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PubMed2004

Approaches and informatics tools to assist in the integration of similar clinical research questionnaires.

OBJECTIVE: The integration of similar clinical research questionnaires is a complex process that can benefit from informatics approaches and tools that provide a systematic structure for performing mapping and integration. This systematic approach is necessary to address complex issues in integration such as data heterogeneity, differing levels of granularity of questions and responses, and other issues involving semantic differences. Informatics tools and approaches have been successfully applied to various standard clinical vocabulary integration processes but not for questionnaire integration or mapping. METHODS: A systematic approach to questionnaire integration was developed in the context of a collaboration of researchers using Trial/DB, a database designed to support clinical research. This approach was applied to the integration of questionnaires involving breast cancer risk factors from each of three research sites. RESULTS: From 375 questions on the three original questionnaires, we identified 65 concepts that were measured by two or three of the sites. An algorithm was developed and used to formalize the process of mapping questions and answers across the questionnaires. The approach was applied to previously collected data and prospective data in disparate data-base systems to import and merge the data from these three sites into Trial/DB. CONCLUSION: Informatics tools that support a systematic approach to mapping questionnaires can be used throughout the research process from questionnaire integration and creation, legacy data integration to data library maintenance and curation.

Biomedical Research↗
PubMed2001

A survey of primary care physicians' perceptions and needs regarding the precepting of medical students in their offices.

OBJECTIVE: To assess the interest, perceptions, and needs of primary care physicians with regard to office-based precepting of medical students. DESIGN: Random survey. SETTING: The New England region of the United States (Maine, New Hampshire, Vermont, Massachusetts, Rhode Island, Connecticut). PARTICIPANTS: Family physicians, general internists and paediatricians. MAIN OUTCOME MEASURES: These included: (1) practice and preceptor demographics; (2) Likert scale agreement or disagreement with various positive and negative perceptions about precepting students; rating (from unimportant to necessary) of potential benefits from medical schools associated with the support of precepting in the office setting, and (3) comparisons among physician groups to determine differences in perceptions and needs. RESULTS: There is a high level of interest in precepting regardless of primary care specialty, practice structure, payment mechanism, or precepting experience. Negative impacts included decreased productivity and increased length of the day by a median of 60 minutes. Positive impacts included keeping one's own knowledge up-to-date and enhanced enjoyment of practice. Benefits such as academic appointments, continuing medical education credits, faculty development, computer linkages for clinical information and medical library access are rated highly. Monetary payment, whether as a modest honorarium or as compensation for lost time/income, was felt to be important by half of our sample. CONCLUSION: A significant interest in precepting medical students on a regular basis is expressed by primary care physicians in the ambulatory medicine setting. The results of this survey can be used by medical schools to address negative perceptions and to develop appropriate benefits packages to recruit and retain these primary care preceptors.

Education, Medical↗
PubMed2004

Oncology studies using siRNA libraries: the dawn of RNAi-based genomics.

High-throughput, human cell-based applications of RNA-mediated interference (RNAi) have emerged in recent years as perhaps the most powerful of a 'second wave' of functional genomics technologies. The available reagents and methodologies for RNAi screening studies now enable a wide range of different scopes and scales of investigation, from single-parameter assays applied to focused subsets of genes, to comprehensive genome-wide surveys based on rich, multiparameter readouts. As such, RNAi-based screens are offering important new avenues for the discovery and validation of novel therapeutic targets for several disease areas, including oncology. By enabling a 'clean' determination of gene function, that is the creation of direct causal links between gene and phenotype in human cells, RNAi investigations promise levels of pathophysiological relevance, efficiency, and range of applicability never before possible on this scale. The field of oncology, with its many assays using readily transfectable cell lines, has offered particularly fertile ground for showcasing the potential of RNAi-based genomics. However, like any other technology before it, RNAi is not without its own challenges, limitations, and caveats. Many of these issues stem directly from the choice of silencing reagent to be used in such studies, and the design of the overall screening strategy. Here, we discuss the basic design issues, potential advantages, and technical challenges of large-scale RNAi screens based on the use of chemically synthesized siRNA libraries.

Gene Library↗
PubMed2005

Mass spectrometry-based approaches to protein-ligand interactions.

One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.

Animals↗
PubMed1989

Reading habits of house-staff: what, where and why.

As in-training evaluations often comment that house-staff do not read enough about cases, this study looked at the reading habits of internal medicine students and house-staff to assess whether they were reading about cases. All 38 trainees at a major teaching hospital were surveyed with a questionnaire. Overall, the house-staff read 8.7 hours/week, of which half is spent reading about cases. They read around approximately half of the cases they see. The more senior house-staff use journals and one major textbook; the medical students use only textbooks. The reading is done mainly at home, except by the senior residents who spent a quarter of their reading time in the library. The major reasons why the house-staff read are to prepare for presentations or for rounds with the attending physicians. These results suggest that contrary to what we anticipated, house-staff do indeed read about the cases they see on the wards.

Education, Medical, Continuing↗
PubMed1991

Yeast artificial chromosome cloning of a two-megabase-size contig within chromosomal band 18q21 establishes physical linkage between BCL2 and plasminogen activator inhibitor type-2.

The construction of large-scale physical maps requires efficient approaches to generate new probes and link informative markers. The mapping of a human chromosomal segment was initiated by using the 18q21.3 probes, plasminogen activator inhibitor type-2 (PLANH2) and BCL2, to screen a yeast artificial chromosome (YAC) library. An inverse polymerase chain reaction technique rescued genomic ends of the YAC inserts. These new probes were used in a chromosomal walking strategy which established that the PLANH2 gene was 600 kb telomeric and in the opposite transcriptional orientation to that of BCL2. Overall, 16 YACs with a mean size of approximately 300 kb were analyzed using rare-cutting restriction endonucleases and 10 end-rescued probes. A contiguous map within 18q21.3 that spans approximately 2 Mb was assembled. This establishes the feasibility of using YACs in the efficient cloning and physical surveying of expanses of the human genome lacking closely spaced, genetic landmarks.

Animals↗
PubMed1983

Two-dimensional gel electrophoretic analysis of the HindIII 1.8-kb repetitive-sequence family in the human genome.

The structure and organization of a human repetitive DNA family containing the HindIII 1.8-kb repetitive sequence were studied, using two-dimensional (2D) gel electrophoresis. The HindIII 1.8-kb sequence proved to be part of a repetitive sequence about 5 kb long and interspersed on the genome. The long repetitive sequence family contained several subgroups, as based on polymorphism of the restriction site. Recombinant phages containing the long repetitive sequence were isolated from the human genomic DNA library. Heteroduplex and restriction analysis showed that the structure of the repetitive sequence carried by the phages was close to that expected from 2D gel electrophoretic analysis. The 2D gel electrophoretic analysis was shown to be a reliable and useful approach for surveying and mass analysis of repetitive sequence families.

DNA Restriction Enzymes↗
PubMed2002

Expressed sequence tag analysis of blood cells in the vanadium-rich ascidian, Ascidia sydneiensis samea--a survey of genes for metal accumulation.

Some species in the family Ascidiidae accumulate vanadium at concentrations in excess of 350 mM, which corresponds to about 10(7) times that found in seawater. The vanadium ions are stored in vacuoles located within vanadium-containing blood cells, vanadocytes. To investigate the phenomenon, an expressed sequence tag analysis (EST) of a cDNA library of Ascidia sydneiensis samea blood cells was carried out. Three hundred clones were obtained and sequenced by EST analysis. A similarity search revealed that 158 of the clones (52.7%) were known genes, and 142 of the clones (47.3%) did not have any similarity to genes registered in the SwissProt database. According to the functions of their genes the identified EST clones were categorized into eight types of clones; these consisted of genes; metal-related proteins (29 clones), signal transduction (22 clones), protein synthesis (17 clones), nuclear proteins (17 clones), cytoskeleton and motility (14 clones), energy conversion (3 clones), hypothetical proteins (11 clones), and others (45 clones). The ferritin homologue has a high degree of similarity to that of mammals; the iron-binding sites of ferritin are well conserved including His-118 which is important for capturing Fe(2+), also works as a ligand for VO(2+).

Amino Acid Sequence↗
PubMed1994

PANG, a gene encoding a neuronal glycoprotein, is ectopically activated by intracisternal A-type particle long terminal repeats in murine plasmacytomas.

Plasmacytomagenesis provides a murine model to decipher progressive genetic events culminating in a B-cell neoplasia. Activation of the c-myc protooncogene by chromosomal translocation is considered an initiating event. Intracisternal A-type particles (IAPs) are defective retroviral-like structures present in the endoplasmic reticulum of plasmacytomas (PCTs). IAP proviral insertions have been documented to engender negative or positive effects on the expression of nearby cellular genes. We have isolated a gene, PANG (plasmacytoma-associated neuronal glycoprotein), that is ectopically transcribed in a number of PCTs due to IAP long terminal repeat (LTR) activation. A full-length PANG cDNA was isolated from an MPC-11 plasma cell tumor cDNA library and encodes a polypeptide of about 113 kDa with six immunoglobulin C2-like and four type III fibronectin-like domains. PANG bears a striking resemblance to axonal glycoproteins TAG-1 and F11 known to function in neuronal outgrowth. An extensive survey revealed a predominant 3.6-kb PANG transcript in 60% (30 of 50) of PCTs as well as unique smaller and larger species. All other normal and transformed lymphoid and nonlymphoid cell lines and normal tissues were negative for PANG expression except for the brain, wherein unique 4.0- and 6.1-kb transcripts were detected. Reverse transcriptase PCR analysis revealed IAP LTR fusion to PANG mRNAs in five PCTs and in a neuroblastoma line. The 5' end of a mouse brain PANG cDNA was identical to the MPC-11 PANG transcript except for the precise replacement of its 5' LTR sequence.

Amino Acid Sequence↗
PubMed1995

cDNA selection from 10 Mb of chromosome 21 DNA: efficiency in transcriptional mapping and reflections of genome organization.

The technique of cDNA hybridization selection has been applied individually to 16 YAC clones mapping to various regions of the long arm of human chromosome 21. YACs represented approximately 10 Mb of non-overlapping DNA, and cDNA sources included fetal brain, whole fetus, and adult testes, thymus, liver and spleen. Sequencing, Northern analysis, RT-PCR and cDNA library screenings have been used to identify and partially characterize a non-redundant set of novel genes. A preliminary analysis strategy of the selected cDNAs has proven rapid and effective for isolation of the more highly represented genes and is suitable for survey transcriptional mapping efforts. By scaling up to screen > 1000 cDNA fragments per 100 kb of YAC DNA, more rare transcripts are identified and lead to comprehensive gene maps. Strong regional variations in transcriptional activity were observed, with gene densities ranging from < 1/2000 kb to > 1/15 kb. This effort has produced a large number of new genes of potential relevance to Down Syndrome.

Adult↗
PubMed2004

High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.

A library of 29,482 T-DNA enhancer trap lines has been generated in rice cv. Nipponbare. The regions flanking the T-DNA left border from the first 12,707 primary transformants were systematically isolated by adapter anchor PCR and sequenced. A survey of the 7480 genomic sequences larger than 30 bp (average length 250 bp), representing 56.4% of the total readable sequences and matching the rice bacterial artificial chromosome/phage artificial chromosome (BAC/PAC) sequences assembled in pseudomolecules allowed the assigning of 6645 (88.8%) T-DNA insertion sites to at least one position in the rice genome of cv. Nipponbare. T-DNA insertions appear to be rather randomly distributed over the 12 rice chromosomes, with a slightly higher insertion frequency in chromosomes 1, 2, 3 and 6. The distribution of 723 independent T-DNA insertions along the chromosome 1 pseudomolecule did not differ significantly from that of the predicted coding sequences in exhibiting a lower insertion density around the centromere region and a higher density in the subtelomeric regions where the gene density is higher. Further establishment of density graphs of T-DNA inserts along the recently released 12 rice pseudomolecules confirmed this non-uniform chromosome distribution. T-DNA appeared less prone to hot spots and cold spots of integration when compared with those revealed by a concurrent assignment of the Tos17 retrotransposon flanking sequences deposited in the National Center for Biotechnology Information (NCBI). T-DNA inserts rarely integrated into repetitive sequences. Based on the predicted gene annotation of chromosome 1, preferential insertion within the first 250 bp from the putative ATG start codon has been observed. Using 4 kb of sequences surrounding the insertion points, 62% of the sequences showed significant similarity to gene encoding known proteins (E-value < 1.00 e(-05)). To illustrate the in silico reverse genetic approach, identification of 83 T-DNA insertions within genes coding for transcription factors (TF) is presented. Based both on the estimated number of members of several large TF gene families (e.g. Myb, WRKY, HD-ZIP, Zinc-finger) and on the frequency of insertions in chromosome 1 predicted genes, we could extrapolate that 7-10% of the rice gene complement is already tagged by T-DNA insertion in the 6116 independent transformant population. This large resource is of high significance while assisting studies unravelling gene function in rice and cereals, notably through in silico reverse genetics.

Base Sequence↗
PubMed2004

[Has the Oslo96 reform brought changes in student satisfaction and study behaviour?].

BACKGROUND: In 1996 the medical school of the University of Oslo introduced a new pedagogical model. The new scheme was more interactive, and partly based on a problem-based learning approach. METHOD: We used a questionnaire survey which is part of a broader study of how Norwegian professional education prepares for work. A class of medical students studying under the new scheme is compared to a class studying under the old model, as well as a class from another Norwegian medical school, that of the University of Bergen. Median values on seven-point scales are used in the comparison, as well as factor analysis with variance analysis of the factor scores. RESULTS: The overall response rate was 76%. Students studying under the new Oslo approach were more satisfied and reported more active learning strategies. They were less curriculum-oriented and used the library more often. INTERPRETATION: Some of the goals of the Oslo reform seem to have been reached. It remains to be seen whether this effect will last.

Curriculum↗
PubMed2003

An EST survey of the sugarcane transcriptome.

Its large genome and high polyploidy makes sugarcane (Saccharum spp.) a singularly challenging crop to study and improve using genetic approaches. To provide large numbers of functionally characterized candidate genes that might be tested for direct association (rather than distant linkage) with economically important traits, we sequenced the 5' ends of 9,216 clones from three cDNA libraries (apex, leaf and mature internode), representing 3,401 non-redundant sequences. About 57% of these sequences could be assigned a tentative function based on statistically significant similarity to previously characterized proteins or DNA sequences. Another 28% corresponded to previously identified, but uncharacterized, sequences. Some of the remaining unidentified sequences were predicted to be genes which could potentially be new to plants or unique to sugarcane. Comparisons of the sugarcane ESTs to a large sorghum EST database revealed similar compositions of expressed genes between some different tissues. Comparison to a detailed Arabidopsis protein database showed some highly conserved sequences, which might be useful DNA markers for pan-angiosperm comparative mapping. These EST sequences provide a foundation for many new studies to accelerate isolation of agronomically important genes from the cumbersome sugarcane genome.

Base Sequence↗
PubMed1991

A human Hox 1 homeobox gene exhibits myeloid-specific expression of alternative transcripts in human hematopoietic cells.

As part of a survey of the expression of homeobox-containing genes in human hematopoietic cells, we identified a novel gene (PL1) expressed only in cells of the myelomonocytic lineage (Shen et al., Proc. Natl. Acad. Sci, USA 86, 8536, 1989). On Northern gel analysis, major transcripts of 3.0 and 2.2 kb length are observed. Alternatively spliced homeobox-containing cDNAs, corresponding to the major transcripts, have been cloned from two myeloid leukemia cell libraries. The two cDNAs share the homeodomain and 3' flanking region but have unique 5' flanking regions. The longer transcript, would encode a 496 amino acid homeobox-containing protein, while the shorter message would encode a 94 amino acid homeobox-containing protein lacking the extended amino-terminal region. These two transcripts are differentially expressed in human leukemia cell lines. The larger transcript is exclusively expressed in cells with myelomonocytic features, while the smaller transcript is expressed in a variety of hematopoietic cell types. PL mRNA is also detectable in normal human bone marrow by RNAse protection. Neither transcript is expressed in uninduced teratocarcinoma cells or in the adult human tissues surveyed. The homeodomain is identical to the genomic sequence for Hox 1H, a newly identified member of the Hox 1 locus (Acampora et al. Nucl. Acids Res. 17, 10385, 1989). The PL1 gene was localized to chromosome 7 using chromosome specific blots and sublocalized to region pI4-21 by in situ hybridization of chromosomal spreads, confirming its location within the Hox 1 complex.

Amino Acid Sequence↗
PubMed2002

Distributions of beta sheets in proteins with application to structure prediction.

We recently developed the Rosetta algorithm for ab initio protein structure prediction, which generates protein structures from fragment libraries using simulated annealing. The scoring function in this algorithm favors the assembly of strands into sheets. However, it does not discriminate between different sheet motifs. After generating many structures using Rosetta, we found that the folding algorithm predominantly generates very local structures. We surveyed the distribution of beta-sheet motifs with two edge strands (open sheets) in a large set of non-homologous proteins. We investigated how much of that distribution can be accounted for by rules previously published in the literature, and developed a filter and a scoring method that enables us to improve protein structure prediction for beta-sheet proteins. Proteins 2002;48:85-97.

Algorithms↗
PubMed2005

Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars.

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P<0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

Chromosome Mapping↗
PubMed2002

German Observational Study of Adult Twins (GOSAT): a multimodal investigation of personality, temperament and cognitive ability.

The German Observational Study of Adult Twins (GOSAT) is the largest population-based observational twin study in Germany to date. Embedded in the Bielefeld Longitudinal Study of Adult Twins (BiLSAT), it addresses the etiology of personality, temperament and cognitive ability in a sample of 300 monozygotic (MZ) and dizygotic (DZ) adult twin pairs between 18 and 70 years of age. A major aim of the GOSAT lies in the utilization of different modes of measurement, (i.e., peer reports and observational data), in addition to self-reports which have been used predominantly in past behavioral genetic research on personality and temperament in adults. Participants completed a full day assessment at the University of Bielefeld including videotaped social interactions and presentations, psychometric intelligence tests and computerized elementary cognitive tasks as well as objective measures and unobtrusive behavior counts. The research design of the GOSAT was devised to reduce the potential impact of systematic rater bias on estimates of genetic and environmental influences to a minimum. In combination with extensive self- and peer report data on key personality and personality related dimensions available from the BiLSAT, the GOSAT provides a rich dataset, which currently includes DNA samples from 80% of its participants.

Adult↗
PubMed2002

Differential diagnosis of Taenia saginata and Taenia solium infections: from DNA probes to polymerase chain reaction.

The objective of this work was the rapid and easy differential diagnosis of Taenia saginata and T. solium. First, a T. saginata size-selected genomic deoxyribonucleic acid (gDNA) library was constructed in the vector lambda gt10 using the 2-4 kb fraction from the parasite DNA digested with EcoR1, under 'star' conditions. After differential screening of the library and hybridization analysis with DNA from T. saginata, T. solium, T. taeniaeformis, T. crassiceps, and Echinococcus granulosus (bovine, porcine, and human), 2 recombinant phages were selected. They were designated HDP1 and HDP2. HDP1 reacted specifically with T. saginata DNA, and HDP2 recognized DNA from both T. saginata and T. solium. The 2 DNA probes were then sequenced and further characterized. HDP1 was a repetitive sequence with a 53 bp monomeric unit repeated 24 times in direct tandem along the 1272 bp fragment, while the 3954 bp HDP2 was not a repetitive sequence. Using the sequencing data, oligonucleotides were designed and used in a polymerase chain reaction (PCR). The 2 selected oligonucleotides from probe HDP1 (PTs4F1 and PTs4R1) specifically amplified gDNA from T. saginata, but not T. solium or other related cestodes, with a sensitivity of < 10 pg of T. saginata gDNA, about the quantity of DNA in one taeniid egg. The 3 oligonucleotides selected from the HDP2 sequence (PTs7S35F1, PTs7S35F2, and PTs7S35R1) allowed the differential amplification of gDNA from T. saginata, T. solium and E. granulosus in a multiplex PCR, again with a sensitivity of < 10 pg. These diagnostic tools have immediate application in the differential diagnosis of T. solium and T. saginata in humans and in the diagnosis of dubious cysts in the slaughterhouse. We also hope to apply them to epidemiological surveys of, for example, soil and water in endemic areas.

Animals↗