The Shape-of-a-Life phenomenon is widely recognized by philosophers of well-being: an upward life trajectory seems better than its downward equivalent if the sum of momentary well-being is held fixed. But what if we hold fixed the sum of momentary well-being in an upward trajectory, are certain ways to improve from the bad times better than the others? Velleman suggests that a redemptive trajectory is better than a bare upward trajectory. In this paper, I elaborate this proposal by developing a mediating (...) factor account of prudential redemption. I argue that, in redemptive trajectories, there is a mediating factor that bears certain relations with the negative and the positive events respectively, one that does not necessarily appear in bare upward trajectories. Prudential redemption, compared to mere improvement, can enhance a person’s lifetime well-being because a redeemed event is made less bad by virtue of the mediating factor. This result has implications for making decisions in the face of equally good options and for evaluating the rationality of honoring sunk costs. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Abstract: Background: Coronary artery disease remains the leading cause of morbidity and mortality Worldwide. Previous reviews pointed that nursing interventions are beneficial for coronary artery patients. However, most interventions focused on education and counselling, but not consistent with the outcome set; still did not consider patient’s coronary artery disease risky characteristics. Related studies in China also difficult to find. Therefore this study was conducted to investigate kinds of nursing interventions delivered to coronary artery patients and match them with patient’s risk (...) factors of coronary artery disease. Results of this study were expected to add new knowledge that will alert nurses to consider coronary artery risk factors which in turn might enable the development of appropriate approaches to improve patient’s wellbeing hence reduce frequent coronary artery morbidity and mortality. Methods: A descriptive, cross-sectional, retrospective design using clinical case notes was employed. Study was undertaken in coronary care wards at the teaching hospital in China from November 2017 to September 2018. Structured-literature supported self-designed questionnaire was utilized for data collection. Chi square (χ2) test and multivariate logistic regression for adjusted odds ratio with 95% confidence interval were used to compare the relationship among independent (patient’s risk coronary artery disease factors) and dependent (nursing interventions) categorical variables. Ethical permission was granted accordingly. Results: A total of 300 coronary artery patients’ case notes were audited with mean age 63±11.2 years. Of these 175 (58.3%) were males. 126(42%) were smoking and 224(74.7%) were hypertensive. More evidence based nursing interventions than education and counselling were found to be delivered to these patients. “Administer coronary artery disease medication and their instructions” was mostly delivered to many patients 291(97%) while “counsel to cope with stress” was the least one 60 (20.0%). Three of eight nursing interventions delivered significantly matched with three or all of these patient’s coronary artery risk variables (age, smoking, hypertension and diabetes) (p < 0.05 and/or < 0.01) with Adjusted odds ratio (95% CI) within their significant ranges. Conclusion: This study delivers valuable insight that, nurses in the studied teaching hospital delivered beneficial evidence based nursing interventions to patients with coronary artery disease which significantly matched with their risk factors of coronary artery illness. However, care for stress was low hence needs improvement. Furthermore, research is needed to get consistency of nursing interventions with patient’s end point clinical outcomes for further appraisal of nursing efforts in caring CAD patients . (shrink)