A Component-Based Approach for Scientific Services for Education and Research (Scientific SEARCH)

Today’s challenge for retrieving digital information by users such as “students,” educators,” or “researchers” is coping, more than ever before, with the excessive data and information available. The problem is further compounded because of the way scientific knowledge is structured, in terms of expert interviews, articles, conference coverage, journal scans etc. Great progress has been made in digital library research. The NSF/NSDL through their initiatives has assembled a great set of tools and techniques that hold significant potential. Many projects are now underway applying these tools and techniques to meet the information needs of different user communities. The primary focus of Scientific SEARCH project is enhancing access to high quality learning materials and resources, modules, and other digital objects targeted towards scientific consumer and scientific producer. The project will use a multi-phased approach to achieve the objective. The paper describes the first-phase work submitted to NSF 04-542 solicitation

Cyberinfrastructure for Preservation of Stream and River Ecology

2008 S.C. Water Resources Conference - Addressing Water Challenges Facing the State and Regio

Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma

<p>Abstract</p> <p>Background</p> <p>The etiology of hemangiosarcoma remains incompletely understood. Its common occurrence in dogs suggests predisposing factors favor its development in this species. These factors could represent a constellation of heritable characteristics that promote transformation events and/or facilitate the establishment of a microenvironment that is conducive for survival of malignant blood vessel-forming cells. The hypothesis for this study was that characteristic molecular features distinguish hemangiosarcoma from non-malignant endothelial cells, and that such features are informative for the etiology of this disease.</p> <p>Methods</p> <p>We first investigated mutations of VHL and Ras family genes that might drive hemangiosarcoma by sequencing tumor DNA and mRNA (cDNA). Protein expression was examined using immunostaining. Next, we evaluated genome-wide gene expression profiling using the Affymetrix Canine 2.0 platform as a global approach to test the hypothesis. Data were evaluated using routine bioinformatics and validation was done using quantitative real time RT-PCR.</p> <p>Results</p> <p>Each of 10 tumor and four non-tumor samples analyzed had wild type sequences for these genes. At the genome wide level, hemangiosarcoma cells clustered separately from non-malignant endothelial cells based on a robust signature that included genes involved in inflammation, angiogenesis, adhesion, invasion, metabolism, cell cycle, signaling, and patterning. This signature did not simply reflect a cancer-associated angiogenic phenotype, as it also distinguished hemangiosarcoma from non-endothelial, moderately to highly angiogenic bone marrow-derived tumors (lymphoma, leukemia, osteosarcoma).</p> <p>Conclusions</p> <p>The data show that inflammation and angiogenesis are important processes in the pathogenesis of vascular tumors, but a definitive ontogeny of the cells that give rise to these tumors remains to be established. The data do not yet distinguish whether functional or ontogenetic plasticity creates this phenotype, although they suggest that cells which give rise to hemangiosarcoma modulate their microenvironment to promote tumor growth and survival. We propose that the frequent occurrence of canine hemangiosarcoma in defined dog breeds, as well as its similarity to homologous tumors in humans, offers unique models to solve the dilemma of stem cell plasticity and whether angiogenic endothelial cells and hematopoietic cells originate from a single cell or from distinct progenitor cells.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A TRUST-RELATIONSHIP MANAGEMENT FRAMEWORK FOR FEDERATED VIRTUAL ORGANIZATIONS

Research collaborations today are virtual organizations (VO’s), formed dynami-cally and crossing institutional and administrative boundaries. Electronic communication is essential for VO members who work at a distance and in different time zones. VO shared resources are owned by and attached to networks managed by enterprise adminis-trative groups who are typically unaware of the VO’s existence or requirements. Assem-bling a computing environment that provides the required tools and data in a manner that is both accessible and secure is a central challenge in distributed computing. This disser-tation addresses that challenge through a novel combination of existing enterprise infra-structure and emerging middleware components that results in a new scalable, VO-centric trust model. Middleware provides a layer of services between applications and underlying systems’ administrative domains, user identity methods, and use policies. Middleware-enabled applications should make it possible for enterprises to manage resources they own while collaborators share communications, resources and data unaware of the organ