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PubMed1987

Automating Veterans Administration libraries: II. Implementation at the Kansas City Medical Center Library.

In 1985, the Kansas City Veterans Administration Medical Center began implementation of the Decentralized Hospital Computer Program (DHCP). An integrated library system, a subset of that program, was started by the medical library for acquisitions and an outline catalog. To test the system, staff of the Neurology Service were trained to use the outline catalog and electronic mail to request interlibrary loans and literature searches. In implementing the project with the Neurology Service, the library is paving the way for many types of electronic access and interaction with the library.

Catalogs, Library↗
PubMed2004

An empirical Bayesian significance test of cDNA library data.

Automated high-throughput sequencing of cDNA clones from numerous libraries has generated a wealth of information about both genome sequence and relative transcript abundances. A common statistical challenge in the analysis of library sequences is to infer whether there is differential expression for the same transcript under two different conditions, such as normal and diseased tissue. In contrast to the continuously variable intensity measurements from microarray experiments, data from cDNA library sequencing presents itself as a discrete count of the incidence of some clone or transcript in a finite sample. In this paper, we first propose a statistical model for data generated from cDNA library sequencing efforts. The model is based on the Poisson mixed with generalized inverse Gaussian (PGIG), introduced by Sichel (1971, 1975). PGIG has been used in modeling population abundance, ecological studies, word frequencies in publications, etc. Using data from the literature, we show that the proposed model provides a good fit to the observed data. Using this new model for cDNA library data, we developed an empirical Bayesian significance test (EBST) for inferring the statistical significance of differential gene expression from discrete data.

Bayes Theorem↗
PubMedDate not supplied

2D and 3D spatially addressed arrays for high-throughput automated synthesis of combinatorial libraries.

One of the key elements in the drug discovery process is the use of automation to synthesize libraries of compounds for biological screening. The "split-and-mix" approaches in combinatorial chemistry have been recognized as extremely powerful techniques to access large numbers of compounds, while requiring only few reaction steps. However, the need for effective encoding/deconvolution strategies and demands for larger amounts of compounds have somewhat limited the use of these techniques in the pharmaceutical industry. In this paper, we describe a concept of directed sort and combine synthesis with spatially arranged arrays of macroscopic supports. Such a concept attempts to balance the number of reaction steps, the confidence in compound identity, and the quantity of synthesized compounds. Using three-dimensional arrays of frames each containing a two-dimensional array of macroscopic solid supports, we have conceptualized and developed a modular semiautomated system with a capacity of up to 100 000 compounds per batch. Modularity of this system enables flexibility either to produce large diverse combinatorial libraries or to synthesize more focused smaller libraries, both as single compounds in 12-15 micromol quantities. This method using sortable and spatially addressed arrays is exemplified by the synthesis of a 15 360 compound library.

Journal Article↗
PubMed2003

Synthesis and analysis of combinatorial libraries performed in an automated micro reactor system.

This paper presents the synthesis of combinatorial libraries performed on a single-channel glass micro reactor under hydrodynamic flow control. The experiments were carried out in a non-well based micro chip and consisted of the preparation of libraries of pyrazoles by means of a Knorr reaction of 1,3-dicarbonyl compounds with hydrazines. The aim of this work is to investigate the capabilities of an automated micro reactor based system to synthesise sequentially multiple analogue reactions. Small slugs of reactants were introduced automatically by an autosampler in a serpentine-etched glass chip. The mobility of the reagents and products was achieved using hydrodynamic driven flow. Reaction slug dilution and UV slug detection took place at the outlet. A sample of the slug was analysed by using an on-line LC-UV-MS system. The degree of conversion was quantified using the UV signal and comparing with standards of starting materials and final products. After the LC-UV-MS analysis, the automated system proceeds to inject the slugs to carry out the next reaction programmed. The results suggest that the micro reactor system is capable of repeating the process of injection, mixing and reaction in an automated manner as many times as required.

Automation↗
PubMed2001

Preparation of 'side-chain-to-side-chain' cyclic peptides by Allyl and Alloc strategy: potential for library synthesis.

Automated and manual deprotection methods for allyl/allyloxycarbonyl (Allyl/Alloc) were evaluated for the preparation of side-chain-to-side-chain cyclic peptides. Using a standard Allyl/Alloc deprotection method, a small library of cyclic peptides with lactam bridges (with seven amino acids) was prepared on an automatic peptide synthesizer. We demonstrate that the Guibe method for removing Allyl/Alloc protecting groups under specific neutral conditions [Pd(PPh3)4/PhSiH3)/DCM] can be a useful, efficient and reliable method for preparing long cyclic peptides on a resin. We have also manually synthesized a cyclic glucagon analogue containing 24 amino acid residues. These results demonstrated that properly controlled palladium-mediated deprotection of Allyl/Alloc protecting groups can be used to prepare cyclic peptides on the resin using an automated peptide synthesizer and cyclic peptides with a long chain.

Amino Acid Sequence↗
PubMed2001

Solid phase synthesis of complex natural products and libraries thereof.

Natural products have served as an important source of medicinal compounds and pharmaceutical leads over the last century. Within the last 10 years, significant interest has developed in applying combinatorial chemistry techniques to the study of natural products and their biological activities. In this review, we examine several representative efforts wherein natural product skeletons have been constructed or immobilized on solid support and subsequently derivatized, giving rise to analog libraries useful in understanding the structure-activity relationships of the parent natural product. Issues such as target selection, library design, linker development, automation, and library characterization are addressed.

Alkaloids↗
PubMed1994

Developing a health information infrastructure for Arizona.

Network connectivity is critical in Arizona, where travel distances are great, academic programs dispersed, and health care practitioners often geographically isolated. Accordingly, the University of Arizona (UA) applied for $50,000.00 in National Library of Medicine/National Science Foundation (NLM/NSF) Connections Program funding to promote statewide collaboration in supporting UA's health sciences education and research programs by expanding network connectivity to hospitals and other health-related institutions. The proposal outlined three strategies: Each major nonuniversity teaching hospital would secure and maintain a leased communications line dedicated to network connectivity, and NSF funds would be used to buy some necessary hardward. NSF funds would be used to establish a modern bank for dial-up Internet access by rural practitioners and teaching sites. Co-principal investigators of the project would promote and support the use of this new statewide connectivity and foster its continued expansion. The proposal was based on a conservative philosophy: familiar technologies and, where possible, existing networks and equipment would be used. The proposal was approved, and NSF funds hastened creation of an expanded health information network in Arizona. Once that network was in place, participants moved quickly from managing the mechanics of connectivity to planning for a computing and communications platform with services. Private funds were obtained to help organize the Arizona Health Information Network to direct these expanded services.

Arizona↗
PubMed2002

Development of combinatorial chemistry methods for coatings: high-throughput optimization of curing parameters of coatings libraries.

An automated analytical system has been implemented for the high-throughput optimization of processing conditions such as curing parameters in fabrication of UV-cured automotive organic protective coatings. Selection of optimum process conditions of combinatorial arrays of coatings is essential to correlate the high-throughput screening and conventional processes and to achieve the desired physical properties of coatings. For monitoring of curing conditions of each coating in the array, a viscosity-sensitive fluorophore 4,4'-bis(2-benzoxazolyl)stilbene was incorporated into coating formulations. This fluorescence tagging approach permitted us to combine a gradient temperature heater and a UV curing system with the full capabilities of our high-throughput screening system, including generation of spectroscopic data and its analysis. This investigation demonstrated the possibility of rapid decoupling of temperature and radiation effects in curing of UV-curable coating formulations by using multiple coatings and process conditions at once. While the system described here was implemented for high-throughput optimization of temperature conditions of radiation curing of arrays of organic protective coatings for automotive applications, this system can be further applied for a variety of other applications where optimization of process parameters can be studied in situ or off-line using optical spectroscopic tools.

Journal Article↗
PubMed1978

The controversy over change.

The full impact of twentieth century technology upon medical libraries was first felt in the late 1950s and early 1960s with the introduction of electronic automation into library methodology. During those years, often the aura of technology for the sake of technology prevailed, and medical librarians did little to inform themselves of capabilities, potentialities, and limitations in relation to cost-effective library usage of automation. Likewise, currently microforms and audiovisuals are frequently acquired for their own sake instead of for their capacity to transmit messages in the most effective and comprehensive way possible. Controversy has raged and still rages over the pros and cons of applying modern technology to library procedures and over the coexistence of the printed page with electronic media. New systems and methodologies, machine or manual, must realistically be evaluated in terms of increased service output by the library to its clientele. Regardless of technological sophistication, any machine that does not significantly contribute to that specific aim has no place in a library. The tradition of the medical librarian has always been to collect, organize, store, and disseminate information in the most efficient manner that the media of the times have had to offer.

Audiovisual Aids↗
PubMed1998

New developments in automated PrepLCMS extends the robustness and utility of the method for compound library analysis and purification.

New developments in the high throughput purification of combinatorial libraries by automated preparative LC-MS is presented. To facilitate high speed purifications at the multimilligram level, short columns operated at ultra high flow rates were incorporated. In order to match the linear velocity of the short analytical columns for high speed separations (operated at 4.0 mL/min), it was required to operate the preparative columns at flow rates in excess of 70 mL/min. For chromatographically well-behaved compounds, analytical LC-MS analyses and preparative LC-MS analyses could be achieved in as little as 5 min. For compounds exhibiting poor chromatographic peak shapes and/or for compound mixtures requiring higher resolution separations, slightly longer preparative LC-MS analysis times were required (8-10 min/sample).

Chemistry, Pharmaceutical↗
PubMedDate not supplied

Automated mass spectrometric sequence determination of cyclic peptide library members.

Cyclic peptides have come under scrutiny as potential antimicrobial therapeutic agents. Combinatorial split-and-pool synthesis of cyclic peptides can afford single compound per well libraries for antimicrobial screening, new lead identification, and construction of quantitative structure-activity relationships (QSAR). Here, we report a new sequencing protocol for rapid identification of the members of a cyclic peptide library based on automated computer analysis of mass spectra, obviating the need for library encoding/decoding strategies. Furthermore, the software readily integrates with common spreadsheet and database packages to facilitate data visualization and archiving. The utility of the new MS-sequencing approach is demonstrated using sonic spray ionization ion trap MS and MS/MS spectrometry on a single compound per bead cyclic peptide library and validated with individually synthesized pure cyclic D,L-alpha-peptides.

Automation↗
PubMed2002

Software for automating analysis of encoded combinatorial libraries.

This paper describes the applications which are used to automate the analysis of encoded combinatorial libraries. Commercial packages from MDL, Oracle and Agilent are linked with application software written in C/C++, in Microsoft Access and in ChemStation macro language. Encoding correspondence lists for each of up to three synthetic steps are conveniently associated with building block lists using the first application, CodeGen. The second application Decode allows the user to identify the individual beads picked onto a 96-well plate and the pool number for each bead. The decoding chromatography data for each well is then loaded into the program. The chromatography data is used to identify the tags used in the synthesis. Along with the building block information from ISIS/Host, the building block used in each step of the synthesis can be identified. A third routine, Code-to-Structure, takes the coded library building blocks and creates the connection table in ISIS for each structure found by the decode program. For quality control of encoded library synthesis, the decoded structures on a set of beads is compared to the LC/UV/MS data for the ligand cleaved from the same bead. CAPTURE, a GlaxoSmithKline proprietary application, is used to display and analyze the decoded structures and associated mass spectral data. This application uses simple isotopic composition and electrospray ionization rule sets to predict mass spectra and judge the concordance of a structure- mass spectrum data set. An ancillary program, EIC, is used to extract predicted single ion chromatograms from the full scan LC/MS data.

Combinatorial Chemistry Techniques↗
PubMed2002

From information jungle trails to superhighways for health caregivers in the Pacific.

Micronesia has very sparse local library services but this is improving. For those libraries with any health science collection, only paper indexes might be available which provide limited search capabilities. Some now provide regional access to knowledge-based information in the health sciences literature with the Guam Medical Library (NHGU Library) staffed by a certified medical librarian. Over the past two decades, the authors, librarians at the NHGU Library and the RFK Library, initiated expanded and timely access to biomedical information for health professionals throughout the Pacific region. Now, health caregivers in the Pacific may affilliate for Loansome Doc service by simply contacting the NHGU Library. In 1996, with the support of the University of Guam, the RFK Library became an NLM resource library and actively began working with the Pacific Southwest Regional Medical Library Service (PSRMLS) of the NLM to provide expanded service to isolated health caregivers in Micronesia. Moreover, NHGU Library belongs to a loose network of (US) federal and Department of Defense libraries that share information and copies of articles among themselves for no cost. In this way medical services can now readily access a wider network of health information.

Guam↗
PubMed2005

Automated design of degenerate codon libraries.

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.

Algorithms↗
PubMed1999

Inventory management and reagent supply for automated chemistry.

Developments in automated chemistry have kept pace with developments in HTS such that hundreds of thousands of new compounds can be rapidly synthesized in the belief that the greater the number and diversity of compounds that can be screened, the more successful HTS will be. The increasing use of automation for Multiple Parallel Synthesis (MPS) and the move to automated combinatorial library production is placing an overwhelming burden on the management of reagents. Although automation has improved the efficiency of the processes involved in compound synthesis, the bottleneck has shifted to ordering, collating and preparing reagents for automated chemistry resulting in loss of time, materials and momentum. Major efficiencies have already been made in the area of compound management for high throughput screening. Most of these efficiencies have been achieved with sophisticated library management systems using advanced engineering and data handling for the storage, tracking and retrieval of millions of compounds. The Automation Partnership has already provided many of the top pharmaceutical companies with modular automated storage, preparation and retrieval systems to manage compound libraries for high throughput screening. This article describes how these systems may be implemented to solve the specific problems of inventory management and reagent supply for automated chemistry.

Automation↗
PubMed2004

The NLM Gateway: a metasearch engine for disparate resources.

The U.S. National Library of Medicine (NLM) has created a metasearch engine called the NLM Gateway at the URL "gateway.nlm.nih.gov". The Gateway allows the user to issue one search that takes place on multiple NLM retrieval engines. A composite result set is presented in several categories of information: journal citations; books, serials and audiovisuals; consumer health; meeting abstracts; and other collections.

Databases as Topic↗