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PubMedDate not supplied

Managing the film library: what to do until the panacea arrives.

Today's imaging departments are complex and often decentralized. Despite such growth, the film library is often overlooked and minimally planned for. The oversight may come from the anticipation of picture archiving and communications systems (PACS), considered by many to be the panacea for film management, but in reality, still only a concept, or at best, in its early stages. Since most departments do not anticipate going filmless for many years and others expect to continue hard copy imaging at a 20 to 30 percent rate, managing the film library remains an important issue. In general, film librarians' daily work remains labor intensive, despite attempts to automate some tasks. Yet when cutbacks are made, this support staff is often cut. One way to deal with service and expansion issues in the film library is to stop and evaluate the situation, assess the decline in the level of service, and determine what issues need improvement. Managers should gather information, analyze the data and listen to all interested parties to be sure they understand the overall problems, often best done by someone from outside the department. Analyzing and evaluating work processes, even observing the design of work areas, can be useful in understanding productivity inside the department. An invaluable way to gather data is to listen to those who carry out the daily tasks and those who use the services. Until their needs are understood by management, further changes will have minimal success. When a list of issues is assembled, managers should establish a team to review and prioritize them. Team members will need to understand departmental long-term plans before making recommendations. While every library's operations are unique, a key problem remains lost films. Policies and procedures for removing films must come from hospital senior administration, while managing film within the department is everyone's job. With the chaos under control, managers will be ready to face the challenge of electronic imaging.

Efficiency, Organizational↗
PubMed1996

Design, synthesis and use of binary encoded synthetic chemical libraries.

With the advent of combinatorial chemistry a new paradigm is evolving in the field of drug discovery. The approach is based on an integration of chemistry, high-throughput screening and automation engineering. The chemistry arm is usually based on solid-phase synthesis technology as the preferred approach to library construction. One of the most powerful of the solid-phase methods is encoded split synthesis, in which the reaction history experience by each polymeric bead is unambiguously recorded. This split-and-pool approach, employing chemically robust tags, was used to construct a 85,000-membered dihydrobenzopyran library.

Benzopyrans↗
PubMed2002

Automated ribotyping of vancomycin-resistant Enterococcus faecium isolates.

Vancomycin-resistant Enterococcus faecium (VREF) strains represent an important threat in hospital infections in the United States and are found at high frequencies in both the community and farm animals in Europe. We evaluated automated ribotyping for interlaboratory reproducibility by using the restriction enzymes EcoRI and BamHI and compared ribotyping to both amplification of fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) to assess its discriminatory power and capacity for the identification of epidemiologically important strains. Of 19 (EcoRI) and 16 (BamHI) isolates tested in duplicate in two laboratories, 18 (95%) and 16 (100%), respectively, showed reproducible ribotypes. These high reproducibility rates were obtained only after manual refinement of the automated fingerprint analysis. A group of 49 VREF strains initially selected to represent 32 distinct AFLP types were separated into 28 EcoRI ribotypes, 25 BamHI ribotypes, and 28 sequence types. Ribotyping with EcoRI and BamHI was able to discern the host-specific genogroups recently disclosed by AFLP typing and MLST and to distinguish most strains containing the esp gene, a marker specific for strains causing hospital outbreaks. An expandable ribotype identification library was created. We recommend EcoRI as the enzyme of choice for automated ribotyping of VREF strains. Given the high level of discrimination of VREF strains, the high rate of interlaboratory reproducibility, and the potential for the identification of epidemiologically important genotypes, automated ribotyping appears to be a very valuable approach for characterizing VREF strains.

Alleles↗
PubMed2002

Phage versus phagemid libraries for generation of human monoclonal antibodies.

Non-immune (naïve) phage antibody libraries have become an important source of antibodies for reagent, diagnostic, and therapeutic use. To date, reported naïve libraries have been constructed in phagemid vectors as fusions to pIII, yielding primarily single copy (monovalent) display of antibody fragments. For this work, we subcloned the single chain Fv (scFv) gene repertoire from a naïve phagemid antibody library into a true phage vector to create a multivalently displayed scFv phage library. Compared to monovalently displayed scFv, multivalent phage display resulted in improved efficiency of display as well as antibody selection. A greater number of antibodies were obtained and at earlier rounds of selection. Such increased efficiency allows the screening for binding antibodies after a single round of selection, greatly facilitating automation. Expression levels of antigen-binding scFv were also higher than from the phagemid library. In contrast, the affinities of scFv from the phage library were lower than from the phagemid library. This could be overcome by utilizing the scFv in a multivalent format, by affinity maturation, or by converting the library to monovalent display after the first round of selection.

Amino Acid Sequence↗
PubMedDate not supplied

Screening of synthetic peptide libraries with radiolabeled acceptor molecules.

A method has been developed for the identification of specific acceptor molecule-binding sequences from a chemically synthesized peptide library. The peptide resin beads, each bead carrying one peptide sequence, are incubated with radiolabeled acceptor molecule and subsequently immobilized in a thin layer of agarose. Resin beads that carry acceptor molecule-specific sequences are identified by autoradiography and subjected to automated gas-phase sequencing. The method was tested by screening a synthetic pentapeptide library with an anti-beta-endorphin monoclonal antibody.

Amino Acid Sequence↗
PubMed1971

New trends in medical libraries in hospitals.

External and internal forces affecting medical library services are examined. Public Law 89-239, the Heart, Cancer and Stroke Amendments of 1965, and Public Law 89-291, the Medical Library Assistance Act of 1965 which was extended by Public Law 91-212 have an impact on medical libraries. The Veterans Administration relationships with primary beneficiaries of these laws are explained. Internally, effort has been expended through automation, networking, and extension of resources by amalgamation of books and audiovisuals to evolve responsive concepts with emphasis on independence through interdependence. The Veterans Administration Library Service plans and accomplishments in these areas are reviewed.

Information Services↗
PubMed1996

A cell-free, nonisotopic, high-throughput assay for inhibitors of type-I interleukin-1 receptor.

A cell-free, nonisotopic assay has been developed to discover molecules that compete with the natural ligands for binding to the active site of the Type-I interleukin-1 receptor. The key reagents are the interleukin-1 receptor antagonist, a recombinant soluble form of the receptor (sIL-1R), and a specific anti-sIL-1R nonneutralizing monoclonal antibody (MAb79). With these molecules a sensitive assay has been developed using a reversed format: the ligand is immobilized and the receptor is in solution. The ligand-bound receptor is detected using MAb79 and an enzyme-linked secondary antibody. Since no cells or cell membranes are used, the assay is very robust, with no interference from membrane-perturbing agents and high resistance to the organic solvents normally used to resuspend compounds of chemical libraries. The microplate format and colorimetric detection have allowed the complete automation of the immobilized-ligand IL-1 receptor binding assay, which has been used for high-throughput screening of synthetic compounds and natural products.

Enzyme-Linked Immunosorbent Assay↗
PubMed1994

Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation.

We describe our production line for the rapid analysis of large cDNA libraries applying robotic techniques to automatically pick, amplify, array, hybridise and analyse the clones. We also outline the current state of the hybridisation techniques and describe anticipated future developments of the system. Our approach faces the large-scale analysis of cDNA clones with partial sequence analysis by oligonucleotide fingerprinting in the following way: after picking of individual colonies and arraying them automatically in quadruple density (384-well) microtitre plates, the cDNA clones are amplified by an automated waterbath polymerase chain reaction (PCR), which allows us to run about 46,000 reactions in parallel. The PCR products are automatically transferred to nylon membranes in a high density pattern using a robotic device. We routinely produce twelve 22 cm x 22 cm membranes in 90 min. Each membrane contains 20,736 clones, although much higher densities might be feasible using both miniaturized glass matrices and fluorescence based hybridisation techniques. Theoretical analysis and preliminary computer simulations indicate that about 100-200 sequence specific hybridisations of octanucleotides to about 100,000 PCR products of 1000-1500 base-pairs length will generate sufficient information for classifying the clones into groups of identical or related genes and to identify a large number of previously uncharacterized cDNA clones.

Biotechnology↗
PubMed2000

Detection of small-molecule enzyme inhibitors with peptides isolated from phage-displayed combinatorial peptide libraries.

BACKGROUND: The rapidly expanding list of pharmacologically important targets has highlighted the need for ways to discover new inhibitors that are independent of functional assays. We have utilized peptides to detect inhibitors of protein function. We hypothesized that most peptide ligands identified by phage display would bind to regions of biological interaction in target proteins and that these peptides could be used as sensitive probes for detecting low molecular weight inhibitors that bind to these sites. RESULTS: We selected a broad range of enzymes as targets for phage display and isolated a series of peptides that bound specifically to each target. Peptide ligands for each target contained similar amino acid sequences and competition analysis indicated that they bound one or two sites per target. Of 17 peptides tested, 13 were found to be specific inhibitors of enzyme function. Finally, we used two peptides specific for Haemophilus influenzae tyrosyl-tRNA synthetase to show that a simple binding assay can be used to detect small-molecule inhibitors with potencies in the micromolar to nanomolar range. CONCLUSIONS: Peptidic surrogate ligands identified using phage display are preferentially targeted to a limited number of sites that inhibit enzyme function. These peptides can be utilized in a binding assay as a rapid and sensitive method to detect small-molecule inhibitors of target protein function. The binding assay can be used with a variety of detection systems and is readily adaptable to automation, making this platform ideal for high-throughput screening of compound libraries for drug discovery.

Alcohol Dehydrogenase↗
PubMed1990

The effect of DOCLINE on interlibrary loan volume and patterns among health sciences libraries in Michigan: preliminary analysis.

Six years of statistics on interlibrary lending and borrowing among basic unit health sciences libraries in Michigan are examined to determine the effect of the availability of an automated interlibrary loan system, DOCLINE, on interlibrary lending volume and patterns within Michigan. A trend analysis projection of expected volume is made and the predicted value compared with the actual value following the adoption of the DOCLINE system. Interlibrary loan (ILL) volume is tested to see if yearly volume increases are statistically significant. The number of libraries changing from net lender to net borrower or the reverse after the adoption of DOCLINE is tracked. Results fail to support the expectation that DOCLINE would produce major change in ILL volume or pattern.

Data Interpretation, Statistical↗
PubMed2025

Using Prime Editing Guide Generator (PEGG) for high-throughput generation of prime editing sensor libraries.

Prime editing enables the generation of nearly any small genetic variant. However, the process of prime editing guide RNA (pegRNA) design is challenging and requires automated computational design tools. We developed Prime Editing Guide Generator (PEGG), a fast, flexible, and user-friendly Python package that enables the rapid generation of pegRNA and pegRNA-sensor libraries. Here, we describe the installation and use of PEGG (https://pegg.readthedocs.io) to rapidly generate custom pegRNA-sensor libraries for use in high-throughput prime editing screens.

Gene Editing↗
PubMed1997

Optimization of the synthesis of peptide combinatorial libraries using a one-pot method.

Conditions for the synthesis of synthetic peptide combinatorial libraries (SPCLs) from mixtures of amino acids were explored. In a one-pot synthesis, the effect of the starting concentrations of amino acids on the resulting library composition was studied, and the optimum balance of amino acids was determined. Protein sequencing, MALDI-TOF, and amino acid analysis were used for the evaluation of the libraries, and their relative merits-are discussed. The effects of continuous-flow automated synthesis instrumentation in conjunction with polyethylene glycol-polystyrene (PEG-PS) graft supports and various cleavage cocktails on the successful synthesis of SPCLs were examined.

Amino Acids↗
PubMed2001

HTPS flow cytometry: a novel platform for automated high throughput drug discovery and characterization.

The flow cytometer is unique among biomedical analysis instruments because it makes simultaneous and multiple optical measurements on individual cells or particles at high rates. High throughput flow cytometry represents a potentially important multifactorial approach for screening large combinatorial libraries of compounds. Limiting this approach has been the availability of instrumentation and methods in flow cytometry for automated sample handling on the scale required for drug discovery applications. Here, we describe an automated system in which a novel patented fluidics-based pharmacology platform, the HTPS (High Throughput Pharmacological System), is coupled to a flow cytometer using a recently described plug flow-coupling valve technology. Individual samples are aspirated sequentially from microplate wells and delivered to a flow cytometer for rapid multiparametric analysis. For primary screening to detect and quantify cell fluorescence in endpoint assays, a high-speed no-wash protocol enabled processing of 9-10 cell samples/min from 96-well microplates. In an alternate primary screening format, soluble receptor ligands were sampled from microplate wells at rates of 3-4 samples/minute and successfully assessed for the ability to elicit intracellular calcium responses. Experiments with fluorescent beads validated the accurate automated production by the HTPS of exponential and linear gradients of soluble compounds. This feature enabled rapid (2- to 3-min) characterization of the intracellular calcium dose response of myeloid cells to formyl peptide as well as the quantitative relationship between formyl peptide receptor occupancy and cell response. HTPS flow cytometry thus represents a powerful high throughput multifactorial approach to increase the efficiency with which novel bioresponse-modifying drugs may be identified and characterized.

Automation↗
PubMed2002

Tagging gene and protein names in biomedical text.

MOTIVATION: The MEDLINE database of biomedical abstracts contains scientific knowledge about thousands of interacting genes and proteins. Automated text processing can aid in the comprehension and synthesis of this valuable information. The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text. This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature. We propose to approach the detection of gene and protein names in scientific abstracts as part-of-speech tagging, the most basic form of linguistic corpus annotation. RESULTS: We present a method for tagging gene and protein names in biomedical text using a combination of statistical and knowledge-based strategies. This method incorporates automatically generated rules from a transformation-based part-of-speech tagger, and manually generated rules from morphological clues, low frequency trigrams, indicator terms, suffixes and part-of-speech information. Results of an experiment on a test corpus of 56K MEDLINE documents demonstrate that our method to extract gene and protein names can be applied to large sets of MEDLINE abstracts, without the need for special conditions or human experts to predetermine relevant subsets. AVAILABILITY: The programs are available on request from the authors.

Abbreviations as Topic↗
PubMed1996

Octamer-primed cycle sequencing: design of an optimized primer library.

This paper describes a novel method of primer walking using octamer oligonucleotides to prime DNA sequencing reactions. Octamer sequencing is compatible with isotopic and fluorescent sequencing chemistry, reaction conditions are optimized such that the samples can be processed in parallel, and the procedure has the potential to be automated. This strategy is faster than the traditional primer walking sequencing strategy, as the existence of a primer library allows immediate access to a primer for the next sequencing reaction, eliminating delays associated with designing and synthesizing gene-specific primers. The octamer library is comprised of optimized sequencing primers, such that octamer sequencing yields results equivalent to or better than traditional primer walking. This technology is more economical because gene-specific sequencing primers, the major cost in the reaction, are replaced by an optimized subset of frequently occurring octamers that are able to prime multiple reactions.

Anabaena↗