Explore it! Building the Next Generation of Sustainable Energy Researchers

This award will establish an REU Site at the University of Maine. The program will engage 10 undergraduates each year for three years in a 10-week summer research experience. This REU site will leverage a focus area represented by the newly established University of Maine Forest Bio-products Research Institute (FBRI). Undergraduate students will conduct research advancing their knowledge of sustainable forest bio-products and will gain a detailed understanding of one of the thematic elements of the research effort as well as a broad understanding of all areas, specifically: 1) sustainable and life cycle analysis; 2) solids extraction/modification; 3) process control and sensing; 4) nanocellulose production and utilization; and 5) new project development. In addition to the hands-on research experience, undergraduate students will participate in a seminar series, field trips to gain practical knowledge of various aspects of sustainable forest bio-products, and a series of evening and weekend recreational activities. Participants will develop and utilize new knowledge to address sustainable energy issues impacting society. The REU site program will specifically target recruitment efforts towards women, minorities and students from undergraduate only institutions. Results of the research will be disseminated via campus presentations, and more broadly through journal articles and symposia

Procedurally Rhetorical Verb-Centric Frame Semantics as a Knowledge Representation for Argumentation Analysis of Biochemistry Articles

The central focus of this thesis is rhetorical moves in biochemistry articles. Kanoksilapatham has provided a descriptive theory of rhetorical moves that extends Swales' CARS model to the complete biochemistry article. The thesis begins the construction of a computational model of this descriptive theory. Attention is placed on the Methods section of the articles. We hypothesize that because authors' argumentation closely follows their experimental procedure, procedural verbs may be the guide to understanding the rhetorical moves. Our work proposes an extension to the normal (i.e., VerbNet) semantic roles especially tuned to this domain. A major contribution is a corpus of Method sections that have been marked up for rhetorical moves and semantic roles. The writing style of this genre tends to occasionally omit semantic roles, so another important contribution is a prototype ontology that provides experimental procedure knowledge for the biochemistry domain. Our computational model employs machine learning to build its models for the semantic roles and rhetorical moves, validated against a gold standard reflecting the annotation of these texts by human experts. We provide significant insights into how to derive these annotations, and as such have contributions as well to the general challenge of producing markups in the domain of biomedical science documents, where specialized knowledge is required

The pedagogical benefits of a lexical database (SciE-Lex) to assist the production of publishable biomedical texts by EAL writers

Faculty Senate Resolution on the LSU System employee benefit plan evaluation, adopted on November 8, 1988

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

Purposive variation in recordkeeping in the academic molecular biology laboratory

This thesis presents an investigation into the role played by laboratory records in the disciplinary discourse of academic molecular biology laboratories. The motivation behind this study stems from two areas of concern. Firstly, the laboratory record has received comparatively little attention as a linguistic genre in spite of its central role in the daily work of laboratory scientists. Secondly, laboratory records have become a focus for technologically driven change through the advent of computing systems that aim to support a transition away from the traditional paper-based approach towards electronic recordkeeping. Electronic recordkeeping raises the potential for increased sharing of laboratory records across laboratory communities. However, the uptake of electronic laboratory notebooks has been, and remains, markedly low in academic laboratories. The investigation employs a multi-perspective research framework combining ethnography, genre analysis, and reading protocol analysis in order to evaluate both the organizational practices and linguistic practices at work in laboratory recordkeeping, and to examine these practices from the viewpoints of both producers and consumers of laboratory records. Particular emphasis is placed on assessing variation in the practices used by different scientists when keeping laboratory records, and on assessing the types of articulation work used to achieve mutual intelligibility across laboratory members. The findings of this investigation indicate that the dominant viewpoint held by laboratory staff other than principal investigators conceptualized laboratory records as a personal resource rather than a community archive. Readers other than the original author relied almost exclusively on the recontextualization of selected information from laboratory records into ‘public genres’ such as laboratory talks, research articles, and progress reports as the preferred means of accessing the information held in the records. The consistent use of summarized forms of recording experimental data rendered most laboratory records as both unreliable and of limited usability in the records management sense that they did not form full and accurate descriptions that could support future organizational activities. These findings offer a counterpoint to other studies, notably a number of studies undertaken as part of technology developments for electronic recordkeeping, that report sharing of laboratory records or assume a ‘cyberbolic’ view of laboratory records as a shared resource

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

The pedagogical benefits of a lexical database (SciE-Lex) to assist the production of publishable biomedical texts by EAL writers

Research has demonstrated that it is challenging for English as an Additional Language (EAL) writers to acquire phraseological competence in academic English and develop a good working knowledge of discipline-specific formulaic language. This paper aims to explore if SciE-Lex, a powerful lexical database of biomedical research articles, can be exploited by EAL writers to enhance their command of formulaic language in biomedical English published writing. Our paper reports on the challenges associated with formulaic language (namely collocations) for EAL writers, it reflects on the benefits of using a lexical database and it evaluates a pedagogical approach to helping EAL writers produce publishable texts. It specifically highlights results from two writing workshops conducted for EAL writers (medical researchers in the present study). The workshops involved medical researchers working on drafts of their writing using SciE-Lex. Our paper reports on the specific benefits of using SciE-Lex as demonstrated by revisions in the writing produced by the EAL medical researchers. This contribution aims to contribute to current discussion on English for Research Publication Purposes (ERPP) for the EAL community who now form the main contributors to research knowledge dissemination

Accessible software frameworks for reproducible image analysis of host-pathogen interactions

Um die Mechanismen hinter lebensgefährlichen Krankheiten zu verstehen, müssen die zugrundeliegenden Interaktionen zwischen den Wirtszellen und krankheitserregenden Mikroorganismen bekannt sein. Die kontinuierlichen Verbesserungen in bildgebenden Verfahren und Computertechnologien ermöglichen die Anwendung von Methoden aus der bildbasierten Systembiologie, welche moderne Computeralgorithmen benutzt um das Verhalten von Zellen, Geweben oder ganzen Organen präzise zu messen. Um den Standards des digitalen Managements von Forschungsdaten zu genügen, müssen Algorithmen den FAIR-Prinzipien (Findability, Accessibility, Interoperability, and Reusability) entsprechen und zur Verbreitung ebenjener in der wissenschaftlichen Gemeinschaft beitragen. Dies ist insbesondere wichtig für interdisziplinäre Teams bestehend aus Experimentatoren und Informatikern, in denen Computerprogramme zur Verbesserung der Kommunikation und schnellerer Adaption von neuen Technologien beitragen können. In dieser Arbeit wurden daher Software-Frameworks entwickelt, welche dazu beitragen die FAIR-Prinzipien durch die Entwicklung von standardisierten, reproduzierbaren, hochperformanten, und leicht zugänglichen Softwarepaketen zur Quantifizierung von Interaktionen in biologischen System zu verbreiten. Zusammenfassend zeigt diese Arbeit wie Software-Frameworks zu der Charakterisierung von Interaktionen zwischen Wirtszellen und Pathogenen beitragen können, indem der Entwurf und die Anwendung von quantitativen und FAIR-kompatiblen Bildanalyseprogrammen vereinfacht werden. Diese Verbesserungen erleichtern zukünftige Kollaborationen mit Lebenswissenschaftlern und Medizinern, was nach dem Prinzip der bildbasierten Systembiologie zur Entwicklung von neuen Experimenten, Bildgebungsverfahren, Algorithmen, und Computermodellen führen wird