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Biomedical subjects

R M Felciano

Publications and source records attributed to R M Felciano.

5 recordsLinked to original sources

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target.

Glioblastoma is the most common primary malignant brain tumor of adults and one of the most lethal of all cancers. Patients with this disease have a median survival of 15 months from the time of diagnosis despite surgery, radiation, and chemotherapy. New treatment approaches are needed. Recent works suggest that glioblastoma patients may benefit from molecularly targeted therapies. Here, we address the compelling need for identification of new molecular targets. Leveraging global gene expression data from two independent sets of clinical tumor samples (n = 55 and n = 65), we identify a gene coexpression module in glioblastoma that is also present in breast cancer and significantly overlaps with the "metasignature" for undifferentiated cancer. Studies in an isogenic model system demonstrate that this module is downstream of the mutant epidermal growth factor receptor, EGFRvIII, and that it can be inhibited by the epidermal growth factor receptor tyrosine kinase inhibitor Erlotinib. We identify ASPM (abnormal spindle-like microcephaly associated) as a key gene within this module and demonstrate its overexpression in glioblastoma relative to normal brain (or body tissues). Finally, we show that ASPM inhibition by siRNA-mediated knockdown inhibits tumor cell proliferation and neural stem cell proliferation, supporting ASPM as a potential molecular target in glioblastoma. Our weighted gene coexpression network analysis provides a blueprint for leveraging genomic data to identify key control networks and molecular targets for glioblastoma, and the principle eluted from our work can be applied to other cancers.

Animals↗

RNA secondary structure as a reusable interface to biological information resources.

The dissemination of biological information has become critically dependent on the Internet and World Wide Web (WWW), which enable distributed access to information in a platform independent manner. The mode of interaction between biologists and on-line information resources, however, has been mostly limited to simple interface technologies such has hypertext links, tables and forms. The introduction of platform-independent runtime environments facilitates the development of more sophisticated WWW-based user interfaces. Until recently, most such interfaces have been tightly coupled to the underlying computation engines, and not separated as reusable components. We believe that many subdisciplines of biology have intuitive and familiar graphical representations of knowledge that can serve as multipurpose user interface elements. We call such graphical idioms "domain graphics". In order to illustrate the power of such graphics, we have built a reusable interface based on the standard two dimensional (2D) layout of RNA secondary structure. The interface can be used to represent any pre-computed layout of RNA, and takes as a parameters the sets of actions to be performed as a user interacts with the interface. It can provide to any associated application program information about the base, helix, or subsequence selected by the user. We show the versatility of this interface by using it as a special purpose interface to BLAST, Medline and the RNA MFOLD search/compute engines. These demonstrations are available at: http://www-smi.stanford.edu/projects/helix/pubs/ gene-combis-96/

Base Sequence↗

Lamprey: tracking users on the World Wide Web.

Tracking individual web sessions provides valuable information about user behavior. This information can be used for general purpose evaluation of web-based user interfaces to biomedical information systems. To this end, we have developed Lamprey, a tool for doing quantitative and qualitative analysis of Web-based user interfaces. Lamprey can be used from any conforming browser, and does not require modification of server or client software. By rerouting WWW navigation through a centralized filter, Lamprey collects the sequence and timing of hyperlinks used by individual users to move through the web. Instead of providing marginal statistics, it retains the full information required to recreate a user session. We have built Lamprey as a standard Common Gateway Interface (CGI) that works with all standard WWW browsers and servers. In this paper, we describe Lamprey and provide a short demonstration of this approach for evaluating web usage patterns.

Computer Communication Networks↗

Optimizing physician access to surgical intensive care unit laboratory information through mobile computing.

Approximately 30 minutes of computer access time are required by surgical residents at Stanford University Medical Center (SUMC) to examine the lab values of all patients on a surgical intensive care unit (ICU) service, a task that must be performed several times a day. To reduce the time accessing this information and simultaneously increase the readability and currency of the data, we have created a mobile, pen-based user interface and software system that delivers lab results to surgeons in the ICU. The ScroungeMaster system, loaded on a portable tablet computer, retrieves lab results for a subset of patients from the central laboratory computer and stores them in a local database cache. The cache can be updated on command; this update takes approximately 2.7 minutes for all ICU patients being followed by the surgeon, and can be performed as a background task while the user continues to access selected lab results. The user interface presents lab results according to physiologic system. Which labs are displayed first is governed by a layout selection algorithm based on previous accesses to the patient's lab information, physician preferences, and the nature of the patient's medical condition. Initial evaluation of the system has shown that physicians prefer the ScroungeMaster interface to that of existing systems at SUMC and are satisfied with the system's performance. We discuss the evolution of ScroungeMaster and make observations on changes to physician work flow with the presence of mobile, pen-based computing in the ICU.

Algorithms↗

Multimedia clinical simulation based on patient records: authoring, user interface, pedagogy.

As an alternative to available computer-based clinical simulations that mimic patient encounters, we developed a clinical case simulation that more closely resembles the patient record. Our system, implemented in a Macintosh program called Short Rounds, features rapid and customized case authoring by editing a structured text file, a dynamic user interface that presents a case-specific screen layout, and a pedagogical model that is suitable for teaching third-year medical students. We believe this approach allows faculty members to create multimedia case simulations in shorter periods of time than in available clinical simulations.

Algorithms↗