Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Library Automation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMed1989

A microcomputer-based, net-lending interlibrary loan system.

A microcomputer-based, net-lending interlibrary loan system was developed at Lane Medical Library, Stanford University. The system, designed to generate the monthly billing invoices and all necessary statistical reports, has reduced the time required for logging-in procedures and compilation of monthly, quarterly, and annual statistics. User menus, help screens, and choice fields were developed explicitly for library staff who have little or no computer experience. The program was written using the DataEase database management software running on IBM PC, XT, AT, or compatible with a minimum of 512K RAM. Described are features of this automated interlibrary loan management system and its use in a net-lending interlibrary loan department. It focuses on data entry in the "Library Directory" and "ILL Log Sheet," details of billing invoices, and statistical reports, and flexibility in modifying tax rates, borrowing fees, and other parameters.

Accounting↗
PubMedDate not supplied

Infrared analysis of urinary stones: a trial of automated identification.

A Search algorithm included in the Opus software of Bruker (Germany) was evaluated for analysis of urinary stones. Three reference libraries containing respectively 85 (single components), 1,059 (binary mixtures) and 4,565 (ternary mixture) digitized spectra were created and used to identify unknown spectra (n=320), applying the automatic procedure. Identification of the major component was correct in 83% of cases but the percentage of identification significantly decreased for the second and the third components. In cases of identification of the two first components, quantitative assessment was correct within tolerance limits +/- 15%. The computer results are judged unsatisfactory with regard to pathology because computer-aided identification is not sufficiently sensitive and specific to differentiate species with similar spectral pattern, even for the identification of main component, and also to detect minor components. It can be of assistance to guide spectral analysis, but it cannot replace human identification.

Algorithms↗
PubMed2005

PCR-based unidirectional deletion method for creation of comprehensive cDNA libraries.

A new strategy for the rapid creation of DNA deletion libraries using a simple PCR-based method is presented. Unidirectional deletion fragments are created and may be cloned into any vector system without the constraint of using restriction enzymes. Our strategy combines methodologies from DNA sequencing, PCR, and homologous recombination (either in vivo or in vitro) to allow for the creation of a library containing fragments representing all possible deletions of a given cDNA. Using this strategy we have successfully constructed a deletion library of the cDNA encoding for the lumenal domain of yeast Ire1p, and have shown that resulting fragments range from 100 bp to the full length cDNA (1557 bp). This method is simple, inexpensive, and can easily be adapted for automated high-throughput research.

Gene Deletion↗
PubMed2000

Investigating the genetic control of stem cell behavior.

The precise control of hematopoietic stem cell fate decisions involves molecules that are differentially expressed in the stem cell versus its non-stem progeny. The construction of representative and high quality cDNA libraries containing stem cell-specific sequences is a first step in elucidating stem cell control mechanisms. Automated bioinformatics in conjunction with high-throughput random sequencing and high-density parallel array hybridization studies make it possible to dissect stem cell molecular pathways and networks. It is the differential analysis of these interacting pathways which will provide the greatest insights into the biological differences underlying stem cell behavior.

Computational Biology↗
PubMed1992

A new approach to understanding T cell development: the isolation and characterization of immature CD4-, CD8-, CD3- T cell cDNAs by subtraction cloning.

During T cell development in the mammalian thymus, immature T cells are observed that lack the cell surface markers CD4, CD8, and CD3. A subtracted cDNA library was constructed to isolate cDNAs that are specific for these immature T cells. Tissue-specific expression of 97 individual cDNAs were examined using different cell types by Northern blot analysis, and six cDNAs were analyzed by reverse transcriptase (RT) polymerase chain reaction (PCR) detection of RNA. Approximately 50% of the clones could not be detected on Northern blots, and 40% of the clones were expressed by at least one other cell-type including monocytes, mature T cells, and B cells. Eight cDNA clones appear to be specific for the CD4-, CD8-, CD3- T cell line, used to construct the library, as determined by Northern blot analysis. In addition, 330 cDNA clones were subjected to partial automated DNA sequence determination. Database searches, with both nucleotide and protein translations, revealed cDNAs that exhibit interesting similarities to human cell-cycle gene 1, platelet-derived growth factor receptor, c-fms oncogene (CSF-1) receptor, and members of the immunoglobulin gene superfamily. This approach of employing subtraction coupled with large scale partial cDNA sequence determination can be useful to identify genes that may be involved in early T cell growth, cellular recognition or differentiation.

Animals↗
PubMed2005

Automated microscopy screening for compounds that partially revert cholesterol accumulation in Niemann-Pick C cells.

Niemann-Pick disease type C (NPC) is an autosomal recessive genetic disorder manifested by abnormal accumulation of unesterified cholesterol and other lipids. We screened combinatorially synthesized chemical libraries to identify compounds that would partially revert cholesterol accumulation. Cultured CHO cells with NPC phenotypes (CT60 and CT43) were used for screening along with normal CHO cells as a control. We developed an automated microscopy assay based on imaging of filipin fluorescence for estimating cholesterol accumulation in lysosomal storage organelles. Our primary screen of 14,956 compounds identified 14 hit compounds that caused significant reduction in cellular cholesterol accumulation at 10 microM. We then screened a secondary library of 3,962 compounds selected based on chemical similarity to the initial hits and identified 7 compounds that demonstrated greater efficacy and lower toxicity than the original hits. These compounds are effective at concentrations of 123 nM to 3 microM in reducing the cholesterol accumulation in cells with a NPC1 phenotype.

Androstenes↗
PubMed1993

PCR buffer optimization with uniform temperature regimen to facilitate automation.

To facilitate PCR(1,2) reactions in large numbers with uniform conditions, the annealing temperature was fixed and the stringency of the reactions was adjusted by optimizing the ion conditions of the reaction. The buffer system is based primarily on Tris (T), ammonium (N), and potassium (K) to adapt assay conditions to different primer pairs. The TNK buffers have permitted successful screening of a 60,000-clone yeast artificial chromosome (YAC) library with more than 200 primer pairs.

Automation↗
PubMed1995

Process redesign: making your film library work for you.

When Riverside Methodist Hospitals in Columbus, Ohio, experienced serious problems in its radiology film library, administrators recognized that poor processes were to blame and used quality management techniques to create a new system. A radiology information system was part of Riverside's long-range plan, but an effective manual process was implemented first. Riverside had decided that closing the library to referring physician access would result in more successful operations. An Operational Changes Planning Committee composed of file clerks, technologists, managers, radiologists and referring physicians planned the redesign. The committee identified four goals: Reduce unmet requests. Improve response time. Benchmark operations of comparable organizations. Implement an effective manual process prior to automation. Steps in the redesign process included identifying the problem, applying statistical tools to the situation and understanding customer requirements. Flow charts, benchmarking, data collection within the department and focus groups provided important quantitative information. Creating an improved process included the following actions: Work simplification. Work elimination (especially non-value-added work). Uncovering and removing causes of delay. Automation of repetitive tasks via the RIS. Reduction and elimination of any rework steps. One important change was to close the library to physician access. There were moderate gains in effectiveness as a result of redesign of the manual process. Results have continued to improve, and the redesign process provided greater commitment and cooperation for the more significant improvements that followed the RIS introduction.

Efficiency, Organizational↗
PubMed2000

Synthesis of highly substituted 5-(trifluoromethyl)ketoimidazoles using a mixed-solid/solution phase motif.

Using a combination of solid phase synthesis for the preparation of N-substituted-N-acylglycines 7 followed by solution-phase ring transformation of trifluoromethylacyl munchnone intermediate 8, a library of 200 trisubstituted-5-trifluoromethylketo (TFMK) imidazoles 9 was prepared. In a sublibrary, bromoacetate resin 4 was treated with 5 amines in parallel to give N-substituted glycines 5 followed by acylation with 12 acid chlorides to provide, upon cleavage from the resin, 60 individual N-substituted-N-acylglycines 7. The glycines 7 were converted to munchnones 8 by treatment with trifluoroacetic anhydride followed by reaction with benzamidine to give trisubstituted-5-TFMK-imidazoles 9. The structural content of the library was analyzed using PlateView of the LCMS results, and individual members were isolated by automated preparative LCMS.

Databases as Topic↗
PubMed2003

Arrhythmia database for algorithm testing: surface leads plus intracardiac leads for validation.

Ann Arbor Electrogram Libraries (AAEL) is a database of over 500 electrocardiographic recordings made during clinical electrophysiology studies over a period of 15 years. These data are used by university researchers and cardiac device research and development laboratories to develop and test arrhythmia detection algorithms. The AAEL library is in use by all major implantable cardioverter defibrillator manufacturers as well as several Automated External Defibrillator developers. In 1996, the USFDA Center for Devices and Radiological Health licensed a portion of Volumes I for proposed device testing. The data consist of 7 channels of signals: surface leads I, III, V1, an intra-atrial high right atrium (bipolar), an intra-atrial high right atrium (unipolar), an intraventricular right ventricular apex (bipolar), and intraventricular right ventricular apex (unipolar) from the distal catheter electrode. Data were recorded under careful engineering quality control continuously (30 min-1.5 hr) on FM magnetic tape at a tape speed of 3.75 in/s after signal amplification at a filter setting of 1-500 Hz. Amplifier gain and filter settings were held constant during the entire recording procedure and a 1 mV calibration signal was entered as a reference at the time of recording. All patient recordings contain a baseline sinus rhythm, and subsequently induced ventricular tachycardia and/or ventricular fibrillation, or less frequently, supraventricular tachycardia, atrial tachycardia, and/or atrial fibrillation. Data are typically made available in digitized format (1,000 Hz); digital or FM recordings are also available. AAEL recordings are the only widespread intracardiac test files in the industry.

Arrhythmias, Cardiac↗
PubMedDate not supplied

Use of statistical design of experiments in the optimization of amide synthesis utilizing polystyrene-supported N-hydroxybenzotriazole resin.

Two fields that routinely perform reaction optimization studies are chemical development (prior to scale-up) and medicinal or combinatorial chemistry (prior to analogue synthesis or library production). To date, the use of statistical design of experiments (DoE) in conjunction with automated synthesizers has been applied in process research to a greater extent than in the medicinal or combinatorial laboratories. We have applied DoE in conjunction with an automated synthesizer to optimize the synthesis of amides employing resin-bound N-hydroxybenzotriazole (PS-HOBt) active esters as intermediates. This methodology allowed the rapid development of an improved protocol for the parallel synthesis of amides by conversion of carboxylic acids to PS-HOBt esters followed by treatment with appropriate amines. Product isolation involved only simple filtration and evaporation.

Amides↗
PubMedDate not supplied

Making "real" molecules in virtual space.

Predicting "realistic" compounds of given chemical reactions with virtual synthesis tools usually requires the manual intervention of experienced chemists in the enumeration phase for the selection of appropriate reactants, assignment of the corresponding reaction sites, and removal of the unlikely products. To automate the virtual synthesis process, we have moved the expertise intensive parts from the compound library design phase to the reaction library design phase. ChemAxon is building an in silico reaction library containing important preparative transformations, where each reaction definition contains a generic transformation scheme and additional rules to handle the various starting compounds according to the corresponding chemo-, regio-, and stereoselectivity issues. Having well designed reaction definitions in hand, our software tool is able to generate synthetically feasible compound libraries with minimal effort in the enumeration phase.

Combinatorial Chemistry Techniques↗
PubMed2003

Migration of volatile degradation products into ozonated water from plastic packaging materials.

Migration of volatile degradation products from poly(ethylene terephthalate) (PET) and high-density polyethylene (HDPE) bottles, polypropylene (PP) caps and ethyl vinyl acetate (EVA) liners into ozonated water was measured. Polymer strips were immersed in deionized and distilled water with ozone concentrations of 0.5, 2.5 and/or 5 mg kg(-1) inside 35-ml vials, which were clamp-sealed and stored at 40 degrees C for 10 days. A purge-and-trap unit was developed to extract volatile products from the ozonated water in vials. The extractables were trapped in an adsorbent tube and analysed using a GC-MS coupled with an automated thermal desorber (ATD). Mass spectra were interpreted by comparison with a NIST mass spectral library, and an internal standard method was used to quantify the extractables of interest. Several volatile compounds found in ozonated water that had been in contact with PP, EVA and HDPE polymers included butanal, pentanal, hexanal, heptanal, octanal, nonanal, 2,2-dimethyl propanal, 3-hexanone, 2-hexanone and heptanone. These compounds could cause off-taste and off-odour with a low organoleptic threshold. In general, the concentrations of these volatile compounds increased with an increased exposure to ozone. The highest concentration found was 14.1 +/- 0.6 microg kg(-1) for hexanal with a 5 mg kg(-1) ozone treatment of PP caps. Even at a treatment level of 5 mg kg(-1) ozone, which is greater than 10 times the current regulatory limits for bottled water, the extractables migrating from those polymers were within the levels permitted by the FDA. For the PET sample, no significant peaks were observed before or after ozonation. These results imply that PP caps containing EVA liners may be major sources of off-odour and taste in ozonated bottled water.

Disinfection↗
PubMed2004

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

MOTIVATION: Several protein function prediction methods employ structural features captured in three-dimensional (3D) descriptors of biologically relevant sites. These methods are successful when applied to high-resolution structures, but their detection ability in lower resolution predicted structures has only been tested for a few cases. RESULTS: A method that automatically generates a library of 3D functional descriptors for the structure-based prediction of enzyme active sites (automated functional templates, 593 in total for 162 different enzymes), based on functional and structural information automatically extracted from public databases, has been developed and evaluated using decoy structures. The applicability to predicted structures was investigated by analyzing decoys of varying quality, derived from enzyme native structures. For 35% of decoy structures, our method identifies the active site in models having 3-4 A coordinate root mean square deviation from the native structure, a quality that is reachable using state of the art protein structure prediction algorithms. AVAILABILITY: See http://www.bioinformatics.buffalo.edu/resources/aft/

Algorithms↗
PubMed1999

An automated sample preparation system for large-scale DNA sequencing.

Recent advances in DNA sequencing technologies, both in the form of high lane-density gels and automated capillary systems, will lead to an increased requirement for sample preparation systems that operate at low cost and high throughput. As part of the development of a fully automated sequencing system, we have developed an automated subsystem capable of producing 10,000 sequence-ready ssDNA templates per day from libraries of M13 plaques at a cost of $0.29 per sample. This Front End has been in high throughput operation since June, 1997 and has produced > 400,000 high-quality DNA templates.

DNA↗
PubMed2006

Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways.

The contamination of waterways with fecal material is a persistent threat to public health. Identification of the sources of fecal contamination is a vital component for abatement strategies and for determination of total maximum daily loads. While phenotypic and genotypic techniques have been used to determine potential sources of fecal bacteria in surface waters, most methods require construction of large known-source libraries, and they often fail to adequately differentiate among environmental isolates originating from different animal sources. In this study, we used pooled genomic tester and driver DNAs in suppression subtractive hybridizations to enrich for host source-specific DNA markers for Escherichia coli originating from locally isolated geese. Seven markers were identified. When used as probes in colony hybridization studies, the combined marker DNAs identified 76% of the goose isolates tested and cross-hybridized, on average, with 5% of the human E. coli strains and with less than 10% of the strains obtained from other animal hosts. In addition, the combined probes identified 73% of the duck isolates examined, suggesting that they may be useful for determining the contribution of waterfowl to fecal contamination. However, the hybridization probes reacted mainly with E. coli isolates obtained from geese in the upper midwestern United States, indicating that there is regional specificity of the markers identified. Coupled with high-throughput, automated macro- and microarray screening, these markers may provide a quantitative, cost-effective, and accurate library-independent method for determining the sources of genetically diverse E. coli strains for use in source-tracking studies. However, future efforts to generate DNA markers specific for E. coli must include isolates obtained from geographically diverse animal hosts.

Animals↗
PubMedDate not supplied

Electronic health record meets digital library: a new environment for achieving an old goal.

Linking the electronic health record to the digital library is a Web-era reformulation of the long-standing informatics goal of seamless integration of automated clinical data and relevant knowledge-based information to support informed decisions. The spread of the Internet, the development of the World Wide Web, and converging format standards for electronic health data and digital publications make effective linking increasingly feasible. Some existing systems link electronic health data and knowledge-based information in limited settings or limited ways. Yet many challenging informatics research problems remain to be solved before flexible and seamless linking becomes a reality and before systems become capable of delivering the specific piece of information needed at the time and place a decision must be made. Connecting the electronic health record to the digital library also requires positive resolution of important policy issues, including health data privacy, government encouragement of high-speed communications, electronic intellectual property rights, and standards for health data and for digital libraries. Both the research problems and the policy issues should be important priorities for the field of medical informatics.

Internet↗