Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding

Peptides that induce and recall T-cell responses are called T-cell epitopes. T-cell epitopes may be useful in a subunit vaccine against malaria. Computer models that simulate peptide binding to MHC are useful for selecting candidate T-cell epitopes since they minimize the number of experiments required for their identification. We applied a combination of computational and immunological strategies to select candidate T-cell epitopes. A total of 86 experimental binding assays were performed in three rounds of identification of HLA-All binding peptides from the six preerythrocytic malaria antigens. Thirty-six peptides were experimentally confirmed as binders. We show that the cyclical refinement of the ANN models results in a significant improvement of the efficiency of identifying potential T-cell epitopes. (C) 2001 by Elsevier Science Inc.

A Delphi study of district nursing research priorities in Australia

This study, using a Delphi approach, sought the opinion of a self-selected panel of 320 district nurses regarding research priorities for district nursing in Australia. Over three rounds of questionnaires, the 419 research clinical problem areas requiring research as suggested by the panel were each rated in importance by the panel and then ranked through analysis from high to low average rating scores, thereby, whittling down the list to the top 15% (68) research questions and to a final list of the top 10 research priorities overall. Research questions focusing on discharge planning are dominant in these top 10 priorities, with documentation issues the second most common focus. Other foci in the top 10 priorities are staffing, aged care, palliative care, and assessment. The organization-specific top 10 research priorities focus on wound care, funding, education, and communication issues. Additionally, the top 68 priorities, which are either finitely practice-based or contextual-issues research questions, were categorized into 20 themes. The results will hopefully lead to scarce human and financial resources being directed to practice-relevant research programs that will facilitate improved health for district nursing (primarily home-nursing) clients in Australia and elsewhere. (c) 2005 Elsevier Inc. All rights reserved.

Population-based mammography screening and breast cancer incidence in New South Wales, Australia

To analyse breast cancer incidence trends in New South Wales (NSW), Australia, in relation to population-based mammography screening targeting women aged 50 to 69 years. Trends in age-specific incidence of invasive breast cancers in NSW women aged >= 40 years were examined in relation to mammography screening rates and screening cancer detection rates. Incidence of invasive breast cancer in NSW women increased in all age-groups over 1972 to 2002. The incidence trend for women aged 50 to 69 years showed that the steepest rise was associated with increased participation in population-based mammography screening, which was implemented from 1988 and achieved state-wide coverage in 1995. The elevated incidence of invasive cancer significantly exceeded pre-screening levels, and persisted after rates of initial screens declined. This elevated incidence was sustained by the contribution of cancers diagnosed through subsequent screening, and resulted from increased cancer detection rates in subsequent screens. The recent increase in invasive breast cancer incidence in NSW is associated with mammography screening, and occurred mostly in the target age-group women. Persistence of higher incidence after 1994 was not explicable by inflation of cancer incidence due to detection of prevalent screen cases, but was associated with a trend of increased cancer detection rates in subsequent screening rounds, probably consequent to quality improvements in mammography screening diagnosis.

Replication of bovine papillomavirus type 1 (BPV-1) DNA in Saccharomyces cerevisiae following infection with BPV-1 virions

Saccharomyces cerevisiae protoplasts exposed to bovine papillomavirus type 1 (BPV-1) virions demonstrated uptake of virions on electron microscopy. S. cerevisiae cells looked larger after exposure to BPV-1 virions, and cell wall regeneration was delayed. Southern blot hybridization of Hirt DNA from cells exposed to BPV-1 virions demonstrated BPV-1 DNA, which could be detected over 80 days of culture and at least 13 rounds of division. Two-dimensional gel analysis of Hirt DNA showed replicative intermediates, confirming that the BPV-1 genome was replicating within S. cerevisiae. Nicked circle, linear, and supercoiled BPV-1 DNA species were observed in Hirt DNA preparations from S. cerevisiae cells infected for over 50 days, and restriction digestion showed fragments hybridizing to BPV-1 in accord with the predicted restriction map for circular BPV-1 episomes. These data suggest that BPV-1 can infect S. cerevisiae and that BPV-1 episomes can replicate in the infected S. cerevisiae cells.

Osteonectin/SPARC induction by ectopic beta(3) integrin in human radial growth phase primary melanoma cells

Expression of the beta(3) integrin subunit in melanoma in situ has been found to correlate with tumor thickness, the ability to invade and metastasize, and poor prognosis. Transition from the radial growth phase (RGP) to the vertical growth phase (VGP) is a critical step in melanoma progression and survival and is distinguished by the expression of beta(3), integrin. The molecular pathways that operate in melanoma cells associated with invasion and metastasis were examined by ectopic induction of the beta(3), integrin subunit in RGP SBcl2 and WM1552C melanoma cells, which converts these cells to a VGP phenotype. We used cDNA representational difference analysis subtractive hybridization between beta(3)-Positive and -negative melanoma cells to assess gene expression profile changes accompanying RGP to VGP transition. Fourteen fragments from known genes including osteonectin (also known as SPARC and BM-40) were identified after three rounds of representational difference analysis. Induction of osteonectin was confirmed by Northern and Western blot analysis and immunohistochemistry and correlated in organotypic cultures with the beta(3)-induced progression from RGP to VGP melanoma. Expression of osteonectin was also associated with reduced adhesion to vitronectin, but not to fibronectin. Osteonectin expression was not blocked when melanoma cells were cultured with anti-alpha(v)beta(3) LM609 mAb, mitogen-activated protein kinase, or protein kinase C inhibitors, indicating that other signaling pathway(s) operate through a(v)beta(3) integrin during conversion from RGP to VGP.

Research utilization among pediatric health professionals

The present study investigated research use and attitudes toward research among pediatric health professionals. All nurses and allied health professionals in a pediatric teaching hospital were surveyed using previously tested and published measures. Over half of the participants had some formal education in research but, for some participants, that education was many years ago. Most participants reported poor or very poor understanding of research design. Two variables were independently associated with a positive attitude towards research: (i) better understanding of how to conduct a literature search; and (ii) higher level of education. Five variables were independently associated with research use: better understanding of research design; having presented at a conference in the past two years; sense of calling to the profession; better understanding of how to conduct a literature search; and attending rounds. A small proportion of variance in both research use and a positive attitude towards research was explained by the independent predicator variables. Further research is required to identify characteristics of the workplace environment that support research use.

Factors influencing PRN medication use in nursing homes

Objective: To identify determinants of PRN ( as needed) drug use in nursing homes. Decisions about the use of these medications are made expressly by nursing home staff when general medical practitioners (GPs) prescribe medications for PRN use. Method: Cross-sectional drug use data were collected during a 7-day window from 13 Australian nursing homes. Information was collected on the size, staffing-mix, number of visiting GPs, number of medication rounds, and mortality rates in each nursing home. Resident specific measures collected included age, gender, length of stay, recent hospitalisation and care needs. Main outcome measures: The number of PRN orders prescribed per resident and the number of PRN doses given per week averaged over the number of PRN medications given at all in the seven-day period. Results: Approximately 35% of medications were prescribed for PRN use. Higher PRN use was found for residents with the lower care needs, recent hospitalisation and more frequent doses of regularly scheduled medications. With increasing length of stay, PRN medication orders initially increased then declined but the number of doses given declined from admission. While some resident-specific characteristics did influence PRN drug use, the key determinant for PRN medication orders was the specific nursing home in which a resident lived. Resident age and gender were not determinants of PRN drug use. Conclusion: The determinants of PRN drug use suggest that interventions to optimize PRN medications should target the care of individual residents, prescribing and the nursing home processes and policies that govern PRN drug use.

Functional promoter analysis using an approach based on an in vitro evolution strategy

In vitro evolution imitates the natural evolution of genes and has been very successfully applied to the modification of coding sequences, but it has not yet been applied to promoter sequences. We propose an alternative method for functional promoter analysis by applying an in vitro evolution scheme consisting of rounds of error-prone PCR, followed by DNA shuffling and selection of mutant promoter activities. We modified the activity in embryogenic sugarcane cells of the promoter region of the Goldfinger isolate of banana streak virus and obtained mutant promoter sequences that showed an average mutation rate of 2.5% after applying one round of error-prone PCR and DNA shuffling. Selection and sequencing of promoter sequences with decreased or unaltered activity allowed us to rapidly map the position of one cis-acting element that influenced promoter activity in embryogenic sugarcane cells and to discover neutral mutations that did not affect promoter Junction. The selective-shotgun approach of this promoter analysis method immediately after the promoter boundaries have been defined by 5' deletion analysis dramatically reduces the labor associated with traditional linker-scanning deletion analysis to reveal the position of functional promoter domains. Furthermore, this method allows the entire promoter to be investigated at once, rather than selected domains or nucleotides, increasing the, prospect of identifying interacting promoter regions.

Increasing male involvement in family planning decision making: trial of a social-cognitive intervention in rural Vietnam

We tested a social-cognitive intervention to influence contraceptive practices among men living in rural communes in Vietnam. It was predicted that participants who received a stage-targeted program based on the Transtheoretical Model (TTM) would report positive movement in their stage of motivational readiness for their wife to use an intrauterine device (IUD) compared to those in a control condition. A quasi-experimental design was used, where the primary unit for allocation was villages. Villages were allocated randomly to a control condition or to two rounds of intervention with stage-targeted letters and interpersonal counseling. There were 651 eligible married men in the 12 villages chosen. A significant positive movement in men's stage of readiness for IUD use by their wife occurred in the intervention group, with a decrease in the proportions in the precontemplation stage from 28.6 to 20.2% and an increase in action/maintenance from 59.8 to 74.4% (P < 0.05). There were no significant changes in the control group. Compared to the control group, the intervention group showed higher pros, lower cons and higher self-efficacy for IUD use by their wife as a contraceptive method (P < 0.05). Interventions based on social-cognitive theory can increase men's involvement in IUD use in rural Vietnam and should assist in reducing future rates of unwanted pregnancy.

Wireless telemedicine for the delivery of specialist paediatric services to the bedside

A mobile interactive online health system was used to conduct virtual ward rounds at a regional hospital which had no specialist paediatrician. The system was wireless, which allowed telepaediatric services to be delivered direct to the bedside. Between December 2004 and May 2005, 43 virtual ward rounds were coordinated between specialists based in Brisbane and local staff at the Gladstone Hospital. Eighty-six consultations were provided for 64 patients. The most common conditions included asthma (27%), chest infections (12%), gastroenteritis (10%) and urinary tract infections (10%). In the majority of cases, there were partial (67%) or complete changes (11%) in the clinical management of patients. Specialist services were offered by a team of 13 clinicians at the Royal Children's Hospital: 10 general paediatricians, two physiotherapists and one registered nurse. Feedback from all consultants involved in the service and local staff in Gladstone was extremely positive. In 43 videoconference calls there were three technical problems, probably due to an intermittent mains power supply at the regional hospital. There appears to be potential for other rural and regional hospitals to adopt this model of service delivery.

Comparison of ASAS improvement criteria for ankylosing spondylitis with clinically relevant improvement according to an expert panel

Objective: To investigate whether the recently developed (statistically derived) "ASsessment in Ankylosing Spondylitis Working Group" improvement criteria (ASAS-IC) for ankylosing spondylitis (AS) reflect clinically relevant improvement according to the opinion of an expert panel. Methods: The ASAS-IC consist of four domains: physical function, spinal pain, patient global assessment, and inflammation. Scores on these four domains of 55 patients with AS, who had participated in a non-steroidal anti-inflammatory drug efficacy trial, were presented to an international expert panel (consisting of patients with AS and members of the ASAS Working Group) in a three round Delphi exercise. The number of (non-) responders according to the ASAS-IC was compared with the final-consensus of the experts. The most important domains in the opinion of the experts were identified, and also selected with discriminant analysis. A number of provisional criteria sets that best represented the consensus of the experts were defined. Using other datasets, these clinically derived criteria sets as well as the statistically derived ASAS-IC were then tested for discriminative properties and for agreement with the end of trial efficacy by patient and doctor. Results: Forty experts completed the three Delphi rounds. The experts considered twice as many patients to be responders than the ASAS-IC (42 v 21). Overall agreement between experts and ASAS-IC was 62%. Spinal pain was considered the most important domain by most experts and was also selected as such by discriminant analysis. Provisional criteria sets with an agreement of greater than or equal to 80% compared with the consensus of the experts showed high placebo response rates (27-42%), in contrast with the ASAS-IC with a predefined placebo response rate of 25%. All criteria sets and the ASAS-IC discriminated well between active and placebo treatment (chi(2) = 36-45; p < 0.001). Compared with the end of trial efficacy assessment, the provisional criteria sets showed an agreement of 71-82%, sensitivity of 67-83%, and specificity of 81-88%. The ASAS-IC showed an agreement of 70%, sensitivity of 62%, and specificity of 89%. Conclusion: The ASAS-IC are strict in defining response, are highly specific, and consequently show lower sensitivity than the clinically derived criteria sets. However, those patients who are considered as responders by applying the ASAS-IC are acknowledged as such by the expert panel as well as by. patients' and doctors' judgments, and are therefore likely to be true responders.

The information specialist in the clinical team: Building expertise in evidence-based healthcare

The Clinician Development Program (CDP) is an initiative of Queensland Health’s Quality Improvement and Enhancement Program. At the Royal Brisbane & Royal Women's Hospital Health Service Districts, evidence-base practice (EBP) is an important CDP area in which several projects were carried out in 2002. This paper describes one such project. A medical librarian was invited to accompany the clinical team on morning rounds in the Medical Assessment & Planning Unit (MAPU). The librarian conducted information skills training in the ward and helped clinicians to answer questions directly related to patient care. Questions not answered during the round were followed-up, usually within 48 hours, and responses emailed to the consultant who led the rounds. At the project’s conclusion the librarian was invited to continue as a member of the MAPU clinical team, thus acknowledging the valuable role an information specialist can play in incorporating research evidence into patient care. Clinical librarianship (CL) creates a space, albeit a contentious one, for the health librarian at the bedside. This paper describes an Australian CL project and attempts to demystify the role of an information specialist in EBP. It also highlights some of the challenges facing librarians and clinicians attempting to embed EBP in clinical settings.