Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Libraries”

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 379 records · Page 21Linked to original sources
PubMed2001

Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.

We developed computer-based methods for constructing a nonredundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3' ends of inserts and clustering, and completing a re-array to generate a nonredundant library from a redundant one. After the cDNA libraries are generated, we sequence the 5' ends of the inserts to check the quality of the library; then we determine the sequencing priority of each library. Selected libraries undergo large-scale sequencing of the 3' ends of the inserts and clustering of the tag sequences. After clustering, the nonredundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters are uniquely identified, and all information is saved in the database according to this identifier. At press time, our system has been in place for the past two years; we have clustered 939,725 3' end sequences into 127,385 groups from 227 cDNA libraries/sublibraries (see http://genome.gse.riken.go.jp/).

5' Untranslated Regions↗
PubMed2006

Diversity of the Clostridium coccoides group in human fecal microbiota as determined by 16S rRNA gene library.

Fecal microbiota were analyzed in seven healthy individuals by 16S rRNA gene libraries (universal library) using universal primers, and the Clostridium coccoides group libraries using the universal primer 27F and the C. coccoides group-specific primer Erec482. The universal libraries were used in our previous studies. The 972 clones obtained from two different primer set libraries belonged to the C. coccoides group and were classified into 139 operational taxonomic units (OTU) (at least 98% sequence similarity). Of these, 41 OTU were detected commonly from universal libraries and C. coccoides group libraries. One hundred and ten OTU were detected from the C. coccoides group libraries. Fifteen new OTU were isolated from the C. coccoides group libraries in human gut. Most of the OTU did not correspond to known species, thus representing as-yet-uncultured bacteria. We also detected OTU that related to the butyrate-producing bacteria. The C. coccoides group consisted of an average of 35 OTU, although there were differences in the number and the type of species in each individual. When fecal microbiota were analyzed using universal libraries, the OTU belonging to the C. coccoides group detected in elderly individuals were fewer than those detected in adult individuals. When C. coccoides group libraries were used, the numbers of OTU in elderly and adult individuals were not different. Interindividual differences in the composition of OTU belonging to the C. coccoides group were also observed in fecal microbiota.

Adult↗
PubMed2006

A comparative analysis of the information content in long and short SAGE libraries.

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on the length of the SAGE tag (10 vs. 17 basepairs). LongSAGE libraries are thought to be more useful than ShortSAGE libraries, but their information content has not been widely compared. To dissect the differences between these two types of libraries, we utilized four libraries (two LongSAGE and two ShortSAGE libraries) generated from the hippocampus of Alzheimer and control samples. In addition, we generated two additional short SAGE libraries, the truncated long SAGE libraries (tSAGE), from LongSAGE libraries by deleting seven 5' basepairs from each LongSAGE tag. RESULTS: One problem that occurred in the SAGE study is that individual tags may have matched to multiple different genes - due to the short length of a tag. We found that the LongSAGE tag maps up to 15 UniGene clusters, while the ShortSAGE and tSAGE tags map up to 279 UniGene clusters. Both long and short SAGE libraries exhibit a large number of orphan tags (no gene information in UniGene), implying the limitation of the UniGene database. Among 100 orphan LongSAGE tags, the complete sequences (17 basepairs) of nine orphan tags match to 17 genomic sequences; four of the orphan tags match to a single genomic sequence. Our data show the potential to resolve 4-9% of orphan LongSAGE tags. Finally, among 400 tSAGE tags showing significant differential expression between AD and control, 79 tags (19.8%) were derived from multiple non-significant LongSAGE tags, implying the false positive results. CONCLUSION: Our data show that LongSAGE tags have high specificity in gene mapping compared to ShortSAGE tags. LongSAGE tags show an advantage over ShortSAGE in identifying novel genes by BLAST analysis. Most importantly, the chances of obtaining false positive results are higher for ShortSAGE than LongSAGE libraries due to their specificity in gene mapping. Therefore, it is recommended that the number of corresponding UniGene clusters (gene or ESTs) of a tag for prioritizing the significant results be considered.

Algorithms↗
PubMed1997

Insight into screening immunoglobulin gene combinatorial libraries in a phage display vector: a tale of two antibodies.

Combinatorial libraries of immunoglobulin genes in "phage display" vectors are a powerful tool for obtaining antigen-specific antibody fragments. To date, this approach has been used to isolate abundant, but not rare, human autoantibodies of IgG class. We have compared the relative efficiencies of panning pComb3 libraries made from intrathyroidal plasma cells for abundant human autoantibodies to thyroid peroxidase (TPO) and rare autoantibodies to the thyrotropin receptor (TSHR). TPO-specific Fab were readily obtained from a library using three different forms of recombinant antigen, (i) purified TPO, (ii) impure TPO in culture medium and, (iii) TPO expressed on the surface of CHO cells. In contrast, TSHR-specific Fab were not isolated. This was the case despite repeated pannings of six libraries from three optimal patients (IgG/kappa and IgG/lambda libraries for each patient). Both purified recombinant TSHR and CHO cells expressing TSHR on their surface were used. Library enrichment was observed on some screenings. However, Fab expressed by individual clones or from enriched libraries were not specific as determined by (i) binding to purified, radio-labeled antigen, (ii) FACS analysis of TSHR on intact CHO cells and, (iii) inhibition of radiolabeled TSH binding. Remarkably, in screening for both TPO- and TSHR-specific Fab, neither library enrichment nor the retention of cDNA inserts of the correct size correlated with obtaining Fab with the antigenic specificity sought. Indeed, excellent enrichment could be observed with conditioned medium from untransfected cells. Our data suggest that the key to isolating rare antibodies from phage display libraries is not the creation of vast libraries of greater diversity or even the development of more stable vectors. Rather, success in this endeavor appears to require reducing the "noise" of non-specific clones in a moderately sized library.

Animals↗
PubMed2002

[cDNA libraries construction and screening in gene expression profiling of disease resistance in wheat].

A wheat line, Bai Nong 3217/Mardler BC5F4 with resistance to powdery mildew, was used to construct a conventional cDNA library and a suppression subtractive hybridization (SSH) cDNA library from wheat leaves inoculated by Erysiphe graminis DC. Three hundred and eighty-seven non-redundant ESTs from the conventional cDNA library and 760 ESTs from the SSH cDNA library were obtained, and the ESTs similarity analysis using BLASTn and BLASTx were conducted by comparing these ESTs with sequences in GenBank. The results showed that the redundancy of some kinds of genes such as photosynthesis related genes and ribosome related genes was higher in the conventional cDNA library but the varieties and quantities of disease resistance genes were less than those in the SSH cDNA library. The SSH cDNA library was found to have obvious advantages in gene expression profiling of disease resistance such as simple library construction procedure, rich specific DRR (disease-resistance-related) genes and decreased sequencing amount. To acquire genes that were involved in the powdery mildew resistance of wheat, hybridization with high-density dots membranes was used to screen the two libraries. The result showed that the method was relatively simple in operation, and the membranes could be used for many times. But some problems also existed with this screening method. For instance, a large amount of mRNA and radioactive isotope were needed and the hybridization procedure must be repeated several times to obtain stable hybridization results. About 54.1% function-known ESTs in the SSH cDNA library were identified to be DRR genes by screening. There were 247 clones of the SSH cDNA library that had positive signal in the repeated hybridizations with the pathogen uninfected probe. The identified DRR genes distributed in the whole procedure of powdery mildew resistance, but mainly focused on the SAR (systemic of acquired resistance).

Ascomycota↗
PubMed1992

Total quality management (TQM) in a hospital library: identifying service benchmarks.

Hospitals are turning to total quality management (TQM) to lower costs of providing care. A hospital library in a TQM environment needs to embrace corporate goals while maintaining its accountability as a contributor to quality patient care. Alliant Health System (AHS) Library at Norton Hospital and Kosair Children's Hospital in Louisville, Kentucky, conducted a study to establish TQM benchmarks and to examine the significance of its role in clinical care. Using a methodology designed to allow both library user and nonuser to respond, 2,091 surveys were distributed to physicians and nursing and allied health personnel. Areas surveyed included frequency of library use, impact of information received on clinical judgments, cognitive value of the information, and satisfaction with library products and services. Results confirm that the library has a substantial clinical role. Eighty-eight percent of reporting physicians agreed that information from the library contributed to higher quality care. Nursing and allied health were less convinced of the importance of the library's clinical role. Sixty-nine percent of nursing personnel and 58% of allied health personnel agreed that the library contributed to higher quality care. Nursing and allied health personnel also used the library less frequently than physicians. With these results as benchmarks, improving the clinical role of the library will take commitment to the TQM process and a willingness to change.

Attitude of Health Personnel↗
PubMed2004

EST analysis of mouse retina and RPE/choroid cDNA libraries.

PURPOSE: cDNA libraries from the mouse retina have recently been reported, but no well characterized library from the retinal pigment epithelium (RPE) or choroid of the mouse has yet appeared in the literature. To complement these libraries and to provide the first mouse RPE/choroid library, we used freshly dissected tissue from adult C57BL/6J mice to construct new retina and RPE/choroid libraries. METHODS: Eyes from 100 six to eight week old C57BL/6J mice were dissected in groups of 10. The whole retina and RPE/choroid were isolated individually and then homogenized before RNA isolation. Over 5000 clones each were sequenced from the unamplified and un-normalized retina and RPE/choroid libraries. All sequences were analyzed using GRIST (GRouping and Identification of Sequence Tags), a bioinformatics program for gene identification and clustering. RESULTS: The RPE/choroid library contained 3145 clusters with 76% of the clusters representing single clones. Nearly 87% of the clusters corresponded to named genes in GenBank, and 8% of the RPE clusters remain unidentified. The retina library contained 3190 clusters of which 78% represented only one clone. Approximately 85% of the clusters matched sequences in GenBank, and 9% of the clusters remain unidentified. The clones most abundant in each library were all well-known sequences and both libraries contained a number of tissue specific or tissue-enhanced genes. CONCLUSIONS: These new libraries should provide a valuable resource for gene discovery and cDNAs for expression analysis and functional studies.

Animals↗
PubMed1996

Health sciences library building projects: 1995 survey.

The Medical Library Association's fifth annual survey of recent health sciences library building projects identified twenty-five libraries planning, expanding, or constructing new library facilities. None of the fifteen new library projects are free standing structures; however, several occupy a major portion of the project space. Ten projects involve renovation of or addition to existing space. Information regarding size, cost of project, type of construction, completion date, and other factual data was provided for twelve projects. The remaining identified projects are in pre-design or early-design stages, or are awaiting funding approval. Library building projects for three hospital libraries, three academic medical libraries, and an association library are described. Each illustrates how considerations of economics and technology are changing the traditional library model from a centrally stored information depository housing a wide range of information under one roof where users come to the information, into an electronic model gradually shifting from investment in the physical presence of resources to investment in creating work space for creditible information specialists who help in-house and distanced users to obtain information electronically from any place and at any time. This new model includes a highly skilled library team to manage, filter, and package the information to users trained by these resident experts.

Canada↗
PubMed1977

Departmental libraries: why do they exist?

In response to an increasing concern on the part of the library staff over the role of the departmental libraries at The Milton S. Hershey Medical Center of The Pennsylvania State University, a questionnaire was developed by the George T. Harrel Library and sent to departmental libraries. From the analyzed responses, the authors were able to define the role of departmental libraries in a medical school/hospital situation, to analyze the Hershey Medical Center situation in an objective manner, to outline areas of possible cooperation between the main and departmental libraries, and to delineate some trends which appear to result from inadequate finding of a central library. Overall, the library found that departmental libraries at Hershey are currently maintaining collections consistent with the functional role of a departmental library.

Book Collecting↗
PubMed2000

In situ generation and screening of a dynamic combinatorial carbohydrate library against concanavalin A.

Dynamic combinatorial chemistry (DCC) is a recently introduced approach that is based on the generation of combinatorial libraries by reversible interconversion of the library constituents. In this study, the implementation of such libraries on carbohydrate-lectin interactions was examined. The dynamic carbohydrate libraries were generated from a small set (four or six compounds) of initial carbohydrate dimers through mild disulfide interchange, and selection was performed under two conditions defining either adaptive or pre-equilibrated libraries. Upon initiation, libraries were formed that contained comparable amounts of 10 or 21 individual dimeric species, dynamically interchanging during the scrambling process. They were probed with respect to binding to the plant lectin concanavalin A, either present during library generation or added after equilibration. The libraries could be generated easily both in the presence and absence of the receptor, and a bis-mannose structure was preferentially bound and selected from the mixture. Scrambling of the library in the presence of the receptor resulted in slightly higher yields than when the receptor was added after scrambling, indicating that the receptor to some extent acts as a thermodynamic trap during library generation. The present results illustrate the extention of the DCC approach to carbohydrate recognition groups, the generation of isoenergetic dynamic libraries, and the implementation of either adaptive or pre-equilibrated procedures.

Carbohydrate Conformation↗
PubMedDate not supplied

PLUMS: a program for the rapid optimization of focused libraries.

PLUMS is a new method to perform rational monomer selection for combinatorial chemistry libraries. The algorithm has been developed to optimize focused libraries with specific two-dimensional and/or three-dimensional properties. A preliminary step is the identification of those molecules in the initial virtual library which satisfy the imposed property constraints; we define these molecules as the virtual hits. From the virtual hits, PLUMS generates a starting library, which is the true combinatorial library that includes all the virtual hits. Monomers are then removed in an iterative fashion, thus reducing the size of the library. At each iteration, the worst monomer is removed. Each sublibrary is selected using a global scoring function, which balances effectiveness and efficiency. The iterative process continues until one is left with a library that consists entirely of virtual hits. The optimal library, which is the best compromise between effectiveness and efficiency, can then be selected according to the score. During the iterative process, equivalent solutions may well occur and are taken into account by the algorithm, according to a user-defined parameter. The number of monomers for each substitution site and the size of the library are parameters that can be either optimized or used to constrain the selection. The results obtained on two test libraries are presented. PLUMS was compared with genetic algorithms (GA) and monomer frequency analysis (MFA), which are widely used for monomer selection. For the two test libraries, PLUMS and GA gave equivalent results. MFA is the fastest method, but it can give misleading solutions. Possible advantages and disadvantages of the different methods are discussed.

Journal Article↗
PubMed2000

Enhancing the hit-to-lead properties of lead optimization libraries

In this paper we address several issues in the design of lead optimization libraries. Multipharmacophore descriptors were first developed in the context of designing diverse compound libraries. One reason for favoring such descriptors is the importance of the pharmacophore hypothesis in understanding the interaction of a compound with a protein target. Allied to this is the proposal that sampling over all potential pharmacophores leads to diversity in a biologically relevant space. We present results in support of this argument and also demonstrate that such methods are applicable to the design of focused libraries where the aim is to design the library toward a known lead or leads. This portability is important because it means that the same descriptors can be used for diverse library design, screening set selection, and focused library design, giving a consistent approach. We also examine the question of designing libraries with improved pharmacokinetic properties and show that it is possible to derive simple and rapidly computable descriptors applicable to the prediction of drug transport properties. Furthermore, these can be applied in the context of library design, although it may be necessary to synthesize libraries in a noncombinatorial manner to obtain the best results. To address this problem, we describe a Monte Carlo search procedure that allows the selection of a near-combinatorial subset in which all library members satisfy the design criteria. We present an example from our own work that illustrates how consideration of calculated log P, molecular weight, and polar surface area in the design of a combinatorial library can lead to compounds with improved absorption characteristics as determined by experimental Caco-2 measurements.

Journal Article↗
PubMed1994

Recursive deconvolution of combinatorial chemical libraries.

A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a solid support. After each coupling, a portion of the resin from each of the four reaction vials was set aside and catalogued. The solid support from each vial is then combined, mixed, and redivided. The steps of (i) coupling, (ii) saving and cataloging, and (iii) randomizing were repeated until a pentapeptide library was obtained. The four pentapeptide libraries where the N-terminal amino acid is defined were screened against the beta-endorphin antibody and quantitated via an ELISA. The amino acid of the four pools that demonstrated the most binding was then coupled to the four tetrapeptide partial libraries that had been set aside and catalogued during the split synthesis. This recursive deconvolution was repeated until the best binders were deduced. Besides the anticipated native binder, two other members of the library displayed significant binding. This recursive method of deconvolution does not use a molecular tag, requires only one split synthesis, and can be applied to the deconvolution of nonlinear small-molecule combinatorial libraries and linear oligomeric combinatorial libraries, since it is based only on the procedure of the synthesis.

Amino Acid Sequence↗
PubMed2026

Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing.

Metagenomic next-generation sequencing (mNGS) is increasingly used in infectious disease diagnostics, yet how library preparation shapes the microbial, functional, and host signals recovered from clinical samples remains poorly defined. Here, we performed a within-sample parallel comparison of three mNGS library preparation strategies-DNA-based libraries (DNAlib), RNA-based libraries (RNAlib), and total nucleic acid-based libraries (TNAlib)-across a diverse range of clinical specimens spanning five sample types. Using a curated clinical infectome as a benchmark, we show that library strategies are not interchangeable but capture distinct biological dimensions of the same specimen. RNAlib provided the most comprehensive standalone recovery of the clinical infectome, with improved detection of RNA viruses and cellular pathogens, enhanced resolution of resistance and virulence signals, and preservation of infection-associated host immune signatures. DNAlib showed stronger baseline recovery of DNA viruses and broader host genome coverage, whereas the TNAlib workflow evaluated here largely behaved as an intermediate strategy rather than a consistent improvement over dedicated DNA- or RNA-based workflows. Together, these results establish that the library preparation protocol is a major determinant of how clinical mNGS data should be interpreted and provide a framework for selecting sequencing strategies according to specific diagnostic and biological questions.IMPORTANCEMetagenomic sequencing is increasingly used in infectious disease research and clinical diagnostics, but different library preparation strategies may recover fundamentally different biological signals from the same sample. These signals include not only pathogens but also background microbes, microbial functional activity, and host immune-response patterns. Here, we systematically compared DNA-, RNA-, and total nucleic acid-based metagenomic sequencing libraries using the same clinical samples processed in parallel. We found that the three strategies did not provide equivalent information. RNA-based sequencing generated the most informative single-library view of infection, particularly for RNA viruses, cellular pathogens, functional microbial signals, and host immune-response patterns. DNA-based sequencing was more effective for DNA virus and host genome recovery, whereas the total nucleic acid sequencing workflow evaluated here generally behaved as an intermediate strategy. These findings show that library preparation can substantially influence the interpretation of metagenomic data.

functional characterization↗
PubMed2004

Creation and development of an All-Wales Health Library Catalogue.

This article focuses on the collaboration between the University of Wales College of Medicine (UWCM) libraries and the Welsh National Health Service (NHS) libraries to create a joint library catalogue. The goal was to create an all-Wales resource that gave users one access point to search for the location and availability of health-related material in any Welsh medical library. This venture grew out of the existing collaborative scheme, the All-Wales Health Information and Library Extension Services (AWHILES). Currently, all seven UWCM libraries and 17 NHS libraries contribute to the catalogue. Four more libraries are due to join in late 2003 or early 2004. All UWCM and AWHILES libraries would then be contributing members of the joint catalogue. The article discusses the background and motivation to the creation of the database. It explores the positives and negatives of the project plus what was learnt as the venture progressed. It reviews the establishment and operations of the Welsh Health Voyager User Group (WHVUG) created to involve all contributing members in the running and future development of the library catalogue.

Catalogs, Library↗
PubMed1970

User services offered by medical school libraries in 1968: results of a national survey employing new methodology.

The breadth and depth of services that ninety-two medical school libraries offer to individual users were ascertained by interviewing the heads of these libraries, employing a standardized inventory procedure developed earlier (Bulletin 56:380-403, Oct. 1968). Selected aspects of the descriptive data obtained on services to faculty and to medical students are presented and commented upon. Comparisons with the findings of earlier surveys suggest that increases in the staffs and budgets of medical school libraries over the past two decades have gone largely to supporting a rapidly increasing volume of service, rather than to any striking increase in the breadth and depth of services. To facilitate summarization and comparisions among libraries the descriptive data were weighted and converted to quantitative measures; the weighting scheme was established by a group of five academic medical librarians to reflect the relative values the group assigned to different services. One of these quantitative measures, the percentage score for overall services relative to the optimal library, summarizes a library's services in a single figure. On this measure, medical school libraries ranged from 38 percent to 87 percent; the median overall score was 63 percent. Results of some exploratory analyses are described; these analyses attempted to find explanations for the observed differences among libraries and among geographical regions on the quantitative measures. Present and potential uses of the survey data for managerial and research purposes are discussed. One of the most important of these uses is in establishing and implementing standards-activities which should be carried out by the library profession itself-and recommendations are made for a program of such activities that is appropriate for the Medical Library Association.

Libraries, Medical↗
PubMed1981

Library instruction within the medical record administration curriculum.

A course for medical record administration (MRA) students has been developed at the University of Tennessee Center for the Health Sciences Library. The course's objectives are: (1) to train students in the use of the resources and services of health sciences libraries and (2) to provide basic instruction in the organization, operation, and management of a small hospital library. These objectives are met by integrating library use instruction within the MRA curriculum and by presenting a five-week hospital library management workshop. Library use instruction includes a library orientation and sessions on the use of major reference sources, writing for publication, and the use and evaluation of the medical record literature. The workshop covers the role of the medical record administrator as manager of the hospital library. Sessions cover basic principles of hospital library administration, technical and public services, and sources of outside assistance. Results are reported of a survey of graduates conducted to determine whether a need for the course still existed and if the changes made as a result of the evaluation process were appropriate. The teaching methods and evaluation techniques used in this course are applicable to library instruction in other disciplines.

Hospitals↗
PubMed1994

[The European Health Information and Library Association--EAHIL/AEIBS].

The authors give a short history of the association, beginning with its establishment (1986) and a survey of its activities up to the summer of 1994, and its organization. They write about conditions and terms of membership, about aims and objectives of the association: to improve co-operation among European medical libraries, to raise standards of library and information services as well as professionality of librarians and information officers and their continuous education, especially in regard to new technologies. The authors also emphasize the European character and principles of tolerance that enable a connection of medical nursing, veterinary and pharmaceutical libraries/librarians in these specializations in various countries. It is necessary for information users to learn modern library methods, including information skills for the learning process (libraries of medical faculties). No less important is the role of libraries for research and evaluation of research. A survey of Czechoslovak and Czech participation in EAHIL is also given here. The course of the Fourth European Conference of Medical and Health Libraries on Oslo (from 28th June to 2nd July, 1994) is shortly described. Further library conference activities are also mentioned: 7th International Congress of Medical Librarianship in Washington, DC, May 10-12, 1995; Fourth Nordic Conference for Medical Libraries, Copenhagen (Denmark), August 21-24, 1995; EAHIL Symposium on Cooperation of Medical Libraries, Prague (Czech Republic), September 21-22, 1995; Fifth European Conference of Medical and Health Libraries, Coimbra (Portugal), September 18-21, 1996.

Czech Republic↗