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PubMed1983

The library and its home computer: automation as if people mattered.

To provide its users with quick and easy access to the library resources, the Muriel and Philip Berman National Medical Library, Jerusalem, between 1978 and 1982 developed an integrated library system (MAIMON) on a minicomputer. Because humans are the most important element of the library system, MAIMON's performance was evaluated in terms of benefits provided to patrons, library management, and library staff. After successfully adopting the system, users' needs and expectations have grown. How the existing system will be used and expanded to meet the new information demands at the library is discussed.

Computers↗
PubMedDate not supplied

Solid-supported benzotriazoles. 2. Synthetic auxiliaries and traceless linkers for the combinatorial synthesis of unsymmetrical ureas.

Resin-bound benzotriazole chemistry applied to the solid-phase synthesis of arrays of unsymmetrical aryl ureas is described here. The chemistry assessment process, the monomer rehearsal, the preparation of a discrete library by automated parallel synthesis, the parallel purification protocol employing solid-phase scavenging, and the complete analytical characterization of the library components are also presented.

Journal Article↗
PubMed2003

SiteLight: binding-site prediction using phage display libraries.

Phage display enables the presentation of a large number of peptides on the surface of phage particles. Such libraries can be tested for binding to target molecules of interest by means of affinity selection. Here we present SiteLight, a novel computational tool for binding site prediction using phage display libraries. SiteLight is an algorithm that maps the 1D peptide library onto a three-dimensional (3D) protein surface. It is applicable to complexes made up of a protein Template and any type of molecule termed Target. Given the three-dimensional structure of a Template and a collection of sequences derived from biopanning against the Target, the Template interaction site with the Target is predicted. We have created a large diverse data set for assessing the ability of SiteLight to correctly predict binding sites. SiteLight predictive mapping enables discrimination between the binding and nonbinding parts of the surface. This prediction can be used to effectively reduce the surface by 75% without excluding the binding site. In 63% of the cases we have tested, there is at least one binding site prediction that overlaps the interface by at least 50%. These results suggest the applicability of phage display libraries for automated binding site prediction on three-dimensional structures. For most effective binding site prediction we propose using a random phage display library twice, to scan both binding partners of a given complex. The derived peptides are mapped to the other binding partner (now used as a Template). Here, the surface of each partner is reduced by 75%, focusing their relative positions with respect to each other significantly. Such information can be utilized to improve docking algorithms and scoring functions.

Algorithms↗
PubMed1993

Screening yeast artificial chromosome libraries with robot-aided automation.

Screening of collections of yeast artificial chromosomes utilizing the polymerase chain reaction (PCR) requires large numbers of reactions in parallel. Four steps were implemented to reduce the labor involved: (a) The number of initial samples for DNA extractions was decreased by compressing libraries up to 12-fold. (b) DNA extraction from yeast clones was robot assisted. (c) A BIOMEK 1000 station was adapted to pipette samples for PCR assays. (d) Sample preparation was integrated with a temperature cycler constructed to carry out up to 576 reactions in six 8 x 12-well trays. The implementation of these steps increases the number of reactions per person per day by an order of magnitude. In tests with X-chromosome-specific probes, the robot-aided screening recovered all of the clones detected by slower manual methods.

Chromosomes, Artificial, Yeast↗
PubMed2001

Automating parallel peptide synthesis for the production of PNA library arrays.

A system was establishedfor the parallel synthesis of peptide library arrays in afully automated manner Synthesis takes place in blocks made of polyoxymethylene that hold during all synthesis steps a polypropylene membrane of 8 x 12 cm. Yields are in the nanomole range, obtained at a low consumption of reagents. The current setup is based on a commercially available pipetting robot and supports the generation of 1536 different oligomers/run. Much higher array densities are possible because the membranes are amicable to spot diameters of down to 200 microm, naturally at a cost of the absolute amount produced of each oligomer The method was put to use for the creation of arrayed libraries of peptide nucleic acids (PNAs). These can be employed both as a source of PNA molecules applied individually in experimentation subsequent to their release or as intact oligomer arrays in hybridization analyses.

Base Sequence↗
PubMed1993

Use of reference libraries and hybridisation fingerprinting for relational genome analysis.

The concept of relational genome analysis by hybridisation has been developed into a working system. Various genomic and cDNA libraries have been generated and are distributed via a reference system. Analysis procedures have been tested successfully in the mapping of the entire Schizosaccharomyces pombe genome. In another test-case for their refinement, analyses on the Drosophila genome are well under way. Human and mouse libraries are being studied on all levels, from generating YAC maps to partially sequencing representative cDNA libraries. The automation of the involved processes and the development of improved image detection and analysis are well advanced.

Animals↗
PubMed1999

Automated parallel synthesis of a tetrahydroisoquinolin-based library: potential prolyl endopeptidase inhibitors.

Solution-phase automated parallel synthesis of a Tic-based library is described. This library comprising 2560 members, was obtained from the combination of 80 carboxylic acids and 32 amines and was screened against Tc80 protease, a parasitic prolyl endopeptidase secreted by Trypanosoma cruzi. Pyrrolidine derivatives proved the most potent inhibitors with IC50 values found in the low nanomolar range.

Isoquinolines↗
PubMed1994

Identification of tryptophan and tyrosine residues in peptides separated by capillary electrophoresis by their second-derivative spectra using diode-array detection.

The use of diode-array detection allows the non-destructive identification of tryptophan and tyrosine residues in complex peptide mixtures separated by capillary electrophoresis. Second-order derivative spectra of both amino acids show significant differences while zero-order spectra are overlapping to a great extent. A mixture of peptides containing tryptophan and/or tyrosine residues was used to evaluate this method. Tryptic peptide maps of carbonic anhydrase and of the bacterial chaperonin protein GroEL, and of an autodigest of trypsin were characterized for tryptophan- and tyrosine-containing peptides. Automated spectra library search was performed successfully.

Amino Acid Sequence↗
PubMed2005

A multi-feature and multi-channel univariate selection process for seizure prediction.

OBJECTIVE: To develop a prospective method for optimizing seizure prediction, given an array of implanted electrodes and a set of candidate quantitative features computed at each contact location. METHODS: The method employs a genetic-based selection process, and then tunes a probabilistic neural network classifier to predict seizures within a 10 min prediction horizon. Initial seizure and interictal data were used for training, and the remaining IEEG data were used for testing. The method continues to train and learn over time. RESULTS: Validation of these results over two workshop patients demonstrated a sensitivity of 100%, and 1.1 false positives per hour for Patient E, using a 2.4s block predictor, and a failure of the method on Patient B. CONCLUSIONS: This study demonstrates a prospective, exploratory implementation of a seizure prediction method designed to adapt to individual patients with a wide variety of pre-ictal patterns, implanted electrodes and seizure types. Its current performance is limited likely by the small number of input channels and quantitative features employed in this study, and segmentation of the data set into training and testing sets rather than using all continuous data available. SIGNIFICANCE: This technique theoretically has the potential to address the challenge presented by the heterogeneity of EEG patterns seen in medication-resistant epilepsy. A more comprehensive implementation utilizing all electrode sites, a broader feature library, and automated multi-feature fusion will be required to fully judge the method's potential for predicting seizures.

Algorithms↗
PubMed2006

FK506-binding protein ligands: structure-based design, synthesis, and neurotrophic/neuroprotective properties of substituted 5,5-dimethyl-2-(4-thiazolidine)carboxylates.

Structure-based design and discovery of novel neuroimmunophilin FK506-binding protein (FKBP) ligands were pursued in the present study. The binding mode of the known FKBP ligand 1 (3-(3-pyridyl)-1-propyl (2S)-1-(3,3-dimethyl-1,2-dioxopentyl)-2-pyrrolidinecarboxylate) in complex with FKBP12 was investigated using LUDI simulation and upon which a novel scaffold structure predicted to possess improved binding affinity was designed. A virtual combinatorial library composed of diverse combinations of two substituted groups was constructed using Project Library, followed by an automated screening of the library against the ligand binding site on FKBP52 using DOCK. Forty-three candidate compounds that displayed favorable binding with the receptor were identified and synthesized. The neurotrophic activity of the candidate compounds was evaluated on chick dorsal root ganglion cultures in vitro. As a result, 15 compounds exhibited positive effects on ganglion neurite outgrowth in the presence of 0.15 ng/mL NGF, among which 7 compounds at testing concentrations of 1 pM and 100 pM showed greater efficacy than 1 at 100 pM. Compound 18 (3-(3-pyridyl)-1-propyl (2S)-5,5-dimethyl-1-(3,3-dimethyl-1,2-dioxobutyl)-2-(4-thiazolidine)carboxylate) afforded the most potent effect in promoting the processes of neurite outgrowth and which was in a concentration-dependent manner from 1 pM to 100 pM. Half-maximal effect occurred at about 10 pM. Moreover, 18 at a dosage of 10 mg/kg was found to be significantly neuroprotective in a mouse peripheral sympathetic nerve injury model induced by 8 mg/kg 6-hydroxydopamine. This study further suggests the clinical potential of novel FKBP ligands as a new therapeutic approach in the treatment of neurodegenerative disorders, such as Parkinson's disease.

Animals↗
PubMed1997

Text and illustration: the digitisation of a medieval manuscript.

This paper considers the choice of the medieval Aberdeen Bestiary as the first project in Aberdeen University Library's digitisation programme, and discusses some of the unusual features of the manuscript itself. Attention is given to the content and depth of the accompanying commentaries, and particular notice is paid to the nature and extent of the textual apparatus (translation and transcription). The factors influencing the choice of (a) PhotoCD as the image capture method, and (b) JPEG as the image format for transmission of the page images across the World Wide Web are examined. The importance of the Web design to the effectiveness of the overall resource is emphasised.

History, 20th Century↗
PubMed1995

Changes in the National Health Service and the effects on the hospital library service: case study based on the Cumberland Infirmary.

The perception of change so often differs from the reality. This article traces the effect on one hospital library of some of the major changes within the NHS during the past 10 years. It explores the importance of external factors such as location and proximity to other professional groups and questions the survival of the multidisciplinary hospital library.

Computer Systems↗
PubMed1995

The organization of the digital library.

As digital information proliferates and the difficulties of managing it threaten to overwhelm traditional publication and information delivery processes, new visions of a digital library are forming. Exactly what a digital library is and how it is to be organized have not yet been determined, and bibliographic organization of digital information has not been sufficiently addressed. Bibliography is the systematic description or classification of writings or publications considered as material objects. In today's digital world, such material objects may no longer be relevant, but the need for systematic description remains. The important issue is not whether digital bibliography is needed but, instead, whether or not existing bibliographic techniques are appropriate for this new media. A second issue is the location of the responsibility for a new digital bibliography. Does it rest with medical informaticians, often the producers of this new digital information, or with librarians, traditionally the classifiers of information? Developments in both medical informatics and medical librarianship indicate a need for greater collaboration between these specialties in order to achieve their common purpose--the creation, classification, and dissemination of scholarly information.

Bibliography of Medicine↗
PubMedDate not supplied

Virtual shelves in a digital library: a framework for access to networked information sources.

OBJECTIVE: Develop a framework for collections-based access to networked information sources that addresses the problem of location-dependent access to information sources. DESIGN: This framework uses a metaphor of a virtual shelf. A virtual shelf is a general-purpose server that is dedicated to a particular information subject class. The identifier of one of these servers identifies its subject class. Location-independent call numbers are assigned to information sources. Call numbers are based on standard vocabulary codes. The call numbers are first mapped to the location-independent identifiers of virtual shelves. When access to an information resource is required, a location directory provides a second mapping of these location-independent server identifiers to actual network locations. RESULTS: The framework has been implemented in two different systems. One system is based on the Open System Foundation/Distributed Computing Environment and the other is based on the World Wide Web. CONCLUSIONS: This framework applies in new ways traditional methods of library classification and cataloging. It is compatible with two traditional styles of selecting information searching and browsing. Traditional methods may be combined with new paradigms of information searching that will be able to take advantage of the special properties of digital information. Cooperation between the library-informational science community and the informatics community can provide a means for a continuing application of the knowledge and techniques of library science to the new problems of networked information sources.

Catalogs, Library↗
PubMed1998

The use of electronic mail at the reference desk: impact of a computer-mediated communication technology on librarian-client interactions.

Commonly recognized computer-mediated communication (CMC) tools include virtual environments, bibliographic databases, listservers, newsgroups, group teleconferencing, interactive messaging systems and electronic mail. The use of these technologies in libraries has grown exponentially over the past decade. Electronic mail has emerged as an especially popular communication tool for librarians, and their colleagues and patrons. This paper explores the use of a reference department electronic mail service and its impact on reference services and librarian-client interactions. Several issues related to the implementation of CMC technologies are presented, including the maintenance and monitoring of reference electronic mail systems, the types of questions that are typically posted, and potential barriers to the implementation and use of reference e-mail.

Academic Medical Centers↗
PubMed2003

Reinventing a health sciences digital library--organizational impact.

What is the organizational impact of becoming a digital library, as well as a physical entity with facilities and collections? Is the digital library an add-on or an integrated component of the overall library package? Librarians see sweeping environmental and technological changes. The staff members feel exhilarated and challenged by the pressures to adapt quickly and effectively. Librarians recognize that a Web presence, like other technology components, must be continuously enhanced and regularly re-engineered. The Health Sciences Library, University of North Carolina at Chapel Hill, is reinventing its digital presence to better meet the needs of the community. This paper provides a case study focusing on major changes in planning processes, organizational structure, staffing, budgeting, training, communications, and operations at the Health Sciences Library.

Computer Communication Networks↗
PubMedDate not supplied

I2Cnet medical image annotation service.

I2Cnet (Image Indexing by Content network) aims to provide services related to the content-based management of images in healthcare over the World-Wide Web. Each I2Cnet server maintains an autonomous repository of medical images and related information. The annotation service of I2Cnet allows specialists to interact with the contents of the repository, adding comments or illustrations to medical images of interest. I2Cnet annotations may be communicated to other users via e-mail or posted to I2Cnet for inclusion in its local repositories. This paper discusses the annotation service of I2Cnet and argues that such services pave the way towards the evolution of active digital medical image libraries.

Computer Communication Networks↗