Revealing the amino acid composition of proteins within an expanded genetic code.

The genetic code can be manipulated to reassign codons for the incorporation of non-standard amino acids (NSAA). Deletion of release factor 1 in Escherichia coli enhances translation of UAG (Stop) codons, yet may also extended protein synthesis at natural UAG terminated messenger RNAs. The fidelity of protein synthesis at reassigned UAG codons and the purity of the NSAA containing proteins produced require careful examination.

YPED: a web-accessible database system for protein expression analysis.

We have developed an integrated web-accessible software system called the Yale Protein Expression Database (YPED) to address the need for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED is an open source system which integrates gel analysis results with protein identifications from DIGE experiments. The system associates the DIGE gel spots and image, analyzed with DeCyder, with mass spectrometric protein identifications from selected gel spots.

Probabilistic enrichment of phosphopeptides by their mass defect.

The mass defect, that is, the difference between the nominal and actual monoisotopic masses, of a phosphorus in a phosphate group is greater than for most other atoms present in proteins. When the mass defects of tryptic peptides derived from the human proteome are plotted against their masses, phosphopeptides tend to fall off the regression line. By calculating the masses of all potential tryptic peptides from the human proteome, we show that regions of higher phosphorylation probability exist on such a plot.

YPED: a proteomics database for protein expression analysis.

We have developed the Yale Protein Expression Database (YPED) to address the storage, retrieval, and integrated analysis of proteomics data generated by Yale's Keck Protein Chemistry and Mass Spectrometry Facility. YPED is Web-accessible and currently handles sample requisition, result reporting and sample comparison for ICAT, DIGE and MUDPIT samples. Sample descriptions are compatible with the evolving MIAPE standards.

Approaches and informatics tools to assist in the integration of similar clinical research questionnaires.

Objective: The integration of similar clinical research questionnaires is a complex process that can benefit from informatics approaches and tools that provide a systematic structure for performing mapping and integration. This systematic approach is necessary to address complex issues in integration such as data heterogeneity, differing levels of granularity of questions and responses, and other issues involving semantic differences. Informatics tools and approaches have been successfully applied to various standard clinical vocabulary integration processes but not for questionnaire integration or mapping.

Exploring the portability of informatics capabilities from a clinical application to a bioscience application.

This report describes XDesc (eXperiment Description), a pilot project that serves as a case study exploring the degree to which an informatics capability developed in a clinical application can be ported for use in the biosciences. In particular, XDesc uses the Entity-Attribute-Value database implementation (including a great deal of metadata-based functionality) developed in TrialDB, a clinical research database, for use in describing the samples used in microarray experiments stored in the Yale Microarray Database (YMD). XDesc was linked successfully to both TrialDB and YMD, and was used to describe the data in three different microarray research projects involving Drosophila.

The integration of similar clinical research data collection instruments.

We devised an algorithm for integrating similar clinical research data collection instruments to create a common measurement instrument. We tested this algorithm using questions from several similar surveys. We encountered differing levels of granularity among questions and responses across surveys resulting in either the loss of granularity or data.

Exploring issues of quality of service in a Next Generation Internet testbed: a case study using PathMaster.

This case study describes a project that explores issues of quality of service (QoS) relevant to the next-generation Internet (NGI), using the PathMaster application in a testbed environment. PathMaster is a prototype computer system that analyzes digitized cell images from cytology specimens and compares those images against an image database, returning a ranked set of "similar" cell images from the database. To perform NGI testbed evaluations, we used a cluster of nine parallel computation workstations configured as three subclusters using Cisco routers.

Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty.

Building a map of restriction sites from double-digest gel data can be a complex and frustrating task, especially when many DNA fragments are detected or when the gel results are ambiguous. 'Double Digester' is an interactive, graphical computer program which helps researchers understand and resolve such data. It explicitly represents the experimental data, the associated uncertainties, the researcher's hypotheses and possible map interpretations.

Building a cooperative institutional model of IAIMS at the Yale-New Haven Medical Center.

The poster describes the cooperative institutional structure which underlies the IAIMS activities at Yale - New Haven Medical Center. Whereas some institutions implement IAIMS via some form of centralized structuring of major computing units, for many institutions this approach may not be viable and a more cooperative model will be required. The poster describes the process through which our IAIMS project evolved, and outlines certain principles underlying such an approach.

PFGE MAPPER: a tool to aid in the analysis of pulse field gel electrophoresis maps.

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA and constructing long-range restriction maps. We have developed a tool, PFGE MAPPER, to aid in the construction of pulse field electrophoresis gel maps. This tool helps construct pulse field gel maps from single and double digest experiments visualized by hybridization with single copy probes.

NetMenu: experience in the implementation of an institutional menu of information sources.

NetMenu is a program, developed at Yale, which enables straightforward access to online information systems. NetMenu has been deployed in several diverse settings within our medical center. In the hospital, NetMenu is functioning as a front-end for our clinical workstation providing access to the hospital information system, the clinical laboratory computer, a drug database and several bibliographic databases.

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper reviews these approaches and develops a straightforward but effective algorithm using the machine-independent parallel programming language, Linda.

CHROMINFO: a database for viewing and editing top-level chromosome data.

CHROMINFO is a prototype database that is intended to serve as a liaison tool for researchers working in different centers on mapping of the same mammalian chromosome. It provides a bird's-eye-view of top-level entities on a chromosome (such as gene loci, chromosome breakpoints and contigs) and relates them to one another in one dimension, the axis of the chromosome. Consensus data can be entered, edited, queried and displayed in a variety of ways.

PFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps.

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA. We have developed two tools to aid in the construction of pulse field electrophoresis gel maps: PFGE READER which stores experimental conditions and calculates fragment sizes and PFGE MAPPER which constructs pulse field gel electrophoresis maps.

Analysis of phospholipids in human amniotic fluid by 31P NMR.

A recently described solvent-reagent system for obtaining narrow linewidths in 31P NMR spectra of phospholipid extracts was applied to human amniotic fluid. Resolution of the major components was achieved by manipulating the solvent composition, and assignments were made by spiking samples with standard compounds. Spin-lattice relaxation times were determined and used to optimize data acquisition.

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda.

Modeling uncertainty in a database for physical gene mapping data.

We are building a database for the storage, retrieval, and graphical display of physical gene mapping data. To allow this information to be analyzed robustly, such a database must confront the inherent uncertainty of the data as a central design issue. The paper describes the overall database design, the types of gene mapping data which the system will contain, the types of uncertainty in the data, and certain of the design issues involved in allowing the database to handle uncertainty in a comprehensive fashion.

TREACT. An expert system consultation program to aid in the diagnosis of transfusion reactions.

We have developed a rule-based, expert system consultation program, TREACT, to aid in the diagnosis of transfusion reactions. Given clinical signs, symptoms, and laboratory results, the program generates diagnoses, alerts the user when a medical director should be called, suggests follow-up actions, and makes recommendations for future transfusion. Diagnoses made by TREACT, including 121 reactions, were compared with those of the medical directors over a 6-month period.

Evaluation of a centrifugal blood cell processor for washing platelet concentrates.

A semiautomated saline wash procedure using a blood cell processor was evaluated as a technique for removing plasma from platelet concentrates. In vitro studies demonstrated 92 to 99.6 percent (mean, 96%) removal of total plasma protein (n = 30) with 84 to 97 percent (mean, 90.

A flagging system for multichannel hematology analyzers.

A flagging system to identify blood specimens requiring a blood film review and/or differential leukocyte count is described. Its utility in avoiding unnecessary differential counts particularly in outpatients is given. Significant reductions in workload can be anticipated without deterioration of patient care.

A critical evaluation of the manual/visual differential leukocyte counting method.

The performance of differential leukocyte counting by 73 technologists and technicians working in 5 different laboratories in a large medical center was evaluated. Good correlation with the reference method was found for neutrophils, normal lymphocytes, and eosinophils. More variability was noted in the estimation of stab neutrophils and variant (atypical) lymphocytes and monocytes.