Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease,using transposonaided capture (TRACA)

The human oral cavity is host to a complex microbial community estimated to comprise > 700 bacterial species, of which at least half are thought to be not yet cultivable in vitro. To investigate the plasmids present in this community, we used a transposon-aided capture system, which allowed the isolation of plasmids from human oral supra- and subgingival plaque samples. Thirty-two novel plasmids and a circular molecule that could be an integrase-generated circular intermediate were isolated

Three (Potential) Pillars of Transnational Economic Justice: The Bretton Woods Institutions as Guarantors of Global Equal Treatment and Market Completion

This essay aims to bring two important lines of inquiry and criticism together. It first lays out an institutionally enriched account of what a just world economic order will look like. That account prescribes, via the requisites to that mechanism which most directly instantiate the account, three realms of equal treatment and market completion - the global products, services, and labor markets; the global investment/financial markets; and the global preparticipation opportunity allocation. The essay then suggests how, with minimal if any departure from familiar canons of traditional international legal mandate interpretation, each of the Bretton Woods institutions - particularly the GATT/WTO and the IMF - can be viewed at least in part as charged with the task of fostering equal treatment and ultimate market completion within one of those three realms. The piece then argues that one of the institutions in particular - the World Bank - has, for reasons of at best negligent and at worst willful injustice on the part of influential state actors in the world community, fallen farthest short in pursuit of what should be viewed as its proper mandate. The article accordingly concludes that a fuller empowerment of the Bank to effect its ideal mission will press the Bretton Woods system more nearly into ethical balance, and with it the world into justice; and that full empowerment of the GATT/WTO and IMF should be partly conditioned upon the fuller empowerment of the Bank

Transformative sensemaking: Development in Whose Image? Keyan Tomaselli and the semiotics of visual representation

The defining and distinguishing feature of homo sapiens is its ability to make sense of the world, i.e. to use its intellect to understand and change both itself and the world of which it is an integral part. It is against this backdrop that this essay reviews Tomaselli's 1996 text, Appropriating Images: The Semiotics of Visual Representation/ by summarizing his key perspectives, clarifying his major operational concepts and citing particular portions from his work in support of specific perspectives on sense-making. Subsequently, this essay employs his techniques of sense-making to interrogate the notion of "development". This exercise examines and confirms two interrelated hypotheses: first, a semiotic analysis of the privileged notion of "development" demonstrates its metaphysical/ ideological, and thus limiting, nature especially vis-a-vis the marginalized, excluded, and the collective other, the so-called Developing Countries. Second, the interrogative nature of semiotics allows for an alternative reading and application of human potential or skills in the quest of a more humane social and global order, highlighting thereby the transformative implications of a reflexive epistemology.Web of Scienc

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

Political Queerness Against Reproductive Futurism in J.M. Coetzee\u27s \u3ci\u3eLife and Times of Michael K.\u3c/i\u3e

In J.M Coetzee\u27s Life and Times of Michael K., Michael interacts with political apparatuses and individuals invested in what Lee Edelman terms reproductive futurism. As both queer sexually, and queer in that he elicits a persistent opposition to the political bias towards reproductive futurism, Michael figures the possibility of a queer resistance to the political ideologies that underwrite state power in the postcolony. He figures what Michael Hardt and Antonio Negri dub the biopolitical event. As he interacts with bureaucrats and others, his incomprehensibility to those characters conjures the biopolitical event via his incomprehensibility to the logic of biopolitics in the postcolony. This arises from his sexual and social queerness. The function of political violence in Life and Times is refigured upon lines that call into question their foundational principles and posit Michael as an alternative to harmful modes of communal action

A Second Look at FAIR in Proteomic Investigations.

Proteomics is, by definition, comprehensive and large-scale, seeking to unravel ome-level protein features with phenotypic information on an entire system, an organ, cells, or organisms. This scope consistently involves and extends beyond single experiments. Multitudinous resources now exist to assist in making the results of proteomics experiments more findable, accessible, interoperable, and reusable (FAIR), yet many tools are awaiting to be adopted by our community. Here we highlight strategies for expanding the impact of proteomics data beyond single studies. We show how linking specific terminologies, identifiers, and text (words) can unify individual data points across a wide spectrum of studies and, more importantly, how this approach may potentially reveal novel relationships. In this effort, we explain how data sets and methods can be rendered more linkable and how this maximizes their value. We also include a discussion on how data linking strategies benefit stakeholders across the proteomics community and beyond

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts.

Clinical case reports (CCRs) are a valuable means of sharing observations and insights in medicine. The form of these documents varies, and their content includes descriptions of numerous, novel disease presentations and treatments. Thus far, the text data within CCRs is largely unstructured, requiring significant human and computational effort to render these data useful for in-depth analysis. In this protocol, we describe methods for identifying metadata corresponding to specific biomedical concepts frequently observed within CCRs. We provide a metadata template as a guide for document annotation, recognizing that imposing structure on CCRs may be pursued by combinations of manual and automated effort. The approach presented here is appropriate for organization of concept-related text from a large literature corpus (e.g., thousands of CCRs) but may be easily adapted to facilitate more focused tasks or small sets of reports. The resulting structured text data includes sufficient semantic context to support a variety of subsequent text analysis workflows: meta-analyses to determine how to maximize CCR detail, epidemiological studies of rare diseases, and the development of models of medical language may all be made more realizable and manageable through the use of structured text data

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Clinical case reports (CCRs) are a valuable means of sharing observations and insights in medicine. The form of these documents varies, and their content includes descriptions of numerous, novel disease presentations and treatments. Thus far, the text data within CCRs is largely unstructured, requiring significant human and computational effort to render these data useful for in-depth analysis. In this protocol, we describe methods for identifying metadata corresponding to specific biomedical concepts frequently observed within CCRs. We provide a metadata template as a guide for document annotation, recognizing that imposing structure on CCRs may be pursued by combinations of manual and automated effort. The approach presented here is appropriate for organization of concept-related text from a large literature corpus (e.g., thousands of CCRs) but may be easily adapted to facilitate more focused tasks or small sets of reports. The resulting structured text data includes sufficient semantic context to support a variety of subsequent text analysis workflows: meta-analyses to determine how to maximize CCR detail, epidemiological studies of rare diseases, and the development of models of medical language may all be made more realizable and manageable through the use of structured text data