dysregulation, and the potential impact of specific microbial species and metabolic pathways. These insights give the way for further research and clinical applications, offering the promise of personalized approaches for diagnosis, and management of OLP, MMP and PV. Future investigations should focus on discovering the mechanistic details underlying these associations and validating the identified biomarkers in larger patient cohorts, ultimately contributing to a deeper understanding of the pathogenesis of these conditions
Managing distributed situation awareness in a team of agents
The research presented in this thesis investigates the best ways to manage Distributed Situation Awareness (DSA) for a team of agents tasked to conduct search activity with limited resources (battery life, memory use, computational power, etc.). In the first part of the thesis, an algorithm to coordinate agents (e.g., UAVs) is developed. This is based on Delaunay triangulation with the aim of supporting efficient, adaptable, scalable, and predictable search. Results from simulation and physical experiments with UAVs show good performance in terms of resources utilisation, adaptability, scalability, and predictability of the developed method in comparison with the existing fixed-pattern, pseudorandom, and hybrid methods. The second aspect of the thesis employs Bayesian Belief Networks (BBNs) to define and manage DSA based on the information obtained from the agents' search activity. Algorithms and methods were developed to describe how agents update the BBN to model the system’s DSA, predict plausible future states of the agents’ search area, handle uncertainties, manage agents’ beliefs (based on sensor differences), monitor agents’ interactions, and maintains adaptable BBN for DSA management using structural learning. The evaluation uses environment situation information obtained from agents’ sensors during search activity, and the results proved superior performance over well-known alternative methods in terms of situation prediction accuracy, uncertainty handling, and adaptability. Therefore, the thesis’s main contributions are (i) the development of a simple search planning algorithm that combines the strength of fixed-pattern and pseudorandom methods with resources utilisation, scalability, adaptability, and predictability features; (ii) a formal model of DSA using BBN that can be updated and learnt during the mission; (iii) investigation of the relationship between agents search coordination and DSA management
Securely extending and running low-code applications with C#
Low-code development platforms provide an accessible infrastructure for the
creation of software by domain experts, also called "citizen developers",
without the need for formal programming education. Development is facilitated
through graphical user interfaces, although traditional programming can still
be used to extend low-code applications, for example when external services or
complex business logic needs to be implemented that cannot be realized with the
features available on a platform. Since citizen developers are usually not
specifically trained in software development, they require additional support
when writing code, particularly with regard to security and advanced techniques
like debugging or versioning. In this thesis, several options to assist
developers of low-code applications are investigated and implemented. A
framework to quickly build code editor extensions is developed, and an approach
to leverage the Roslyn compiler platform to implement custom static code
analysis rules for low-code development platforms using the .NET platform is
demonstrated. Furthermore, a sample application showing how Roslyn can be used
to build a simple, integrated debugging tool, as well as an abstraction of the
version control system Git for easier usage by citizen developers, is
implemented. Security is a critical aspect when low-code applications are
deployed. To provide an overview over possible options to ensure the secure and
isolated execution of low-code applications, a threat model is developed and
used as the basis for a comparison between OS-level virtualization, sandboxing,
and runtime code security implementations
VMTools-RA: a Reference Architecture for Software Variability Tools
Currently, software systems must be appropriately developed to support an amount of variability for accommodating different requirements. To support such development, a diversity of tools has already been designed for variability management (i.e., identification, modeling, evaluation, and realization). However, due to this diversity, there is a lack of consensus on what in fact software variability tools are and even what functionalities they should provide. Besides that, the building of new tools is still an effort- and time-consuming task. To support their building, we present VMTools-RA, a reference architecture that encompasses knowledge and practice for developing and evolving variability tools. Designed in a systematic way, VMTools-RA was evaluated throughout: a controlled experiment with software developer practitioners; and an instantiation of the VMTools-RA architecture to implement a software variability tool, named SMartyModeling. As a result, VMTools-RA is evidenced to be feasible and it can be considered an important contribution to the software variability and developers of variability-intensive software systems community, which require specific tools developed in a faster manner with less risk, what a reference architecture could provide
Adaptation of the human nervous system for self-aware secure mobile and IoT systems
IT systems have been deployed across several domains, such as hospitals and industries, for the management of information and operations. These systems will soon be ubiquitous in every field due to the transition towards the Internet of Things (IoT). The IoT brings devices with sensory functions into IT systems through the process of internetworking. The sensory functions of IoT enable them to generate and process information automatically, either without human contribution or having the least human interaction possible aside from the information and operations management tasks. Security is crucial as it prevents system exploitation. Security has been employed after system implementation, and has rarely been considered as a part of the system. In this dissertation, a novel solution based on a biological approach is presented to embed security as an inalienable part of the system.
The proposed solution, in the form of a prototype of the system, is based on the functions of the human nervous system (HNS) in protecting its host from the impacts caused by external or internal changes. The contributions of this work are the derivation of a new system architecture from HNS functionalities and experiments that prove the implementation feasibility and efficiency of the proposed HNS-based architecture through prototype development and evaluation.
The first contribution of this work is the adaptation of human nervous system functions to propose a new architecture for IT systems security. The major organs and functions of the HNS are investigated and critical areas are identified for the adaptation process. Several individual system components with similar functions to the HNS are created and grouped to form individual subsystems. The relationship between these components is established in a similar way as in the HNS, resulting in a new system architecture that includes security as a core component. The adapted HNS-based system architecture is employed in two the experiments prove its implementation capability, enhancement of security, and overall system operations.
The second contribution is the implementation of the proposed HNS-based security solution in the IoT test-bed. A temperature-monitoring application with an intrusion detection system (IDS) based on the proposed HNS architecture is implemented as part of the test-bed experiment. Contiki OS is used for implementation, and the 6LoWPAN stack is modified during the development process. The application, together with the IDS, has a brain subsystem (BrSS), a spinal cord subsystem (SCSS), and other functions similar to the HNS whose names are changed. The HNS functions are shared between an edge router and resource-constrained devices (RCDs) during implementation. The experiment is evaluated in both test-bed and simulation environments. Zolertia Z1 nodes are used to form a 6LoWPAN network, and an edge router is created by combining Pandaboard and Z1 node for a test-bed setup. Two networks with different numbers of sensor nodes are used as simulation environments in the Cooja simulator.
The third contribution of this dissertation is the implementation of the proposed HNS-based architecture in the mobile platform. In this phase, the Android operating system (OS) is selected for experimentation, and the proposed HNS-based architecture is specifically tailored for Android. A context-based dynamically reconfigurable access control system (CoDRA) is developed based on the principles of the refined HNS architecture. CoDRA is implemented through customization of Android OS and evaluated under real-time usage conditions in test-bed environments.
During the evaluation, the implemented prototype mimicked the nature of the HNS in securing the application under threat with negligible resource requirements and solved the problems in existing approaches by embedding security within the system. Furthermore, the results of the experiments highlighted the retention of HNS functions after refinement for different IT application areas, especially the IoT, due to its resource-constrained nature, and the implementable capability of our proposed HNS architecture.---
IT-järjestelmiä hyödynnetään tiedon ja toimintojen hallinnassa useilla aloilla, kuten sairaaloissa ja teollisuudessa. Siirtyminen kohti esineiden Internetiä (Internet of Things, IoT) tuo tällaiset laitteet yhä kiinteämmäksi osaksi jokapäiväistä elämää. IT-järjestelmiin liitettyjen IoT-laitteiden sensoritoiminnot mahdollistavat tiedon automaattisen havainnoinnin ja käsittelyn osana suurempaa järjestelmää jopa täysin ilman ihmisen myötävaikutusta, poislukien mahdolliset ylläpito- ja hallintatoimenpiteet. Turvallisuus on ratkaisevan tärkeää IT-järjestelmien luvattoman käytön estämiseksi. Valitettavan usein järjestelmäsuunnittelussa turvallisuus ei ole osana ydinsuunnitteluprosessia, vaan otetaan huomioon vasta käyttöönoton jälkeen. Tässä väitöskirjassa esitellään uudenlainen biologiseen lähestymistapaan perustuva ratkaisu, jolla turvallisuus voidaan sisällyttää erottamattomaksi osaksi järjestelmää.
Ehdotettu prototyyppiratkaisu perustuu ihmisen hermoston toimintaan tilanteessa, jossa se suojelee isäntäänsä ulkoisten tai sisäisten muutosten vaikutuksilta. Tämän työn keskeiset tulokset ovat uuden järjestelmäarkkitehtuurin johtaminen ihmisen hermoston toimintaperiaatteesta sekä tällaisen järjestelmän toteutettavuuden ja tehokkuuden arviointi kokeellisen prototyypin kehittämisen ja toiminnan arvioinnin avulla.
Tämän väitöskirjan ensimmäinen kontribuutio on ihmisen hermoston toimintoihin perustuva IT-järjestelmäarkkitehtuuri. Tutkimuksessa arvioidaan ihmisen hermoston toimintaa ja tunnistetaan keskeiset toiminnot ja toiminnallisuudet, jotka mall-innetaan osaksi kehitettävää järjestelmää luomalla näitä vastaavat järjestelmäkomponentit. Nä-istä kootaan toiminnallisuudeltaan hermostoa vastaavat osajärjestelmät, joiden keskinäinen toiminta mallintaa ihmisen hermoston toimintaa. Näin luodaan arkkitehtuuri, jonka keskeisenä komponenttina on turvallisuus. Tämän pohjalta toteutetaan kaksi prototyyppijärjestelmää, joiden avulla arvioidaan arkkitehtuurin toteutuskelpoisuutta, turvallisuutta sekä toimintakykyä.
Toinen kontribuutio on esitetyn hermostopohjaisen turvallisuusratkaisun toteuttaminen IoT-testialustalla. Kehitettyyn arkkitehtuuriin perustuva ja tunkeutumisen estojärjestelmän (intrusion detection system, IDS) sisältävä lämpötilan seurantasovellus toteutetaan käyttäen Contiki OS -käytöjärjestelmää. 6LoWPAN protokollapinoa muokataan tarpeen mukaan kehitysprosessin aikana. IDS:n lisäksi sovellukseen kuuluu aivo-osajärjestelmä (Brain subsystem, BrSS), selkäydinosajärjestelmä (Spinal cord subsystem, SCSS), sekä muita hermoston kaltaisia toimintoja. Nämä toiminnot jaetaan reunareitittimen ja resurssirajoitteisten laitteiden kesken. Tuloksia arvioidaan sekä simulaatioiden että testialustan tulosten perusteella. Testialustaa varten 6LoWPAN verkon toteutukseen valittiin Zolertia Z1 ja reunareititin on toteutettu Pandaboardin ja Z1:n yhdistelmällä. Cooja-simulaattorissa käytettiin mallinnukseen ymp-äristönä kahta erillistä ja erikokoisuta sensoriverkkoa.
Kolmas tämän väitöskirjan kontribuutio on kehitetyn hermostopohjaisen arkkitehtuurin toteuttaminen mobiilialustassa. Toteutuksen alustaksi valitaan Android-käyttöjärjestelmä, ja kehitetty arkkitehtuuri räätälöidään Androidille. Tuloksena on kontekstipohjainen dynaamisesti uudelleen konfiguroitava pääsynvalvontajärjestelmä (context-based dynamically reconfigurable access control system, CoDRA). CoDRA toteutetaan mukauttamalla Androidin käyttöjärjestelmää ja toteutuksen toimivuutta arvioidaan reaaliaikaisissa käyttöolosuhteissa testialustaympäristöissä.
Toteutusta arvioitaessa havaittiin, että kehitetty prototyyppi jäljitteli ihmishermoston toimintaa kohdesovelluksen suojaamisessa, suoriutui tehtävästään vähäisillä resurssivaatimuksilla ja onnistui sisällyttämään turvallisuuden järjestelmän ydintoimintoihin. Tulokset osoittivat, että tämän tyyppinen järjestelmä on toteutettavissa sekä sen, että järjestelmän hermostonkaltainen toiminnallisuus säilyy siirryttäessä sovellusalueelta toiselle, erityisesti resursseiltaan rajoittuneissa IoT-järjestelmissä
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Proceedings of the 33rd Annual Workshop of the Psychology of Programming Interest Group
This is the Proceedings of the 33rd Annual Workshop of the Psychology of Programming Interest Group (PPIG). This was the first PPIG to be held physically since 2019, following the two online-only PPIGs in 2020 and 2021, both during the Covid pandemic. It was also the first PPIG conference to be designed specifically for hybrid attendance. Reflecting the theme, it was hosted by Music Computing Lab at the Open University in Milton Keynes
Fine-Grained Source Code Tracking and Visualization in Commit History
CodeTracker is the current state-of-the-art program element change history generator with a reported precision and recall of 99.9% in method and variable tracking [1]. In this thesis, we extend the granularity of CodeTracker to support the tracking of control-flow blocks (e.g., for, while, if, try, catch, etc.) with a precision and recall of 98.12% and 97.62% respectively, providing researchers and developers with finer-grained information about the evolution of source code. We accompany this extension with a manually validated oracle, which includes the change histories of 1280 code blocks. These code blocks are contained within 200 methods from 20 open-source Java projects (10 methods from each project) comprising the method change history oracle created by Grund et al. [2]. We also present a code change history visualization and navigation tool for CodeTracker, named CodeTracker Visualizer, that overlays the GitHub user interface with change history information enabling users to track code elements directly from the commit page by simply selecting the desired code element. Finally, we compare CodeTracker’s block tracking precision and recall using two different tools that provide statement mappings, namely RefactoringMiner [3, 4], the current state-of-the-art refactoring detection tool, and GumTree [5], the current state-of-the-art Abstract Syntax Tree (AST) Diff tool. The enhanced version of CodeTracker along with the extended oracle are made publicly available to facilitate reproducibility and future research on code element tracking techniques [6]
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