Reasoning by analogy in the generation of domain acceptable ontology refinements

Refinements generated for a knowledge base often involve the learning of new knowledge to be added to or replace existing parts of a knowledge base. However, the justifiability of the refinement in the context of the domain (domain acceptability) is often overlooked. The work reported in this paper describes an approach to the generation of domain acceptable refinements for incomplete and incorrect ontology individuals through reasoning by analogy using existing domain knowledge. To illustrate this approach, individuals for refinement are identified during the application of a knowledge-based system, EIRA; when EIRA fails in its task, areas of its domain ontology are identified as requiring refinement. Refinements are subsequently generated by identifying and reasoning with similar individuals from the domain ontology. To evaluate this approach EIRA has been applied to the Intensive Care Unit (ICU) domain. An evaluation (by a domain expert) of the refinements generated by EIRA has indicated that this approach successfully produces domain acceptable refinements

An Ontology for Supporting Knowledge Discovery and Evolution

Knowledge Discovery and Evolution (KDE) is of interest to a broad array of researchers from both Philosophy of Science (PoS) and Artificial Intelligence (AI), in particular, Knowledge Representation and Reasoning (KR), Machine Learning and Data Mining (ML-DM) and the Agent Based Systems (ABS) communities. In PoS, Haig recently pro- posed a so-called broad theory of scientific method that uses abduction for generating theories to explain phenomena. He refers to this method of scientific inquiry as the Abductive Theory of Method (ATOM). In this paper, we analyse ATOM, align it with KR and ML-DM perspec- tives and propose an algorithm and an ontology for supporting agent based knowledge discovery and evolution based on ATOM. We illustrate the use of the algorithm and the ontology on a use case application for electricity consumption behaviour in residential households

An Ontology for Supporting Knowledge Discovery and Evolution

Knowledge Discovery and Evolution (KDE) is of interest to a broad array of researchers from both Philosophy of Science (PoS) and Artificial Intelligence (AI), in particular, Knowledge Representation and Reasoning (KR), Machine Learning and Data Mining (ML-DM) and the Agent Based Systems (ABS) communities. In PoS, Haig recently pro- posed a so-called broad theory of scientific method that uses abduction for generating theories to explain phenomena. He refers to this method of scientific inquiry as the Abductive Theory of Method (ATOM). In this paper, we analyse ATOM, align it with KR and ML-DM perspec- tives and propose an algorithm and an ontology for supporting agent based knowledge discovery and evolution based on ATOM. We illustrate the use of the algorithm and the ontology on a use case application for electricity consumption behaviour in residential households

ACLRO: An Ontology for the Best Practice in ACLR Rehabilitation

Indiana University-Purdue University Indianapolis (IUPUI)With the rise of big data and the demands for leveraging artificial intelligence (AI), healthcare requires more knowledge sharing that offers machine-readable semantic formalization. Even though some applications allow shared data interoperability, they still lack formal machine-readable semantics in ICD9/10 and LOINC. With ontology, the further ability to represent the shared conceptualizations is possible, similar to SNOMED-CT. Nevertheless, SNOMED-CT mainly focuses on electronic health record (EHR) documenting and evidence-based practice. Moreover, due to its independence on data quality, the ontology enhances advanced AI technologies, such as machine learning (ML), by providing a reusable knowledge framework. Developing a machine-readable and sharable semantic knowledge model incorporating external evidence and individual practice’s values will create a new revolution for best practice medicine. The purpose of this research is to implement a sharable ontology for the best practice in healthcare, with anterior cruciate ligament reconstruction (ACLR) as a case study. The ontology represents knowledge derived from both evidence-based practice (EBP) and practice-based evidence (PBE). First, the study presents how the domain-specific knowledge model is built using a combination of Toronto Virtual Enterprise (TOVE) and a bottom-up approach. Then, I propose a top-down approach using Open Biological and Biomedical Ontology (OBO) Foundry ontologies that adheres to the Basic Formal Ontology (BFO)’s framework. In this step, the EBP, PBE, and statistic ontologies are developed independently. Next, the study integrates these individual ontologies into the final ACLR Ontology (ACLRO) as a more meaningful model that endorses the reusability and the ease of the model-expansion process since the classes can grow independently from one another. Finally, the study employs a use case and DL queries for model validation. The study's innovation is to present the ontology implementation for best-practice medicine and demonstrate how it can be applied to a real-world setup with semantic information. The ACLRO simultaneously emphasizes knowledge representation in health-intervention, statistics, research design, and external research evidence, while constructing the classes of data-driven and patient-focus processes that allow knowledge sharing explicit of technology. Additionally, the model synthesizes multiple related ontologies, which leads to the successful application of best-practice medicine

T cells in rheumatoid arthritis

Over the past decade and a half, advances in our understanding of the pathogenesis of immune-mediated diseases such as rheumatoid arthritis (RA) have translated directly into benefit for patients. Much of this benefit has arisen through the introduction of targeted biological therapies. At the same time, technological advances have made it possible to define, at the cellular and molecular levels, the key pathways that influence the initiation and persistence of chronic inflammatory autoimmune reactions. As our understanding grows, it is likely that this knowledge will be translated into a second generation of biological therapies that are tailor-made for the patient. This review summarizes current perspectives on RA disease pathogenesis, with particular emphasis on what RA T cells look like, what they are likely to see, and how they contribute to persistence of the chronic inflammatory response

Exploring the motivation behind cybersecurity insider threat and proposed research agenda

Cyber exploitation and malicious activities have become more sophisticated. Insider threat is one of the most significant cyber security threat vector, while posing a great concern to corporations and governments. An overview of the fundamental motivating forces and motivation theory are discussed. Such overview is provided to identify motivations that lead trusted employees to become insider threats in the context of cyber security. A research agenda with two sequential experimental research studies are outlined to address the challenge of insider threat mitigation by a prototype development. The first proposed study will classify data intake feeds, as recognized and weighted by cyber security experts, in an effort to establish predictive analytics of novel correlations of activities that may lead to cyber security incidents. It will also develop approach to identify how user activities can be compared against an established baseline, the user’s network cyber security pulse, with visualization of simulated users’ activities. Additionally, the second study will explain the process of assessing the usability of a developed visualization prototype that intends to present correlated suspicious activities requiring immediate action. Successfully developing the proposed prototype via feeds aggregation and an advanced visualization from the proposed research could assist in the mitigation of malicious insider threat

Evaluating Differential Gene Expression Using RNA-Sequencing: A Case Study in Diet-Induced Mouse Model Associated with Non-Alcoholic Fatty Liver Disease (NAFLD) and CXCL12-Vs- TGFβ Induced Fibroblast to Myofibroblast Phenoconversion

Unlike the genome, cell transcriptome is dynamic and specific for a given cell developmental stage. Transcriptomics study is crucial to understand the functional elements of the genome to divulge molecular constituents of cells. The recent development of high-throughput sequencing technologies has provided an unprecedented method to sequence RNA and it has been emerging as the preferred technology for both characterization and quantification of the cell transcripts. Using “Tailor_Pipeline” we have analyzed diet-induced mouse and stromal fibroblast RNA-Seq samples and deciphers the differentially expressed genes that were significantly up- and downregulated and associated with several metabolic immune responses that presumably associated with liver disease. Analyzing the diet-induced mice model allowed us to encapsulate the transcriptional differences between diet-induced mice that can aid in the understanding of NAFLD and consequent liver pathogenesis. Identification of genes downregulated in metabolic processes and upregulated in immune responses indicate that mice model exhibiting liver disease. Moreover, the finding of a premalignant signature suggests that NAFLD may begin to progress towards hepatocellular carcinoma much earlier than earlier consideration. Tissue fibrosis arises due to overgrowth, scarring of various tissues and is attributed to deposition of the extracellular matrix including collagen, influenced by the actions of several pro-fibrotic proteins that can induce myofibroblast phenoconversion. Though recent transcriptomics analysis reveals the cellular identity, its ability to provide biologically meaningful insights in fibrosis is largely unexplored. To unravel the mechanisms at the genetic level, we have considered TGFβ/TGFβR and CXCL12/CXCR4 transcriptomes in human stromal fibroblasts. Transcriptome profiling technology revealed CXCL12/CXCR4 axis is responsible for the activation of COPII vesicle formation, ubiquitination, and Golgi/ER localization/targeting. Especially, identification of CUL3 and KLHL12 are responsible for the transportation of procollagen from ER to the Golgi. Interestingly, over-expression of CUL3 and KLHL12 are highly correlated with procollagen secretion by CXCL12-treated cells, but not in TGFβ-, treated cells. Moreover, this analysis showed how activation of the CXCL12/CXCR4 axis promotes procollagen I secretion that responsible for the deposition of ECM which is a characteristic of fibrosis

Concepts, Frames and Cascades in Semantics, Cognition and Ontology

This open access book presents novel theoretical, empirical and experimental work exploring the nature of mental representations that support natural language production and understanding, and other manifestations of cognition. One fundamental question raised in the text is whether requisite knowledge structures can be adequately modeled by means of a uniform representational format, and if so, what exactly is its nature. Frames are a key topic covered which have had a strong impact on the exploration of knowledge representations in artificial intelligence, psychology and linguistics; cascades are a novel development in frame theory. Other key subject areas explored are: concepts and categorization, the experimental investigation of mental representation, as well as cognitive analysis in semantics. This book is of interest to students, researchers, and professionals working on cognition in the fields of linguistics, philosophy, and psychology

Acts of killing, acts of meaning:an application of corpus pattern analysis to language of animal-killing

We are currently witnessing unprecedented levels of ecological destruction and violence visited upon nonhumans. Study of the more-than-human world is now being enthusiastically taken up across a range of disciplines, in what has been called the ‘scholarly animal turn’. This thesis brings together concerns of Critical Animal Studies – along with related threads of posthumanism and new materialist thinking – and Corpus Linguistics, specifically Corpus Pattern Analysis (CPA), to produce a data-driven, lexicocentric study of the discourse of animal-killing. CPA, which has been employed predominantly in corpus lexicography, provides a robust and empirically well-founded basis for the analysis of verbs. Verbs are chosen as they act as the pivot of a clause; analysing them also uncovers their arguments – in this case, participants in material-discursive ‘killing’ events. This project analyses 15 ‘killing’ verbs using CPA as a basis, in what I term a corpus-lexicographical discourse analysis. The data is sampled from an animal-themed corpus of around 9 million words of contemporary British English, and the British National Corpus is used for reference. The findings are both methodological and substantive. CPA is found to be a reliable empirical starting point for discourse analysis, and the lexicographical practice of establishing linguistic ‘norms’ is critical to the identification of anomalous uses. The thesis presents evidence of anthropocentrism inherent in the English lexicon, and demonstrates several ways in which distance is created between participants of ‘killing’ constructions. The analysis also reveals specific ways that verbs can obfuscate, deontologise and deindividualise their arguments. The recommendations, for discourse analysts, include the adoption of CPA and a critical analysis of its resulting patterns in order to demonstrate the precise mechanisms by which verb use can either oppress or empower individuals. Social justice advocates are also alerted to potentially harmful language that might undermine their cause

Conflict within psychosis treatment in the English NHS: investigating the experiences of patients and psychiatrists

The vociferous psychiatric Service User Movement and critical elements within psychiatry form evidence of conflict within the field of psychosis treatment. Psychiatric treatment of psychosis within the English NHS was investigated to understand the conflict-ridden relationships between psychiatrists and patients. The hope was to form a bridge of understanding and dialogue between mainstream psychiatry, its fringes and the Service User Movement. People diagnosed with psychosis who subsequently sought support from the Movement and Consultant Psychiatrists working within the NHS were interviewed, focussing upon their experiences of psychosis treatment. The patients were asked about their experiences of and feelings about their NHS treatment and help received from the Movement and, how and if the experiences had affected their self-understanding. The psychiatrists were asked about their motivations for choosing the speciality, experiences of working with those diagnosed with psychosis and their relationships with patients and other psychiatrists. Interviews were analysed using Framework Analysis, a qualitative method designed to probe individual as well as organisational processes and make policy recommendations. The conflictual dynamic was found to result from a fundamental neglect of existential needs for meaning, hope and relationships in psychiatric training and NHS treatment. The patients felt harmed in treatment because their anxieties about psychic annihilation and need to understand their suffering were ignored. Such harms were found to derive from the lack of focus upon relationships in psychiatric services and training. The psychiatrists suffered low morale and vocational dissatisfaction because their training and work systems left them ill equipped to understand or bear the essential difficulties of the work. Psychoanalytic and other literature is cited to explore unconscious betrayals of human needs in the design of care systems. Ideas are offered to support all involved in the difficult work with psychosis, based upon interventions in psychiatry and other disciplines