Conceptual Modelling and The Quality of Ontologies: Endurantism Vs. Perdurantism

Ontologies are key enablers for sharing precise and machine-understandable semantics among different applications and parties. Yet, for ontologies to meet these expectations, their quality must be of a good standard. The quality of an ontology is strongly based on the design method employed. This paper addresses the design problems related to the modelling of ontologies, with specific concentration on the issues related to the quality of the conceptualisations produced. The paper aims to demonstrate the impact of the modelling paradigm adopted on the quality of ontological models and, consequently, the potential impact that such a decision can have in relation to the development of software applications. To this aim, an ontology that is conceptualised based on the Object-Role Modelling (ORM) approach (a representative of endurantism) is re-engineered into a one modelled on the basis of the Object Paradigm (OP) (a representative of perdurantism). Next, the two ontologies are analytically compared using the specified criteria. The conducted comparison highlights that using the OP for ontology conceptualisation can provide more expressive, reusable, objective and temporal ontologies than those conceptualised on the basis of the ORM approach

The design and engineering of innovative mobile data services: An ontological framework founded on business model thinking

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This research investigates mobile service design and engineering in the mobile telecommunications industry. The mobile telecommunication business is shifting from one that was voice-centric to one that is almost all data-centric; thanks to recent rapid advances in Information and Communication Technologies (ICTs). The underlying reasons behind this shift can be traced back to two main issues that are interlinked. The first and major reason is that telecoms (telecommunication companies) are trying to generate new revenue streams based on data and information transmissions, given the saturation of the voice market. This is rational given the market opportunities in one direction and the pressures being generated by the current economic downturn from the other direction. The second reason relates to the flexibility of data, compared to voice. Indeed, the number of services that can be developed on the basis of data are much greater than those that can be developed on the basis of voice. However, the design and engineering of successful and innovative mobile data services has proven to be a complex undertaking. The number of effective mobile data services is relatively small and the revenue generated from such offerings has generally been below expectations. This research develops an ontological framework to help in changing this situation, and making mobile services engineering more effective and successful, following the design-science research paradigm. Design-science research, in general, aims to solve unstructured but relevant organizational or social problems through the development of novel and useful artefacts. As the current research aims to help in solving the mobile data services engineering dilemma by developing a purposeful ontological framework, the design-science research paradigm is deemed fitting. Within this paradigm, the author develops a novel design approach specified for ontology engineering, termed “OntoEng”. This design approach is used in this research for developing the ontological framework. The developed ontological framework is founded on business model thinking. The idea is that creating innovative mobile data services requires developing innovative business models. Indeed, innovative business models can help translate technological potential into economic value and allow telecoms to achieve their strategic objectives. The ontological framework includes the development of an ontology, termed “V4 Mobile Service BM Ontology” as well as “Mobile Key Value Drivers” for designing and engineering innovative mobile data services. The V4 Mobile Service BM Ontology incorporates four design dimensions: (1) value proposition including targeting; (2) value architecture including technological and organizational infrastructure; (3) value network dealing with aspects relating to partnerships and co-operations; and finally (4) value finance relating to costs, pricing, and revenue structures. Within these four dimensions, sixteen design concepts are identified along with their constituent elements. Relationships and interdependencies amongst the identified design constructs are established and clear semantics are produced. The research then derives six key value drivers for mobile service engineering as follows: (a) Market Alignment; (b) Cohesion; (c) Dynamicity; (d) Uniqueness; (e) Fitting Network-Mode; and (f) Explicitness. The developed ontological framework in this research is evaluated to ensure that it can be successfully implemented and performs correctly in the real world. The research mainly utilizes case analysis methods to ensure the semantic correctness of the ontological framework. Indeed, the developed ontological framework is employed as an analytical lens to examine the design and engineering of three key real-life cases in the mobile telecommunications industry. These cases are: (1) Apple’s iPhone Services and Applications; (2) NTT DoCoMo’s i-mode Services; and (3) Orange Business Services. For further validation, the developed ontological framework is evaluated against a set of criteria synthesized from ontology engineering and evaluation literature. These criteria are: Clarity; Coherence; Conciseness; Preciseness; Completeness; and Customizability. The developed ontological framework is argued to make significant contributions for theory, practice, and methodology. For theory, this research provides (1) a novel ontological framework for designing and engineering mobile data services; (2) a unified framework of the business model concept; and (3) a new design approach for ontology engineering in information systems. For practice, the current research provides practitioners in the telecommunications industry with systematic and customizable means to design, implement, analyze, evaluate, and change new and existing mobile data services to make them more manageable, effective, and creative. For methodology, the use of the design- science research paradigm for ontology engineering signifies the focal methodological contribution in this research given its novelty. This research also contributes to the understanding of the design-science research paradigm in information systems as it is relatively new. It provides a working example in which the author illustrates how recognizing design-science research as a paradigm is essential and useful to the research in information systems discipline

Insights into the epigenetic role of H2A.J in radiation-induced premature senescence

This thesis provides molecular insight into the H2A.J histone variant and its involvement in some biological processes as a reaction to ionizing radiation. The in-vitro study was conducted using WI-38 (no target (NT), knockdown (KD) and overexpressing (OE) H2A.J) cell line irradiated with 20Gy and labelled with several markers for investigating DNA damage and cell senescence. RNA-seq and enzyme-linked immunosorbent assay (ELISA) were used to examine the effect of H2A.J on the inflammatory response in cells. In addition, the study used assays for transposase-accessible chromatin sequencing (ATAC-seq) to investigate the role of H2A.J in the global chromatin conformation changes after IR. It was found that those cells, which have H2A.J involvement after radiation, show more resistance against senescence and apoptosis. Moreover, the conformational structure of the chromatin changes the global status of the transcription in the cells, especially for the senescence-associated secretory phenotype (SASP) genes in case of overexpressing H2A.J. Many changes occur in the cells during senescence, including disruptions in the nucleus and cytoplasmic organelles. Disruption in the nuclear morphology was noticed in the radiation-induced senescent cells. Mass spectrometry-based proteomics and high-resolution tools were used to look into the relation between the disrupted nuclear membrane and the characteristic markers of senescence. Our study found that the cells lost their laminB1 during senescence, which may disrupt the nuclear envelope, leading to the ejection of chromatin fragments in the cytoplasm, and activating the cGAS-STING-dependent interferon signalling. Moreover, serial block-face scanning electron microscopy (SBF-SEM) revealed the establishment of nanotubes as a result of the nucleus envelope disruption. These nanotubes may have role in the cytoplasmic chromatin fragments (CCF) ejection into the cytoplasm. After high-LET IR, the fibroblasts showed low electron density domains (LEDDs) in the nucleus caused by the centralized energy emitted next to the particle trajectories. Automated image analysis software with transmission electron microscopy (TEM) micrographs was used to detect the dynamics of DNA repair chromatin conformation. Fibroblasts were irradiated with low- and high-LET photons, and then they were labelled nanoparticles-tagged with DNA repair markers. The automated software tools were used to analyze the TEM micrographs to determine the pattern of the DNA damage post-low-LET versus high-LET IR. Most DNA double-strand breaks (DSBs) were repaired totally and no changes in chromatin condensation were visible after low-LET irradiation, but compound DNA damages were detected along the particle trajectories induced by high-LET IR causing clear-bordered LEDDs. The chromatin densities and the distribution of nanoparticles (related to LEDDs and based on size and shape) in the nucleus were determined using an AI tool. These results showed the ability of the automated precise analysis for the nanoparticles and LEDDs in micrographs to describe the DNA damage patterns in the nucleus after radiation. Additionally, an in-vivo study of H2A.J's role in senescence was conducted using H2A.J-knock-out (KO) mice. Skinfold of wildtype (WT) and KO mice were irradiated with 20Gy, and then for two weeks, the skin reactions were noticed macroscopically. Skin samples were collected, embedded, and labelled with several senescence and DNA damage markers. Transcriptome profile was examined using RNA-seq and RT-PCR, moreover, flow cytometry was used to explore the immune cell infiltration. An intensive reaction was observed on the skin of KO mice compared to WT, accompanied by enlargement of the epidermal thickness. More loss of hair follicles and their stem cells after radiation was found in KO skin which led to follicle vanishing. Also, increasing senescence gene expression was found in KO mice, which was associated with increased releasing of SASP factors. High numbers of infiltrated immune cells were found in both KO and WT; however, KO skin showed more induction of neutrophil numbers, irregular differentiation of and cornification of keratinocytes with increasing transcription of JunB after radiation in comparison to WT. In conclusion, the absence of H2A.J in irradiated keratinocytes is related to increasing senescence, SASP secretion, and immune response, combined with higher proliferation as an inflammatory reaction during radiation dermatitis.In dieser Arbeit wurden die Histonvariante H2A.J, deren molekularbiologische Prozessierung und Beteiligung als Reaktion auf ionisierende Strahlung analysiert. Hierzu wurden in einer in-vitro-Studie WI-38-Zellen (Fibroblasten) verwendet, die unterschiedliche genetisch Modifikationen für die Histonvariante H2AJ aufwiesen (Non-Target, Knock-down, Over-expressing). Die Bestrahlung der Zellen erfolgte hochpräzise mit 20 Gy (6 MV Photonen) am Linearbeschleuniger der Klinik für Strahlentherapie und Radioonkologie um anschließend in unterschiedlichen Zeitabständen die Auswirkungen der strahleninduzierten DNA-Schäden und Prozesse der Zellalterung mikroskopisch zu untersuchen. RNA-Seq und ELISA wurden darüber hinaus verwendet, um eine mögliche Beteiligung von H2A.J auf die Entzündungsreaktion in den Zellen zu analysieren. Ebenfalls wurde ATAC-Seq angewendet, um die Rolle von H2A.J an den strahleninduzierten Modifikationen der Chromatinstruktur zu erforschen. Hierbei wurde festgestellt, dass die Zellen, in welchen eine Beteiligung von H2A.J auf molekularer Ebene nachweisbar ist, resistenter gegenüber Alterungsprozessen und Apoptoseinduktion aufweisen. Darüber hinaus konnte beobachtet werden, dass die Modifikationen des Chromatins auch die Transkription der zellulären DNA beeinflussen, insbesondere die SASP-Gene bei einer H2A.J-Überexpression. Alterungsbedingt teilungs-unfähige seneszente Zellen weisen eine Vielzahl an Veränderungen in den zytoplasmatischen Organellen und den intra-nukleären Vorgängen auf. Bei strahleninduzierter Seneszenz wird insbesondere die Kernmorphologie beeinflusst, was mit Hilfe von massenspektrometischer Proteomanalyse und hochauflösender Mikroskopie untersucht wurde, um die Verbindung zwischengeschädigter Kernmembran und den charakteristischen Seneszenz-Markern besser zu verstehen. Hierbei wurde nachgewiesen, dass die Veränderungen in der Kernlamina durch Lamin-B1-Verlust hervorgerufen werden, was in Folge zu einem Verlust von Chromatinfragmenten (CCFs) in das Zytoplasma führen und die cGAS-STING-abhängige Interferonsignalisierung aktivieren kann. Darüber hinaus konnten mittels Serial-Blockface-Rasterelektronenmikroskopie (SBF-SEM) Nanoröhren visualisiert werden, die bei dem Transport von CCFs aus dem Zellkern in das Zytoplasma beteiligt sind. Nach der Bestrahlung von Fibroblasten mit Schwerionen, die einen hohen linearen Energietransfer (high-LET) aufweisen, wurden mittels elektronenmikroskopischer Analyse in der homogenen Chromatinstruktur Bereiche mit niedriger Elektronendichte (LEDDs) sichtbar, welche durch die Ionisationsereignisse entlang der Partikelbahn verursacht wurden. Um diese zu untersuchen, wurde eine automatisierte Bildanalysesoftware (HALO) verwendet, um in den elektronen¬mikroskopischen Aufnahmen die Dynamik in der Veränderung der Chromatin¬struktur zu beobachten. Hierzu wurden DNA-Reparaturproteinen antikörperbasiert mit kolloidalen Goldpartikeln markiert, um hochaufgelöst die Induktion und Reparatur von DNA-Schäden, insbesondere Doppelstrangbrüche (DSBs), zu untersuchen und die hierdurch gewonnen Erkenntnisse mit denen nach low-LET-Bestrahlung zu vergleichen. Nach low-LET-Bestrahlung (Photonen) wurden fast alle DSBs repariert und es verblieben keine sichtbaren Chromatinveränderungen zurück. Hingegen waren nach high-LET-Bestrahlung (Schwerionen) entlang der Partikelbahn eine Vielzahl an Schäden nachweisbar, die zur Bildung der LEDDs führten. Innerhalb von diesen wurde die Chromatindichte sowie die Verteilung der mit kolloidalem Gold markierten Reparaturfaktoren mit Hilfe eines KI-basiertem Softwaretool ausgewertet. Der Einfluss von H2A.J auf die vielfältigen intrazellulären Prozesse bei Seneszenz wurde darüber hinaus in einer in-vivo-Studie an genetisch modifizierten H2A.J-knock-out-Mäusen (KO) durchgeführt und die Ergebnisse mit Wildtyp-Mäusen (WT) verglichen. Die Haut von WT- und KO-Mäusen wurden mit 20 Gy lokal bestrahlt, makroskopisch wurde über einen Zeitraum von 14 Tagen die Hautreaktion beobachtet, um anschließend entnommene Haut mittels RNA-Sequenzierung und RT-PCR auf Seneszenz und DANN-Reparatur zu untersuchen, ein Transkriptomprofil zu erstellen und die Infiltration von Immunzellen mit Hilfe von Durchflouzytometre zu analysieren. Die Haut der KO-Mäuse zeigte hierbei eine intensivere Reaktion auf die Strahlung und eine Veränderung in der Epidermisdicke, einhergehend mit einem Verlust der Haarfollikelstammzellen und Haarfollikeln, im Vergleich zu den WT-Mäusen. Ebenso konnte eine erhöhte Genexpression von Seneszenz Faktoren und die Freisetzung von SASP-Faktoren festgestellt werden. Sowohl in den KO- wie auch bei den WT-Mäusen wurde eine vermehrte Infiltration der Haut durch Immunzellen nachgewiesen, jedoch zeigte die Haut der KO-Mäuse eine Vermehrung der Neutrophilen, eine unregelmäßige Differenzierung und Verhornung von Keratinozyten sowie eine Zunahme der JunB-Transkription im Vergleich zur Haut der WT-Mäuse. Zusammenfassend wurde die Erkenntnis gewonnen, dass das Fehlen von H2A.J in bestrahlten murinen Keratinozyten, die zunehmende Seneszenz, SASP-Sekretion und Immunreaktionen sowie die erhöhte Proliferation mit der Entzündungsreaktion während der Strahlendermatitis zusammenhängt

A business model perspective for ICTs in public engagement

This is the post-print version of the Article. The official published article can be accessed from the link below - Copyright @ 2012 ElsevierPublic institutions, in their efforts to promote meaningful citizen engagement, are increasingly looking at the democratic potential of Information and Communication Technologies (ICTs). Previous studies suggest that such initiatives seem to be impeded by socio-technical integration barriers such as low sustainability, poor citizen acceptance, coordination difficulties, lack of understanding and failure to assess their impact. Motivated by these shortcomings, the paper develops and applies a business model perspective as an interceding framework for analysis and evaluation. The underlying principle behind this approach is that it is not technology per se which determines success, but rather the way in which the businessmodel of the technological artifact is configured and employed to achieve the strategic goals. The business model perspective is empirically demonstrated with the case of an online petitioning system implemented by a UK local authority. The case illustrates the importance of considering ICTs in public engagement from a holistic view to make them more manageable and assessable

Method development and validation of simultaneous determination of seventeenmetals in water by ICP/MS

A simple, precise, accurate, and sensitive method is developed and validated for simultaneous determination of seventeen metals (Li, Sr, Ba, Tl, Pb, Bi, Al, K, Cr, Mn, Co, Ni, Cu, Zn, Mo, Ag, and Cd) in water by ICP-MS. The optimum conditions of the ICP-MS are as follows: nebulizer gas (argon) flow rate: 0.9 L/min, auxiliary gas (argon) flow 0.3 L/min, plasma (argon) gas flow: 15 L/min, reaction gas flow (helium) 4mL/min. This method is validated according to the requirements for new methods, which include linearity and range, accuracy, precision, selectivity, limit of detection (LOD), and limit of quntitation (LOQ). The current method demonstrates good linearity over the range of 1-1000 ppb with r2 greater than 0.999 for the seventeen metals. The recovery of the metals from water samples ranges from 97.5 to 101.7%. The method is selective where minimal interferences between the metals is observed (CeO/Ce = 1%, and Ce+2/Ce+1 = 1%), and with good resolution (0.8 amu at 10% height). The method is also precise where the RSD of the responses (cps) of replicates of the metals at three concentration levels is less than 1%. Low LOD and LOQ of metals using this method enable the detection and quantitation of these metals at low concentrations. Real water samples from West Bank in Palestine (groundwater) were analyzed for their trace metals content using this method

Determination of trace heavy metals in harvested rainwater used for drinking in Hebron (south West Bank, Palestine) by ICP-MS

Rainwater samples harvested for drinking from the west part of Hebron (south of West Bank in Palestine), the largest city in the West Bank, were analyzed for the content of different trace heavy metals (Cr, Mn, Co, Ni, Cu, Zn, Mo, Ag, Cd, Bi, and Pb) by inductively coupled plasma mass spectrometry (ICPMS). This study was conducted to determine the water quality of harvested rainwater used for drinking of south West Bank (case study, Hebron area).A total of 44water samples were collected in November 2012 from 44 house cisterns used to collect rainwater from the roofs of houses. The samples were analyzed for their pH, temperature, electrical conductivity, total dissolved solids, and different heavy metal contents. The pH of all water samples was within the US Environmental Protection Agency limits (6.5–8.5), while some water samples were found to exceed the allowed WHO limit for total dissolved solids (TDSs) in drinking water. Results showed that concentrations of the heavy metals vary significantly between the 44 samples. Results also showed that the concentration of five heavy metals (Cr, Mn, Ni, Ag, and Pb) is higher than the WHO limits for these heavy metals in drinking water. Overall, our findings revealed that harvested rainwater used for drinking of this part of south West Bank is contaminated with heavy metals that might affect human health.The authors are grateful for the German research funding organization (Deutsche Forschungsgemeinschaft (DFG)) for their financial support through TRION project