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Paul Bradley

Publications and source records attributed to Paul Bradley.

12 recordsLinked to original sources
PubMed2005

InterPro, progress and status in 2005.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Databases, Protein↗
PubMed2005

Assessment of progress tests.

BACKGROUND: Progress testing is a form of longitudinal examination which, in principle, samples at regular intervals from the complete domain of knowledge considered a requirement for medical students on completion of the undergraduate programme. Over the course of the programme students improve their scores on the test, enabling them, as well as staff, to monitor their progress. AIM: We aimed to review methods which have been used to assess the results of individual tests, and to make recommendations on best practice. DISCUSSION: In assessing progress tests, there are a variety of choices that must be made. These include whether the test is norm- or criterion-referenced; whether marking is negative or "number-right"; whether the grades are reported on a continuous or a discontinuous scale, and whether the grades are weighted towards the most recent observations, or the entire set of grades is used to determine the final grade. Grade boundary setting in the context of progress tests is also considered, using a mathematical model to predict the consequences of different approaches. The relationships between boundary setting, progression and remediation rules are considered. CONCLUSIONS: We concluded that norm referencing is preferable to criterion referencing, negative marking preferable to number-right marking, a discontinuous scale preferable to a continuous scale and that grades should be weighted to favour the most recent outcomes, although there should still be a degree of persistence (earlier grades should not disappear all together). Grade boundaries should be established with regard to rules on remediation and progression.

Clinical Competence↗
PubMed2004

Mitochondrial DNA mutations in breast cancer tissue and in matched nipple aspirate fluid.

Unlike nuclear (n)DNA, of which there is one paired copy per cell, there are many copies of mitochondrial (mt)DNA per cell, making PCR amplification of mtDNA easier in samples of limited cellularity. The aims of this study were to (i) determine the mutation patterns of breast cancers through a comprehensive screen of mtDNA mutations, and (ii) assess if mutations in the cancers are also detectable in breast nipple aspirate fluid (NAF), a physiologic fluid which contains shed ductal epithelial cells. Fifteen breast cancers, matched benign tissues and NAF were collected. Nine overlapping primer sets were used to sequence the entire mitochondrial genome from tissue samples. For NAF samples, we focused on the 19 nucleotide positions (np) where mutations were found in a 3701 bp region (np 15331 to 2463), which includes the displacement (D)-loop, a mtDNA mutation hot spot. Fourteen of the fifteen (93%) cancer samples had > or =1 somatic mtDNA mutation for a total of 45 at 35 np (9 np reported previously, 26 new). Nine of fifteen tumors had > or =2 mutations. The D-loop contained 17 of 45 (38%) and non-D-loop (coding) regions contained 28 (62%) mutations. Of the 28 mutations in the coding loci, 11 led to an amino acid change. The frequency of mtDNA mutations was higher in the D-loop region (1.5 versus 0.18% of loci). 155 polymorphisms were identified (98 reported previously, 57 new). Sixteen of forty-five (36%) mutations were located at polymorphism sites. Four of nineteen mtDNA mutations in 10 cancers located between np 15331 and 2463 were found in matched NAF (two of eleven mutations in the D-loop and two of eight in non-D-loop regions). No mutations were found in five matched NAF samples from women whose cancers lacked a mutation in the same region. In conclusion, mtDNA mutations in breast cancer occur both within and outside of the D-loop, though the mutation rate in the D-loop is over 7-fold higher than in coding areas. We identified 26 new mutation loci (25 in regions sequenced by others, one in an area not). The high frequency of mtDNA mutations at polymorphic loci requires further investigation. Specific mtDNA mutations can be detected in a subset of NAF samples from women with breast cancer.

Base Sequence↗
PubMed2004

Teaching anatomy without cadavers.

BACKGROUND: Anatomy learning is generally seen as essential to medicine, and exposure to cadavers is generally seen as essential to anatomy learning around the world. Few voices dissenting from these propositions can be identified. AIMS: This paper aims to consider arguments relating to the use of cadavers in anatomy teaching, and to describe the rationale behind the decision of a new UK medical school not to use cadaveric material. DISCUSSION: First, the background to use of cadavers in anatomy learning is explored, and some general educational principles are explored. Next, arguments for the use of human cadaveric material are summarised. Then, possible arguments against use of cadavers, including educational principles as well as costs, hazards and practicality, are considered. These are much less well explored in the existing literature. Next, the rationale behind the decision of a new UK medical school not to use cadaveric material is indicated, and the programme of anatomy teaching to be employed in the absence of the use of human remains is described. Curriculum design and development, and evaluation procedures, are briefly described. Issues surrounding pathology training by autopsy, and postgraduate training in surgical anatomy, are not addressed in this paper. FUTURE DIRECTIONS: Evidence relating to the effect on medical learning by students not exposed to cadavers is scant, and plainly opportunities will now arise through our programme to gather such evidence. We anticipate that this discussion paper will contribute to an ongoing debate, in which virtually all previous papers on this topic have concluded that use of cadavers is essential to medical learning.

Anatomy↗
PubMed2004

Exploring medical students' attitudes towards peer physical examination.

With opportunities for dissection and examination of sick patients decreasing, the role of peer physical examination (PPE) is increasing. This study explores students' attitudes towards PPE and the relationship between attitudes and demographics. A total of 129 first-year medical students from the Peninsula Medical School completed the Examining Fellow Students (EFS) questionnaire. At least 97% of students were comfortable participating in PPE of all body parts except breast and inguinal regions. Over 20% of students were unwilling to participate in PPE of the breast and inguinal regions. Students were more comfortable with PPE within gender than across gender. Females were more likely to be uncomfortable with PPE. Further research with larger sample sizes is required to determine whether attitudes are related to age and religious faith.

Adolescent↗
PubMed2003

The InterPro Database, 2003 brings increased coverage and new features.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Animals↗
PubMed2003

Early introduction to interprofessional learning: a simulated ward environment.

OBJECTIVES: To develop an interprofessional simulated ward environment for junior medical and nursing students and to identify themes for future evaluations and modify criteria for formative assessment of the exercise. SUBJECTS: Second year medical and nursing students. SETTING: The multiprofessional Clinical Skills Centre at the Faculty of Medicine, and Nursing, University of Dundee, Scotland. METHOD: A simulated ward environment was created in the Clinical Skills Centre around patients with common medical conditions. Students were allocated to interprofessional teams and, after a briefing given in the form of a ward report, were asked to take responsibility for the ward for 'a shift'. Observers from the Schools of Medicine and Nursing charted their progress in relation to evidence of collaborative team working, effective leadership, the ability to prioritise workload and competence in clinical performance. Evaluations of the exercise were taken from all participants. The criteria for formative assessment were reviewed by the observers after the exercise and a focus group was used to generate additional criteria and modify those piloted. RESULTS: The exercise was perceived positively by all participating groups. Themes for evaluation of future exercises and modified criteria for future assessment were identified. CONCLUSIONS: The exercise gave students their first experience of participating independently in a realistic and safe operational ward setting. It proved to be a powerful learning experience for the students.

Clinical Competence↗
PubMed2002

InterPro: an integrated documentation resource for protein families, domains and functional sites.

The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for classification of the resulting protein sequences. There are several signature and sequence cluster-based methods for protein classification, each resource having distinct areas of optimum application owing to the differences in the underlying analysis methods. In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein signature database projects. The member databases - PRINTS, PROSITE, Pfam, ProDom, SMART and TIGRFAMs - form the InterPro core. Related signatures from each member database are unified into single InterPro entries. Each InterPro entry includes a unique accession number, functional descriptions and literature references, and links are made back to the relevant member database(s). Release 4.0 of InterPro (November 2001) contains 4,691 entries, representing 3,532 families, 1,068 domains, 74 repeats and 15 sites of post-translational modification (PTMs) encoded by different regular expressions, profiles, fingerprints and hidden Markov models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (2,141,621 InterPro hits from 586,124 SWISS-PROT and TrEMBL protein sequences). The database is freely accessible for text- and sequence-based searches.

Algorithms↗