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PubMed1994

Bibliographic instruction in the hospital library.

The nature of bibliographic instruction in this hospital library continues to evolve. As the library makes easy-to-master, menu-driven tools for online searching available to end users, the demand for this service and the accompanying training increases. The demand for formal sessions covering research techniques is also increasing. Upon request, the library offered an extended research orientation to the housestaff in Obstetrics and Gynecology in May of 1993. An introduction to the use of CD-ROM was included to highlight its usefulness for citation verification, author searches, and for periodic current awareness searches on a particular topic. The UMH Library staff strive to offer the most current and comprehensive facilities and services to their users. These include automated access to the library's book, journal, and audiovisual holdings using the Data Trek system; online bibliographic searching by library staff and end users using CD Plus MEDLINE on CD-ROM and Grateful MED software; participation in clinical rounds to provide research support for clinical care; and several types of bibliographic instruction. In addition to the informal teaching of library research techniques that the library staff offers on a daily basis, the Library at Union Memorial Hospital is pleased to be able to provide a formalized and evolving bibliographic instruction program.

Computer User Training↗
PubMed2002

Unravelling the composition of very complex samples by comprehensive gas chromatography coupled to time-of-flight mass spectrometry. Cigarette smoke.

The potential and current limitations of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-TOF-MS) for the analysis of very complex samples were studied with the separation of cigarette smoke as an example. Because of the large number of peaks in such a GC x GC chromatogram it was not possible to perform manual data processing. Instead, the GC-TOF-MS software was used to perform peak finding, deconvolution and library search in an automated fashion; this resulted in a peak table containing some 30000 peaks. Mass spectral match factors were used to evaluate the library search results. The additional use of retention indices and information from second-dimension retention times can substantially improve the identification. The combined separation power of the GC x GC-TOF-MS system and the deconvolution algorithm provide a system with a most impressive separation power.

Automation↗
PubMed1991

Integrating CD-ROM Medline with electronic mail: first step in implementing new strategy for online reference library.

Simultaneous ACCESS to and DISSEMINATION of electronically available PROFESSIONAL KNOWLEDGE, in a productive, Cost-of-Ownership effective, and affordable manner are now achievable. Emerging MANAGEMENT-OF-INFORMATION and SYSTEMS-INTEGRATION disciplines are essential contributing factors to devising and implementing NEW STRATEGIES for ONLINE REFERENCE LIBRARIES. Bringing integrated information closer to the ultimate user and RESHAPING the electronic databases and full-text management systems MARKETPLACE are the most significant outcomes. Key technology attributes are advancements in CD-ROM, Networking, and office automation. We have proven this concept by developing an INTERFACE between MEDLINE from COMPACT CAMBRIDGE and ALL-IN-1 from DIGITAL EQUIPMENT CORPORATION. Saved search results are automatically routed to the individual's ALL-IN-1 account where further DOCUMENT MANAGEMENT and electronic mail functions may be performed. A 486Ware system from Logicraft and a five-members VAX-Cluster (respectively), are linked in a DECNet environment that is the foundation of Children's Integrated Hospital Information System. In phase one of the project up to 8 SIMULTANEOUS USERS may access the 8 RECENT YEARS, from any one of 1500 ACCESS POINTS (local and remote), and utilize any one of 150 NETWORKED PRINTERS. Opportunities are now within reach to expand the electronic library services while utilizing progressive methods and taking advantage of the best available technologies.

Boston↗
PubMed2002

Approaches to library screening.

Fuelled by the drive to complete the Human Genome Project, many laboratories have developed new methods of screening clone libraries. From PCR-based strategies to pooling schemes and increased automation, the tedious task of library screening has become less labour-intensive and more cost-efficient. Currently, two main screening methods dominate: hybridization and polymerase chain reaction (PCR). In the following article, we present a brief overview of hybridization and PCR-based screening of yeast and bacterial libraries. Multi-faceted approaches combining different techniques, as well as less frequently employed methods such as fingerprinting are also described.

Chromosomes, Artificial, Bacterial↗
PubMed2000

Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.

In the course of site-directed mutagenesis or directed evolution experiments, large numbers of protein variants are often generated. To characterize functional properties of individual mutant proteins in vitro, a rapid and reliable protein purification system is required. We have developed an automated method for the parallel purification of 96 different protein variants that takes about two hours. Using a 96-well format, the whole process can be performed automatically by a pipetting robot. Coupled with a suitable assay, again using a 96-well format, all variants can be functionally characterized within a few hours. The protein purification procedure described here is based on the interaction between His6-tagged proteins and Ni-NTA-coated microplates. Typical yields are 3-8 pmol purified protein/well, which is sufficient to analyze most enzymatic activities. Using this procedure, we have purified and characterized variants of the restriction endonuclease EcoRV, which were produced in an effort to enhance the selectivity of this enzyme. For this purpose, three amino acid residues were randomized in a region known from the co-crystal structure to be located at the protein-DNA interface. From a library of about 1200 variants, predominantly single and double mutants, more than 1000 variants were purified and characterized in parallel, which corresponds to an almost complete screening of the library.

Automation↗
PubMed1997

A genome-based resource for molecular cardiovascular medicine: toward a compendium of cardiovascular genes.

BACKGROUND: Large-scale partial sequencing of cDNA libraries to generate expressed sequence tags (ESTs) is an effective means of discovering novel genes and characterizing transcription patterns in different tissues. To catalogue the identities and expression levels of genes in the cardiovascular system, we initiated large-scale sequencing and analysis of human cardiac cDNA libraries. METHODS AND RESULTS: Using automated DNA sequencing, we generated 43,285 ESTs from human heart cDNA libraries. An additional 41,619 ESTs were retrieved from public databases, for a total of 84,904 ESTs representing more than 26 million nucleotides of raw cDNA sequence data from 13 independent cardiovascular system-based cDNA libraries. Of these, 55% matched to known genes in the Genbank/EMBL/DDBJ databases, 33% matched only to other ESTs, and 12% did not match to any known sequences (designated cardiovascular system-based ESTs, or CVbESTs). ESTs that matched to known genes were classified according to function, allowing for detection of differences in general transcription patterns between various tissues and developmental stages of the cardiovascular system. In silico Northern analysis of known gene matches identified widely expressed cardiovascular genes as well as genes putatively exhibiting greater tissue specificity or developmental stage specificity. More detailed analysis identified 48 genes potentially overexpressed in cardiac hypertrophy, at least 10 of which were previously documented as differentially expressed. Computer-based chromosomal localizations of 1048 cardiac ESTs were performed to further assist in the search for disease-related genes. CONCLUSIONS: These data represent the most extensive compilation of cardiovascular gene expression information to date. They further demonstrate the untapped potential of genome research for investigating questions related to cardiovascular biology and represent a first-generation genome-based resource for molecular cardiovascular medicine.

Blotting, Northern↗
PubMedDate not supplied

Preliminary investigation of submerged aquatic vegetation mapping using hyperspectral remote sensing.

The use of airborne hyperspectral remote sensing imagery for automated mapping of submerged aquatic vegetation (SAV) in the tidal Potomac River was investigated for near to real-time resource assessment and monitoring. Airborne hyperspectral imagery and field spectrometer measurements were obtained in October of 2000. A spectral library database containing selected ground-based and airborne sensor spectra was developed for use in image processing. The spectral library is used to automate the processing of hyperspectral imagery for potential real-time material identification and mapping. Field based spectra were compared to the airborne imagery using the database to identify and map two species of SAV (Myriophyllum spicatum and Vallisneria americana). Overall accuracy of the vegetation maps derived from hyperspectral imagery was determined by comparison to a product that combined aerial photography and field based sampling at the end of the SAV growing season. The algorithms and databases developed in this study will be useful with the current and forthcoming space-based hyperspectral remote sensing systems.

Algorithms↗
PubMed2005

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics.

MOTIVATION: The key to MS -based proteomics is peptide sequencing. The major challenge in peptide sequencing, whether library search or de novo, is to better infer statistical significance and better attain noise reduction. Since the noise in a spectrum depends on experimental conditions, the instrument used and many other factors, it cannot be predicted even if the peptide sequence is known. The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues. RESULTS: We designed RAId to identify peptides from their associated tandem mass spectrometry data. RAId performs a novel de novo sequencing followed by a search in a peptide library that we created. Through de novo sequencing, we establish the spectrum-specific background score statistics for the library search. When the database search fails to return significant hits, the top-ranking de novo sequences become potential candidates for new peptides that are not yet in the database. The use of spectrum-specific background statistics seems to enable RAId to perform well even when the spectral quality is marginal. Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications.

Algorithms↗
PubMed2004

Intensity-based protein identification by machine learning from a library of tandem mass spectra.

Tandem mass spectrometry (MS/MS) has emerged as a cornerstone of proteomics owing in part to robust spectral interpretation algorithms. Widely used algorithms do not fully exploit the intensity patterns present in mass spectra. Here, we demonstrate that intensity pattern modeling improves peptide and protein identification from MS/MS spectra. We modeled fragment ion intensities using a machine-learning approach that estimates the likelihood of observed intensities given peptide and fragment attributes. From 1,000,000 spectra, we chose 27,000 with high-quality, nonredundant matches as training data. Using the same 27,000 spectra, intensity was similarly modeled with mismatched peptides. We used these two probabilistic models to compute the relative likelihood of an observed spectrum given that a candidate peptide is matched or mismatched. We used a 'decoy' proteome approach to estimate incorrect match frequency, and demonstrated that an intensity-based method reduces peptide identification error by 50-96% without any loss in sensitivity.

Algorithms↗
PubMed1968

Problems of medical subject cataloging.

The subject catalog of the University of Colorado Medical Center Library is examined in considerable detail. Annual revisions of the subject catalog required by annual revisions of the subject heading authority list used, NLM's MeSH, are analyzed in terms of man-hours required for the effort and the effect on the catalog's structure. It is contended that, in a divided catalog, changes of headings on a one-for-one equivalency basis are no more difficult than they would be in a computerized catalog, but that in many-for-one changes the manual catalog and the machine catalog face exactly the same dilemma and in the same magnitude, the only solution in either case being the reexamination of many entries. The proliferation of subheadings is shown to present particularly vexing problems in catalog revision. A plea is made to recognize the MeSH system for what it is, a legitimate compromise between the descriptor-oriented terms of a computer coordinate-indexing system, and the subject-heading-oriented terms of the conventional card catalog.

Automation↗
PubMed1994

Growth patterns in the National Library of Medicine's serials collection and in Index Medicus journals, 1966-1985.

Data from the National Library of Medicine (NLM) automated Master Serials System and its MEDLINE database were used to chart the growth of NLM's serials collection and of the journals indexed in Index Medicus from 1966 to 1985. The number of live serial titles in the subset of NLM's collection examined increased 30% in the twenty years. The average number of articles per Index Medicus journal increased 56%. The average number of articles in U.S. Index Medicus journals grew more rapidly than the average number in journals published elsewhere. The NLM data provide clear evidence that the years from 1966 to 1985 saw a substantial increase in the percentage of the biomedical serial literature published in English. The period from 1966 to 1985 saw substantial but uneven growth in the number of serial titles in the NLM collection and in the average number of articles in Index Medicus journals. Although data on the number of articles published in Index Medicus journals is unlikely to reflect the number of articles in other journals, the pattern of growth in the number of serials held by NLM probably reflects trends in the universe of all biomedical serials.

Abstracting and Indexing↗
PubMedDate not supplied

A new strategy for the preparation of peptide-targeted technetium and rhenium radiopharmaceuticals. The automated solid-phase synthesis, characterization, labeling, and screening of a peptide-ligand library targeted at the formyl peptide receptor.

A new solid-phase synthetic methodology was developed that enables libraries of peptide-based Tc(I)/Re(I) radiopharmaceuticals to be prepared using a conventional automated peptide synthesizer. Through the use of a tridentate ligand derived from N-alpha-Fmoc-l-lysine, which we refer to as a single amino acid chelate (SAAC), a series of 12 novel bioconjugates [R-NH(CO)ZLF(SAAC)G, R = ethyl, isopropyl, n-propyl, tert-butyl, n-butyl, benzyl; Z = Met, Nle] that are designed to target the formyl peptide receptor (FPR) were prepared. Construction of the library was carried out in a multiwell format on an Advanced ChemTech 348 peptide synthesizer where multi-milligram quantities of each peptide were isolated in high purity without HPLC purification. After characterization, the library components were screened for their affinity for the FPR receptor using flow cytometry where the K(d) values were found to be in the low micromolar range (0.5-3.0 microM). Compound 5j was subsequently labeled with (99m)Tc(I) and the product isolated in high radiochemical yield using a simple Sep-Pak purification procedure. The retention time of the labeled compound matched that of the fully characterized Re-analogue which was prepared through the use of the same solid-phase synthesis methodology that was used to construct the library. The work reported here is a rare example of a method by which libraries of peptide-ligand conjugates and their rhenium complexes can be prepared.

Automation↗
PubMed2003

Micropreparative capillary gel electrophoresis of DNA: rapid expressed sequence tag library construction.

A capillary gel electrophoresis based automated DNA fraction collection technique was developed to support a novel DNA fragment-pooling strategy for expressed sequence tag (EST) library construction. The cDNA population is first cleaved by BsaJ I and EcoR I restriction enzymes, and then subpooled by selective ligation with specific adapters followed by polymerase chain reaction (PCR) amplification and labeling. Combination of this cDNA fingerprinting method with high-resolution capillary gel electrophoresis separation and precise fractionation of individual cDNA transcript representatives avoids redundant fragment selection and concomitant repetitive sequencing of abundant transcripts. Using a computer-controlled capillary electrophoresis device the transcript representatives were separated by their size and fractions were automatically collected in every 30 s into 96-well plates. The high resolving power of the sieving matrix ensured sequencing grade separation of the DNA fragments (i.e., single-base resolution) and successful fraction collection. Performance and precision of the fraction collection procedure was validated by PCR amplification of the collected DNA fragments followed by capillary electrophoresis analysis for size and purity verification. The collected and PCR-amplified transcript representatives, ranging up to several hundred base pairs, were then sequenced to create an EST library.

Animals↗
PubMed1989

Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor.

Two cDNA clones (3.7 kb and 4.8 kb) encoding a Drosophila muscarinic acetylcholine receptor were isolated from a Drosophila head cDNA library and characterized by automated DNA sequence analysis. The Drosophila muscarinic receptor contains 788 amino acids with a calculated Mr of 84,807 and displays greater than 60% homology with mammalian muscarinic receptors. The muscarinic receptor maps to the tip of the right arm of the second chromosome of the Drosophila genome.

Amino Acid Sequence↗
PubMed2001

The application of non-combinatorial chemistry to lead discovery.

Non-combinatorial chemistry is a powerful technology for the synthesis of large numbers of compounds, with complete control over the properties of those compounds. We have developed a Library Creation, Registration and Automation system (LiCRA), which harnesses an efficient non-combinatorial chemistry design and synthesis engine, together with high-throughput automated purification. This LiCRA system also operates in a closed loop mode for hit-to-lead optimization, and contains an integrated IT system that controls and facilitates all aspects of the operation from design to registration. Quality has been our watchword, from the quality of compound design through to the quality of the products.

Journal Article↗
PubMed2001

Genome and genetic resources from the Cancer Genome Anatomy Project.

The Cancer Genome Anatomy Project (CGAP) is a collaborative network of cancer researchers with a common goal: to decipher the genetic changes that occur during cancer formation and progression. The project brings together several recent technologies capable of high-throughput analysis to help achieve this goal. Automated sequencing of cDNA libraries is a primary focus and is geared towards providing a comprehensive and annotated set of human and mouse transcribed sequences. This effort includes full-length transcript sequence generated by CGAP's new Mammalian Gene Collection initiative. Single nucleotide polymorphisms (SNPs) within human gene sequences (Genetic Annotation Initiative) and chromosomal rearrangements within cancer cells (Cancer Chromosome Aberration Project) are also being cataloged as part of CGAP. Finally, to help determine gene expression patterns related to cancer, CGAP provides a quantitative catalog of data through its SAGEmap initiative. The genome and genetic analysis tools listed in this review are all freely distributed by CGAP (http://cgap.nci.nih.gov/) without restriction.

Animals↗