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PubMed2002

Use of the Cochrane electronic library in complementary and alternative medicine courses in medical schools: is the giant lost in cyberspace?

Courses in complementary and alternative medicine (CAM) are increasing in medical schools in the United States and, currently, approximately two thirds of U.S. medical schools offer at least one such course. As these courses grow in popularity, however, concerns are also growing that these courses lack an evidence-based perspective. We propose that one interesting and easy way to bring an evidence-based perspective to the CAM classroom is to utilize the Cochrane Electronic Library (CLIB), which is available in many medical libraries, as a teaching tool. The CLIB currently houses more than 80 CAM-related, full-text systematic reviews and approximately 5000 CAM-related clinical trials, making it a valued resource for people who seek CAM evidence. Moreover, the CLIB commitment to publishing reviews regardless of the results make it a resource where one can find reviews concluding there is strong evidence of benefit or no evidence of benefit. In addition to the access to CAM evidence which the CLIB provides, students can learn basic critical appraisal skills by learning the rationale behind Cochrane systematic reviews. A survey of CAM course directors, however, shows that almost one half of these directors have never used the CLIB. For those who have never used the CLIB, this editorial explains the four main databases within the CLIB and presents ideas for using them in CAM school courses.

Complementary Therapies↗
PubMed2004

From library to discharge: a managing care student project.

BACKGROUND AND OBJECTIVES: The Patient Care Project (PCP) was a central component of the Undergraduate Medical Education for the 21st Century (UME-21) grant project at the University of Nebraska. With the primary goal of improving students' critical thinking skills, the PCP was directed more toward an understanding of managing care than the business aspects of managed care and emphasized written communication skills, clinical hypothesis testing, and exploring ways to solve medical and ethical questions. METHODS: All 239 students graduating in 2000 and 2001 were required to analyze the medical care received by one of their hospitalized patients. Using a criterion-based evaluation tool, students' written critiques were assessed in five specific areas, all of which required critical thinking skills. Students also received an overall grade for the project. The UME-21 Graduation Survey was used to assess changes in attitudes and behavior. Students graduating in 1999, prior to the institution of the PCP graduation requirement, served as a control group. RESULTS: The most frequently discussed topic of the PCPs was cardiovascular disease. The mean overall rating by the faculty for the PCPs was 3.7 and 3.8 in academic years 2000 and 2001, respectively (maximum=5). In a qualitative analysis of the PCPs, students demonstrated insight into their patients' overall medical care, including the use of evidence-based medicine (EBM), quality improvement, and cost containment. There were no statistically significant differences, however, between the PCP and control groups on the UME-21 Graduation Survey. Nonetheless, more students who had completed the PCP reported that they had identified the total cost of a patient's stay, designed a quality improvement loop, and obtained clinical evidence from an EBM computer database. On this same survey, all students agreed with the use of clinical practice guidelines and cost containment. CONCLUSIONS: The PCP appeared to be relevant to the students' learning needs, and they provided cogent critiques of the medical care they had rendered as well as critical analyses of their patients' discharge summaries and the cost of care including ways to reduce cost. On the other hand, we were unable to demonstrate any substantial differences in the results of the UME-21 Graduation Survey given to both the PCP and control groups. In spite of this lack of effect on students' attitudes, the PCP was perceived by the faculty to be valuable and has been incorporated into the required third-year family medicine clerkship at the University of Nebraska.

Clinical Clerkship↗
PubMed1992

cDNA surveying of specific tissue expression of human chromosome 19 sequences.

cDNA surveying is a straightforward approach for identifying sequences in genomic clones expressed in specific tissues. It has been applied to a subchromosomal region of human chromosome 19 (19q13.2-q13.4), a region that contains several known expressed sequences including the locus for myotonic dystrophy (DM). Genomic clones were selected from this region by probing a human placental cosmid library with a chromosome 19q-specific minisatellite sequence, or human genomic clones were isolated from a cosmid library constructed from a human chromosome 19q13.2-q13.3 hamster hybrid cell line using human repetitive DNA as probe. Pooled cDNAs synthesized from RNA of specific tissues characteristically affected in DM were depleted in repetitive sequences and used as hybridization probes against gridded cosmid arrays. DNA from the cDNA-positive cosmid clones was transferred to nylon filters and reprobed with cDNAs to identify restriction fragments that were expressed in these tissues. Hybridizing restriction fragments were subcloned, sequenced, and demonstrated to be nonrepetitive. Primer pairs complementary to subcloned sequences were constructed and used for PCR amplification of cDNA synthesized from RNA of tissues affected in myotonic dystrophy. PCR products were sequenced to verify the identity of expressed genomic DNA and its corresponding cDNA.

Animals↗
PubMed2006

Open source tools and toolkits for bioinformatics: significance, and where are we?

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Algorithms↗
PubMed2002

Undermethylated DNA as a source of microsatellites from a conifer genome.

Developing microsatellites from the large, highly duplicated conifer genome requires special tools. To improve the efficiency of developing Pinus taeda L. microsatellites, undermethylated (UM) DNA fragments were used to construct a microsatellite-enriched copy library. A methylation-sensitive restriction enzyme, McrBC, was used to enrich for UM DNA before library construction. Digested DNA fragments larger than 9 kb were then excised and digested with RsaI and used to construct nine dinucleotide and trinucleotide libraries. A total of 1016 microsatellite-positive clones were detected among 11 904 clones and 620 of these were unique. Of 245 primer sets that produced a PCR product, 113 could be developed as UM microsatellite markers and 70 were polymorphic. Inheritance and marker informativeness were tested for a random sample of 36 polymorphic markers using a three-generation outbred pedigree. Thirty-one microsatellites (86%) had single-locus inheritance despite the highly duplicated nature of the P. taeda genome. Nineteen UM microsatellites had highly informative intercross mating type configurations. Allele number and frequency were estimated for eleven UM microsatellites using a population survey. Allele numbers for these UM microsatellites ranged from 3 to 12 with an average of 5.7 alleles/locus. Frequencies for the 63 alleles were mostly in the low-common range; only 14 of the 63 were in the rare allele (q < 0.05) class. Enriching for UM DNA was an efficient method for developing polymorphic microsatellites from a large plant genome.

DNA Methylation↗
PubMed1993

A genetic survey of the pathogenic fungus Ophiostoma ulmi across a Dutch elm disease front in western Canada.

The natural population structure of the Dutch elm pathogen Ophiostoma ulmi was determined from isolated collected from across a Western Canadian disease front through an analysis of restriction-site polymorphisms in the ribosomal DNA repeat, length mutations in the mitochondrial genomes, and through DNA fingerprinting of the nuclear genomes using a minisatellite DNA probe. The 8.8-kbp rDNA repeat was selected from a genomic library, and restriction-site and genic maps were constructed for the nonaggressive and aggressive subgroups of O. ulmi. There were only three restriction-site differences that distinguished these two subgroups and no intrasubgroup variation was detected. All of the isolates collected from the disease front were of the aggressive subgroup and were represented by two distinct nuclear and four mitochondrial genotypes. The minority of the isolates were of a single genotype (type A nuclear DNA; type I mtDNA), indicating the presence of a single very large clone extending across much of Manitoba and into Saskatchewan.

Ascomycota↗
PubMed1996

Genes expressed in Brugia malayi infective third stage larvae.

We have used a tag sequencing approach to survey genes expressed in the third stage infective larvae of the human filarial nematode parasite Brugia malayi. RNA was isolated from late vector-stage L3 larvae after days 9 or 10 of infection in mosquitos, and converted to cDNA by reverse transcriptase. Double-stranded cDNA was produced by either conventional methods (non-SL cDNA library) or by PCR using the nematode spliced leader (SLI) and oligo(dT) primers (SL cDNA library). Two clone libraries (one from SL and one from non-SL cDNAs) were constructed in lambda ZapII. A set of these full-length clones was selected and 596 inserts were sequenced from the 5' end. We have identified 364 B. malayi genes (the majority of which are new) that encode housekeeping proteins, structural proteins, proteins of immediate immunological or drug-discovery interest as well as a large class of novel sequences which may prove to have significant involvement in host invasion. Extensive, genome-wide approaches to the analysis of larval gene expression are now possible for B. malayi. We present several examples of this approach.

Amino Acid Sequence↗
PubMed1998

Oral ibuprofen and diclofenac in post-operative pain: a quantitative systematic review.

Surveys show consistently that pain is not treated well. Improvement depends on knowing which treatments are the most effective. We used systematic review to compare the relative efficacy of two common analgesics, ibuprofen and diclofenac, in post-operative pain. Studies were identified by searching MEDLINE (1966 to Dec 1996), EMBASE (1980 to Jan 1997), the Cochrane Library (Aug 1996), Biological Abstracts (Jan 1985 to Dec 1996) and the Oxford Pain Relief Database (1950 to 1994). We sought randomised, controlled, single-dose comparisons of oral ibuprofen or diclofenac against placebo. Summed pain relief or pain intensity difference over 4-6 h was extracted and converted into dichotomous information yielding the number of patients with at least 50% pain relief. This was then used to calculate the relative benefit and the number-needed-to-treat for one patient to achieve at least 50% pain relief. Thirty-four reports compared ibuprofen and placebo (3591 patients), six compared diclofenac with placebo (840 patients), and there were two direct comparisons of diclofenac 50 mg and ibuprofen 400 mg (130 patients). In post-operative pain, the numbers-needed-to-treat for ibuprofen 200 mg were 3.3 (95% confidence interval 2.8-4.0) compared with placebo, for ibuprofen 400 mg 2.7 (2.5-3.0), for ibuprofen 600 mg 2.4 (1.9-3.3), for diclofenac 50 mg 2.3 (2.0-2.7) and for diclofenac 100 mg 1.8 (1.5-2.1). Direct comparisons of diclofenac 50 mg with ibuprofen 400 mg showed no significant difference between the two. Both drugs worked well. Choosing between them is an issue of dose, safety and cost. Copyright 1998 European Federation of Chapters of the International Association for the Study of Pain.

Journal Article↗
PubMed1996

An assessment of practice support and continuing medical education needs of rural Pennsylvania family physicians.

Family physicians provide the greatest proportion of care in rural communities. Yet, the number of physicians choosing family practice and rural practice has continued to decline. Undesirable aspects of rural practice, such as professional isolation and a lack of or inadequate resources, are assumed to be associated with this decline. This article reports on the practice support and continuing medical education needs of rural family physicians. A mail survey was conducted in 1993 on a purposive sample of family physicians in 39 of 67 rural-designated or urban Pennsylvania counties with low population densities. The physicians identified needs that included patient education materials and programs, community health promotion, federal regulation updates, technical assistance with computers and business management, database software and a videotape lending library, a drug hotline, and mini-fellowships on clinical skill development. A majority of respondents were willing to participate in clinical educational experiences for students and residents. Some physicians indicated a lack of interest in access to information through telecommunications, e.g., video conference referrals and consultations. Overall, findings revealed that family physicians need and are receptive to a variety of practice support and continuing education programs. A practice support program coupled with policy coordination among public and private organizations is likely to lessen complaints by rural primary care physicians.

Clinical Competence↗
PubMed2006

Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.

I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale ( approximately 100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

Bacteria↗
PubMed2004

Identification of Birds through DNA Barcodes.

Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10x average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

Animals↗
PubMed2003

Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics.

Acidobacteria have been established as a novel phylum of Bacteria that is consistently detected in many different habitats around the globe by 16S rDNA-based molecular surveys. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important ecological role and extensive metabolic versatility. However, the genetic and physiological information about Acidobacteria is scarce. In order to gain insight into genome structure, evolution and diversity of these microorganisms we have initiated an environmental genomic approach by constructing large insert libraries directly from DNA of a calcerous grassland soil. Genomic fragments of Acidobacteria were identified with specific 16S rDNA probes and sequence analyses of six independently identified clones were performed, representing in total more than 210,000 bp. The 16S rRNA genes of the genomic fragments differed between 2.3% and 19.9% and were placed into two different subgroups of Acidobacteria (groups III and V). Although partial co-linearity was found between genomic fragments, the gene content around the rRNA operons was generally not conserved. Phylogenetic reconstructions with orthologues that were encoded on two of the six genomic fragments (PurF, PurL, PurB and formamidopyrimidine-DNA glycosylase) confirmed the coherence of the acidobacterial phylum. One genomic fragment harboured a cluster of eight genes which was syntenic and highly homologous to genomic regions in Rhodopseudomonas palustris and Bradyrhizobium japonicum, including a conserved two-component system. Phylogenetic analysis of the putative response regulator confirmed that this similarity between Rhizobiales and Acidobacteria might be due to a horizontal gene transfer. In total, our data give first insight into the genome content and diversity of the ubiquitously distributed but poorly characterized phylum of Acidobacteria. Furthermore they support the phylogenetic inferences made from 16S rRNA gene libraries, suggesting that Acidobacteria form a broad group in the same sense and with a similar diversity as that of many well-studied bacterial phyla.

Bacteria↗
PubMed1999

Bacterial diversity within the human subgingival crevice.

Molecular, sequence-based environmental surveys of microorganisms have revealed a large degree of previously uncharacterized diversity. However, nearly all studies of the human endogenous bacterial flora have relied on cultivation and biochemical characterization of the resident organisms. We used molecular methods to characterize the breadth of bacterial diversity within the human subgingival crevice by comparing 264 small subunit rDNA sequences from 21 clone libraries created with products amplified directly from subgingival plaque, with sequences obtained from bacteria that were cultivated from the same specimen, as well as with sequences available in public databases. The majority (52.5%) of the directly amplified 16S rRNA sequences were <99% identical to sequences within public databases. In contrast, only 21.4% of the sequences recovered from cultivated bacteria showed this degree of variability. The 16S rDNA sequences recovered by direct amplification were also more deeply divergent; 13.5% of the amplified sequences were more than 5% nonidentical to any known sequence, a level of dissimilarity that is often found between members of different genera. None of the cultivated sequences exhibited this degree of sequence dissimilarity. Finally, direct amplification of 16S rDNA yielded a more diverse view of the subgingival bacterial flora than did cultivation. Our data suggest that a significant proportion of the resident human bacterial flora remain poorly characterized, even within this well studied and familiar microbial environment.

Adult↗
PubMedDate not supplied

Tissue and gene specificity of mouse renin expression.

The Ren-1 locus of mice encodes the protease renin, which with converting enzyme processes angiotensinogen to the potent vasopressor angiotensin II. Some strains of mice appear to carry a duplication of the renin structural gene (Ren-2) near the Ren-1 locus. Strains with the gene duplication can exhibit as much as 100-fold higher levels of submaxillary gland renin compared to strains with a single gene copy. In contrast, kidney renin levels appear to be unaffected by the gene duplication. Sequence analysis of a 319 bp renin cDNA recombinant isolated from a kidney library from the two-gene strain DBA/2Ha corresponds to a transcript of the Ren-1 gene. Moreover, a single base substitution of A for G at residue #996 in the kidney renin mRNA creates a potential glycosylation recognition site that may, in part, account for the differential glycosylation of kidney and submaxillary gland renins. In addition, our tissue surveys indicate that mature mRNAs from the Ren loci are detectable in adrenal gland and testes, as well as sublingual and parotid salivary glands, and reveal length variation for the renin transcripts in at least the submaxillary gland.

Animals↗
PubMed1976

A review of small canned computer programs for survey research and demographic analysis.

A variety of small canned computer programs for survey research and demographic analysis appropriate for use in developing countries are reviewed in this article. The programs discussed are SPSS (Statistical Package for the Social Sciences); CENTS, CO-CENTS, CENTS-AID, CENTS-AIE II; MINI-TAB EDIT, FREQUENCIES, TABLES, REGRESSION, CLIENT RECORD, DATES, MULT, LIFE, and PREGNANCY HISTORY; FIVFIV and SINSIN; DCL (Demographic Computer Library); MINI-TAB Population Projection, Functional Population Projection, and Family Planning Target Projection. A description and evaluation for each program of uses, instruction manuals, computer requirements, and procedures for obtaining manuals and programs are provided. Such information is intended to facilitate and encourage the use of the computer by data processors in developing countries.

Computers↗
PubMed2005

[The use of bibliographic databases by Spanish-speaking Latin American biomedical researchers: a cross-sectional study].

OBJECTIVE: To describe how Spanish-speaking biomedical professionals in Latin America access and utilize bibliographic databases. METHODS: Based on a MEDLINE search, 2 515 articles published between August 2002 and August 2003 were identified that dealt with and/or had authors from 16 countries: Argentina, Bolivia, Chile, Colombia, Costa Rica, Cuba, Ecuador, Guatemala, Honduras, Mexico, Nicaragua, Panama, Paraguay, Peru, Uruguay, and Venezuela. The search was limited to references to basic science, clinical science, or social medicine. A survey was sent by e-mail to researchers who lived in 15 of the 16 countries (the exception being Nicaragua). The survey asked about the researcher's area of work (basic science, clinical science, or public health), the level of skill in using databases, the frequency and type of access to the databases most utilized, the impact from not having access to the full text of articles when preparing a manuscript, and how the respondent usually obtained the full-text version of articles. RESULTS: A total of 586 e-mail messages with the survey were sent out, and 185 responses were received (32%). The databases most utilized to obtain biomedical information were MEDLINE (34.1%), general search engines (Google, Yahoo!, and AltaVista) (15.9%), on-line journals (9.8%), BIREME-LILACS (6.0%), BioMedNet (5.4%), the databases of the Centers for Disease Control and Prevention of the United States of America (5.2%), and the Cochrane Library (4.9%). Of the respondents, 64% said they had average or advanced abilities in using MEDLINE. However, 71% of the respondents did not use or were not aware of the MEDLINE Medical Subject Headings (MeSH), a controlled vocabulary established by the National Library of Medicine of the United States of America for indexing articles. The frequency of accessing the databases was similar in all the countries studied, without significant differences in terms of the type of access (authorized access to commercial databases, unauthorized access to those databases, or access to databases available for free) or the level of abilities. Of the respondents, 87% said they had not included important references in the articles that they had published because they had not had access to the full text of those items, and 56% said they had cited articles that they had not read in full. In addition, 7.6% of the respondents admitted to unauthorized use of limited-access databases, such as through borrowed passwords or copied disks. More than two-thirds of the respondents said they obtained the full text of articles through photocopies or directly from the authors. CONCLUSIONS: In order to encourage scientific output by Latin American researchers, more of them need to be trained in the use of the most frequently used databases, especially MEDLINE. Those researchers also need to have expanded access to the biomedical literature.

Biomedical Research↗
PubMed2004

A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics.

Comparative nematode genomics has thus far been largely constrained to the genus Caenorhabditis, but a huge diversity of other nematode species, and genomes, exist. The Brugia malayi genome is approximately 100 Mb in size, and distributed across five chromosome pairs. Previous genomic investigations have included definition of major repeat classes and sequencing of selected genes. We have generated over 18,000 sequences from the ends of large-insert clones from bacterial artificial chromosome libraries. These end sequences, totalling over 10 Mb of sequence, contain just under 8 Mb of unique sequence. We identified the known Mbo I and Hha I repeat families in the sequence data, and also identified several new repeats based on their abundance. Genomic copies of 17% of B. malayi genes defined by expressed sequence tags have been identified. Nearly one quarter of end sequences can encode peptides with significant similarity to protein sequences in the public databases, and we estimate that we have identified more than 2700 new B. malayi genes. Importantly, 459 end sequences had homologues in other organisms, but lacked a match in the completely sequenced genomes of Caenorhabditis briggsae and Caenorhabditis elegans, emphasising the role of gene loss in genome evolution. B. malayi is estimated to have over 18,500 protein-coding genes.

Animals↗