Ethnic slur terms and other group-based slurs must be differentiated from general pejoratives and pure expressives. As these terms pejoratively refer to certain groups of people, they are a typical feature of hate speech contexts where they serve xenophobic speakers in expressing their hatred for an entire group of people. However, slur terms are actually far more frequently used in other contexts and are more often exchanged among friends than between enemies. Hate speech can be identified as the most central, (...) albeit not the most frequent, mode of use. I broadly distinguish between hate speech, other pejorative uses, parasitic uses, neutral mentioning, and unaware uses. In this paper, authentic examples of use and frequency estimates from empirical research will help provide accurate definitions and insight into these different modes that purely theoretical approaches cannot achieve. (shrink)

The role of Brachyury and other T-box genes in the differentiation of mesoderm and endoderm of vertebrates is well established. Recently, homologues of Brachyury have been isolated from an increasing number of diverse organisms ranging from Cnidaria to vertebrates and insects. Comparative expression and function analysis allows the origin of the mesoderm and the evolution of the developmental role of Brachyury gene family in metazoans to be traced. The data suggest that an ancestral function of Brachyury was to designate a (...) blastoporal region that had distinct properties in induction and axis elongation. A subset of blastoporal cells expressing Brachyury and other genes that convey specific mesodermal functions may have segregated as a distinct cell population from this region in the course of mesoderm evolution. BioEssays 23:788–794, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

For researchers who study technology designs, the application and execution of so-called design-oriented research projects are a common way of funding their research. Against this background, we propose a new methodical approach with which VSD can easily be implemented in such projects and which we call “value declaration”. We share our experience with this method which we gained in two design-oriented research projects.

The Drosophila embryo provides a useful model system to study the mechanisms that lead to pattern and cell diversity in the central nervous system (CNS). The Drosophila CNS, which encompasses the brain and the ventral nerve cord, develops from a bilaterally symmetrical neuroectoderm, which gives rise to neural stem cells, called neuroblasts. The structure of the embryonic ventral nerve cord is relatively simple, consisting of a sequence of repeated segmental units (neuromeres), and the mechanisms controlling the formation and specification of (...) the neuroblasts that form these neuromeres are quite well understood. Owing to the much higher complexity and hidden segmental organization of the brain, our understanding of its development is still rudimentary. Recent investigations on the expression and function of proneural genes, segmentation genes, dorsoventral‐patterning genes and a number of other genes have provided new insight into the principles of neuroblast formation and patterning during embryonic development of the fly brain. Comparisons with the same processes in the trunk help us to understand what makes the brain different from the ventral nerve cord. Several parallels in early brain patterning between the fly and the vertebrate systems have become evident. BioEssays 26:739–751, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

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)

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)

Ecological developmental biology (eco‐devo) explores the mechanistic relationships between the processes of individual development and environmental factors. Recent studies imply that some of these relationships have deep evolutionary origins, and may even pre‐date the divergences of the simplest extant animals, including cnidarians and sponges. Development of these early diverging metazoans is often sensitive to environmental factors, and these interactions occur in the context of conserved signaling pathways and mechanisms of tissue homeostasis whose detailed molecular logic remain elusive. Efficient methods for (...) transgenesis in cnidarians together with the ease of experimental manipulation in cnidarians and sponges make them ideal models for understanding causal relationships between environmental factors and developmental mechanisms. Here, we identify major questions at the interface between animal evolution and development and outline a road map for research aimed at identifying the mechanisms that link environmental factors to developmental mechanisms in early diverging metazoans.Also watch the Video Abstract. (shrink)

Distractibility is one of the key features of attention deficit hyperactivity disorder and has been associated with alterations in the neural orienting and alerting networks. Task-irrelevant stimuli are thus expected to have detrimental effects on the performance of patients with ADHD. However, task-irrelevant presentation of novel sounds seems to have the opposite effect and improve subsequent attentional performance particularly in patients with ADHD. Here, we aimed to understand the neural modulations of the attention networks underlying these improvements. Fifty boys participated (...) in a functional magnetic resonance imaging study in which unique or repeatedly presented sounds were placed before a visual flanker task in 2/3 of the trials. We found that presenting any sound improved task performance in all participants, but the underlying neural mechanisms differed for the type of sound. Familiar sounds led to a stronger increase in activity in the left posterior insula in patients with ADHD compared to typically developing peers. Novel sounds led to activations of the fronto-temporoparietal ventral attention network, likewise in ADHD and TD. These changes in signaling by novelty in the right inferior frontal gyrus were directly related to improved response speed showing that neural orienting network activity following novel sounds facilitated subsequent attentional performance. This mechanism of behavioral enhancement by short distractions could potentially be useful for cognitive trainings or homework situations. (shrink)

The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (shrink)

The biannual international workshop entitled “The diversification of early emerging metazoans: A window into animal evolution?” took place at the Evangelische Akademie Tutzing, Germany, 11–14. September 2017. It was organized by Thomas Bosch (Kiel), Thomas Holstein (Heidelberg), and Ulrich Technau (Vienna), and it was sponsored by the Deutsche Forschungsgemeinschaft (DFG). The meeting gathered over 140 researchers to discuss the contribution of non‐bilaterian metazoan models (Porifera, Ctenophora, Placozoa, and Cnidaria) to our understanding of: a. The evolution of metazoan developmental processes; (...) b. Fundamental molecular mechanisms underlying metazoan features; and c. The complex interactions that animals establish with their environment. (shrink)