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PubMed1993

Automatic knowledge acquisition from MEDLINE.

Construction of medical knowledge bases for use in expert systems is an arduous task. We propose a procedure for obtaining medical knowledge via automated analysis of citations found in the National Library of Medicine's MEDLINE database. In this method, simple pattern of keywords and subheading co-occurrences are detected in the keyword descriptor portion of the citations. Each pattern corresponds to a fact, expressed as a semantic relationship between medical concepts. We have constructed a set of 504 pattern-matching rules and applied it to a set of 673 MEDLINE citations to produce 2,795 such facts. The results are presented of an analysis of the syntactic and semantic features of these facts to understand the kinds of knowledge than can be obtained through our method and speculate on the potential uses and pitfalls for knowledge of this type.

Artificial Intelligence↗
PubMed1972

Mechanization of library procedures in the medium-sized medical library. 8. Computer applications in hospital departmental libraries.

To test the hypothesis that a standard library system could be designed for hospital departmental libraries, a system was developed and partially tested for four departmental libraries in the Washington University School of Medicine and Associated Hospitals. The system from determination of needs through design and evaluation, is described. The system was limited by specific constraints to control of the monograph collection. Products of control include catalog cards, accessions list, new book list, location list, fund list, missing book list, and discard book list. Sample data form and pages from a procedure manual are given, and conversion from a manual to an automated system is outlined. The question of standardization of library records and procedures is discussed, with indications of the way in which modular design, as utilized in this system, could contribute to greater flexibility in design of future systems. Reference is made to anticipating needs for organizing departmental libraries in developing regional medical library programs and to exploring the role of the departmental library in a medical library network.

Computers↗
PubMedDate not supplied

Tapping allergen repertoires by advanced cloning technologies.

BACKGROUND: Complex allergenic sources such as moulds, foods and mites contain complex panels of IgE-binding molecules which need to be cloned, produced and characterized in order to mimic the entire allergenicity of whole extracts reconstituted by mixing single standardized recombinant allergens. METHODS: Phage surface display of cDNA libraries selectively enriched for allergen-expressing clones using IgE from allergic patients allows rapid isolation of large panels of allergens. For the characterization of all different clones present in enriched cDNA libraries in a fast and cost-effective way, high-throughput screening technology is required. RESULTS: The combination of selective enrichment of cDNA libraries based on biopanning against serum IgE from sensitized patients and automated robot technology for picking and high-density gridding of clones onto filter membranes, followed by hybridization, enables fast identification of all the different clones present in an enriched library. The consequent application of selective enrichment and robotic-based screening allows, within weeks, cloning and characterization of the whole allergenic repertoire of any organisms. CONCLUSIONS: Robotic-based high-throughput screening of clones selected for IgE-binding capacity from phage surface-displayed cDNA libraries of Aspergillus fumigatus, Cladosporium herbarum, Coprinus comatus, Malassezia furfur, peanut and human lung tissue allowed rapid characterization of 81, 28, 37, 27, 8 and 151 different sequences, respectively. All these cDNAs bear a high probability to encode allergens derived from the respective allergenic source.

Allergens↗
PubMed1986

The National Library of Medicine and medical informatics.

Medical informatics attempts to provide the theoretic and scientific basis for the use of automated information systems in biomedicine. Even though a new field, its roots are in the 19th century. The National Library of Medicine (NLM) began classifying the medical literature and publishing the Index Medicus in 1897; in the early 1960s, the growth of the index gave rise to MEDLARS, the first successful, large-scale, computerized bibliographic system. In 1971, about the time MEDLARS evolved into a nationwide on-line retrieval system known as MEDLINE, a committee of the Association of American Medical Colleges published a report calling for the NLM to exert strong leadership in developing computer applications for information transfer in medicine. The NLM has sponsored several training and research programs in this area and is now developing the concept of "centers of excellence" in medical informatics. In addition, there are a number of current research and development activities within the NLM internal and extramural programs that may influence the progress of medical informatics.

History, 19th Century↗
PubMed1988

Study of living single cells in culture: automated recognition of cell behavior.

An automated system capable of analyzing the behavior, in real time, of single living cells in culture, in a noninvasive and nondestructive way, has been developed. A large number of cell positions in single culture dishes were recorded using a computer controlled, robotized microscope. During subsequent observations, binary images obtained from video image analysis of the microscope visual field allowed the identification of the recorded cells. These cells could be revisited automatically every few minutes. Long-term studies of the behavior of cells make possible the analysis of cellular locomotary and mitotic activities as well as determination of cell shape (chosen from a defined library) for several hours or days in a fully automated way with observations spaced up to 30 minutes. Short-term studies of the behavior of cells permit the study, in a semiautomatic way, of acute effects of drugs (5 to 15 minutes) on changes of surface area and length of cells.

Animals↗
PubMed2003

Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles.

The non-supervised construction of a mass spectral and retention time index data base (MS/RI library) from a set of plant metabolic profiles covering major organs of potato (Solanum tuberosum), tobacco (Nicotiana tabaccum), and Arabidopsis thaliana, was demonstrated. Typically 300-500 mass spectral components with a signal to noise ratio > or =75 were obtained from GC/EI-time-of-flight (TOF)-MS metabolite profiles of methoxyaminated and trimethylsilylated extracts. Profiles from non-sample controls contained approximately 100 mass spectral components. A MS/RI library of 6205 mass spectral components was accumulated and applied to automated identification of the model compounds galactonic acid, a primary metabolite, and 3-caffeoylquinic acid, a secondary metabolite. Neither MS nor RI alone were sufficient for unequivocal identification of unknown mass spectral components. However library searches with single bait mass spectra of the respective reference substance allowed clear identification by mass spectral match and RI window. Moreover, the hit lists of mass spectral searches were demonstrated to comprise candidate components of highly similar chemical nature. The search for the model compound galactonic acid allowed identification of gluconic and gulonic acid among the top scoring mass spectral components. Equally successful was the exemplary search for 3-caffeoylquinic acid, which led to the identification of quinic acid and of the positional isomers, 4-caffeoylquinic acid, 5-caffeoylquinic acid among other still non-identified conjugates of caffeic and quinic acid. All identifications were verified by co-analysis of reference substances. Finally we applied hierarchical clustering to a complete set of pair-wise mass spectral comparisons of unknown components and reference substances with known chemical structure. We demonstrated that the resulting clustering tree depicted the chemical nature of the reference substances and that most of the nearest neighbours represented either identical components, as judged by co-elution, or conformational isomers exhibiting differential retention behaviour. Unknown components could be classified automatically by grouping with the respective branches and sub-branches of the clustering tree.

Arabidopsis↗
PubMed2001

Reading factor: a bibliometric tool to manage a virtual library.

UNLABELLED: Among the many bibliometric criteria used to evaluate biomedical journals, the impact factor is the most commonly used. Despite its limitations, it quantifies the influence of a journal on secondary publications. It does not however evaluate the practical usefulness of primary documents. Usefulness is field-related and varies greatly among specialities. We introduce a new bibliographic criterion, the "reading factor", and define it as the ratio between the number of electronic consultations of a particular journal (i.e., number of clicks on a hyper-link) and the mean number of electronic consultations of all the journals studied (itself calculated by dividing the total number of electronic accesses by the number of journals in the database). We describe its observed distribution, relative to that of the impact factor, based on electronic consultation records from our University Hospital medical digital library, where full-text electronic versions of 45 major biomedical journals have been available since December 1997. From this analysis we found no correlation between the 1999 reading factor and the 1998 impact factor of these 45 journals, and we observed a dramatic change in the hierarchy of journals upon using the reading factor as the yardstick rather than the impact factor. Moreover, we describe how using the reading factor has helped in managing the collection of our University Hospital's virtual library. The selection of journals to be discarded from the virtual library for the year 2001 was based on journals' RF values and this process will repeated over the coming years. The reading factor also permits a cost-analysis of a virtual library. CONCLUSION: The measurement of the reading factor is highly automated, practical and efficient. It appears as a new tool for electronic collection management by librarians, well fitting with economical data.

Bibliometrics↗
PubMed1993

Automated production of high density cosmid and YAC colony filters using a robotic workstation.

We report here on a system for automated preparation of high-density colony filters of arrayed libraries using the high density replicating system (HDR) for the Beckman Biomek 1000 robotic workstation. This system, consisting of a 96-pin tool, a sterilization station and controlling software, transfers samples from microplates onto target membranes in arrays up to 36 times the density of a 96-well microplate. The transfer operation can be completely automated with the addition of the Biomek Side Loader System, which consists of a robotic arm capable of transferring plates and filters between the Biomek working tablet and a storage area. Using the complete system, we are able to plate 32 replica filters (8 x 12 cm), each containing the clones from 16 different microplates (i.e., 1536 clones per filter), in a 16-h overnight run without any operator intervention. We describe conditions used for transfer of bacterial yeast colonies and fixation of DNA to the membranes, and we illustrate hybridization results obtained with cosmid and YAC filters.

Biotechnology↗
PubMed2001

High-throughput purification of compound libraries.

Synthesis of combinatorial libraries by parallel synthesis, followed by high- throughput biological screening, is the new paradigm for drug discovery. Purity of these libraries is an important consideration to obtain high-quality assay data. Liquid-liquid extraction and solid-phase capture reagents are useful in special cases for small numbers of compounds. However, for libraries of a few thousand compounds, HPLC is a viable alternative. Beyond these numbers, factors such as solvent requirements, the number of fractions and tracking become prohibitive. Supercritical fluid chromatography has been successfully employed in automated purification instrumentation and is expected to be capable of purifying libraries of tens-of-thousands of compounds.

Journal Article↗
PubMed2001

Development of an optimized interaction-mating protocol for large-scale yeast two-hybrid analyses.

BACKGROUND: Protein-protein interactions have decisive roles in almost all aspects of the structural and functional organization of cells. But in spite of the increasing amount of complete genome sequence data, the ability to predict protein function from sequences alone is limited. Therefore comprehensive analysis of protein-protein interactions, as derived from the yeast two-hybrid mating system, will yield valuable information for functional biology on a proteomic scale. RESULTS: We have developed an optimized interaction mating protocol for the yeast two-hybrid system, which gives increased mating efficiencies. This significantly reduces the effort and cost of cDNA library screening and allows multiple parallel approaches. Improved preincubation conditions before mating, and optimal cell densities and cell ratios enable almost quantitative mating of the yeast cells carrying the cDNA library. We have proved the applicability of this technology using 20 bait proteins to screen an Arabidopsis thaliana cDNA library, in spite of bait-dependent variations in mating efficiency. CONCLUSIONS: The improved yeast two-hybrid interaction-mating protocol presented here allows the multiple parallel screening of cDNA libraries. It can be carried out without specialized equipment and has the potential to be standardized and automated.

Arabidopsis↗
PubMedDate not supplied

Sector spin coating for fast preparation of polymer libraries.

The feasibility of sector spin coating (or combinatorial spin-coating) is demonstrated (i.e., spin coating of various samples onto one single substrate using a metal template to divide the substrate into sectors). Film thickness increases in an angular direction against the sense of rotation. In the radial direction, the film thickness is constant within 2%. A library of 8 poly(methyl methacrylate)/polystyrene-blends with varying composition was spin coated and subsequently analyzed using automated atomic force microscopy: 24 measurements could be performed within 72 min. The contact angles of a library of 16 polyoxazoline diblock copolymers were measured using one substrate with 16 spin-coated sectors. Forty-eight measurements could be performed within 50 min. On the basis of the surface energies calculated using the Owens-Wendt-Rath-Kaeble method, the library can be divided into three groups of polymers: those containing a dispersive nonyloxazoline block, those containing a polar phenyloxazoline block, and those containing neither.

Journal Article↗
PubMed2000

Automated knowledge extraction from MEDLINE citations.

As part of preliminary studies for the development of a digital library, we have studied the possibility of using the co-occurrence of MeSH terms in MEDLINE citations associated with the search strategies optimal for evidence-based medicine to automate construction of a knowledge base. We use the UMLS semantic types in order to analyze search results to determine which semantic types are most relevant for different types of questions (etiology, diagnosis, therapy, and prognosis). The automated process generated a large amount of information. Seven to eight percent of the semantic pairs generated in each clinical task group co-occur significantly more often than can be accounted for by chance. A pilot study showed good specificity and sensitivity for the intended purposes of this project in all groups.

Electronic Data Processing↗
PubMed1998

Octamer-primed cycle sequencing using dye-terminator chemistry.

Octamer Sequencing Technology, OST, is a method of DNA sequencing using single octamer oligonucleotides to prime cycle sequencing reactions. This sequencing strategy is faster than a traditional primer-walking strategy, since access to this optimized octamer library eliminates delays associated with designing and synthesizing gene specific primers. In this report, OST has been optimized for fluorescent, dye-terminator cycle sequencing reactions to facilitate parallel processing of samples. The successful adaptation of OST to an automated sequencing platform and the design of and access to an octamer library are critical steps towards developing an efficient 'closed-loop' DNA sequencing system.

Animals↗
PubMed2004

Modular tube/plate-based sample management: a business model optimized for scalable storage and processing.

Modular approaches to sample management allow staged implementation and progressive expansion of libraries within existing laboratory space. A completely integrated, inert atmosphere system for the storage and processing of a variety of microplate and microtube formats is currently available as an integrated series of individual modules. Liquid handling for reformatting and replication into microplates, plus high-capacity cherry picking, can be performed within the inert environmental envelope to maximize compound integrity. Complete process automation provides ondemand access to samples and improved process control. Expansion of such a system provides a low-risk tactic for implementing a large-scale storage and processing system.

Automation↗
PubMed2006

A collaborative hit-to-lead investigation leveraging medicinal chemistry expertise with high throughput library design, synthesis and purification capabilities.

High throughput screening (HTS) campaigns, where laboratory automation is used to expose biological targets to large numbers of materials from corporate compound collections, have become commonplace within the lead generation phase of pharmaceutical discovery. Advances in genomics and related fields have afforded a wealth of targets such that screening facilities at larger organizations routinely execute over 100 hit-finding campaigns per year. Often, 10(5) or 10(6) molecules will be tested within a campaign/cycle to locate a large number of actives requiring follow-up investigation. Due to resource constraints at every organization, traditional chemistry methods for validating hits and developing structure activity relationships (SAR) become untenable when challenged with hundreds of hits in multiple chemical families per target. To compound the issue, comparison and prioritization of hits versus multiple screens, or physical chemical property criteria, is made more complex by the informatics issues associated with handling large data sets. This article describes a collaborative research project designed to simultaneously leverage the medicinal chemistry and drug development expertise of the Novartis Institutes for Biomedical Research Inc. (NIBRI) and ArQule Inc.'s high throughput library design, synthesis and purification capabilities. The work processes developed by the team to efficiently design, prepare, purify, assess and prioritize multiple chemical classes that were identified during high throughput screening, cheminformatics and molecular modeling activities will be detailed.

Chemistry, Pharmaceutical↗
PubMed2005

Identification of novel binding partners for tuberous sclerosis complex 2 (TSC2) by yeast two-hybrid approach.

AIM: To identify novel tuberous sclerosis complex (TSC2) binding partners by yeast two-hybrid screening. METHODS: The yeast two-hybrid system DupLEX-A developed by OriGene Technologies and Mouse embryo and HeLa cells cDNA libraries were used in this study. The "bait" constructs, containing full-length and truncated form of TSC2 were prepared. The expression of all constructs in yeast was confirmed by immunoblotting with specific anti-LexA antibodies. The suitability of generated constructs for screening was tested in autoactivation and nuclear translocation assays. Screening of mouse embryo and HeLa cDNA libraries with selected baits was carried out according to manufacturer's recommendations. Positive clones were selected using double selection procedure and further confirmed in mating assay. Isolated cDNA clones were identified by automated DNA sequencing and database searching. RESULTS: Extensive screening of two cDNA libraries from mouse embryo and HeLa cells with TSC2 baits led to the isolation of 102 positives clones. The specificity of interaction between TSC2 and binding proteins of selected clones was confirmed by mating assay for 83 clones. Sequencing of these clones indicated that they encode already known and novel TSC2-binding partners. CONCLUSION: The isolation of several known TSC2-binding partners, such as several isoforms of 14-3-3, demonstrates the validity of generated bait constructs and screening conditions. In addition, we have found a number of novel interactors, which encode cytoskeletal proteins and signaling molecules, such as Ser/Thr phosphatases.

Animals↗
PubMed2000

Automated solid-phase synthesis of linear nitrogen-linked compounds.

A synthetic library motif has been developed to create linear, nitrogen-linked compounds as screening libraries to target structured RNA for drug discovery. Scaffolds were created in situ from suitably protected bifunctional compounds linked together either by acyl or amine links. Acyl links were created from amino acids, which also introduce one degree of functionality. Amine links from the amino acid nitrogen were created from an N-protected amino alcohol via Fukuyama Mitsunobu alkylation. Each amine site can then be used for introducing functionality or extending the scaffold. This synthetic scheme can be used to create a wide variety of modified-backbone PNA in situ, as shown by the synthesis of a PNA-type monomer. The synthesis steps have been enabled on a 96-well parallel-array synthesizer for high-throughput synthesis. The present study represents a versatile synthetic approach to a wide variety of potential RNA-binding molecules.

Amides↗