Intelligent Systems

This book is dedicated to intelligent systems of broad-spectrum application, such as personal and social biosafety or use of intelligent sensory micro-nanosystems such as "e-nose", "e-tongue" and "e-eye". In addition to that, effective acquiring information, knowledge management and improved knowledge transfer in any media, as well as modeling its information content using meta-and hyper heuristics and semantic reasoning all benefit from the systems covered in this book. Intelligent systems can also be applied in education and generating the intelligent distributed eLearning architecture, as well as in a large number of technical fields, such as industrial design, manufacturing and utilization, e.g., in precision agriculture, cartography, electric power distribution systems, intelligent building management systems, drilling operations etc. Furthermore, decision making using fuzzy logic models, computational recognition of comprehension uncertainty and the joint synthesis of goals and means of intelligent behavior biosystems, as well as diagnostic and human support in the healthcare environment have also been made easier

SYSTEMATIC LITERATURE REVIEW: DATA STANDARDIZATION IN HEALTH INFORMATION SYSTEMS

Digitalization within the healthcare sector has resulted in the accumulation of vast amounts of data that can be utilized towards the improvement of health outcomes. Meaningful use of such data, however, requires that it is standardized. Standardization plays a key role in providing a universal language for data that is exchanged through different health systems. Through a systematic literature review, this paper identifies practices that are vital for an effective standardization process. Ontological development, governance and organizational practices are identified as pertinent to the process of standardization and are analyzed and explained through the lens of a multi-thread social activity model by Fomin et al. (2003). This model provides a comprehensive view of related aspects of design, sense-making, and negotiation. The analysis shows that all these aspects take place in all stages of the standardization process, and they are highly dependent on each other and can occur simultaneously

Operations Management and Decision Making in Deployment of an On-Site Biological Analytical Capacity

Deployment of an on-site laboratory to contain an expanding outbreak and protect public health through rapid diagnosis of infected patients and identification of their contacts is a challenging and complex response, further complicated by time limitation and dramatic consequences of failure. Effective operations management and decision-making are critical for a successful Fieldable Laboratory (FL) mission at each phase of the mission. To analyze the principles and challenges of the operations management and associated decision-making process, the FL mission has been broken down into five successive interlinked phases defined as the “FL mission cycle” (FL-MC). Each phase comprises a set of operational functions (OFs) corresponding to the mission activities. Some decisions are associated with a single OF, whereas others are taken across different OFs and FL-MC phases. All decisions are treated as logical entities inherently linked to each other and to the whole situational context within the FL operational domain. Being part of the laboratory information management system (LIMS), the FL domain ontology is developed as the main knowledge management tool supporting the decision-making process. This is an essential way to promote interoperability and scalability between different FL modules and health care capacities during cross-border biological crises

The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world

Biotechnology has empirically established that it is easier to construct and evaluate variant genes and proteins than to account for the emergence and function of wild-type macromolecules. Systematizing this constructive approach, synthetic biology now promises to infer and assemble entirely novel genomes, cells and ecosystems. It is argued here that the theoretical and computational tools needed for this endeavor are missing altogether. However, such tools may not be required for diversifying organisms at the basic level of their chemical constitution by adding, substituting or removing elements and molecular components through directed evolution under selection. Most importantly, chemical diversification of life forms could be designed to block metabolic cross-feed and genetic cross-talk between synthetic and wild species and hence protect natural habitats and human health through novel types of containment

Knowledge-based modelling applied to synucleinopathies

The adoption of telemedicine technologies has enabled collaborative programs involving a variety of links among distributed medical structures and health officials and professionals. The use for telemedicine for transmission of medical data and the possibility for several distant physicians to share their knowledge on given medical cases provides clear benefits, but also raises several unsolved conceptual and technical challenges. The seamless exchange and access of medical information between medical structures, health professionals, and patients is a prerequisite for the harmonious development of this new medical practice. This paper proposes a new approach of semantic interoperability for enabling mutual understanding of terminologies and concepts used. The proposed semantic interoperability approach is based on conceptual graph to support collaborative activities by describing how different health specialists can apply appropriate strategies to eliminate differential medical diagnosis. Intelligent analysis strategies are used to narrow down and pinpoint medical disorders. The model proposed is fully verified by a case study in the context of elderly patients and specifically dealing with synucleinopathies, a group of neurodegenerative diseases that include Parkinson's disease (PD), dementia with Lewy bodies (DLB), pure autonomic failure (PAF) and multiple system atrophy (MSA)

A FAIR approach to genomics

The aim of this thesis was to increase our understanding on how genome information leads to function and phenotype. To address these questions, I developed a semantic systems biology framework capable of extracting knowledge, biological concepts and emergent system properties, from a vast array of publicly available genome information. In chapter 2, Empusa is described as an infrastructure that bridges the gap between the intended and actual content of a database. This infrastructure was used in chapters 3 and 4 to develop the framework. Chapter 3 describes the development of the Genome Biology Ontology Language and the GBOL stack of supporting tools enforcing consistency within and between the GBOL definitions in the ontology (OWL) and the Shape Expressions (ShEx) language describing the graph structure. A practical implementation of a semantic systems biology framework for FAIR (de novo) genome annotation is provided in chapter 4. The semantic framework and genome annotation tool described in this chapter has been used throughout this thesis to consistently, structurally and functionally annotate and mine microbial genomes used in chapter 5-10. In chapter 5, we introduced how the concept of protein domains and corresponding architectures can be used in comparative functional genomics to provide for a fast, efficient and scalable alternative to sequence-based methods. This allowed us to effectively compare and identify functional variations between hundreds to thousands of genomes. In chapter 6, we used 432 available complete Pseudomonas genomes to study the relationship between domain essentiality and persistence. In this chapter the focus was mainly on domains involved in metabolic functions. The metabolic domain space was explored for domain essentiality and persistence through the integration of heterogeneous data sources including six published metabolic models, a vast gene expression repository and transposon data. In chapter 7, the correlation between the expected and observed genotypes was explored using 16S-rRNA phylogeny and protein domain class content as input. In this chapter it was shown that domain class content yields a higher resolution in comparison to 16S-rRNA when analysing evolutionary distances. Using protein domain classes, we also were able to identify signifying domains, which may have important roles in shaping a species. To demonstrate the use of semantic systems biology workflows in a biotechnological setting we expanded the resource with more than 80.000 bacterial genomes. The genomic information of this resource was mined using a top down approach to identify strains having the trait for 1,3-propanediol production. This resulted in the molecular identification of 49 new species. In addition, we also experimentally verified that 4 species were capable of producing 1,3-propanediol. As discussed in chapter 10, the here developed semantic systems biology workflows were successfully applied in the discovery of key elements in symbiotic relationships, to improve functional genome annotation and in comparative genomics studies. Wet/dry-lab collaboration was often at the basis of the obtained results. The success of the collaboration between the wet and dry field, prompted me to develop an undergraduate course in which the concept of the “Moist” workflow was introduced (Chapter 9).</p

Information society and personal security

В статье авторы акцентировали внимание на современных трансформациях социальной реальности и процессах интеграции, цифровизации, которые детерминируют структурные изменения сферы безопасности. Развитие информационно-телекоммуникационных технологий и цифровизация изменяют существующую ментальную среду и духовную сферу социума, что приводит к трансмутации традиционных ценностей, инициируя деструктивные социальные взаимодействия в сфере информационной безопасности личности.In the article, the authors focused on the modern transformations of social reality and the processes of integration, digitalization, which determine the structural changes in the security sphere. The development of information and telecommunications technologies and digitalization change the existing mental environment and the spiritual sphere of society, which leads to the transmutation of traditional values, initiating destructive social interactions in the field of information security of the individual