The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.

Objective findings with malpositioning of a nucleus 24RE(CA) cochlear implant.

BACKGROUND: Proper intracochlear placement of cochlear implant electrode arrays is believed to be important for optimum speech perception results. However, objective tests of cochlear implant function typically provide little or no information about the intracochlear placement of the array. We report the results for a variety of objective tests, including averaged electrode voltage (AEV) measurements, in a patient where the electrode array had folded up on itself during insertion. PURPOSE: To determine whether any of the objective measures provided evidence of incorrect electrode placement. RESEARCH DESIGN: Objective test data are reported for a patient with an incorrectly positioned electrode array, prior to and following reimplantation, and compared to data obtained in 42 patients with normal insertions. STUDY SAMPLE: One patient with an incorrectly placed electrode array, prior to and following reimplantation, and a sample of 42 implant recipients with correct insertions. INTERVENTION: The patient with the malpositioned electrode array was explanted and reimplanted. The results for the first and the second implant, with regards to objective test results, are compared. The results are also compared to the data obtained on 42 implant recipients with normal insertions. DATA COLLECTION AND ANALYSIS: The objective test data (primarily AEV data) are compared with AEV results obtained in 42 patients with normal electrode insertions. RESULTS AND CONCLUSIONS: Although the electrode array had folded up on itself during insertion, intraoperative electrode impedances and VIII nerve responses, as well as postoperative electrically evoked auditory brainstem responses, were within normal limits. However, averaged electrode voltages, obtained with the Nucleus Crystal Integrity Test system, were abnormal and consistent with a low-impedance pathway between the apical and middle portions of the electrode array.

The Impact of the Roast Levels of Coffee Extracts on their Potential Anticancer Activities.

Coffee is one of the most widely consumed beverages in the world and contains numerous phytochemicals that are beneficial to consumer health. The phytochemical profile of coffee, however, can be affected by the roast level. In this study, we compared the effect of roasting level on the growth inhibitory activity of HT-29 (colon) and SCC-25 (oral) cancer cell lines. The different roasting stages selected for this study were green, cinnamon/blonde, city/medium, full city/medium-dark, and full city plus/dark. Cancer cells were treated with various concentrations of coffee extracts for 72 hr. Cell viability was quantified using the thiazolyl blue tetrazolium bromide assay. It was found that the lighter roast extracts, Cinnamon in particular, reduced cell growth more than darker roast extracts. The Cinnamon extract had the greatest amount of total phenolic content and antioxidant activity. Relative levels of gallic, caffeic, and chlorogenic acid in the extracts were also compared. The Cinnamon coffee extract had the highest levels of gallic and caffeic acids, which have both been widely-regarded as bioactive phytochemicals. In conclusion, the consumption of lighter roasted coffee, may contribute to the prevention of certain types of cancer such as oral and colon. PRACTICAL APPLICATION: Chemical compounds in coffee may reduce the risk for certain types of cancers. These compounds may be particularly abundant in lighter roasted coffee. Therefore, lighter roasted coffee could contribute to the prevention of cancer through a healthy diet.

Perspectives on leadership in organizations providing services to people with disabilities: an exploratory study.

As leaders from the Baby Boomer generation prepare for retirement over the next decade, emerging leaders must be identified and supported in anticipation of a major organizational transition. Authentic leadership is a construct that informs the development of values-driven leaders who will bring organizations into the future, just as the previous generation of leaders oversaw the movement of services away from state institutions and into networks of community-based service delivery organizations. The purpose of this exploratory study was to examine executive and emerging leaders' opinions about the unique leadership values, skills, and challenges in organizations that serve individuals with intellectual and developmental disabilities. Themes of defining, developing, and sustaining leaders emerged from the data and are explored through an authentic leadership framework.

A formal ontology of subcellular neuroanatomy.

The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.