Informationist: Informationist Breakout Session

In this session Leah will discuss her experiences working on an NIH Supplement for Informationist Services grant, what was accomplished, and what she learned along the way. Within the psychiatric neuroimaging research community, data and resource sharing have become accepted as standard, but issues related to attribution and citing data in novel research are still hindering meaningful reuse. This project aimed to illustrate a system of data identification that would not only allow for proper citation of whole datasets, but maintain the chain of attribution in derived and remixed datasets, allowing for a more complete picture of research impact and author contribution. Leah Honor is Library Fellow and Informationist Liaison to the Child and Adolescent Neurodevelopment Initiative, University of Massachusetts Medical School

Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution

Data sharing and reuse, while widely accepted as good ideas, have been slow to catch on in any concrete and consistent way. One major hurdle within the scientific community has been the lack of widely accepted standards for citing that data, making it difficult to track usage and measure impact. Within the neuroimaging community, there is a need for a way to not only clearly identify and cite datasets, but also to derive new aggregate sets from multiple sources while clearly maintaining lines of attribution. This work presents a functional prototype of a system to integrate Digital Object Identifiers (DOI) and a standardized metadata schema into a XNAT-based repository workflow, allowing for identification of data at both the project and image level. These item and source level identifiers allow any newly defined combination of images, from any number of projects, to be tagged with a new group-level DOI that automatically inherits the individual attributes and provenance information of its constituent parts. This system enables the tracking of data reuse down to the level of individual images. The implementation of this type of data identification system would impact researchers and data creators, data hosting facilities, and data publishers, but the benefit of having widely accepted standards for data identification and attribution would go far toward making data citation practical and advantageous

An assessment of the autism neuroimaging literature for the prospects of re-executability

Background: The degree of reproducibility of the neuroimaging literature in psychiatric application areas has been called into question and the issues that relate to this reproducibility are extremely complex. Some of these complexities have to do with the underlying biology of the disorders that we study and others arise due to the technology we apply to the analysis of the data we collect. Ultimately, the observations we make get communicated to the rest of the community through publications in the scientific literature. Methods: We sought to perform a ‘re-executability survey’ to evaluate the recent neuroimaging literature with an eye toward seeing if the technical aspects of our publication practices are helping or hindering the overall quest for a more reproducible understanding of brain development and aging. The topic areas examined include availability of the data, the precision of the imaging method description and the reporting of the statistical analytic approach, and the availability of the complete results. We applied the survey to 50 publications in the autism neuroimaging literature that were published between September 16, 2017 to October 1, 2018. Results: The results of the survey indicate that for the literature examined, data that is not already part of a public repository is rarely available, software tools are usually named but versions and operating system are not, it is expected that reasonably skilled analysts could approximately perform the analyses described, and the complete results of the studies are rarely available. Conclusions: We have identified that there is ample room for improvement in research publication practices. We hope exposing these issues in the retrospective literature can provide guidance and motivation for improving this aspect of our reporting practices in the future

WT1 regulates epicardial epithelial to mesenchymal transition through β-catenin and retinoic acid signaling pathways

AbstractAn epithelial sheet, the epicardium, lines the surface of the heart. In the developing embryo, the epicardium expresses the transcriptional regulator Wilm's Tumor Gene 1 (Wt1). Through incompletely understood mechanisms, Wt1 inactivation derails normal heart development. We investigated mechanisms by which Wt1 regulates heart development and epicardial epithelial to mesenchymal transition (EMT). We used genetic lineage tracing approaches to track and isolate epicardium and epicardium derivatives in hearts lacking Wt1 (Wt1KO). Wt1KO hearts had diminished proliferation of compact myocardium and impaired coronary plexus formation. Wt1KO epicardium failed to undergo EMT. Wt1KO epicardium expressed reduced Lef1 and Ctnnb1 (β-catenin), key components of the canonical Wnt/β-catenin signaling pathway. Wt1KO epicardium expressed decreased levels of canonical Wnt downstream targets Axin2, Cyclin D1, and Cyclin D2 and exhibited decreased activity of the Batgal Wnt/β-catenin reporter transgene, suggestive of diminished canonical Wnt signaling. Hearts with epicardium-restricted Ctnnb1 loss of function resembled Wt1KO hearts and also failed to undergo epicardial EMT. However, Ctnnb1 inactivation did not alter WT1 expression, positioning Wt1 upstream of canonical Wnt/β-catenin signaling. Wnt5a, a prototypic non-canonical Wnt with enriched epicardial expression, and Raldh2, a key regulator of retinoic acid signaling confined to the epicardium, were also markedly downregulated in Wt1KO epicardium. Hearts lacking Wnt5a or Raldh2 shared phenotypic features with Wt1KO. Although Wt1 has been proposed to regulate EMT by repressing E-cadherin, we detected no change in E-cadherin in Wt1KO epicardium. Collectively, our study shows that Wt1 regulates epicardial EMT and heart development through canonical Wnt, non-canonical Wnt, and retinoic acid signaling pathways

Engaging digital artworks through emotion: interface design case study

Artworks are often created to solicit emotional responses, yet the emotional elements are largely missing from artworks’ description and access options. In an effort to advance the design of emotion-based image retrieval systems, our study developed several research proposals for incorporating emotion into the description and access features of a digital artwork collection. Most of the proposed solutions for developing emotion metadata for artworks were informed by the current practices in information organization, including crowdsoursing and expert classifications. Being grounded in various emotion theories, the proposals offer a variety of ways to integrate emotion descriptors and navigation features into the interface design of a museum website. While the proposed solutions for integrating emotion features into online collections are not exhaustive, they highlight some of the design choices for developing emotion metadata, coding schemas and navigation features, and offer innovative ways to engage virtual visitors with museum digital collection.ye

Clinical Support During COVID-19

Background: The Lamar Soutter Library serves UMass Memorial Healthcare and the University of Massachusetts Medical School, which consists of the Schools of Nursing, Medicine, and Biomedical Sciences. In pursuit of our mission to help our community during the COVID-19 pandemic, we were called upon to provide clinical support in new ways as we also adapted to the “new normal” of working from home, social distancing, and remote interactions. Description: The Education and Clinical Services department (ECS) typically supports the clinical system by attending clinical rounds, staffing multiple library locations, providing education around information resources, and supporting literature searches. During COVID-19, many of our usual methods of support were not possible because we could not be there in person, and because educational pursuits were repurposed to answer the call for staffing and training during the pandemic. The need for immediate information and the desire to help meant demands for evidence-based information increased. To answer the call, ECS librarians had to learn new skills, come up with creative approaches, and stay up to date with an ever-changing information landscape. Conclusion: The COVID-19 pandemic was a force for change in the relationship between ECS and the clinical environment we support. Although it is wrong to say there is a silver lining to this tragedy, we have become more creative, more adaptive, and more flexible. We better understand the needs of our clinical community and are more proactive and confident in our approach to working with them. It was evident that our impact was felt by the response to our offers for new resident orientations. There was an almost 200% increase in the number of sessions (7 to 20) during March to September 2020 as compared to the same period in 2019. The skills we learned and the relationships we formed have changed the way we will approach clinical support going forward

Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution

Data sharing and reuse, while widely accepted as good ideas, have been slow to catch on in any concrete and consistent way. One major hurdle within the scientific community has been the lack of widely accepted standards for citing that data, making it difficult to track usage and measure impact. Within the neuroimaging community, there is a need for a way to not only clearly identify and cite datasets, but also to derive new aggregate sets from multiple sources, while clearly maintaining lines of attribution. This work presents a functional prototype of a system to integrate Digital Object Identifiers (DOI) and a standardized metadata schema into a XNAT-based repository workflow, allowing for identification of data at both the project and image level. These item and source level identifiers allow any newly defined combination of images, from any number of projects, to be tagged with a new group-level DOI that automatically inherits the individual attributes and provenance information of its constituent parts. This system enables the tracking of data reuse, down to the level of individual images. The implementation of this type of data identification system would impact researchers and data creators, data hosting facilities, and data publishers, but the benefit of having widely accepted standards for data identification and attribution would go far towards making data citation practical and advantageous

ReproNim

This is the OSF embodiment of ReproNim, A Center for Reproducible Neuroimaging Computation