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At least 199 records · Page 11Linked to original sources

The preparation of a series of nitrostilbene ester compounds using micro reactor technology.

The synthesis of stilbene esters using Wittig chemistry has been used to illustrate the generic diversity micro reactors offer in terms of chemical control and rapid method development. The micro reactor consisted of a 'T' design based on channel geometries 200 microns wide and 100 microns deep, etched into borosilicate glass and sealed with a borosilicate top plate using a thermal bonding technique. The movement of the reagent and products was achieved using electroosmotic flow (EOF), assisted by the incorporation of micro porous silica frits within the micro-channels to allow accurate solution control. To optimise the operating conditions methyl 4-formylbenzoate, premixed with sodium methoxide, was reacted with 2-nitrobenzyl-triphenylphosphonium bromide in dry degassed MeOH using flow conditions for both reagents of 0.40 microL min-1 for 20 min. A product yield of 70% (2:1 reaction stoichiometry with the aldehyde in excess) was obtained representing a 10% increase compared with the traditional batch synthesis. To demonstrate the capability of micro reactors to perform atom efficient synthesis a series of experiments based on an injection methodology (optimised to 30 s) were performed in the micro reactor at 1:1 stoichiometry resulting in a yield of 59%. Finally, the capability of micro reactors to perform a series of analogue reactions was investigated. The yields for a further three aldehydes indicated that the technology will be suitable for the development of automated device to support the generation of combinatorial libraries and rapid high throughput synthetic methods.

Journal Article↗

Navigating the Brookhaven Protein Data Bank.

The Protein Data Bank maintained at Brookhaven National Laboratories has expanded to the point where even experienced users have difficulty understanding, exploring, and exploiting it. This paper describes a text file, an annotation of the Protein Data Bank, which helps users find information on related files and structures. The most recent version of this file includes information on homologous structures, including both sequence homology and structural homology. This file is in ASCII format and is available electronically. It is easy to search locally on any type of computer, using an editor or a pattern-matching program, such as grep.

Base Sequence↗

Automatic evaluation of protein sequence functional patterns.

A procedure that automatically provides an evaluation of the diagnostic ability of a protein sequence functional pattern is described. The procedure relies on the identification of the closest definable set in terms of a (protein sequence) database functional annotation to the set of database instances containing a given pattern. Assuming annotation correctness and completeness in the protein sequence database, the degree of statistical association between these sets provides an appropriate measure of the diagnostic ability of the pattern. An experimental implementation of the procedure, using the NBRF/PIR protein database, has been applied to a diverse collection of published sequence patterns. Results obtained reveal that frequently it is not possible to define (in NBRF/PIR database terminology) the set of database instances containing a given pattern, suggesting either lack of pattern diagnostic ability or protein database annotation incompleteness and/or inconsistencies.

Algorithms↗

On approximate string matching of unique oligonucleotides.

The current research considers the approximate string matching search for important subsequences from DNA sequences, which is essential for numerous bioinformatics computation tasks. We tested several approximate string matching algorithms and furthermore developed one for DNA data. Run times of the algorithms are important, since the amount of data is very large.

Algorithms↗

Meeting the urgency for document delivery in clinical medicine.

A Document Delivery library project was designed to improve delivery of information to health professionals in the Washington DC/Baltimore area. The project goals were to enhance delivery of full text documents and accelerate interlibrary loan services. The aim was to provide direct library services in the clinical arena by facilitating access to the articles needed by practitioners and clinical investigators. The objectives were to (1) design, develop and implement a comprehensive Document Delivery System (DDS) for the Library Information System (LIS) which included interlibrary loan, photocopy services and facsimile transmission capabilities; (2) establish a multi-university Library Knowledge Network for resource sharing; and (3) evaluate the project. The DDS and facsimile service are described and project data and outcomes are reported. Today, the participating libraries can use electronic means to share interlibrary loans. Georgetown users have responded favorably to the DDS and Fax services.

Clinical Medicine↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗