Papers

• Adam Craig and Carl Taswell, 2022, Inclusion and Exclusion Criteria for Automating Adherence to Scope of Conference Calls for Papers presented September 2022 at the 4th IEEE Conference on Transdisciplinary Artificial Intelligence (TransAI), also available via DOI 10.1109/TransAI54797.2022.00018.

  To conduct a well-designed and reproducible study, researchers must define and adhere to clear inclusion and exclusion criteria for subjects. Similarly, a well-run journal or conference should publish easily understood inclusion and exclusion criteria that determine which submissions will receive more detailed peer review. This will empower authors to identify the conferences and journals that are the best fit for their manuscripts while allowing organizers and peer reviewers to spend more time on the submissions that are of greatest interest. To provide a more systematic way of representing these criteria, we extend the syntax for concept-validating constraints of the Nexus-PORTAL-DOORS-Scribe cyberinfrastructure, which already serve as criteria for inclusion of records in a repository, to allow description of exclusion criteria.

• Adam Craig, S. Koby Taswell, Anousha Athreya, and Carl Taswell, 2022, Who are the Guardians of Truth and Integrity? a half-day workshop hosted October 2022 online for the 85th Annual Meeting of the Association for Information Science & Technology held in Pittsburgh, Pennsylvania.

  Brain Health Alliance (BHA), a US 501c3 nonprofit organization, will host an online virtual workshop at ASIST 2022 for the library, data, and information sciences community to discuss the now tragically prevalent information cyberwars impacting global citizens of planet earth. These online information wars have resulted in real deaths with loss of life and destruction of entire cities that many believe should have been prevented, whether in the current fight to stop the spread of viral disease, in political election voting disputes and the fight to stop the spread of polarizing and extremified propaganda, and in military campaigns and the fight by freedom-loving peoples who defend their sovereign territory to stop unnecessary wars of aggression, invasion, and criminal genocide. We believe that when some choose to spread propaganda and lies for autocratic dictators, others must stand up and fight to defend truth and integrity in support of democracy and the freedom to live in safety without fear of being imprisoned or poisoned to death for speaking and writing the truth with integrity that should save lives. The BHA workshop on guardians of truth and integrity will provide tutorials with training sessions on open-source PDP-DREAM software and open-access NPDS data repositories from the PORTAL-DOORS Project with its mission to promote transparency, reproducibility, accountability, and citational justice in scholarly communications. In order to support democratic societies for all global citizens of planet earth who wish to be free and safe from unnecessary wars of criminal genocide, we must build the necessary software systems and electronic digital cyberinfrastructure to assure that all citizens of planet earth in every society and country have access to the free flow of information without censorship by any single person, organization, or government.

• Aniruddh Anand and Carl Taswell, 2022, An Information-Resilient Big-Data Workbench with PDP-DREAM Software presented October 2022 at the 85th ASIS&T Annual Meeting of the Association for Information Science and Technology

  PORTAL-DOORS Project DREAM Software, available as an open-source C#-centric codebase from a Github public repository at PDP-DREAM, implements the PDP-DREAM principles and PDP-FAIR metrics with web-enabled workbench software for distributed data repositories in the Nexus-PORTAL-DOORS-Scribe Cyberinfrastructure. PDP-DREAM Software has been developed for Microsoft platform technologies with ASP.NET Core, SQL Server, and Internet Information Server. As a web-enabled workbench, PDP-DREAM provides many features for big data management with tools and services to support information resilience in defense of truth in science and integrity in research.

• Adam Craig, Christina Lee, Nithyaa Bala, and Carl Taswell, 2022, Motivating and Maintaining Ethics, Equity, Effectiveness, Efficiency, and Expertise in Peer Review Brainiacs Journal 2022 Volume 3 Issue 1 Edoc I5B147D9D, also available via DOI 10.48085/I5B147D9D.

  Scientists who engage in science and the scientific endeavor should seek truth with conviction of morals and commitment to ethics. While the number of publications continues to increase, the number of retractions has increased at a faster rate. Journals publish fraudulent research papers despite claims of peer review and adherence to publishing ethics. Nevertheless, appropriate ethical peer review will remain a gatekeeper when selecting research manuscripts in scholarly publishing and approving research applications for grant funding. However, this peer review must become more open, fair, transparent, equitable, and just with new recommendations and guidelines for reproducible and accountable reviews that support and promote fair citation and citational justice. We should engineer this new peer-review process with modern informatics technology and information science to provide and defend better safeguards for truth and integrity, to clarify and maintain the provenance of information and ideas, and to rebuild and restore trust in scholarly research institutions. Indeed, this new approach will be necessary in the current post-truth era to counter the ease and speed with which mis-information, dis-information, anti-information, caco-information, and mal-information spread through the internet, web, news, and social media. The most important question for application of new peer-review methods to these information wars should be ‘Who does what when?’ in support of reproducible and accountable reviews. Who refers to the authors, reviewers, editors, and publishers as participants in the review process. What refers to disclosure of the participants' identities, the material content of author manuscripts and reviewer commentaries, and other communications between authors and reviewers. When refers to tracking the sequential points in time for which disclosure of whose identity, which content, and which communication at which step of the peer-review process for which audience of readers and reviewers. We believe that quality peer review, and peer review of peer review, must be motivated and maintained by elevating their status and prestige to an art and a science. Both peer review itself and peer review analyses of peer reviews should be incentivised by publishing peer reviews as citable references separately from the research report reviewed while crossreferenced and crosslinked to the report reviewed.

• Carl Taswell, 2021, Research Scholar's Oath Brainiacs Journal 2021 Volume 2 Issue 1 Edoc P3F95585B, also available via DOI 10.48085/P3F95585B.
• S. Koby Taswell, Anousha Athreya, Madhavi Akella, and Carl Taswell, 2021, Truth in Science Brainiacs Journal 2021 Volume 2 Issue 1 Edoc M85EC99EE, also available via DOI 10.48085/M85EC99EE.

  Truth, honesty, and integrity remain crucial to the pursuit of science as a self-correcting discipline to explore, discover, and process information about the world around us. When following the scientific method, we hypothesize, experiment, and repeatedly retest our results, investigating whether or not those results can be confirmed as reproducible and valid. Conducting this process rigorously with unbiased and objective investigations enables greater confidence in obtaining results we consider more reliable and trustworthy. Such truthful information can be used to avoid harm and prevent injury by those who may wish to apply it in their daily lives in the form of a medicine, machine, or method of some kind. However, in recent years, some scientists and lay persons have violated these tenets of truth in science to further their professional or personal agenda by spreading false information in scientific literature and on social media. This misconduct can be evaluated by assessing the authors' awareness of the document's truthfulness prior to publishing it and their willingness to correct the mistakes and false information when brought to their attention. Identifying these key characteristics about incidents of scientific misconduct enables analysis and introduction of a consistent collection of definitions and criteria for the terms mis-information, dis-information, anti-information, caco-information, and mal-information. Clarifying different categories of misconduct in this manner should enable more effective interventions to remediate and/or prevent each one appropriately. Without adequate safeguards to maintain reproducible science as a self-correcting endeavor with retractions of publications when necessary, false information will continue to pollute the published literature and threaten the core of science.

• Adam Craig and Carl Taswell, 2021, PDP-DREAM Software for Integrating Multimedia Data with Interoperable Repositories Brainiacs Journal 2021 Volume 2 Issue 1 Edoc HA46280EF, also available via DOI 10.48085/HA46280EF.

  Integrating multimedia data in a meaningful way requires keeping track of the who, what, where, when, and how of many kinds of data and metadata in different formats. The PORTAL-DOORS-Project (PDP) was formed to design and build the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure for managing and distributing resource data and metadata in a manner compatible with both the established lexical web and the developing semantic web. PDP-DREAM software, archived at github.com/bhavius/pdp-dream, represents the first publicly available, open-source implementation of NPDS. It provides RESTful web services for software agents and user-friendly web applications for human agents so that individuals and organizations can create and publish their own problem-oriented and domain-specific repositories customized for their own purposes. In this report, we also introduce the NpdsQuads format with an approach to formatting the comments of N-quads files as name-value pairs for content from NPDS records which can be exported from and imported to NPDS repositories. We then describe the use of these tools in the curation of the PDP-DREAM ontology, which serves as the foundational ontology for the NPDS cyberinfrastructure. Finally, we discuss the planned use of PDP-DREAM software in a medical imaging clinical trial for multiple sclerosis.

• Anousha Athreya, S. Koby Taswell, Andrew Kang, Ishani Das, and Carl Taswell, 2021, Ashurbanipal: A Diristry to Document Multimedia Metadata Tools for Transdisciplinary Archives presented December 2021 at the International Conference on Computational Science and Computational Intelligence (CSCI) Symposium on Computational Science (CSCI-ISCS) in Las Vegas, Nevada.

  In historical artifact conservation, archiving objects using entity metadata plays a significant role in managing the related versions of the artifacts preserved, recorded and documented at various time points. In this paper, we discuss five fields of study to display the importance of related versions in identifying patterns over time through events in history, cultural heritage, biomedical research, performing arts, and fine arts. We describe our use of the Ashurbanipal diristry to document scholarly research on archiving tools and technologies. We highlight the importance of the provenance infosubset in tracing metadata for cultural objects managed in NPDS repositories and enabling interoperability with existing multimedia bibliographic formats including MARC and BIBFRAME.

• Anousha Athreya, S. Koby Taswell, and Carl Taswell, 2021, Management Software for Monitoring Related Versions of Cultural Heritage Artifacts for Libraries and Museums also available via DOI 10.1002/pra2.526 presented November 2021 at the 84th Annual Meeting of the Association for Information Science & Technology in Salt Lake City, Utah.

  In cultural object conservation, tracking provenance has served as the foundational method of managing information for historical artifacts. To find data points, archivists identify related versions of an artifact at various time points. In this paper, we discuss four categories with versioned examples to display the importance of data points for identifying patterns over time through events in history, cultural heritage, performing arts, and fine arts. We describe our use of the Ashurbanipal diristry to document scholarly research regarding library tools and technologies for the preservation of cultural objects as well as the implementation of PORTAL-DOORS Project (PDP) utilities for tracing provenance and distribution of cultural objects and interoperability with bibliographic formats such as BIBFRAME and MARC from existing archival methods.

• Anousha Athreya, S. Koby Taswell, Sohyb Mashkoor, and Carl Taswell, 2020, The Essential Enquiry 'Equal or Equivalent Entities?' About Two Things as Same, Similar, Related, or Different Brainiacs Journal 2020 Volume 1 Issue 1 Edoc PEDADC885, also available via DOI 10.48085/PEDADC885.

  We discuss definitions of entities, equality, and equivalence as used by a transdisciplinary diversity of research fields including mathematics, statistics, computational linguistics, computer programming, knowledge engineering, music theory, and genomics. Declaring definitions for these concepts in the situational context of each domain specific field supports the essential question 'Equal or equivalent entities?' about two things as same, similar, related, or different for that field. Pattern recognition performed by artificial intelligence applications whether with supervised and unsupervised learning or with deductive and inferential logic, with machine learning or logical reasoning, can be described as the automated process of answering this fundamental question about the similarity, relatedness, or difference between two things.

• Shreya Choksi and Carl Taswell, 2020, The Nexus-PORTAL-DOORS-Scribe (NPDS) Learning Intelligence aNd Knowledge System (LINKS) Brainiacs Journal 2020 Volume 1 Issue 1 Edoc B61CA3D89, also available via DOI 10.48085/B61CA3D89.

  With the continuing growth in use of large complex data sets for artificial intelligence applications (AIA), unbiased methods should be established for assuring the validity and reliability of both input data and output results. Advancing such standards will help to reduce problems described with the aphorism 'Garbage In, Garbage Out' (GIGO). This concern remains especially important for AIA tools that execute within the environment of interoperable systems which share, exchange, convert, and/or interchange data and metadata such as the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure and its associated Learning Intelligence aNd Knowledge System (LINKS) applications. The PORTAL-DOORS Project (PDP) has developed the NPDS cyberinfrastructure with lexical PORTAL registries, semantic DOORS directories, hybrid Nexus diristries, and Scribe registrars. As a self-referencing and self-describing system, the NPDS cyberinfrastructure has been designed to operate as a pervasive distributed network of data repositories compliant with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style. Building on the foundation of the NPDS cyberinfrastructure with its focus on data, PDP has now introduced LINKS applications with their focus on algorithms and analysis of the data. In addition, PDP has launched a pair of new websites at NPDSLINKS.net and NPDSLINKS.org which will serve respectively as the root of the NPDS cyberinfrastructure and the home for definitions and standards on quality descriptors and quantitative measures to evaluate the data contained within NPDS records. Prototypes of these descriptors and measures for use with NPDS and LINKS are described in this report. PDP envisions building better AIA and preventing the unwanted phenomenon of GIGO by using the combination of metrics to detect and reduce bias from data, the NPDS cyberinfrastructure for the data, and LINKS applications for the algorithms.

• Adam Craig, Peter Hong, Shreya Choksi, Anousha Athreya, and Carl Taswell, 2020, Survey, Analysis, and Requirements for Semantic Enhancement to Support Machine Understanding of Scientific Literature Brainiacs Journal 2020 Volume 1 Issue 1 Edoc D11DABE6D, also available via DOI 10.48085/D11DABE6D.

  Adoption of the proposed recommendations with standards set forth by the World Wide Web Consortium (W3C) regarding the semantic web remains a work in progress, especially with regard to their use in the published research literature. Proponents of the semantic enhancement of scholarly publishing have described it as a visionary breakthrough for the way in which both individuals and machines should be able to obtain meaningful information from data, text, and content management systems. However, the availability and prevalence of useful real-world resources remains limited. In this report, we present a survey of those scholarly research journals that focus on the semantic web and ontology engineering. We highlight noteworthy examples of publishers offering semantic enhancement and markup services in hopes of shedding light on tools that could revolutionize how both academic scholars and the lay public find and understand the published results of scientific research. We then consider the implications of these findings for the growth and development of the semantic web as a whole. We also review proposals for how the semantic web could accelerate the advancement of brain sciences and brain health. Finally, we propose a novel approach to scholarly publishing represented by our planned semantic enhancement workflow process for the Brainiacs Journal. By surveying the current use of the semantic web, we show the need for more motivated and enthusiastic adoption of semantic enhancement in scholarly publishing in order to 'stand on the shoulders of giants' and reap the benefits of published research.

• S. Koby Taswell, Brian Hsiao, and Carl Taswell, 2020, Augmented and Virtual Reality Environments for Healthcare Brainiacs Journal 2020 Volume 1 Issue 1 Edoc GCF086AF4, also available via DOI 10.48085/GCF086AF4.

  Contemporary life with modern technology has benefited from dramatic advances with electronic devices including the rise in availability and quality of augmented reality (AR) and virtual reality (VR) headsets capable of simulating environments for use in healthcare. By integrating AR/VR headsets into existing educational programs and medical therapies, we can enable new approaches for teaching students and delivering care to patients. This report provides definitions for AR and VR, reviews common device specifications, and discusses a variety of applications described in the biomedical engineering, healthcare, and telehealth literature.

• Anousha Athreya, S Koby Taswell, Sohyb Mashkoor, and Carl Taswell, 2020, Essential Question: 'Equal or Equivalent Entities?' About Two Things as Same, Similar, or Different also available via DOI 10.1109/TransAI49837.2020.00028 presented September 2020 at the 2nd International Conference on Transdisciplinary Artificial Intelligence (TransAI)

  We discuss definitions of entities, equality, and equivalence as used by a transdisciplinary diversity of research fields including mathematics, statistics, computational linguistics, computer programming, knowledge engineering, and music theory. Declaring definitions for these concepts in the situational context of each domain specific field supports the essential question 'Equal or equivalent entities?' about two things as same, similar, related, or different for that field. Pattern recognition performed by artificial intelligence applications can be described as the automated process of answering this fundamental question about the similarity or difference between two things.

• Shreya Choksi, Peter Hong, Sohyb Mashkoor, and Carl Taswell, 2020, NPDSLINKS: Nexus-PORTAL-DOORS-Scribe Learning Intelligence aNd Knowledge System also available via DOI 10.1109/TransAI49837.2020.00027 presented September 2020 at the 2nd International Conference on Transdisciplinary Artificial Intelligence (TransAI)

  With the continuing growth in use of large complex data sets for artificial intelligence applications (AIA), unbiased methods should be established for assuring the validity and reliability of both input data and output results. Advancing such standards will help to reduce problems described with the aphorism 'Garbage In, Garbage Out' (GIGO). This concern remains especially important for AIA tools that execute within the environment of interoperable systems which share, exchange, convert, and/or interchange data and metadata such as the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure and its associated Learning Intelligence aNd Knowledge System (LINKS) applications. The PORTAL-DOORS Project (PDP) has developed the NPDS cyberinfrastructure with lexical PORTAL registries, semantic DOORS directories, hybrid Nexus diristries, and Scribe registrars. As a self-referencing and self-describing system, the NPDS cyberinfrastructure has been designed to operate as a pervasive distributed network of data repositories compliant with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style. Building on the foundation of the NPDS cyberinfrastructure with its focus on data, PDP has now introduced LINKS applications with their focus on algorithms and analysis of the data. In addition, PDP has launched a pair of new websites at NPDSLINKS.net and NPDSLINKS.org which will serve respectively as the root of the NPDS cyberinfrastructure and the home for definitions and standards on quality descriptors and quantitative measures to evaluate the data contained within NPDS records. Prototypes of these descriptors and measures for use with NPDS and LINKS are introduced in this report. PDP envisions building better AIA and preventing the unwanted phenomenon of GIGO by using the combination of metrics to detect and reduce bias from data, the NPDS cyberinfrastructure for the data, and LINKS applications for the algorithms.

• S. Koby Taswell, Kelechi Uhegbu, Sohyb Mashkoor, Shiladitya Dutta, and Carl Taswell, 2020, Storing Bibliographic Data in Multiple Formats with the NPDS Cyberinfrastructure also available via DOI 10.1002/pra2.428 presented with poster October 2020 at the 83rd ASIS&T Annual Meeting of the Association for Information Science and Technology

  The PORTAL-DOORS Project (PDP) aims to develop the Nexus-PORTAL-DOORS-Scribe (NPDS) Cyberinfrastructure as a distributed network of data repositories that communicate with each other using a common message exchange standard. These data repositories include a collection of servers with a system of registries, directories, and diristries for diverse resources including bibliographic information records. Examples of resource metadata representations can be viewed at PDP participating websites. Until now, PDP has not supported convenient import or export of bibliographic records to or from any of the common bibliographic standards. In this report, we describe our progress on our new PDP utilities for interoperability between the format for NPDS records and various bibliographic formats such as BIBFRAME, MARC, RIS, and BibLaTeX. We will detail the import process when using a converter that transforms bibliographic citations in other formats and stores them in an NPDS diristry. Improved interoperability for conversion between bibliographic records in other traditional formats with the NPDS format will support a variety of use cases that require either lexical and/or semantic parsing of cited references.

• S. Koby Taswell, Christopher Triggle, June Vayo, Shiladitya Dutta, and Carl Taswell, 2020, The Hitchhiker's Guide to Scholarly Research Integrity also available via DOI 10.1002/pra2.223 presented with hyperlinked version and slides October 2020 at the 83rd ASIS&T Annual Meeting of the Association for Information Science and Technology

  The pursuit of truth in research should be both an ideal in aspiration and also a reality in practice. The PORTAL-DOORS Project (PDP) strives to promote creative authenticity, fair citation, and adherence to integrity and ethics in scholarly research publishing using the FAIR family of quantitative metrics with acronym FAIR for the phrases Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records, and the DREAM principles with acronym DREAM for the phrase Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata. This report presents formalized definitions for idea-laundering plagiarism by authors, idea-bleaching censorship by editors, and proposed assertion claims for authors, reviewers, editors, and publishers in ethical peer-reviewed publishing to support integrity in research. All of these principles have been implemented in version 2 of the PDP-DREAM ontology written in OWL 2. This PDP-DREAM ontology will serve as the model foundation for development of a software-guided workflow process intended to manage the ethical peer-reviewed publishing of web-enabled open access journals operated online with PDP software.

• Carl Taswell, 2020, Research Protocol for Exploratory Study of Entire-body PET Scans for Multiple Sclerosis (EPSMS) with accompanying informed consent for research participants.

  Basic question: Can an entire-body positron emission tomography (PET) scanner be exploited to improve evaluation, monitoring and measurement of both peripheral and central demyelination in multiple sclerosis (MS) patients? We assume here that demyelination outside the brain may involve the spinal cord if not also possibly some of the larger peripheral nerves outside the spinal column in a manner that may be detected with the greater sensitivity and resolution of the most recent state-of-the-art PET scanners.
  Initial approach: Adopt a cost-effective and reduced-risk approach initially for an exploratory study by using commercially available and already FDA-approved PET amyloid imaging radiopharmaceuticals that also bind to myelin to follow radiotracer uptake in white matter, thereby tracking demyelination versus remyelination for MS patients in comparison with normal healthy subjects. This initial approach with the greater sensitivity and resolution of modern entire-body PET scanners when used for amyloid/myelin imaging should hypothetically enable monitoring of increased versus decreased activity in both the peripheral nervous system (PNS) and the central nervous system (CNS), rather than only imaging the brain as performed in most conventional imaging evaluations for MS patients.
  Future approach: Investigate other possible radiotracers (including those not yet FDA approved) that may be useful for monitoring demyelination, neuroinflammation and/or microglial activation in both the PNS and CNS of MS patients. In addition, PET myelin imaging by PET-CT scanners will be compared with analogous imaging by PET-MR scanners.
  Significance: Improved molecular imaging with new entire-body PET scanners that provide improved detection sensitivity and spatial resolution for quantitative measurement of demyelination and remyelination will support better decision-making for patient care with more robust outcome measures for monitoring therapeutic drugs evaluated in clinical trials for the treatment of multiple sclerosis.

• Shiladitya Dutta, Kelechi Uhegbu, Sathvik Nori, Sohyb Mashkoor, S. Koby Taswell, and Carl Taswell, 2020, DREAM Principles from the PORTAL-DOORS Project and NPDS Cyberinfrastructure also available via DOI 10.1109/ICSC.2020.00044 presented February 2020 at the 14th IEEE International Conference on Semantic Computing in San Diego, California.

  The PORTAL-DOORS Project (PDP) has been pursued to develop the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure as a distributed network system of data repositories to manage lexical and semantic data and metadata from and/or about online and offline resources. Designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style in a manner analogous to IRIS-DNS, the NPDS cyberinfrastructure provides distributed multilevel metadata management as an open, flexible, and extensible networked system of independent community customizable who-what-where registries, directories, and diristries for identifying, describing, locating, and linking things on the internet, web and grid. In the current work reported here, we combined our original principles from PDP, HDMM, and NPDS together with additional principles for scientific reproducibility and social engineering related to our family of quantitative metrics with acronym FAIR for Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records.We call this new consolidated collection of principles the DREAM principles with acronym DREAM for the phrase Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata . To codify these DREAM principles as a concrete artifact for the semantic web, and thus to operationalize their use, we developed an OWL 2.0 ontology that we named the PDP-DREAM ontology.

• Adam Craig, Adarsh Ambati, Shiladitya Dutta, Arush Mehrotra, S. Koby Taswell, and Carl Taswell, 2019, Definitions, Formulas, and Simulated Examples for Plagiarism Detection with FAIR Metrics also available via DOI 10.1002/pra2.6 presented with slides October 2019 at the 82nd Annual Meeting of the Association for Information Science & Technology in Melbourne, Australia.

  In prior work, we proposed a family of metrics as a tool to quantify adherence to or deviation from good citation practices in scholarly research and publishing. We called this family of metrics FAIR as an acronym for Fair Attribution to Indexed Reports and Fair Acknowledgment of Information Records, and introduced definitions for these metrics with counts of instances of correct or incorrect attribution or nonattribution in primary research articles with citations for previously published references. In the present work, we extend our FAIR family of metrics by introducing a collection of ratio-based metrics to accompany the count-based metrics described previously. We illustrate the mathematical properties of the ratio-based metrics with various simulated examples in order to assess their suitability as a means of identifying papers under peer review as more or less likely to be suspicious for plagiarism. These FAIR metrics would alert peer reviewers to prioritize low-scoring manuscripts for closer scrutiny. Finally, we outline our planned strategy for future validation of the FAIR metrics with an approach using both expert human analysts and automated algorithms for computerized analysis.

• Shiladitya Dutta, Pooja Kowshik, Adarsh Ambati, Sathvik Nori, S. Koby Taswell, and Carl Taswell, 2019, Managing Scientific Literature with Software from the PORTAL-DOORS Project also available via DOI 10.1109/eScience.2019.00081 presented with slides and demo video September 2019 at the Bridging from Concepts to Data and Computation for eScience (BC2DC'19) Workshop of the IEEE 15th International Conference on eScience in San Diego, California. See also IEEE Xplore eScience conference series proceedings.

  Scholarly research associated with finding and citing scientific literature in the 21st century requires new approaches to address the continuing problems that occur with the provenance of content in the literature as well as the peer and editorial review process for publishing this literature. The PORTAL-DOORS Project (PDP) has developed software for the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure in support of identifying, describing, locating and linking things on the internet, web and grid with both lexical and semantic tools and applications. This presentation of our PDP software will highlight Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata with the DREAM principles, and the Fair Acknowledgment of Information Records also called the Fair Attribution to Indexed Reports with the FAIR metrics. This software demonstration will explain use of the network of metadata repositories for scientific literature accessible from www.portaldoors.org, and use of the open source software that powers the NPDS cyberinfrastructure, PDP websites and PDP web services. Our PDP software for the NPDS cyberinfrastructure will be released publicly at this presentation of the software where we will also discuss challenges in the peer review process that include plagiarism detection.

• S. Koby Taswell and Carl Taswell, 2019, Generalizing Effect Sizes for Differences with an Alternative to Cohen's d Coefficient presented September 2019 at the International Biometric Society XXXIst Conference of the Austro-Swiss Region (ROeS) in Lausanne, Switzerland.

  Data obtained for population samples studied in clinical trials may not fit normal distributions. These non-normal distributions of samples create analytic and practical difficulties when estimating effect sizes for differences between sampled comparison groups. In these situations, it would be preferable to adopt a non-parametric model-free method to estimate an effect size for the difference between comparison groups in a manner that relies solely on computational analysis of the empirical data.

  We generalize the classical effect size for differences as described by Cohen's d coefficient for the difference of the means divided by the standard deviation. Instead, we take an analogous approach for our estimate that we call the Robust Generalized Effect Size (RGES) by calculating the difference of the medians divided by the maximum of the peak half widths for the distributions of the two comparison groups. Thus, we use medians instead of means for the estimates of the measure of central tendency, and peak half widths instead of standard deviations for estimates of the measure of dispersion. Moreover, we define the peak half widths as a generalization of the traditional half width at half maximum (HWHM) of the main peak. Specifically, we propose use of the half width at half absolute height for measures of dispersion around the center of the data distribution. Our method has been defined with both mathematical formulas and MATLAB code with a function rghwhah for the Robust Generalized Half Width Half Absolute Height, and the function rges for the Robust Generalized Effect Size. The function rghwhah finds the width, height and center point of the main peak of the data distribution defined by the rectangular box with width determined by all data points with absolute values greater than half the height of the box. A peak half width obtained from rghwhah does not necessarily equal a peak half width obtained from a traditional HWHM. Then, the function rges computes the effect size comparing the difference between the two distributions each of which may have a different rghwhah width and height for their main peaks. Our method has been generalized sufficiently to analyse multi-modal and other non-normal distributions of data.

  We have tested our approach for the estimation of effect sizes with computer simulations comparing pairs of two different normal distributions with a wide range of varying means and standard deviations for the normal distributions. Results for our estimates of effect sizes have also been tabulated for a diverse variety of non-normal distributions compared with each other. These tabulated results of rges coefficient values will provide a reference for comparison of effect sizes for those statisticians and other clinical trial investigators who do not wish to rely solely on estimates for effect sizes based on standard deviations that might not be appropriate for non-normal distributions.

• Adam Craig, Adarsh Ambati, Shiladitya Dutta, Pooja Kowshik, Sathvik Nori, S. Koby Taswell, Qiyuan Wu, and Carl Taswell, 2019, DREAM Principles and FAIR Metrics from the PORTAL-DOORS Project for the Semantic Web also available via DOI 10.1109/ECAI46879.2019.9042003 presented with slides June 2019 at the 11th Annual IEEE International Conference on Electronics, Computers and Artificial Intelligence in Pitesti, Romania.

  Articles published in Scientific Data by Wilkinson et al. argued for the adoption of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles of data management without citing any of the prior work published by Taswell. However, these principles were first proposed and described by Taswell in 2006 as the foundation for work on the PORTAL-DOORS Project (PDP) and the Nexus-PORTAL-DOORS-Scribe (NPDS) cyberinfrastructure, and have been published in numerous conference presentations, journal articles, and patents. This work on PDP and NPDS has been continuously available since 2007 from a publicly accessible web site at www.portaldoors.org, and discussed in person at conferences with several key authors of the Wilkinson et al. papers. Paraphrasing without citing the PDP and NPDS principles while renaming them as the FAIR principles raises questions about both the ‘FAIRness’ and the fairness of the authors of the Wilkinson et al. papers. Promoting these principles with the use of the term ‘metrics’, which are not metrics by definition of the term metric as used in most fields of science, also raises questions about their commitment to maintaining consistency of usage for basic terminology across different fields of science as should be expected for terms in ontology mapping with knowledge engineering for the semantic web. Therefore, in the present report, we clarify the origin of their FAIR principles by identifying our PDP and NPDS principles that constitute the historical precedent for their FAIR principles. Moreover, as the comprehensively summarizing phrase for all of our PDP and NPDS principles, we rename them the DREAM principles with the acronym DREAM for Discoverable Data with Reproducible Results for Equivalent Entities with Accessible Attributes and Manageable Metadata. Finally, we define numerically valid quantitative FAIR metrics to monitor and measure the DREAM principles from the perspective of the most important principle, ie, the Fair Acknowledgment of Information Records and Fair Attribution to Indexed Reports, for maintaining fair standards of citation in scholarly research and publishing.

• Carl Taswell, Cheryl Donohue, Maree T Mastwyk, Andrea G Louey, Jacqueline Giummarra, Joanne Robertson, David G Darby, Colin L Masters, Christopher C Rowe, 2019, Avoiding Methodological Bias in Studies of Amyloid Imaging Results Disclosure, published in Alzheimer's Research & Therapy Volume 11 Article 52 with DOI 10.1186/s13195-019-0495-y.

  A commentary and discussion of methodological bias in clinical research trials for dementia and Alzheimer's disease with particular attention to studies of amyloid imaging results disclosure. See also Safety of Disclosing Amyloid Imaging Results to MCI and AD Patients.

• S Koby Taswell, Adam Craig, Carl Taswell, 2019, Brain Health Alliance Virtual Institute: Teaching Students Medical Informatics via Collaborative Research Projects with slides presented June 2019 at the AMIA 2019 Informatics Educators Forum in St Louis, Missouri.

  During program years 2014–2018, a total of 45 high school, college and graduate students have participated in the Brain Health Alliance Virtual Institute (BHAVI), a project-based learning and research training program. BHAVI students have published 14 conference papers in clinical and translational research informatics and data sciences. BHAVI uses frequent videoconferencing between students and mentors as its primary collaboration tool, and overcomes obstacles to on-line education with support from on-site advisors.

• Carl Taswell, 2019, Total-Body PET Imaging of Both Peripheral and Central Demyelination in Multiple Sclerosis

  Basic question: Can a total-body PET scanner be exploited to improve evaluation, monitoring and measurement of both peripheral and central demyelination in multiple sclerosis (MS) patients? We assume here that demyelination outside the brain may involve at least the spinal cord if not also possibly some of the larger peripheral nerves outside the spinal column in a manner that might be detected with the greater sensitivity and resolution of the Explorer PET-CT scanner. Initial approach: Adopt a cost-effective and reduced-risk approach initially for a pilot study by using commercially available and already FDA-approved amyloid PET tracers to follow radiotracer uptake in white matter, thereby tracking demyelination versus remyelination for MS patients in comparison with normal healthy subjects. This initial approach with the Explorer total-body PET scanner used for amyloid imaging should hypothetically enable monitoring of increased versus decreased activity in both the peripheral nervous system (PNS) and the central nervous system (CNS), rather than only imaging the brain as performed in most conventional imaging evaluations for MS patients. Total-body amyloid PET imaging by the Explorer PET-CT scanner will be compared with analogous imaging by PET-MRI scanners. Future approach: Investigate other possible radiotracers (including those not yet FDA approved) that might be useful for monitoring demyelination, neuroinflammation and/or microglial activation in both the PNS and CNS of MS patients. Significance: Improved molecular imaging with new total-body PET scanners that provide greater sensitivity and better spatial resolution for quantitative measurement of demyelination and remyelination will support better decision-making for patient care and improved outcome measures for monitoring therapeutic drugs evaluated in clinical trials for the treatment of multiple sclerosis.

• Tathya Shah, S Koby Taswell, Carl Taswell, 2018, Optimal Contrast Color Maps for Coregistered PET and MRI Brain Scans presented December 2018 as Abstract B279 at the 11th International Conference on Brain Informatics in Arlington, Texas.

  To maximize the contrast and clarity of coregistered PET (Positron Emission Tomography) and MR (Magnetic Resonance) brain scans, the application of certain color maps have been tested. Twelve of Matlab’s predefined color maps were applied on a PET-MR overlay to discover which are the easiest to read, yet are informative. The experiments are carried out in three phases, or constructs. These constructs have been executed on Matlab by functions within a custom-built library, which allows for the overlaying and resizing of brain scans. The first and second constructs consist of gray scale PET over colored MR and gray scale MR over colored PET, respectively. These first two constructs determine which type of scan, PET or MR, should be colored in an overlay, as well as the type of color map that should be applied. The third construct performs a fusion between colored PET and colored MR scans. A clinical trial consisting of twentyfive high school students has been completed. Students answered questions based on images generated by the Matlab software. Results confirm that the second construct, gray scale MR over colored PET, was preferred over the first. Next, students compared different color maps to identify which one allows for the best distinction between PET and MR scans in their overlay. Participants ranked the color maps, summer, copper, and cool, as first, second, and third, based on the contrast and clarity of the scans. Future studies will examine responses from brain imaging professionals and test custom-designed color maps on PET-MR overlays.

• Shiladitya Dutta and Carl Taswell, 2018, SPARQL-Based Search Engine and Agent for Finding Brain Literature and Converting References to NPDS Metadata Records presented December 2018 as Abstract B277 at the 11th International Conference on Brain Informatics in Arlington, Texas.

  We describe CoVaSEA (Concept-Validating Search Engine Agent): an automated web crawler/query engine that is interoperable with the Nexus-PORTAL-DOORS System. The Nexus-PORTAL-DOORS System (NPDS) is a data management system that organizes repositories of lexical metadata (in PORTAL servers) and semantic representations (in DOORS servers) of resources. Due to the purpose built hybridized nature of NPDS, it is well placed to perform a variety of data analysis tasks. However, many of these tasks require records of semantic descriptions which are labor intensive to create and maintain due to the substantial and rapidly increasing quantities of brain related literature available on the open web. To remedy this, we created CoVaSEA with the intention of providing an automated method for users to navigate and expand the semantic records of brain literature in the NPDS directories. To this end, CoVaSEA integrates multiple features which benefit NPDS including: (A) An implementation of SPARQL query based search to allow retrieval and manipulation of RDF descriptions, (B) Targeted web-crawling for relevant articles from external biomedical literature databases to broaden NPDS records, and (C) Translation of free-form text into RDF triples to derive the semantic portrayals of lexical data. CoVaSEA consists of three principal components: the web-crawler, the lexical to semantic converter, and the SPARQL query engine. The web crawler retrieves articles along with their basic metadata (title, abstract, author(s), etc.) from several of biomedical literature databases via REST API. However, in order to capture a full semantic description of the data in each article, key RDF triples which describe the abstract are constructed. First, each of the unique nouns in the passage are registered via coreference resolution and pronomial anaphora. Then the sentences are parsed into constituency tree format so that the subject(s), verb(s), and object(s) can be extracted. Once the SVO triples are extracted, they are transformed into valid RDF by assigning unique resource identifiers (URI) to each part of the triples. This is accomplished by using various databases (i.e. MeSH) for terminology and select named entities, word sense disambiguation for standard words, and literals for any other sections. These triples are stored via the Scribe API in either a DOORS directory or a localized triplestore where they can be retrieved via the SPARQL query engine. In order to create a more conducive user experience, the query engine supports the capability to construct SPARQL queries from expressions in conjunctive normal form, thus circumventing the need to know SPARQL syntax. With the distinct advantage that the system is automated, CoVaSEA presents the capability to search “externally” to furnish large numbers of brain-related literature descriptions on a regular basis and search “internally” to provide a method of retrieving those descriptions, thus laying the groundwork for a variety of future NPDS applications for which semantic metadata stores of brain literature are a functional necessity.

• Adam Craig and Carl Taswell, 2018, Formulation of FAIR Metrics for Primary Research Articles also available via DOI 10.1109/BIBM.2018.8621399 presented December 2018 at the SEPDA Workshop held at the IEEE 2018 BIBM Conference in Madrid, Spain.

  Measuring the merits of a scholarly article only by how often other articles or social media posts cite it creates a perverse incentive for authors to avoid citing potential rivals. To uphold established standards of scholarship, institutions should also consider one or more metrics of how appropriately an article cites relevant prior work. This paper describes the general characteristics of the FAIR Attribution to Indexed Reports (FAIR) family of metrics, which we have designed for this purpose. We formulate five FAIR metrics suitable for use with primary research articles. Two measure adherence to best practices: number of correctly attributed background statements and number of genuinely original claims. Three measure specific deviations from best practices: number of misattributed background statements, number of background statements with missing references, and number of claims falsely indicated as original. We conclude with a discussion of plans to implement a web application for calculating metric values of scholarly works described by records in Nexus-PORTAL-DOORS System (NPDS) servers.

• Adam Craig and Carl Taswell, 2018, The FAIR Metrics of Adherence to Citation Best Practices with poster presented November 2018 at the SIGMET Workshop Metrics 2018 held at the 2018 ASIS&T Annual Meeting of the Association for Information Science & Technology in Vancouver, British Columbia.

  Measuring the merits of scholarly research articles only by citation counts and how often other research articles or social media messages cite a particular publication creates a perverse incentive for some authors to refrain from citing potential rivals. This dilemma has developed despite the historical publishing standard expected in peer review for citing and discussing related prior work. To encourage and support a countervailing incentive, research organizations should also consider metrics for how well and appropriately a scholarly article cites relevant prior work in the spirit of the classic phrase and metaphor standing on the shoulders of giants. We present a proposal for a family of such article-level metrics called the FAIR metrics and described as the FAIR Attribution to Indexed Reports or the FAIR Acknowledgment of Information Records.

• Carl Taswell, Cheryl Donohue, Maree T Mastwyk, Andrea G Louey, Jacqueline Giummarra, Joanne Robertson, David G Darby, Colin L Masters, Christopher C Rowe, 2018, Safety of Disclosing Amyloid Imaging Results to MCI and AD Patients published as MHFM 2018 Volume 14 Issue 2 pages 748-756.

  Objective: To assess the psychological impact of disclosing a positive or negative amyloid brain scan result to symptomatic individuals with mild cognitive impairment (MCI) or mild Alzheimer’s disease (AD). Design: Prospective longitudinal cohort study. Setting: Florey Institute of Neuroscience & Mental Health, University of Melbourne, Australia. Participants: A total of 133 individuals aged 50–85 with MCI or mild AD enrolled in the study with data collected between October 2014 and June 2016. Interventions: Disclosure of amyloid imaging results to participants. Measurements: Positron emission tomography (PET) brain amyloid imaging with [18F]-NAV4694; psychometric scales including the Center for Epidemiologic Studies Depression (CES-D) scale, Geriatric Depression Scale (GDS), Hospital Anxiety and Depression Scales (HADS-A and HADS-D) and State-Trait Anxiety Inventory (STAI) performed before and after disclosure of amyloid imaging results. Results: We did not observe any worsening of psychological health with a panel of psychometric scales assessed on individuals to whom amyloid brain scan results were disclosed. Conclusions: We consider it safe, without apparent risk of harm to patients, to disclose amyloid imaging results to patients who have no prior history of neuropsychiatric illness.

• Adam G Craig, Seung-Ho Bae, Carl Taswell, 2017, Message Exchange between Independent Implementations of Servers in the Nexus-PORTAL-DOORS System presented December 2017 at the 10th International SWAT4HCLS Conference in Rome, Italy; published as CEUR Workshop Proceedings Vol 2042 Paper 6.

  To search and summarize research on biomedical questions, reasoning agents require access to high-quality semantic markup. The Nexus-PORTAL-DOORS v1.0 API and message exchange format empower organizations to manage and share their own collections of lexical metadata and RDF descriptions of knowledge resources. In this systems demonstration, NPDS servers built on Microsoft’s .NET framework distribute records to NPDS servers built on the MEAN solution stack for caching and distribution to clients.

• Adam G Craig, Seung-Ho Bae, Carl Taswell, 2017, Bridging the Semantic and Lexical Webs: Concept-Validating and Hypothesis-Exploring Ontologies for the Nexus-PORTAL-DOORS System presented July 2017 at the Special Track on Bio- and Medical Informatics and Cybernetics: BMIC 2017 in the context of the 21st Multi-conference on Systemics, Cybernetics and Informatics: WMSCI 2017 Orlando, Florida; published as JSCI 2017 Vol 15 Num 5 pages 8-13; see also XML and RDF files for NPDS v0.9.3 schemas and ontologies.

  The Nexus-PORTAL-DOORS System (NPDS) has been designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style to provide an infrastructure system for managing both lexical and semantic metadata about both virtual and physical entities. We describe here how compatibility between version 0.9 of the NPDS schema, the new NPDS-interfacing ontologies, and the domain-specific concept-validating hypothesis-exploring ontologies allows NPDS to bootstrap the semantic web onto the more developed lexical web. We then describe how this system will serve as the foundation of a planned platform for automated meta-analysis.

• Seung-Ho Bae, Adam G Craig, Carl Taswell, 2017, Expanding Nexus Diristries of Dementia Literature with the NPDS Concept-Validating Search Engine Agent with poster presented July 2017 at the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society in Jeju Island, South Korea; see also a video demo of CoVaSEA Software.

  Even though online databases make it easier than ever to access the biomedical and scientific literature about dementia, accelerating growth in the size of these databases has made it more difficult for humans to gather and analyze manually all articles relevant to any given topic. We document a Nexus-PORTAL-DOORS System (NPDS) Concept-Validating Search Engine Agent that can populate Nexus diristries with concept-validated metadata records for citations of journal articles found in literature databases.

• Teja Veeramacheneni, S Koby Taswell, Carl Taswell, 2017, Evaluating the Effect of Alzheimer’s Disease Status on Co-Registration Accuracy of PET and MRI Brain Scans with poster presented July 2017 at the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society in Jeju Island, South Korea.

  Does the clinical status of patients with either Alzheimer’s disease or mild cognitive impairment when compared with the normal healthy status of control subjects have an effect on the co-registration accuracy of the participants PET and MRI brain scans? An initial evaluation reveals that a statistically significant difference may exist in co-registration accuracy with some popular algorithms for the different groups of participants’ brain scans. These differences suggest that investigators should use appropriate caution when reviewing fusion studies of co-registered PET and MRI brain scans.

• S Koby Taswell, Teja Veeramacheneni, Carl Taswell, 2017, BrainWatch Software for Interactive Exploration of Brain Scans in 3D Virtual Reality Systems presented July 2017 at the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society in Jeju Island, South Korea; see also a video demo of BrainWatch VR Software.

  The ability to view medical images as 3D objects, which can be explored interactively, has now become possible due to the advent of rapidly emerging virtual reality (VR) technologies. In the past, VR has been used as an educational tool for learning anatomy, a visualization tool for assisting surgery, and a therapeutic tool for rehabilitating patients with motor disorders. However, these older systems were either expensive to build or difficult to acquire and use. Exploiting the arrival of new consumer devices such as the Oculus Rift that are now affordable, we have developed a software application called BrainWatch for VR ready computers to enable 3D visualization and interactive exploration of DICOM data sets focusing on PET and MRI brain scans. BrainWatch software provides a unique set of 3 approaches for interacting with the virtual object which we have named the observatory scenario with an external camera, the planetarium scenario with an internal camera, and the voyager scenario with a mobile camera. A live interactive demonstration of BrainWatch VR with the Oculus Rift CV1 will be available for conference attendees to experience at EMBC 2017.

• Adam Craig, Seung-Ho Bae, Teja Veeramacheneni, S Koby Taswell, Carl Taswell, 2016, Web Service APIs for Scribe Registrars, Nexus Diristries, PORTAL Registries and DOORS Directories in the NPD System presented December 2016 at the 9th International SWAT4LS Conference in Amsterdam, Netherlands.

  The Nexus-PORTAL-DOORS System (NPDS) has been designed with the Hierarchically Distributed Mobile Metadata (HDMM) architectural style to provide an infrastructure system for managing both lexical and semantic metadata about both virtual and physical entities. We describe version 0.8 of NPDS, including the separation of concerns between the original Problem-Oriented Registry of Tags And Labels (PORTAL) registries and the Domain Ontology Oriented Resource System (DOORS) directories, the combined registry and directory functionality of Nexus diristries, and the RESTful read-only web service API through which resource representation metadata records can be retrieved from these NPDS servers. We also introduce Scribe registrars with a corresponding RESTful read-write web service API for management of metadata records by both software agents accessing the web services directly and human users accessing them indirectly via web applications.

• Teja Veeramacheneni, S Koby Taswell, Carl Taswell, 2016, Performance Evaluation Comparison of Registration Methods for PET and MRI Brain Scans presented October 2016 at the Annual Meeting of the Western Region Society of Nuclear Medicine in Anaheim, California.

  In routine clinical imaging, PET and MR images often undergo co-registration, however, methods for co-registration may vary. The significance of differences between methods has not been previously determined. Registration accuracy was calculated both qualitatively and quantitatively using different metrics. Both the quantitative metrics and subsequent visual inspection confirm that there exists a significant difference between different registration methods. Because a difference does exist across co-registration methods, clinicians and researchers must take appropriate care when choosing what method to use for PET-MR co-registration.

• S Koby Taswell, Matthew Garvey, Carl Taswell, 2016, Interactive Exploration of PET and MRI Brain Scans with a 3D Virtual Reality System presented October 2016 at the Annual Meeting of the Western Region Society of Nuclear Medicine in Anaheim, California.

  In a world of rapidly emerging commercial Virtual Reality (VR) technologies, such as Oculus Rift, the ability to view medical images as an interactive 3D object, which can be virtually entered, becomes a possibility. In the past, virtual reality has been used as an educational tool, for therapy in motor disorders, and also as a visualization tool for surgery, however, many of these systems have been a combination of incredibly costly and often difficult to come by. Using these improved and more readily available technologies, we have created an application for use with a VR enabled computer and Oculus Rift to allow the 3D visualization of DICOM datasets, specifically MRI and PET brain scans.

• Martin Skarzynski, Adam Craig, Carl Taswell, 2015, SOLOMON: An Ontology for Sensory-Onset, Language-Onset and Motor-Onset Dementias also available via DOI 10.1109/BIBM.2015.7359814 presented November 2015 at the IEEE International Conference on Bioinformatics and Biomedicine in Washington DC.

  The PORTAL-DOORS system (PDS) has been designed as a resource metadata management system intended to support applications such as automated searches of online resources and meta-analyses of published literature. PDS comprises a network of Problem Oriented Registry of Tags and Labels (PORTAL) lexical registries and Domain Ontology Oriented Resource System (DOORS) semantic directories. Here we introduce a PDS-compliant concept-validating registry and hypothesisexploring ontology that organizes focal-onset dementias including Sensory-Onset, Language-Onset and Motor-ONset (SOLOMON) dementias with novel classifying and relating concepts. This approach facilitates semantic search of resources and exploration of hypotheses related to neurodegeneration. SOLOMON interoperates with other PDS registries and ontologies including BrainWatch, ManRay and GeneScene.

• S Koby Taswell, Adam Craig, Diana Leung, Stephan Loh, Martin Skarzynski, Sara Gharabaghi, Bohan Zhou, Carl Taswell, 2015, Hypothesis-Exploring Methods for Automated Meta-Analyses of Brain Imaging Literature presented October 2015 at the Annual Meeting of the Western Region Society of Nuclear Medicine in Monterey, California.

  The PORTAL-DOORS system (PDS) has been designed as a resource metadata management system intended to support applications such as automated searches of online resources and meta-analyses of published literature. We present a methodological approach with a PDS-compliant concept-validating registry and hypothesis-exploring ontology that organizes focal-onset dementias including Sensory-Onset, Language-Onset and Motor-ONset(SOLOMON) dementias with novel classifying and relating concepts. This approach facilitates semantic search of resources and exploration of hypotheses related to neurodegeneration. SOLOMON interoperates with other PDS registries and ontologies including BrainWatch, ManRayand GeneScene.

• Linda Xu, Stephan Loh, Carl Taswell, 2015, Web-Enabled Software for Clinical Telegaming Evaluation of Multisensory Integration and Response to Auditory and Visual Stimuli with poster presented April 2015 at the 7th International IEEE EMBS Neural Engineering Conference in Montpelier, France; see also STEP Software.

  Clinical telegaming integrates telecare and videogaming to enable a more convenient and enjoyable experience for patients when providers diagnose, monitor, and treat a variety of health problems via web-enabled telecommunications. In recent years, clinical telegaming systems have been applied to physical therapy and rehabilitation, evaluation of mental health, and prevention and management of obesity and diabetes. Parkinson’s disease (PD) is suitable for development of new clinical telegaming applications because PD patients are known to experience motor symptoms that can be improved by physical therapy. Recent research suggests that sensory processing deficits may also play an important role in these motor impairments because successful motor function requires multisensory integration. In this paper, we describe a new web-enabled software system that uses clinical telegaming to evaluate and improve multisensory integration ability in users. This software has the potential to be used in diagnostic and therapeutic telegaming for PD patients.

• Carl Taswell, Victor L Villemagne, Paul Yates, Hitoshi Shimada, Cristian E Leyton, Kirrie J Ballard, Olivier Piguet, James R Burrell, John R Hodges, Christopher C Rowe, 2015, 18F-FDG PET Improves Diagnosis in Patients with Focal-Onset Dementias published as Journal of Nuclear Medicine 2015 Volume 56 Number 10 pages 1547-1553.

  Alzheimer disease is the cause of up to one-third of cases of primary progressive aphasia or corticobasal syndrome. The primary objective of this study was to determine the accuracy of 18F-FDG PET metabolic imaging for the detection of Alzheimer disease in patients with primary progressive aphasia or corticobasal syndrome. Methods: A cohort of patients (n = 94), including those with an expert clinical diagnosis of logopenic (n = 19), nonfluent (n = 16), or semantic (n = 13) variants of primary progressive aphasia, corticobasal syndrome (n = 14), or Alzheimer disease (n = 24), underwent 18F-FDG metabolic and 11C-labeled Pittsburgh compound B (11C-PiB) amyloid PET brain imaging. 18F-FDG PET scans interpreted with Neurostat and 3D-SSP displays were classified as revealing Alzheimer disease or “other” by interpreters who were unaware of the clinical assessments and 11C-PiB PET results. 11C-PiB PET imaging was considered to be the diagnostic reference standard, with a threshold standardized uptake value ratio of 1.5 being indicative of Alzheimer disease pathology. To address possible bias from subgroup selection for the Alzheimer disease binary classifier, we calculated both conventional and balanced accuracies. Results: Diagnoses of Alzheimer disease based on 18F-FDG PET resulted in 84% accuracy (both conventional and balanced). In comparison, diagnoses based on clinical assessments resulted in 65% conventional accuracy and 67% balanced accuracy. Conclusion: Brain 18F-FDG PET scans interpreted with Neurostat and 3D-SSP displays accurately detected Alzheimer disease in patients with primary progressive aphasia or corticobasal syndrome as focal-onset dementias. In such diagnostically challenging cohorts, 18F-FDG PET imaging can provide more accurate diagnoses, enabling more appropriate therapy.