Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Initial responses to questionnaires used to assess participants' understanding of informed consent for malaria vaccine trials conducted in the United States and Mali were tallied. Total scores were analyzed by age, sex, literacy (if known), and location. Ninety-two percent (92%) of answers by United States participants and 85% of answers by Malian participants were correct. Questions more likely to be answered incorrectly in Mali related to risk, and to the type of vaccine. For adult participants, independent predictors of higher scores (...) were younger age and female sex in the United States, and male sex in Mali. Scores in the United States were higher than in Mali (P = 0.005). Despite this difference participants at both sites were well informed overall. Although interpretation must be qualified because questionnaires were not intended as research tools and were not standardized among sites, these results do not support concerns about systematic low understanding among research participants in developing versus developed countries. (shrink)

The idea that causation involves the production of changes due to the exertion of influence of something on something else—the core idea of causal realism—used to be the default view. Today this idea is at the heart of (i) transmission/causal process accounts, (ii) mechanistic accounts, and (iii) powers-based accounts. However, as I have previously argued (Ingthorsson 2021) the above-mentioned approaches are based—to varying degree—on the very problematic assumption that causal influence is essentially unidirectional; that it passes from whatever is the (...) cause to the effect. As first pointed out be Mario Bunge (1959), the idea that causal influence is unidirectional is incompatible with what is today considered a scientific fact, notably that all interactions are perfectly reciprocal; whenever any object exerts an influence on any other object, the latter simultaneously exerts the same kind of influence, of the same magnitude, on the former. Drawing on Bunge’s result, I have developed a fourth approach to efficient causation that accepts the reciprocity of interactions (Ingthorsson 2002 & 2021). According to this view a cause is not the action of something on something else that receives the influence, but the reciprocal action between powerful particulars which results in a modification of both sides, producing a new state of affairs. In this paper, I present the core ideas of the four different approaches to causal efficacy, what I think is problematic with the first three and finally attempt to compare how well the four approaches fare in explaining two often discussed types of causal interactions: (i) collisions between billiard balls, and (ii) how water dissolves salt. I argue that only reciprocal actions between powerful particulars can plausibly claim to fully account for these phenomena, in a manner compatible with the theories and findings of the natural sciences. (shrink)

Jag tror att det är ett misstag att kräva av humanvetenskaperna (d.v.s. humaniora, samhälls- och beteendevetenskaperna) att de imiterar naturvetenskapernas forskningsmetodik. Humanvetenskaperna studerar meningsfulla fenomen vilkas natur är på ett grundläggande sätt annorlunda än de blott fysiska fenomen som naturvetenskapen studerar. Den största skillnaden är att meningsfulla fenomen inte uppenbarligen är lagbundna på samma sätt som fysiska fenomen och uppvisar därför inte samma regelbundenhet och förutsägbarhet som fysiska fenomen. För att studera meningsfulla fenomen krävs därför andra forskningsmetoder. Trots att humanvetenskaperna (...) studerar fenomen som inte är lagbundna och är på ett visst sätt subjektiva, så vill jag mena att de studerar objektivt verkliga fenomen och kan få giltig kunskap om dem. Att subjektiva fenomen också kan vara objektivt verkliga kan låta märkligt för vissa läsare, varför jag rundar av med en diskussion om vad det egentligen innebär för något att vara objektivt verkligt. Enligt den definition jag föreslår så framstår att meningsfulla fenomen, också de som kallas ”sociala konstruktioner”, kan förstås som objektivt verkliga företeelser trots att de på ett betydelsefullt sätt också är subjektiva. (shrink)

According to metaphysical tensism, there is an objective, albeit ever changing, present moment corresponding to our phenomenal experiences :635–642, 2013). One of the principle objections to metaphysical tensism has been Einstein’s argument from special relativity, which says that given that the speed of light is constant, there is no absolute simultaneity defined in terms of observations of light rays . In a recent paper, Brogaard and Marlow :635–642, 2013) argue that this objection fails. We argue that Brogaard and Marlow’s argument (...) fails to show that special relativity does not pose a threat to metaphysical tensism. (shrink)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: -/- The main aim of this review will be to assess the effects of changing practitioner empathy or patient expectations for all conditions. The main objective is to conduct a systematic review of randomised trials where the intervention involves manipulating either (a) practitioner empathy or (b) patient expectations, or (c) both.

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Shortages of new therapeutics to treat coronavirus disease (COVID-19) have forced clinicians, public health officials, and health systems to grapple with difficult questions about how to fairly allocate potentially life-saving treatments when there are not enough for all patients in need (1). Shortages have occurred with remdesivir, tocilizumab, monoclonal antibodies, and the oral antiviral Paxlovid (2) -/- Ensuring equitable allocation is especially important in light of the disproportionate burden experienced during the COVID-19 pandemic by disadvantaged groups, including Black, Hispanic/Latino and (...) Indigenous communities, individuals with certain disabilities, and low-income persons. However, many health systems have resorted to first-come, first-served approaches to allocation, which tend to disadvantage individuals with barriers in access to care (3). There is mounting evidence of racial, ethnic, and socioeconomic disparities in access to medications for COVID-19 (4, 5). -/- One potential method to promote equitable allocation is to use a weighted lottery, which is an allocation strategy that gives all eligible patients a chance to receive the scarce treatment while also allowing the assignment of higher or lower chances according to other ethical considerations (6). We sought to assess the feasibility of implementing a weighted lottery to allocate scarce COVID-19 medications in a large U.S. health system and to determine whether the weighted lottery promotes equitable allocation. (shrink)

Transoral laser microsurgery applies to the piecemeal removal of malignant tumours of the upper aerodigestive tract using the CO2 laser under the operating microscope. This method of surgery is being increasingly popularised as a single modality treatment of choice in early laryngeal cancers (T1 and T2) and occasionally in the more advanced forms of the disease (T3 and T4), predomi- nantly within the supraglottis. Thomas Kuhn, the American physicist turned philosopher and historian of science, coined the phrase ‘paradigm shift’ in (...) his groundbreaking book The Structure of Scientific Revolutions. He argued that the arrival of the new and often incompatible idea forms the core of a new paradigm, the birth of an entirely new way of thinking. This article discusses whether Steiner and col- leagues truly brought about a paradigm shift in oncological surgery. By rejecting the principle of en block resection and by replacing it with the belief that not only is it oncologically safe to cut through the substance of the tumour but in doing so one can actually achieve better results, Steiner was able to truly revolutionise the man- agement of laryngeal cancer. Even though within this article the repercussions of his insight are limited to the upper aerodigestive tract oncological surgery, his willingness to question other peoples’ dogma makes his contribution truly a genuine paradigm shift. (shrink)

Loneliness in medicine is a serious problem not just for patients, for whom illness is intrinsically isolating, but also for physicians in the contemporary condition of medicine. We explore this problem by investigating the ideal physician-patient relationship, whose analogy with friendship has held enduring normative appeal. Drawing from Talbot Brewer and Nir Ben-Moshe, we argue that this appeal lies in a dynamic form of companionship incompatible with static models of friendship-like physician-patient relationships: a mutual refinement of embodied virtue that draws (...) both persons together. The ideal physician-patient relationship has a dialectical character that fosters each member's improvement of phenomenologically recognizing and embodying moral virtues. A key component of this dynamic is a commitment to the common goal of the patient's health, realized through joint interactivities and conversations over time. The physician's presence to the patient's suffering—understood best as an alienating phenomenological condition for the patient—orients and discloses possibilities for virtuous caregiving by structuring the meanings of the goals, conversations, and joint narrative constitutive of their relationship. Presence to suffering, paradoxically, is perhaps an important prerequisite for this dynamic partnership. These activities dialectically build an interpretive horizon of understanding through which moral goods and character refinement—in and for the other—may become revealed for both persons in their shared being-in-the-world. This analysis of suffering, mood, and revealing of (possible) moral goods has implications for addressing the modern problem of loneliness for patients and physicians, who are increasingly inhibited from building flourishing relationships with each other. (shrink)

A nested mode ontology allows one to make sense of apparently contradictory Christological claims such as that Christ knows everything and there are some things Christ does not know.

There is an important sense in which one can be sure without being certain, i.e., without assigning unit probability. I will offer an explication of this sense of sureness, connecting it with the level of credence that a rational agent would need to have to be confident that she won’t ever lose her confidence. A simple formal result then gives us an explicit formula connecting the threshold α for credence needed for confidence with the threshold needed for being sure: one (...) needs 1−(1−α) to be sure. I then suggest that stepping between α and 1−(1−α) gives a procedure that generates an interesting hierarchy of credential thresholds. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Appearing for the first time in English, Art and the Working Class is the work of Alexander Bogdanov, a revolutionary polymath and co-founder, with Vladimir Lenin, of the Bolshevik faction of the Russian Social Democratic Labor Party. Bogdanov was a strong proponent of the arts, co-founding the Proletarian Culture (Proletkult) organization to provide political and artistic education to workers. In this book, Bogdanov discusses the origins of art, its class characteristics, and how it might be created within a revolutionary (...) socialist context. (shrink)

We discuss potential biorisks from large language models (LLMs). AI assistants based on LLMs such as ChatGPT have been shown to significantly reduce barriers to entry for actors wishing to synthesize dangerous, potentially novel pathogens and chemical weapons. The harms from deploying such bioagents could be further magnified by AI-assisted misinformation. We endorse several policy responses to these dangers, including prerelease evaluations of biomedical AIs by subject-matter experts, enhanced surveillance and lab screening procedures, restrictions on AI training data, and access (...) controls on biomedical AI. We conclude with a suggestion about future research directions in bioethics. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

Teachers encountered numerous challenges posed by the COVID-19 outbreak. Herewith, this study aimed to determine the challenges encountered by Filipino teachers in the new normal and their coping mechanisms. This study employed a qualitative inquiry to determine the challenges encountered and coping mechanisms employed by teachers amid modular instruction, involving 10 teachers from five secondary schools in the Philippines who participated voluntarily. Data were gathered through a written narrative from each participant and were analyzed thematically. Themed findings showed that these (...) teachers are greatly challenged in terms of learning quality transfer, module distribution and retrieval, students’ difficulties in following instruction, power disruption, internet connection, and health risks posed by the pandemic. Nevertheless, these teachers dealt with these difficulties by employing their own coping techniques. Teaching can be challenging and frustrating, especially in these difficult times, but as these teachers demonstrated, everything is possible. Hence, educators must be ready for any situation that may arise. This situation is unlikely to get better anytime soon; instead, teachers will need to adjust to and accept this reality. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

In this paper I contend that the 'superfluity' of triangles is only apparent; all those specified are indeed required for the smallest sub-units, so long as the symmetry of the final body to be constructed is taken into account at earlier stages.

This paper sets mathematics among the sciences, despite not being empirical, because it studies relations of various sorts, like the sciences. Each empirical science studies the relations among objects, which relations determining which science. The mathematical science studies relations as such, regardless of what those relations may be or be among, how relations themselves are related. This places it at the extreme among the sciences with no objects of its own (A Subject with no Object, by J.P. Burgess and G. (...) Rosen). Examples are discussed. The historical development of written mathematics from algorithms on clay tablets to theorems with proofs is said to show that application of algorithms to specific problems and theorems to scientific objects is like allegorical interpretation. Mathematics fits into the modern scientific context because the sciences, beginning with Galileo, have been constructed in imitation of mathematics. Viewing mathematics this way does not solve any ontological problems, but it does show how mathematics avoids them. Epistemological problems, insuperable for object realism, are simplified. For example, we have access to relations among any objects that we can consider objectively, first physical objects and then mathematical objects of greater and greater abstraction. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: (...) this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper. (shrink)

This paper explores an emerging sub-field of both empirical bioethics and experimental philosophy, which has been called “experimental philosophical bioethics” (bioxphi). As an empirical discipline, bioxphi adopts the methods of experimental moral psychology and cognitive science; it does so to make sense of the eliciting factors and underlying cognitive processes that shape people’s moral judgments, particularly about real-world matters of bioethical concern. Yet, as a normative discipline situated within the broader field of bioethics, it also aims to contribute to substantive (...) ethical questions about what should be done in a given context. What are some of the ways in which this aim has been pursued? In this paper, we employ a case study approach to examine and critically evaluate four strategies from the recent literature by which scholars in bioxphi have leveraged empirical data in the service of normative arguments. (shrink)

Translators’ Abstract: This is a translation of Hans-Georg Gadamer’s recently discovered 1952 Berlin speech. The speech includes several themes that reappear in Truth and Method, as well as in Gadamer’s later writings such as Reason in the Age of Science. For example, Gadamer criticizes positivism, modern philosophy’s orientation toward positivism, and Enlightenment narratives of progress, while presenting his view of philosophy’s tasks in an age of crisis. In addition, he discusses structural power, instrumental reason, the objectification of nature and human (...) beings, the reduction of both to mere means, and the colonization of scientific-technological ways of knowing and being—all of which continue to impact our social and political lives together and threaten the very existence of every living being. This speech is essential reading for Gadamer scholars interested in the social, political, and ethical dimensions of his thought and for those interested in bringing Gadamer into conversation with critical theory. (shrink)

Objectives: To explore individuals’ perception of the personal, family and societal educational needs following a spinal cord injury. Methods: Sixty-one patients who sustained a traumatic SCI between March 2015 and June 2016 referred to Brain and Spinal Cord Injury Research Center were included in a cross sectional study and completed an online survey containing open-and closed-ended questions, in Iran. Participants’ responses were analyzed i using a qualitative approach with a thematic analysis. Results: Following a thematic analysis of the patient’s perceived (...) educational needs, 3 themes and 14 subthemes were identified. The 3 themes included personal, family, and societal educational perceived needs. Within personal educational needs, there were 7 subthemes which included personal independence and transportation, financial independence, life skills modification, knowledge about SCI, prevention of SCI complications, relationships and sexual function, and psychological adjustments. Among family educational needs, the 3 subthemes were caregiver skills and communication, first aid and emergency skills, and emotional and psychological support. For societal educational needs, the 4 subthemes described were social integration, interpersonal communication skills, SCI awareness and injury prevention, sympathize while avoiding pity. Conclusion: According to our findings, people with SCI have various needs that need to be addressed. Educational support should be a part of a comprehensive rehabilitation program and geared towards addressing the patients’ personal and family needs, while educating the community about SCI in order to allow for reintegration into society. (shrink)

Bilim ve din arasındaki etkileşimler hem tarihsel olarak hem de günümüzde çeşitli ve karmaşıktır. Modeller, verileri anlamlandırmak için faydalı olabilir. Bu makale, bilim-din etkileşimlerini tanımlamak için önerilen dört ana model türünü karşılaştırarak, onların güçlü ve zayıf yönlerini vurgulamaktadır. Bilimsel ve dini bilgiyi ilişkilendirme görevinde 'bütünleyici' modelin en verimli olduğu sonucuna varılmıştır.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Since its publication, the Psychopathic Personality Inventory and its revision (Lilien- feld & Andrews, 1996; Lilienfeld & Widows, 2005) have become increasingly popular such that it is now among the most frequently used self-report inventories for the assessment of psychopathy. The current meta-analysis examined the relations between the two PPI factors (factor 1: Fearless Dominance; factor 2: Self-Centered Impulsivity), as well as their relations with other validated measures of psychopathy, internalizing and externalizing forms of psychopathology, general personality traits, and antisocial (...) personality disorder symptoms. Across 61 samples reported in 49 publications, we found support for the convergent and criterion validity of both PPI factor 2 and the PPI total score. Much weaker validation was found for PPI factor 1, which manifested limited convergent validity and a pattern of correlations with central criterion variables that was inconsistent with many conceptualizations of psychopathy. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

This dissertation discusses the work of Thomas Hobbes, and has two main themes. The first is Hobbes's materialism, and the second is Hobbes's relationships to other philosophers, in particular his place in the mechanist movement that is said to have replaced Aristotelianism as the dominant philosophy in the seventeenth century. -/- I argue that Hobbes does not, for most of his career, believe the general materialist view that bodies are the only substances. He believes, rather, that ideas, which are our (...) main mechanism for thinking about the world, allow us to understand many bodies, but not to understand every thing we recognize to exist. The incomprehensible things include God---and, early in Hobbes's career, the human mind. Discussing materialism and our knowledge of God leads me to engage with the debate over Hobbes's alleged atheism. I argue that the evidence for Hobbes's atheism is weak at best. Hobbes is a sincere theist, though his view is sometimes unusual. -/- My discussion of Hobbes's relationships to other philosophers has three parts. In chapter five I argue that Hobbes's views about method are in important ways similar to Zabarella's. In chapter six I look at Hobbes's rejection of the view, held by some scholastic Aristotelians, that accidents can sometimes exist without inhering in substances. Thus we see two sides of Hobbes's interaction with the Aristotelian tradition. Sometimes that interaction is just rejection, but at other times Hobbes takes over views from that tradition. Then in chapter seven I consider whether, and in what sense, Hobbes is a mechanist. I argue that the narrative of mechanism and Aristotelianism is a less powerful explanation than it has seemed to some to be, because it is hard to see what mechanists have in common. (shrink)

This study emphasizes the importance of enhancing food safety and hygiene practices among sidewalk vendors to safeguard public health in Balayan Public Market. Employing a mixed-methods approach, with both quantitative and qualitative components, a diverse sample of 55 consumers, 5 sidewalk vendors, and 5 market administrators was selected using a combination of purposive and random sampling techniques under non-probability sampling. Microbial investigations were conducted during both the initial sampling and testing phase (A) and subsequent sampling and testing phase (B) on (...) popular street food items at Lipa Quality Control Inc., including chicken nuggets, chicken nugget sauce (sweet and vinegar), Isaw, Isaw sauce, Proben, Proben sauce, Calamares, Calamares Vinegar Sauce, Kwek- Kwek, and Kwek-Kwek sauce. The findings reveal that “Isaw and Chicken Nuggets Sauce (Sweet)” had a result of “Too Numerous To Count (TNTC),” indicating an extraordinarily high bacteria count. This underscores the imperative need to raise awareness and provide targeted guidance to sidewalk vendors regarding essential food handling, storage, and sanitation practices. Therefore, a sanitary action plan is developed to promote community engagement, educational initiatives, and regulatory support, enhancing food safety practices among sidewalk vendors and ensuring a safer and healthier food environment. (shrink)

(1996). What the prophet and the philosopher told their nations: A multi‐modal systems view of norms and civilisation. World Futures: Vol. 47, Unity and Diversity in Contemporary Systems Tinking: Systematic Pictures at an Exhibition, pp. 53-67.

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

In response to the COVID-19 pandemic threat, the Department of Education (DepEd) established the Basic Education - Learning Continuity Plan (BE-LCP) to allow students to continue their education and teachers to conduct instruction in a safe working and learning environment. As a result, DepEd implemented the distance learning approach, including Modular Distance Learning (MDL), for the School Year 2020-2021. This paper investigated the practices, challenges, and coping mechanisms of teachers and students involved in the implementation of the MDL in Schools (...) Division of Laoag City. This qualitative research utilized semi-structured interview guide to collect data from 20 teachers and 20 learners from elementary, junior high and senior high schools. Using the phenomenological study, data were analyzed and organized into themes. The study's major themes revealed that teachers and students began familiarizing themselves with the features of MDL but encountered challenges such as printing, distribution, and retrieval of modules, as well as monitoring of student progress on the part of the teacher and answering overloaded activities on the part of the students. They claimed, however, that they have unique coping mechanisms in dealing with the identified challenges by resolving issues independently and seeking help from family and colleagues. Finally, the Modular Distance Learning Adoption Framework (MDLAF) was developed and validated for teachers and students to effectively adopt MDL. The researchers recommended that relevant scaffolding such as capacity building, counseling and instructional support be provided to both teachers and students to effectively adopt different learning modalities such as MDL. (shrink)

Online education has become an essential component of education. Thus, several factors, such as the student’s learning strategy and motivation, generally contribute to their academic success. This study investigates the relationship between learning strategies, motivation, and online learning environment among 150 first-year college students. Employing correlational design, the statistical findings of the study reveal that the r coefficient of 0.59 indicates a moderate positive correlation between the variables. The p-value of 0.00, which is less than 0.05, leads to the decision (...) to reject the null hypothesis. Hence, a significant relationship exists between learning strategies, motivation, and the online learning environment. (shrink)

Abstract: Colombia's armed conflict, one of the longest in the world, requires a special approach to transitional justice strategies. Institutionalized practices customs. Approach it from a perspective that, with the legislative and judicial actions, give rise to political-educational and ethical-cultural actions is key. Recognition and legitimacy are complementary. With Carlos S. Nino, we see the law as a collective action in time.

IPCC SPECIAL REPORT ON CLIMATE CHANGE AND LAND (SRCCL) -/- Chapter 3: Climate Change and Land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.