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PubMed1978

The use of a subscription agent's computer facilities in creating and maintaining a library's subscription profile.

A library's subscription profile should reflect the needs of library clientele, but creating such a profile can require extensive clerical work. It was found that a subscription agent's computerized facilities could be used to facilitate a program of this type by providing initial serial listings for use in a survey, by manipulating data obtained from such a survey, and by producing listings identifying resulting serial titles and costs according to requesting disciplines. The data base thus created is updated as subscriptions are added or deleted so that the profile remains current.

Computers↗
PubMed2006

Not just for celebrities: collaborating with a PR representative to market library education services.

Hardin Library for the Health Sciences offers an education service called Hardin House Calls. In collaboration with the University of Iowa libraries' public relations coordinator, the education team developed a marketing campaign for Hardin House Calls. Marketing strategies included designing a new logo, meeting with external relations representatives and faculty, distributing a user survey, and producing and distributing posters and advertisements. These marketing strategies greatly increased the visibility and use of Hardin House Calls. The campaign also led to a series of faculty development sessions, education collaborations with smaller health sciences departments, and collection development opportunities. Promoting an instructional service through a public relations frameworkwas found to be a highly successful strategy.

Cooperative Behavior↗
PubMed1995

The construction and analysis of M13 libraries prepared from YAC DNA.

Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomic DNA and their use in genome analysis is now extensive. We modified a series of procedures to produce high quality shotgun libraries from small amounts of YAC DNA. Clones from several different libraries have been sequenced and analyzed for distribution, sequence integrity and degree of contamination from yeast DNA. We describe these procedures and analyses and show that sequencing at about 1-fold coverage, followed by database comparison (survey sequencing) offers a relatively quick method to determine the nature of previously uncharacterized cosmid or YAC clones.

Bacteriophage M13↗
PubMedDate not supplied

A client/server system for Internet access to biomedical text/image databanks.

Internet access to mixed text/image databanks is finding application in the medical world. An example is a database of medical X-rays and associated data consisting of demographic, socioeconomic, physician's exam, medical laboratory and other information collected as part of a nationwide health survey conducted by the government. Another example is a collection of digitized cryosection images, CT and MR taken of cadavers as part of the National Library of Medicine's Visible Human Project. In both cases, the challenge is to provide access to both the image and the associated text for a wide end user community to create atlases, conduct epidemiological studies, to develop image-specific algorithms for compression, enhancement and other types of image processing, among many other applications. The databanks mentioned above are being created in prototype form. This paper describes the prototype system developed for the archiving of the data and the client software to enable a broad range of end users to access the archive, retrieve text and image data, display the data and manipulate the images. System design considerations include; data organization in a relational database management system with object-oriented extensions; a hierarchical organization of the image data by different resolution levels for different user classes; client design based on common hardware and software platforms incorporating SQL search capability, X Window, Motif and TAE (a development environment supporting rapid prototyping and management of graphic-oriented user interfaces); potential to include ultra high resolution display monitors as a user option; intuitive user interface paradigm for building complex queries; and contrast enhancement, magnification and mensuration tools for better viewing by the user.

Anatomy, Cross-Sectional↗
PubMed1989

The type-specific epitopes of the Epstein-Barr virus nuclear antigen 2 are near the carboxy terminus of the protein.

The Epstein-Barr virus nuclear antigen 2 (EBNA 2) shows serotype variation and two serologically distinct groups of viruses have been identified. These correspond to the two hybridization groups of viruses (A and B) that are distinguished by a highly substituted nucleic acid sequence in the middle of the open reading frame of the EBNA 2 gene. An epitope survey of the EBNA 2-coding region was carried out using a new prokaryotic expression vector tailored to express DNA fragments from the M13 sequencing libraries of the B95-8 (type A) and Jijoye (type B) prototype virus strains. Short overlapping stretches of EBNA 2 sequence were expressed as fusion proteins and used in Western blotting with human sera that contained serotype-specific antibodies. The type A-specific epitope was located between residues 378 and 435 of the B95-8 EBNA 2 polypeptide and the type B-specific epitope mapped between residues 390 and 454, at the carboxy terminus of the Jijoye polypeptide chain. All of the type-specific anti-EBNA 2 sera tested reacted with fusion proteins containing one or other of these epitopes. Despite the direct correlation between the hybridization and serological phenotypes, the type-specific epitopes appear to lie in the relatively conserved carboxy-terminal region of EBNA 2. There was no indication that the residues of the non-homologous region contributed to the formation of antibody-combining sites.

Amino Acid Sequence↗
PubMed2000

Gene survey of the pathogenic protozoan Trypanosoma cruzi.

We have performed a survey of the active genes in the important human pathogen Trypanosoma cruzi by analyzing 5013 expressed sequence tags (ESTs) generated from a normalized epimastigote cDNA library. Clustering of all sequences resulted in 771 clusters, comprising 54% of the ESTs. In total, the ESTs corresponded to 3054 transcripts that might represent one-fourth of the total gene repertoire in T. cruzi. About 33% of the T. cruzi transcripts showed similarity to sequences in the public databases, and a large number of hitherto undiscovered genes predicted to be involved in transcription, cell cycle control, cell division, signal transduction, secretion, and metabolism were identified. More than 140 full-length gene sequences were derived from the ESTs. Comparisons with all open reading frames in yeast and in Caenorhabditis elegans showed that only 12% of the T. cruzi transcripts were shared among diverse eukaryotic organisms. Comparison with other kinetoplastid sequences identified 237 orthologous genes that are shared between these evolutionarily divergent organisms. The generated data are a useful resource for further studies of the biology of the parasite and for development of new means to combat Chagas' disease.

Animals↗
PubMed2004

Degenerate peptide recognition by Candida albicans adhesins Als5p and Als1p.

Candida albicans and Saccharomyces cerevisiae expressing the adhesins Als5p or Als1p adhere to immobilized peptides and proteins that possess appropriate sequences of amino acids in addition to a sterically accessible peptide backbone. In an attempt to further define the nature of these targets, we surveyed the ability of yeast cells to adhere to 90- micro m-diameter polyethylene glycol beads coated with a 7-mer peptide from a library of 19(7) unique peptide-beads. C. albicans bound to ca. 10% of beads from the library, whereas S. cerevisiae expressing Als5p or Als1p bound to ca. 0.1 to 1% of randomly selected peptide-beads. S. cerevisiae expressing Als1p had a distinctly different adherence phenotype than did cells expressing Als5p. The former adhered in groups or clumps of cells, whereas the latter adhered initially as single cells, an event which was followed by the build up of cell-cell aggregates. Beads with adherent cells were removed, and the peptide attached to the bead was determined by amino acid sequencing. All adhesive beads carried a three-amino-acid sequence motif (tau phi+) that possessed a vast combinatorial potential. Adherence was sequence specific and was inhibited when soluble peptide identical to the immobilized peptide was added. The Als5p adhesin recognized some peptides that went unrecognized by Als1p. The sequence motif of adhesive peptides identified by this method is common in proteins and offers so many possible sequence combinations that target recognition by the Als proteins is clearly degenerate. A degenerate recognition system provides the fungi with the potential of adhering to a multitude of proteins and peptides, an advantage for any microorganism attempting to establish a commensal or pathogenic relationship with a host.

Amino Acid Sequence↗
PubMed2003

Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients.

BACKGROUND: Plasmodium vivax is the most widely distributed human malaria, responsible for 70-80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected. METHODS: A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10(-30) was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology RESULTS: A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them. CONCLUSION: These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.

AT Rich Sequence↗
PubMed2001

[Antepartum perineal massage: review of randomized trials].

OBJECTIVE: To assess the effectiveness of ante partum perineal massage to reduce the number of perineal injuries and episiotomies through a survey of the existing literature. MATERIAL AND METHODS: [corrected] A search both in English and French on randomized clinical trials using the Medline and Cochrane Library databases. The key words: "Perineum", "massage", "perineum injuries", "randomized controlled trial" were selected from the years 1966 to November 2000. RESULTS: Four randomized controlled trials were found. The definition of the selected issues, as well as the included and excluded criteria varied according to the authors. Perineal massages seemed to reduce the occurrence of perineal injuries and episiotomies, mostly among primipara: Labrecque et al. in 1999, noted an OR of 0.56; 95% CI: 0.61-1.31 and at the opposite an increased rate of intact perineum in the massage group (OR = 1.79; 95% CI 1.27-2.52]; and Shipman et al. in 1997 stressed among women of > or = 30 years old an augmentation of intact perineum in the intervention group (OR = 1.93; 95% CI 1.08-3.48), and in the logistic regression taking into account age and birth weight they found a reduction of episiotomies and important perineal injuries (p = 0.02). CONCLUSION: Ante partum perineal massages would seem valid but further studies would be necessary to evaluate the utility of this intervention in the avoidance of serious perineal injuries and the women's satisfaction.

Adult↗
PubMed2003

Benchmarking information needs and use in the Tennessee public health community.

OBJECTIVE: The objective is to provide insight to understanding public health officials' needs and promote access to data repositories and communication tools. METHODS: Survey questions were identified by a focus group with members drawn from the fields of librarianship, public health, and informatics. The resulting comprehensive information needs survey, organized in five distinct broad categories, was distributed to 775 Tennessee public health workers from ninety-five counties in 1999 as part of the National Library of Medicine-funded Partners in Information Access contract. RESULTS: The assessment pooled responses from 571 public health workers (73% return rate) representing seventy-two of ninety-five counties (53.4% urban and 46.6% rural) about their information-seeking behaviors, frequency of resources used, computer skills, and level of Internet access. Sixty-four percent of urban and 43% of rural respondents had email access at work and more than 50% of both urban and rural respondents had email at home (N = 289). Approximately 70% of urban and 78% of rural public health officials never or seldom used or needed the Centers for Disease Control (CDC) Website. Frequency data pooled from eleven job categories representing a subgroup of 232 health care professionals showed 72% never or seldom used or needed MEDLINE. Electronic resources used daily or weekly were email, Internet search engines, internal databases and mailing lists, and the Tennessee Department of Health Website. CONCLUSIONS: While, due to the small sample size, data cannot be generalized to the larger population, a clear trend of significant barriers to computer and Internet access can be identified across the public health community. This contributes to an overall limited use of existing electronic resources that inhibits evidence-based practice.

Attitude to Computers↗
PubMedDate not supplied

Resident education in transfusion medicine: a multi-institutional needs assessment.

A survey was conducted among resident physicians at nine academic medical centers to assess their perceptions of their knowledge of transfusion medicine (TM), their confidence in using various blood bank resources, and their ratings of the contribution of various learning resources to their knowledge of TM. A total of 320 residents completed the survey; nearly 90 percent were in an internal medicine, surgery, or anesthesiology residency. Respondents placed a high value on the relevance of TM to patient care, although they rated their knowledge and learning opportunities as only moderate. They rated senior residents as the most useful educational resource, with undergraduate medical school education, formal conferences, and journals and library resources being the three next most useful. Residents had the greatest confidence in using packed red cells, platelets, and fresh-frozen plasma. Surgery and anesthesiology residents generally had greater confidence in using blood bank resources than internal medicine residents. The findings of the survey can be used, along with the results of medical care evaluations of transfusion practice and opinions of education experts, to create an optimally relevant and effective curriculum for resident education in transfusion medicine.

Academic Medical Centers↗
PubMedDate not supplied

A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface.

We have initially sequenced approximately 8,000 canine expressed sequence tags (ESTs) from several complementary DNA (cDNA) libraries: testes, whole brain, and Madin-Darby canine kidney (MDCK) cells. Analysis of these sequences shows that they provide partial sequence information for about 5%-10% of the canine genes. An analysis pipeline has been created to cluster the ESTs and to map individual ESTs as well as clustered ESTs to both the human genome and the human proteome. Gene ontology (GO) terms have been assigned to the ESTs and clusters based on their top matches to the International Protein Index (IPI) set of human proteins. The data generated is stored in a MySQL relational database for analysis and display. A Web-based Perl script has been written to display the analyzed data to the scientific community.

Animals↗
PubMed1999

GaIN (Georgia Interactive Network for Medical Information) study on health professionals' search requests and continuing education needs.

Health sciences librarians are being called upon to be more proactive in their institutions' continuing education efforts. In an effort to identify whether search requests indicated CE needs, a study was conducted by a group of members of GaIN (Georgia Interactive Network for Medical Information). MEDLINE requests from health care professionals for subject specific clinical topics were collected during a six-month period via a standard search request form created for the study. Copies of all completed requests were collected and broad ICD-9 codes assigned to the search topics. Institutional reports were generated for each participating library to share with hospital CE coordinators. They were also compiled for the group as a whole, and reflected the "hottest" topics requested during the study period for physicians and for non-physicians (nurses, allied health, administrators). A survey to hospital librarians and CE educators showed some value in the reports, but greater potential for further collaboration between librarians and CE coordinators.

Allied Health Personnel↗
PubMed2005

Library design for fragment based screening.

According to Hann's model of molecular complexity an increased probability of detection binding to a target protein can be expected when small, low complex molecular fragments are screened with high sensitivity instead of full-sized ligands with lower sensitivity. Analysis of the HTS summary data of Novartis and comparison with NMR screening results obtained on generic fragment libraries indicate this expectation to be true with hitrates of 0.001% - 0.151% observed in the identification of ligands with an IC(50) threshold in the micromolar range in an HTS setup and hitrates above or equal to 3% observed in NMR screening of fragments with an affinity threshold in the millimolar range. It is however necessary to keep in mind that the sets of target studied were not identical for both method and the experience in NMR screening is too limited for a final conclusion. The term hitrate as used here reflects only the success rate in the observation of ligand binding event. It must not be confused with the overall success rate of fragment and high throughput screening in the lead finding process, which can be entirely different, since the steps required to follow-up a ligand binding event to a lead are different for both methods. A survey of fragment-based lead discovery case studies given in the literature shows that in approximately half of the cases the initial hit fragment was discovered by screening a generic library, whereas in the other cases some knowledge about an initial ligands or the protein binding site has been used, whereas systematic virtual screening of fragment databases has been only rarely reported. As comparatively high hitrates were obtained, further consideration to optimize the generic fragment screening library were directed to the chemical tractability of the fragment. As several functional groups preferred by chemists for modification and linking of the fragments are also preferentially involved in interactions between the fragments and the target protein, a set of screening fragments was derived from chemical building blocks by masking its linker group by a chemical transformation which can be later on used in the chemical follow-up of the fragment hit. For example primary amines can be masked as acetamides. If the screening fragment is active the related building block can then be used for synthesis of a follow-up library.

Combinatorial Chemistry Techniques↗
PubMed1986

1,25-Dihydroxyvitamin D3-stimulated mRNAs in rat small intestine.

The technique of differential hybridization has been employed to study gene expression associated with vitamin D action on the mammalian intestine. A cDNA library consisting of 10(6) independent recombinants was constructed from poly(A)+ RNA extracted from vitamin D-deficient rats given 1,25-dihydroxyvitamin D3. A survey of 20,000 clones resulted in identification of four distinct cDNAs whose corresponding mRNAs are significantly increased 12 h after an intrajugular dose of 1,25-dihydroxyvitamin D3 given to vitamin D-deficient rats. DNA sequence analysis identified these mRNAs as mitochondrial ATP synthetase, vitamin D-dependent calcium binding protein, cytochrome oxidase subunit I, and cytochrome oxidase subunit III. The time course of response of three of these mRNAs was similar, with maximum values at 12 h after dosing, while that of cytochrome oxidase subunit I showed two peaks at 6 and 18 h following a single dose of 1,25-dihydroxyvitamin D3. The levels of all four mRNAs were elevated in rats supplied with vitamin D when hypocalcemia was produced by dietary calcium restriction.

Animals↗
PubMedDate not supplied

The fetal imaging workstation demonstration project.

Congenital birth defects are a leading cause of infant mortality. Early detection of fetal anomalies by prenatal ultrasound may improve clinical outcome in selected cases. However, many training programs are hindered by curriculum weaknesses which include: (1) limited physician exposure to ultrasound anomalies; (2) inadequate postnatal correlation with prenatal findings; (3) constraints imposed by static images for ultrasound training; and (4) difficulty with understanding complex three-dimensional anatomy. The Fetal Imaging Workstation Demonstration Project addresses these problems by illustrating how computers can supplement traditional prenatal ultrasound training through interactive multimedia. The project uses a laserdisc library of ultrasound video images as source material for a variety of interactive software tutorials. An educational testing module has been developed that can evaluate diagnostic skills through simulated ultrasound studies provided by the laserdisc library. An interactive three-dimensional fetal heart model also provides a new way for physicians to better understand their two-dimensional ultrasound studies. A survey suggests that this prototype has been widely accepted by housestaff physicians and that there is a perceived need for this supplementary training. Future work will address the educational effectiveness of these materials and will consider cost-effective ways to disseminate the software for other institutions. However, future development must be implemented against a background of rapidly emerging technologies involving faster computers, digital video, and virtual reality applications.

Computer Systems↗
PubMed1995

The value of information supplied to clinicians by health libraries: devising an outcomes-based assessment of the contribution of libraries to clinical decision-making.

The Value project, a study funded by the British Library Research and Development Department and a group of postgraduate medical deans, has examined the effectiveness of NHS library and information services. Clinicians at 11 hospital library sites were asked to describe the purposes for which they needed information, the steps they took to obtain it, and to assess the value of the information obtained from interlibrary loan requests, database searches and end-user searches. A sample of non-library users and of users of the BMA Dial-Up MEDLINE service were also asked similar questions. Results show that information did, or would in the future, assist in personal clinical decision-making and which kinds of decisions were most supported. Information new to clinicians was often provided. Follow-up interviews provided illustrations of the ways in which developments aimed at more cost-effective patient care were supported by information obtained from the library. Results are being used to guide the production of a quality assurance toolkit to help libraries audit their services and improve the delivery of information to clinicians.

Clinical Medicine↗