Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Library Automation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources

The Oxford clinical intranet: providing clinicians with access to patient records and multiple knowledge bases with internet technology.

The Oxford Clinical Intranet provides clinicians in primary and secondary care across Oxfordshire with: Access to information about their patients held on multiple remote disparate computer systems, including admissions and episodes, Laboratory Medicine reports, Radiology reports and hospital discharge letters. The patient records are managed using CSW Case Notes. Access to support and advisory information, developed both within the organization and collected from other sites and projects, a wide range of internal handbooks, directories and guidelines and links to external resources, including evidence-based resources, the Cochrane Collaboration and the NHS National electronic Library of Health. Automated retrieval and presentation of the support information that is contextually appropriate to the task being carried out by the clinician and the information held about the patient. For example laboratory reports are linked to handbooks and other reference sources using eLABook, a web-interfaced database subsystem. Internet technology has been used throughout, thus providing a thin-client architecture with cross-platform ability. Appropriate data standards have been used across the communicating systems and the intranet is compliant with the UK eGovernment Interoperability Framework. The intranet was developed at low cost and is now in routine use. This approach appears to be transferable across systems and organisations.

England↗

Better library design: data-driven protein engineering.

Data-driven protein engineering is increasingly used as an alternative to rational design and combinatorial engineering because it uses available knowledge to limit library size, while still allowing for the identification of unpredictable substitutions that lead to large effects. Recent advances in computational modeling and bioinformatics, as well as an increasing databank of experiments on functional variants, have led to new strategies to choose particular amino acid residues to vary in order to increase the chances of obtaining a variant protein with the desired property. Strategies for limiting diversity at each position, design of small sub-libraries, and the performance of scouting experiments, have also been developed or even automated, further reducing the library size.

Computational Biology↗

Analysis of a sequenced cDNA library from multiple sclerosis lesions.

To identify genes that are expressed in MS pathogenesis, we have analyzed a normalized cDNA library made from mRNA obtained from CNS lesions of a patient with primary progressive MS. Complementary DNA clones obtained from this library were subjected to automated DNA sequencing to generate expressed sequence tags. Analysis of this MS cDNA library revealed the presence of 54 cDNAs that were associated with immune activation and indicated the presence of an ongoing inflammatory response with evidence of both cell-mediated and humoral immune responses. The surprising finding was that 16 of the cDNAs encoded autoantigens associated with seven other autoimmune disorders, while only three of these 16 autoantigen cDNAs were present in a similarly constructed adult brain library. Such aberrant autoantigen expression could provide a source of secondary autoimmune stimulation that could contribute to the ongoing inflammatory response in MS. In addition, two cDNAs were found that mapped to a known MS susceptibility locus (5p14-p12): one encoded an excitatory amino acid transporter and the other a human homologue of the Drosophila disabled gene. This approach to the molecular biology of MS pathogenesis may help to illuminate previously unappreciated aspects of this disease.

Cloning, Molecular↗

High-throughput screening of surface displayed gene products.

With the human genome project approaching completion, there is a growing interest in functional analysis of gene products. The characterization of large numbers of proteins, their expression patterns and in vivo localisations, demands the use of automated technology that maintains a logistic link to the encoding genes. As a complementary approach, phage display is used for recombinant protein expression and the selection of interacting (binding) molecules. Cloning of libraries in filamentous bacteriophage or phage mid vectors provides a physical link between the expressed protein and its encoding DNA sequence. High-throughput technology for automated library handling and phage display selection has been developed using picking-spotting robots and a module for pin-based magnetic particle handling. This system enables simultaneous interaction screening of libraries and the selection of binders to different target molecules at high throughput. Target molecules are either displayed on high-density filter membranes (protein filters) or tag-bound to magnetic particles and can be handled as native ligands. Binding activity is confirmed by magnetic particle ELISA in the microtitre format. The whole procedure from immobilisation of target molecules to confirmed clones of binders is automatable. Using this technology, we have selected human scFv antibody fragments against expression products of human cDNA libraries.

Bacteriophages↗

OCLC for the hospital library: the justification plan for hospital administration.

This paper delineates the necessary steps to provide hospital administrators with the information needed to evaluate an automated system, OCLC, for addition to the medical library. Based on experience at the Norton-Children's Hospitals, included are: (1) cost analyses of present technical processing systems and cost comparisons with OCLC; (2) delineation of start-up costs for installing OCLC; (3) budgetary requirements for 1981; (4) the impact of automation on library systems, personnel, and services; (5) potential as a shared service; and (6) preparation of the proposal for administrative review.

Budgets↗

High-throughput purification of single compounds and libraries.

The need for increasing productivity in medicinal chemistry and associated improvements in automated synthesis technologies for compound library production during the past few years have resulted in a major challenge for compound purification technology and its organization. To meet this challenge, we have recently set up three full-service chromatography units with the aid of in-house engineers, different HPLC suppliers, and several companies specializing in custom laboratory automation technologies. Our goal was to combine high-throughput purification with the high attention to detail which would be afforded by a dedicated purification service. The resulting final purification laboratory can purify up to 1000 compounds/week in amounts ranging from 5 to 300 mg, whereas the two service intermediate purification units take 100 samples per week from 0.3 to 100 g. The technologies consist of normal-phase and reversed-phase chromatography, robotic fraction pooling and reformatting, a bottling system, an automated external solvent supply and removal system, and a customized, high-capacity freeze-dryer. All work processes are linked by an electronic sample registration and tracking system.

Automation↗

Multidimensional chromatography coupled with mass spectrometry for target-based screening.

The synthesis of structural analogs and the process of drug discovery have evolved dramatically through recent advances in solid-phase synthesis reagents and automated screening systems. As molecular diversity strategies emerge, the need for automated target-based selection of lead candidates becomes equally important. Multidimensional automated chromatographic techniques coupled to electrospray ionization mass spectrometry facilitate the selection process and provide maximum characterization information in a single screening run. The capture of tightly bound affinity leads by target biomolecules, followed by subsequent release and high-resolution separation with sensitive detection, significantly reduces the time required to identify and characterize lead compounds. This automated multidimensional chromatographic approach coupled with mass spectrometry, Selectronics, was used with several organic and natural libraries to demonstrate an automated target-based screening technique to select for high-affinity binders as potential lead compounds.

Amino Acid Isomerases↗

A human heart cDNA library--the development of an efficient and simple method for automated DNA sequencing.

A direct polymerase chain reaction (PCR) amplification of the human heart cDNA clones was used to generate lambda PCR product. By the use of the first set of primers derived from lambda gt11, each cDNA insert can readily be obtained. Using millipore filters, primers and nucleotides are removed and this purified PCR product can then be subjected to a second set of fluorescent primers in the generation of nucleotides in the auto-cycle reactions for automated DNA sequencing.

Base Sequence↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗