Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution

Artequakt: Generating tailored biographies from automatically annotated fragments from the web

The Artequakt project seeks to automatically generate narrativebiographies of artists from knowledge that has been extracted from the Web and maintained in a knowledge base. An overview of the system architecture is presented here and the three key components of that architecture are explained in detail, namely knowledge extraction, information management and biography construction. Conclusions are drawn from the initial experiences of the project and future progress is detailed

SENSORS: Detecting Microbial Pathogens with Novel Surface Acoustic Wave Devices in Liquid Environments

This SENSORS proposal integrates research and education to exploit the sensitivity of a new family of LGX crystal devices operated in novel Shear Horizontal Surface Acoustic Wave (SH-SAW) propagation directions by combining them with highly selective molecular padlock probes to detect specific nucleic acid sequences associated with bacteria such as Escherichia coli O157:H7, Salmonella typhi, and Vibrio cholerae in aqueous solutions. The anticipated fundamental advances in sensor science and engineering will be relevant to numerous applications, including rapid response to bioterrorism, healthcare, epidemiology, agriculture, food safety, and pollution avoidance and mitigation. This SENSORS program builds upon the initial proof-of-concept results provided by an NSF SGER project funded by the divisions of Electrical and Communication Systems, and Bioengineering and Environmental Systems. The intellectual merit of this proposal rests in the creative, integrated research and education activities related to combining the recently identified LGX SH-SAW devices with molecular padlock probe technology to permit the design, fabrication, testing, and optimization of prototype biosensors. The specific research objectives of this SENSORS program are to: (i) Identify the surface density chemistry for increased sensitivity; (ii) Investigate and identify the optimal LGX SH-SAW orientation and device design for operation with the padlock technology; (iii) Study and develop the molecular padlock probe system to operate effectively in conjunction with the LGX SH-SAW device; (iv) Fabricate and test the prototype SH-SAW liquid biosensors; (v) Identify and optimize a procedure for sensor regeneration; and (vi) Characterize and optimize the sensor\u27s dynamic range and cross-effects due to temperature and other physical and chemical factors. The educational objective of this SENSORS program is to provide a multidisciplinary learning experience to students ranging from high school to graduate student level in the area of sensors in general, and biosensors in particular. Broader impacts will be achieved through the following programs and activities to: (i) Train and interact with high school audiences through two major ongoing programs at University of Maine (UMaine), NSF Research Experiences for Teachers (RET) and the GK-12 Sensors; (ii) Involve undergraduates from Maine and other institutions directly into the research project under the umbrella of the ongoing NSF Research Experience for Undergraduates (REU) program at the UMaine; (iii) Expand existing undergraduate Sensor Technology and Instrumentation and Biochemical Engineering Engineering courses at the UMaine by adding modules relating to biosensors devices and systems; (iv) Identify appropriate Capstone projects for undergraduates involving cross-disciplinary research and design projects; (v) Enhance existing graduate level courses Microscale Bioengineering and Design and Fabrication of Acoustic Wave Devices by incorporating research results into the course; (vi) Contribute to the new interdisciplinary multi-institutional NSF Integrative Graduate Education and Research Traineeship (IGERT) program in functional genomics, which involves UMaine, the Jackson Laboratory, and the Maine Medical Center Research Institute; (vi) Provide a experimental and/or theoretical thesis topics for Masters and Ph.D. students; (vii) Disseminate the research and educational material on a project website, and through conferences and printed literature. The SENSORS project proposed here is designed to result in tangible research and educational benefits. It will provide a knowledge base critical to creation of the next generation of biosensors for single unit production and future integration into arrays. It also seeks to establish a model program whereby cross-disciplinary education is integrated with a state-of-the-art research program, providing a rich learning experience for students ranging from high school to graduate student level. Finally, the project will help to strengthen U.S. research and educational capabilities in an area of high technology that currently is in need of highly trained industry and academic professionals

SGER: Detection of Bioterrorism-Linked Microbial Pathogens Using Surface Acoustic Wave Liquid Sensors

Bioterrorism threats and attacks in civilian environments require sensors that can rapidly and accurately detect minute quantities of pathological bioagents. Selective and inexpensive sensors are urgently needed to detect pathogens in liquid environments, including food and water supplies. Conventional laboratory analyses are time-consuming, labor-intensive and inconsistent with the expedient response required in the wake or possibility of a bioterrorist act.The activities proposed in this Small Grant for Exploratory Research (SGER) are multidisciplinary and involve two faculty members from the University of Maine. Dr. Mauricio Pereira da Cunha, from the Department of Electrical and Computer Engineering, will provide expertise in the area of sensor platform development in general, and acoustic wave sensors in particular. Pereira DaCunha is a 2002 NSF CAREER award recipient, who has worked for more than 16 years in the acoustics microwave area. Dr. Paul Millard, from the Department of Chemical and Biological Engineering, is a microbiologist with more than 15 years of experience in microbial detection and analysis. Both Pereira da Cunha and Millard are affiliated with the University of Maine\u27s Laboratory for Surface Science and Technology, a multidisciplinary laboratory with appropriate facilities for the realization of the proposed tasks. This project determined the validity of integrating biomolecular technology with a novel SH-SAW sensor platform. This NSF SGER initiative permitted proof-of-concept verification of the LGS SH-SAW biosensor device and the results gave rise to a full proposal. It is expected that research and development of this particular sensor will permit the further creation of sensors for use in a wide range of environmental, medical, industrial, homeland security, and military applications. By providing a rapid, reliable and ultimately, inexpensive sensor, the development of this technology will contribute to general well-being of the population at large, and serve as a starting point for the development of an important new class of biosensors

Motion optimization and parameter identification for a human and lower-back exoskeleton model

Designing an exoskeleton to reduce the risk of low-back injury during lifting is challenging. Computational models of the human-robot system coupled with predictive movement simulations can help to simplify this design process. Here, we present a study that models the interaction between a human model actuated by muscles and a lower-back exoskeleton. We provide a computational framework for identifying the spring parameters of the exoskeleton using an optimal control approach and forward-dynamics simulations. This is applied to generate dynamically consistent bending and lifting movements in the sagittal plane. Our computations are able to predict motions and forces of the human and exoskeleton that are within the torque limits of a subject. The identified exoskeleton could also yield a considerable reduction of the peak lower-back torques as well as the cumulative lower-back load during the movements. This work is relevant to the research communities working on human-robot interaction, and can be used as a basis for a better human-centered design process

Using Protege for automatic ontology instantiation

This paper gives an overview on the use of Protégé in the Artequakt system, which integrated Protégé with a set of natural language tools to automatically extract knowledge about artists from web documents and instantiate a given ontology. Protégé was also linked to structured templates that generate documents from the knowledge fragments it maintains

Web based knowledge extraction and consolidation for automatic ontology instantiation

The Web is probably the largest and richest information repository available today. Search engines are the common access routes to this valuable source. However, the role of these search engines is often limited to the retrieval of lists of potentially relevant documents. The burden of analysing the returned documents and identifying the knowledge of interest is therefore left to the user. The Artequakt system aims to deploy natural language tools to automatically ex-tract and consolidate knowledge from web documents and instantiate a given ontology, which dictates the type and form of knowledge to extract. Artequakt focuses on the domain of artists, and uses the harvested knowledge to gen-erate tailored biographies. This paper describes the latest developments of the system and discusses the problem of knowledge consolidation

Automatic extraction of knowledge from web documents

A large amount of digital information available is written as text documents in the form of web pages, reports, papers, emails, etc. Extracting the knowledge of interest from such documents from multiple sources in a timely fashion is therefore crucial. This paper provides an update on the Artequakt system which uses natural language tools to automatically extract knowledge about artists from multiple documents based on a predefined ontology. The ontology represents the type and form of knowledge to extract. This knowledge is then used to generate tailored biographies. The information extraction process of Artequakt is detailed and evaluated in this paper

Generating adaptive hypertext content from the semantic web

Accessing and extracting knowledge from online documents is crucial for therealisation of the Semantic Web and the provision of advanced knowledge services. The Artequakt project is an ongoing investigation tackling these issues to facilitate the creation of tailored biographies from information harvested from the web. In this paper we will present the methods we currently use to model, consolidate and store knowledge extracted from the web so that it can be re-purposed as adaptive content. We look at how Semantic Web technology could be used within this process and also how such techniques might be used to provide content to be published via the Semantic Web