Nonparametric tests of structure for high angular resolution diffusion imaging in Q-space

High angular resolution diffusion imaging data is the observed characteristic function for the local diffusion of water molecules in tissue. This data is used to infer structural information in brain imaging. Nonparametric scalar measures are proposed to summarize such data, and to locally characterize spatial features of the diffusion probability density function (PDF), relying on the geometry of the characteristic function. Summary statistics are defined so that their distributions are, to first-order, both independent of nuisance parameters and also analytically tractable. The dominant direction of the diffusion at a spatial location (voxel) is determined, and a new set of axes are introduced in Fourier space. Variation quantified in these axes determines the local spatial properties of the diffusion density. Nonparametric hypothesis tests for determining whether the diffusion is unimodal, isotropic or multi-modal are proposed. More subtle characteristics of white-matter microstructure, such as the degree of anisotropy of the PDF and symmetry compared with a variety of asymmetric PDF alternatives, may be ascertained directly in the Fourier domain without parametric assumptions on the form of the diffusion PDF. We simulate a set of diffusion processes and characterize their local properties using the newly introduced summaries. We show how complex white-matter structures across multiple voxels exhibit clear ellipsoidal and asymmetric structure in simulation, and assess the performance of the statistics in clinically-acquired magnetic resonance imaging data.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS441 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Open Content in Open Context

This article presents the challenges and rewards of sharing research content through a discussion of Open Context, a new open access data publication system for field sciences and museum collections. Open Context is the first data repository of its kind, allowing self-publication of research data, community commentary through tagging, and clear citation and stable hyperlinks, and Creative Commons licenses that make reusing content legal and easy.The Nov-Dec 2007 issue of Educational Technology magazine is an entire special issue dedicated to "Opening Educational Resources." A series of articles in this issue highlight open educational models, including OpenCourseWare, Connexions and this piece on Open Context, co-authored by Sarah Whitcher Kansa and Eric Kansa

Enhancing Humanities Research Productivity in a Collaborative Data Sharing Environment

This project represents a multi-organizational, interdisciplinary effort to enhance collaborative research in cultural heritage fields by exploring user experience with Web-based technologies. The objective of this project is to document user needs around online systems for sharing primary data and documentation of cultural heritage collections. To this end, we will draw upon the experience and insights of representatives from different stakeholder groups in three broad arenas: academic researchers, heritage managers, and specialist communities. Investigations undertaken in this study will result in best-practice guidelines to guide humanities computing efforts on how to best meet the diverse user needs in future online data sharing systems. Using an iterative cycle of development, deployment, and evaluation, this project will enhance Open Context, a collaborative, open-access data sharing system already in use for archaeology and related disciplines

An Open Context for Near Eastern Archaeology

The common use by archaeologists of ubiquitous technologies such as computers and digital cameras means that archaeological research projects now produce huge amounts of diverse, digital documentation. However, while the technology is available to collect this documentation, we still largely lack community-accepted dissemination channels appropriate for such torrents of data. Open Context aims to help fill this gap by providing open access data publication services for archaeology. Open Context has a flexible and generalized technical architecture that can accommodate most archaeological datasets, despite the lack of common recording systems or other documentation standards. It includes a variety of tools to make data dissemination easier and more worthwhile. Authorship is clearly identified through citation tools, including web-based publication systems that enable individuals to upload their own data for review, and collaboration is facilitated through easy download and "tagging" features. Near Eastern archaeologists will benefit from Open Context's flexibility to share a variety of content from diverse projects, no matter how large or small. This article was originally published in Near Eastern Archaeology (ISSN 1094-2076), Volume 70, Number 4, December 2007

Gaps in Adolescent Tobacco Prevention and Counseling in Vermont

Introduction. Tobacco use remains the leading cause of preventable death in Vermont. While the Vermont Blueprint for Health includes compensation for adult tobacco counseling, it includes no specific mention of pediatric populations. Research questions: To what extent are tobacco assessment and cessation efforts occurring in the primary care setting with pediatric patients? What factors influence their practices?Methods. A 12-question electronic survey, modeled on an American Academy of Pediatrics survey, was distributed to primary care providers throughout Vermont; through the UVM departments of pediatrics, family medicine, the Vermont Medical Society and the Vermont Area Health Education Center. We received 70 completed surveys.Results. 70% of the surveyed primary care providers begin tobacco counseling at the age recommended (11 years) by the Vermont Department of Health. Only 45.71% of providers are confident in their understanding of the recommendations for adolescent health screening written in the Blueprint for Health. Additionally, only 67.1% of the providers expressed confidence in their ability to provide guidance regarding the harmful effects of E-cigarettes, compared to 92.8% feeling confident regarding conventional cigarettes. 70% of providers listed time restraints as a significant factor in their decision not to counsel adolescents on tobacco use.Discussion. The Blueprint for Health is a guiding document for provider practices that is not well understood and does not specifically include pediatric tobacco prevention. In an environment where youth E-cigarette use is rising, especially among adolescents, it is especially critical that physicians are confident in their counseling practices.https://scholarworks.uvm.edu/comphp_gallery/1237/thumbnail.jp

Publishing and Pushing: Mixing Models for Communicating Research Data in Archaeology

We present a case study of data integration and reuse involving 12 researchers who published datasets in Open Context, an online data publishing platform, as part of collaborative archaeological research on early domesticated animals in Anatolia. Our discussion reports on how different editorial and collaborative review processes improved data documentation and quality, and created ontology annotations needed for comparative analyses by domain specialists. To prepare data for shared analysis, this project adapted editor-supervised review and revision processes familiar to conventional publishing, as well as more novel models of revision adapted from open source software development of public version control. Preparing the datasets for publication and analysis required significant investment of effort and expertise, including archaeological domain knowledge and familiarity with key ontologies. To organize this work effectively, we emphasized these different models of collaboration at various stages of this data publication and analysis project. Collaboration first centered on data editors working with data contributors, then widened to include other researchers who provided additional peer-review feedback, and finally the widest research community, whose collaboration is facilitated by GitHub’s version control system. We demonstrate that the “publish” and “push” models of data dissemination need not be mutually exclusive; on the contrary, they can play complementary roles in sharing high quality data in support of research. This work highlights the value of combining multiple models in different stages of data dissemination

Publishing and pushing: Mixing models for communicating research data

We present a case study of data integration and reuse involving 12 researchers who published datasets in Open Context, an online data publishing platform, as part of collaborative archaeological research on early domesticated animals in Anatolia. Our discussion reports on how different editorial and collaborative review processes improved data documentation and quality, and created ontology annotations needed for comparative analyses by domain specialists. To prepare data for shared analysis, this project adapted editor-supervised review and revision processes familiar to conventional publishing, as well as more novel models of revision adapted from open source software development of public version control. Preparing the datasets for publication and analysis required significant investment of effort and expertise, including archaeological domain knowledge and familiarity with key ontologies. To organize this work effectively, we emphasized these different models of collaboration at various stages of this data publication and analysis project. Collaboration first centered on data editors working with data contributors, then widened to include other researchers who provided additional peer-review feedback, and finally the widest research community, whose collaboration is facilitated by GitHub’s version control system. We demonstrate that the “publish” and “push” models of data dissemination need not be mutually exclusive; on the contrary, they can play complementary roles in sharing high quality data in support of research. This work highlights the value of combining multiple models in different stages of data dissemination

Village-Integrated Eye Worker trial (VIEW): rationale and design of a cluster-randomised trial to prevent corneal ulcers in resource-limited settings.

IntroductionCorneal opacity is a leading cause of blindness worldwide. In resource-limited settings, untreated traumatic corneal abrasions may result in infection and ultimately, opacity. Although antimicrobial treatment of corneal ulcers may successfully cure infections, the scarring that accompanies the resolution of infection can still result in visual impairment. Prevention may be the optimal approach for reducing corneal blindness. Studies have employed community health workers to provide prompt administration of antimicrobials after corneal abrasions to prevent infections, but these studies were not designed to determine the effectiveness of such a programme.Methods and analysisThe Village-Integrated Eye Worker trial (VIEW) is a cluster-randomised trial designed to assess the effectiveness of a community health worker intervention to prevent corneal ulcers. Twenty-four Village Development Committees (VDCs) in Nepal were randomised to receive a corneal ulcer prevention programme or to no intervention. Female Community Health Volunteers (FCHVs) in intervention VDCs are trained to diagnose corneal abrasions, provide antimicrobials and to refer participants when needed. An annual census is conducted over 3 years in all study VDCs to assess the incidence of corneal ulceration via corneal photography (primary outcome). Masked outcome assessors grade corneal photographs to determine the presence or absence of incident corneal opacities. The primary analysis is negative binomial regression to compare the incidence of corneal ulceration by study arm.Ethics and disseminationThe University of California San Francisco Committee on Human Research, Nepal Netra Jyoti Sangh and the Nepal Health Research Council have given ethical approval for the trial. The results of this trial will be presented at local and international meetings and submitted to peer-reviewed journals for publication.Trial registration numberNCT01969786; Pre-results

Gazetteer of the Ancient Near East

This grant will support the creation of the Gazetteer of the Ancient Near East. The project’s goal is to develop an authoritative, open access geospatial index of archaeological sites and historical places in the Near East, spanning some twelve thousand years (c. 12,500-600 BCE). The project is based on software developed by the Pleiades project (http://pleiades.stoa.org/), an extant and successful model for open access Web-based gazetteers. By developing a gazetteer of Ancient Near East places, researchers will be able to link events, persons, and archaeological evidence through shared notions of place and time. Thus, this project will help scholars to bring together disparate lines of historical and archaeological evidence. In doing so, this project represents critically needed infrastructure to catalyze research in the Ancient Near East and serves as an exemplar for open, collaborative scholarship