We present explorable multiverse analysis reports, a new approach to statistical reporting where readers of research papers can explore alternative analysis options by interacting with the paper itself. This approach draws from two recent ideas: i) multiverse analysis, a philosophy of statistical reporting where paper authors report the outcomes of many different statistical analyses in order to show how fragile or robust their findings are; and ii) explorable explanations, narratives that can be read as normal explanations but where the reader can also become active by dynamically changing some elements of the explanation. Based on five examples and a design space analysis, we show how combining those two ideas can complement existing reporting approaches and constitute a step towards more transparent research papers.

/pdf/increasing-the-transparency-of-research-papers-with-55uwmrhrp3.pdf

Increasing the Transparency of Research Papers with Explorable Multiverse Analyses

Until fairly recently, medical publications have been handicapped by being restricted to non-electronic formats, effectively preventing the dissemination of complex audiovisual and three-dimensional data. However, authors and readers could significantly profit from advances in electronic publishing that permit the inclusion of multimedia content directly into an article. For the first time, the de facto gold standard for scientific publishing, the portable document format (PDF), is used here as a platform to embed a video and an audio sequence of patient data into a publication. Fully interactive three-dimensional models of a face and a schematic representation of a human brain are also part of this publication. We discuss the potential of this approach and its impact on the communication of scientific medical data, particularly with regard to electronic and open access publications. Finally, we emphasise how medical teaching can benefit from this new tool and comment on the future of medical publishing.

/pdf/effectively-incorporating-selected-multimedia-content-into-3p87oqyvyw.pdf

Effectively incorporating selected multimedia content into medical publications.

Objective 
This study informs efforts to improve the discoverability of and access to biomedical datasets by providing a preliminary estimate of the number and type of datasets generated annually by research funded by the US National Institutes of Health (NIH) It focuses on those datasets that are “invisible” or not deposited in a known repository


Methods 
We analyzed NIH-funded journal articles that were published in 2011, cited in PubMed and deposited in PubMed Central (PMC) to identify those that indicate data were submitted to a known repository After excluding those articles, we analyzed a random sample of the remaining articles to estimate how many and what types of invisible datasets were used in each article


Results 
About 12% of the articles explicitly mention deposition of datasets in recognized repositories, leaving 88% that are invisible datasets Among articles with invisible datasets, we found an average of 29 to 34 datasets, suggesting there were approximately 200,000 to 235,000 invisible datasets generated from NIH-funded research published in 2011 Approximately 87% of the invisible datasets consist of data newly collected for the research reported; 13% reflect reuse of existing data More than 50% of the datasets were derived from live human or non-human animal subjects


Conclusion 
In addition to providing a rough estimate of the total number of datasets produced per year by NIH-funded researchers, this study identifies additional issues that must be addressed to improve the discoverability of and access to biomedical research data: the definition of a “dataset,” determination of which (if any) data are valuable for archiving and preservation, and better methods for estimating the number of datasets of interest Lack of consensus amongst annotators about the number of datasets in a given article reinforces the need for a principled way of thinking about how to identify and characterize biomedical datasets

/pdf/sizing-the-problem-of-improving-discovery-and-access-to-nih-5awfpgzszv.pdf

Sizing the Problem of Improving Discovery and Access to NIH-Funded Data: A Preliminary Study.

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D – it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.

/pdf/simplified-generation-of-biomedical-3d-surface-model-data-3wgjx6zets.pdf

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

Introduction: In the digital age, information retrieval is dominated by digital data and the demand for digital media is continually growing, consequently the dynamics are very different and e-journals can take advantage of this transition phase as an opportunity to explore ways more effective.Methods: A bibliographic review was carried out in the main databases and other search services. The terms “interactive formats”, “data visualization”, “interactive graphics”, “scientific publication” were used as search descriptors.Results: An interactive publication could contain many multimedia objects: text, video, audio, bitmap images, spreadsheets, presentation graphics, or animation sequences. These objects can be in different file formats. Interactive media can be defined as the integration of various digital media content, including multimedia elements (text, graphics, audio, animation and video) into structured and engaging computerized digital content, facilitating dynamic interaction for specific purposes. An interactive approach is interesting and desirable, because users will get dynamic reactions. They have been revealed and demonstrated that the use of 3D technology for academic publications is useful and necessary. However, widespread application is yet to come. The new academic contexts can serve as a starting point for many scientific journals to redefine their position and open new fields of dissemination and financing.Conclusions: Scientific journals must take advantage of the new virtual scenarios to reorganize their communication processes and face new formats of scientific dissemination.

Interactive formats: considerations for scientific publications

Invited paper: Interactive publication: The document as a research tool

As envisioned here, an "interactive publication" has similarities to multimedia documents that have been in existence for a decade or more, but possesses specific differentiating characteristics. In common usage, the latter refers to online entities that, in addition to text, consist of files of images and video clips residing separately in databases, rarely providing immediate context to the document text. While an interactive publication has many media objects as does the "traditional" multimedia document, it is a self-contained document, either as a single file with media files embedded
within it, or as a "folder" containing tightly linked media files. The main characteristic that differentiates an interactive publication from a traditional multimedia document is that the reader would be able to reuse the media content for analysis and presentation, and to check the underlying data and possibly derive alternative conclusions leading, for example, to more in-depth peer reviews. We have created prototype publications containing paginated text and several media types encountered in the biomedical literature: 3D animations of anatomic structures; graphs, charts and tabular data; cell development images (video sequences); and clinical images such as CT, MRI and ultrasound in the DICOM format. This paper presents developments to date including: a tool to convert static tables or graphs into interactive entities, authoring procedures followed to create prototypes, and advantages and drawbacks of each of these platforms. It also outlines future work including meeting the challenge of network distribution for these large files.

Interactive publications: creation and usage

The increasing prevalence of multimedia and research data generated by scientific work affords an opportunity to reformulate the idea of a scientific article from the traditional static document, or even one with links to supplemental material in remote databases, to a self-contained, multimedia-rich interactive publication. This paper describes our concept of such a document, and the design of tools for authoring (Forge) and visualization/analysis (Panorama). They are platform-independent applications written in Java, and developed in Eclipse1 using its Rich Client Platform (RCP) framework. Both applications operate on PDF files with links to XML files that define the media type, location, and action to be performed. We also briefly cite the challenges posed by the potentially large size of interactive publications, the need for evaluating their value to improved comprehension and learning, and the need for their long-term preservation by the National Library of Medicine and other libraries.

Interactive Publication: The Document As a Research Tool

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Invited paper: Interactive publication: The document as a research tool

Interactive publications: creation and usage

Interactive Publication: The Document As a Research Tool