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)
BackgroundIn the Canadian Alliance for Healthy Hearts and Minds cohort, participants underwent magnetic resonance imaging of the brain, heart, and abdomen, that generated incidental findings. The approach to managing these unexpected results remain a complex issue. Our objectives were to describe the CAHHM policy for the management of IFs, to understand the impact of disclosing IFs to healthy research participants, and to reflect on the ethical obligations of researchers in future MRI studies.MethodsBetween 2013 and 2019, 8252 participants were recruited with (...) a follow-up questionnaire administered to 909 participants at 1-year. The CAHHM policy followed a restricted approach, whereby routine feedback on IFs was not provided. Only IFs of severe structural abnormalities were reported.ResultsSevere structural abnormalities occurred in 8.3% of participants, with the highest proportions found in the brain and abdomen. The majority of participants informed of an IF reported no change in quality of life, with 3% of participants reporting that the knowledge of an IF negatively impacted their quality of life. Furthermore, 50% reported increased stress in learning about an IF, and in 95%, the discovery of an IF did not adversely impact his/her life insurance policy. Most participants would enrol in the study again and perceived the MRI scan to be beneficial, regardless of whether they were informed of IFs. While the implications of a restricted approach to IF management was perceived to be mostly positive, a degree of diagnostic misconception was present amongst participants, indicating the importance of a more thorough consent process to support participant autonomy.ConclusionThe management of IFs from research MRI scans remain a challenging issue, as participants may experience stress and a reduced quality of life when IFs are disclosed. The restricted approach to IF management in CAHHM demonstrated a fair fulfillment of the overarching ethical principles of respect for autonomy, concern for wellbeing, and justice. The approach outlined in the CAHHM policy may serve as a framework for future research studies.Clinical trial registrationhttps://clinicaltrials.gov/ct2/show/nct02220582. (shrink)
In this article, we develop an approach for the moral assessment of research and development networks on the basis of the reflective equilibrium approach proposed by Rawls and Daniels. The reflective equilibrium approach aims at coherence between moral judgments, principles, and background theories. We use this approach because it takes seriously the moral judgments of the actors involved in R & D, whereas it also leaves room for critical reflection about these judgments. It is shown that two norms, namely reflective (...) learning and openness and inclusiveness, which are used in the literature on policy and technological networks, contribute to achieving a justified overlapping consensus. We apply the approach to a case study about the development of an innovative sewage treatment technology and show how in this case the two norms are or could be instrumental in achieving a justified overlapping consensus on relevant moral issues. (shrink)
An appropriate kind of curved Hilbert space is developed in such a manner that it admits operators of $\mathcal{C}$ - and $\mathfrak{D}$ -differentiation, which are the analogues of the familiar covariant and D-differentiation available in a manifold. These tools are then employed to shed light on the space-time structure of Quantum Mechanics, from the points of view of the Feynman ‘path integral’ and of canonical quantisation. (The latter contains, as a special case, quantisation in arbitrary curvilinear coordinates when space is (...) flat.) The influence of curvature is emphasised throughout, with an illustration provided by the Aharonov-Bohm effect. (shrink)
We investigate a possible form of Schrödinger’s equation as it appears to moving observers. It is shown that, in this framework, accelerated motion requires fictitious potentials to be added to the original equation. The gauge invariance of the formulation is established. The example of accelerated Euclidean transformations is treated explicitly, which contain Galilean transformations as special cases. The relationship between an acceleration and a gravitational field is found to be compatible with the picture of the ‘Einstein elevator’. The physical effects (...) of an acceleration are illustrated by the problem of the uniformly-accelerated harmonic oscillator. (shrink)
This paper presents a new formal model for D–N explanation that gives intuitive criteria of acceptability, avoids the known trivializations, and links explanation with confirmation theory. Although set in the twenty-five year tradition of attempts to formalize D–N explanation, it proposes a new direction for the model that is to be distinguished from the syntactical and informational approaches by its introduction of restrictions which derive from the use which the D–N model can have in hypothesis testing. This model, illustrating the (...) verificational approach, revises the classic H–O requirements and amends the notion of partial self-explanation to meet a criticism to which the H–O notion is vulnerable. (shrink)
This paper analyzes several properties of infima in Dn, the n-r.e. degrees. We first show that, for every n> 1, there are n-r.e. degrees a, b, and c, and an -r.e. degree x such that a < x < b, c and, in Dn, b c = a. We also prove a related result, namely that there are two d.r.e. degrees that form a minimal pair in Dn, for each n < ω, but that do not form a minimal pair (...) in Dω. Next, we show that every low r.e. degree branches in the d.r.e. degrees. This result does not extend to the low2 r.e. degrees. We also construct a non-low r.e. degree a such that every r.e. degree b a branches in the d.r.e. degrees. Finally we prove that the nonbranching degrees are downward dense in the d.r.e. degrees. (shrink)
