Nathan Wilson - US grants

Develop a repository of human cardiovascular and cardiopulmonary computer models consisting of realistic, image-based anatomic models of large arteries and airways, generic, distal vascular beds, and representative blood and tissue properties. Simulations based on repository data will have significant impact on our understanding of cardiopulmonary pathologies, diagnostic methods and therapy development, and ultimately, allow physicians to design optimal, prearsonalized treatment plans based on predictive methods. The project will yield a critical data resource for scientist, engineers, industry and physicians seeking to use simulation methods to aid in preventing, diagnosing and treating patients with cardiopulmonary dieseases.

This INSPIRE award is partially funded by the Science, Technology, and Society Program in the Division of Social and Economic Sciences in the Directorate for Social, Behavioral, and Economic Sciences; and by the Advances in Biological Informatics Program in the Division of Biological Infrastructure in the Directorate for Biological Sciences.

Intellectual Merit

This will be the first large scale computational project in Science and Technology Studies. Although the focus of this project is on Biodiversity and on History and Philosophy of science, the approach would extend well beyond these areas. The project will establish a repository and a research system based on computational tools and digital sources, and it will develop education and training modules. The goal is to move beyond separate small collections that reside on individual computers in dispersed places, and bring together the objects of study as well as scholarly interpretations of those objects. The materials are to be openly available for efficiency and also to stimulate new kinds of research and discovery. The repository will link to existing large and widely-used databases such as the Biodiversity Heritage Library and the Encyclopedia of Life. Researchers at Arizona State University and the Marine Biological Laboratory will collaborate in bringing together the robustly integrative methods that combine history and philosophy of science, informatics, and biology of biodiversity. It will transform the way that scholarship and training is done in the areas, and lead to a new kind of scientific history based in open access publishing. The repository, tools, and training modules will be widely available for other projects in Science and Technology Studies for the full range of STEM disciplines.

Potential Broader Impacts

This project will produce scholarly results, a repository, informatics tools, and training manuals for others to customize and contribute their own projects. Scholarly results are to be produces that would be available through different websites for multiple user groups, from specialized scholars to the wider public. For educators and students, the project will connect with Arizona State University's Ask A Biologist project, as well as to Encyclopedia of Life and the Biodiversity Heritage Library, and to other existing databases. Undergraduate and Graduate students will be trained to contribute interpretive articles. Informatics Training courses, manuals, and other educational approaches will make the system and repository available widely.

In the mid-18th century biology as a science was revolutionized by Carl Linneaus and the use of binomial scientific names. Such names consist of two words in Latin - genus name and specific epithet - for example, Homo sapiens for humans. For higher classifications Linneaus adopted names consisting of a single Latin word. This nomenclatural system dramatically simplified handling species information, and gave scientists from different countries a standard way of communication. This system has been so successful it has persisted for over 250 years and is still in very active use today. An enormous amount of scientific and popular science literature uses scientific names. In the electronic age scientific names enable the effective organization of biodiversity information from various sources, as demonstrated by the Encyclopedia of Life (http://eol.org) and Biodiversity Heritage Library (http://bhl.org). However the naming system introduced by Linnaeus is far from perfect. For example, if scholars decide to move a particular species to different genus - the name changes, and finding information about it becomes much more difficult. For example, a very prominent model organism of modern science Drosophila melanogaster (fruit fly) is now recommended to be placed in the genus Sophophora, changing its name to Sophophora melanogaster. Such changes are inevitable in Linnaean nomenclature, and they create a significant amount of confusion. The project aims to create a system which would allow a user to enter a name, and find out if it is a known scientific name, if another name should be used instead, if there are other historical synonyms, and if this name is a misspelling of a known scientific name. The system will also display which data sources contain information related to a name, and will provide a list of relevant web-pages (URLs). This project aims to make significant strides in removing ambiguity and confusion from biodiversity data. Teaching activities are planned with college students at Arizona State and there are opportunities for participation in Google Summer of Code and Biodiversity informatics training courses developed at MBL.

The first stage of the research was also funded by NSF and it allowed the development of a prototype and 'proof of concept' algorithms for finding and verifying scientific names in texts, images, species lists. This second phase aims to make production version of the algorithms, make them precise, fast, and scale them up to serve the global biological community. The task of scientific name disambiguation is not a simple one. It requires cooperation of many researchers. Discovery of scientific names in texts uses natural language processing algorithms which we plan to improve. The project aims to collect all known spellings and renderings of scientific names (20 million are currently collected) and organizes them into groups belonging to the same sets of organisms. It also catalogues where each spelling was used and stores information as a global name index. The database is powered by a search engine which uses fuzzy matching algorithms, and name parsing algorithms to find that names like 'Carek scirpoidea Michx. var. convoluta Kük.' and 'Carex scirpoidea subsp. convoluta (Kukenth) D. A. Dunlop' refer to the same
subspecies. The project's URL is: http://globalnames.org/

Researchers seek to understand how interaction between large states and small polities impacts populations of said small polities at the local and regional level. With increased global interconnectedness and the continued development of world-wide economic systems, the impacts of these systems on local populations, both positive and negative, have become an increasingly important focus of study. Archaeology is particularly well-suited to examine similar processes of interaction in the past and can therefore inform on these processes of economic and political expansion in the present. In the Classic Period (AD 300-900) of ancient Mesoamerica, the large city of Teotihuacan (located near present-day Mexico City), engaged in various forms of contact with many other regions. Forms of interaction included trade, conquest, and cultural dissemination. This project will focus on one location of interaction with Teotihuacan, the Sierra de los Tuxtlas Region of Southern Veracruz, Mexico. It will address the impacts of Teotihuacan influence on local populations in the region and assess the ways in which this influence altered regional social and economic systems. In doing so, this project will contribute to the general study of economic expansion and implements an approach to examine foreign-induced regional economic change from the local perspective, which can be applied broadly. This research will be conducted by Arizona State University doctoral student Nathan D. Wilson, under the direction of Dr. Michael E. Smith. Data from this project will serve as the basis for Mr. Wilson's doctoral dissertation.

This research addresses the issue of peripheral incorporation into larger systems and how this process is manifest regionally. It implements a world-systems framework in quantifying interaction between core-affiliated populations and a negotiated periphery. To evaluate this, it will study peripheral consumption of imported goods in the Western Tuxtlas Region (WTR) of southern Veracruz, Mexico. Through multiple lines of evidence, this research will ascertain the regional economic effects for two WTR polities that were connected to an intrusive center (Matacapan) displaying cultural affiliation to the Mexican highland capital of Teotihuacan. Prior research in the region has focused on intensive production and regional, interpolity distribution of specific pottery types associated with Matacapan. This project will build upon this previous research by: (1) more effectively quantifying consumption of these products in two neighboring polities and (2) assessing distribution and consumption of other Matacapan-produced goods. In doing so, it will construct a regional, diachronic view of the different ways through which these two indigenous polities (and different populations within one of the polities) incorporated into a Teotihuacan world-system via interaction with Matacapan. The proposed research is geared toward analytical methods (e.g., attribute analysis, Instrumental Neutron Activation Analysis [INAA], and petrography) to help differentiate between Early and Middle Classic Period contexts, assess the accuracy of visual sourcing of obsidian, and separate local utilitarian pottery types from imported versions. Sample selection from previously excavated materials will be done in Mexico, while sample preparation and chemical and mineralogical analyses will be completed by laboratories in the United States.

Intellectual Merit:
This project establishes an I-Corps Site at the University of California-Los Angeles (UCLA).

NSF Innovation Corps (I-Corps) Sites are NSF-funded entities established at universities whose purpose is to nurture and support multiple, local teams to transition their technology concepts into the marketplace. Sites provide infrastructure, advice, resources, networking opportunities, training and modest funding to enable groups to transition their work into the marketplace or into becoming I-Corps Team applicants. I-Corps Sites also strengthen innovation locally and regionally and contribute to the National Innovation Network of mentors, researchers, entrepreneurs and investors.

This project at UCLA provides mechanisms for thirty teams a year to receive seed funding to accelerate translational research in the fields of Science, Technology, Engineering, and Mathematics (STEM) across campus. The additional funding and entrepreneurial instruction enabled by this grant complements existing programs at UCLA and prepares the selected teams to benefit from a variety of resources available on campus, facilitating commercialization and new business formation.

Led by the Price Center for Entrepreneurial Studies in the UCLA Anderson School of Management, the goals of the Site are to establish: 1. An interdisciplinary UCLA I-Corps Site Team Selection Committee to oversee the annual award of thirty grants to competitively selected UCLA I-Corps Site Teams per year that will use the grants for STEM related projects to prepare applications for UCLA?s collection of entrepreneurial plan competitions, on campus accelerators and incubators, and translational governmental funding; 2. A new UCLA I-Site Lean Startup Course that will be taught three times annually for UCLA I-Corps Site Teams by Price Center entrepreneurship faculty; 3. Three existing UCLA entrepreneurial courses enhanced to enable enrolled UCLA I-Corps Site Teams to utilize grants during the course.

Broader Impacts:
This grant may benefit society given that sponsored translational research and training at UCLA will directly impact the Southern California Economic Region which consists of 18.4M people (5.9% of the U.S. population) and contributes $924B in GDP (16th largest economy in the world). With 28,700 undergraduates (11.8% are international students) and 12,000 graduate students representing all fifty states and nearly 80 countries worldwide, this grant in conjunction with entrepreneurial education at UCLA impacts beyond the borders of California.