Description and critical appraisal of principal components analysis (PCA) methodology applied to pulsed-field gel electrophoresis profiles of methicillin-resistant Staphylococcus aureus isolates

Principal components analysis (PCA) has been described for over 50 years; however, it is rarely applied to the analysis of epidemiological data. In this study PCA was critically appraised in its ability to reveal relationships between pulsed-field gel electrophoresis (PFGE) profiles of methicillin- resistant Staphylococcus aureus (MRSA) in comparison to the more commonly employed cluster analysis and representation by dendrograms. The PFGE type following SmaI chromosomal digest was determined for 44 multidrug-resistant hospital-acquired methicillin-resistant S. aureus (MR-HA-MRSA) isolates, two multidrug-resistant community-acquired MRSA (MR-CA-MRSA), 50 hospital-acquired MRSA (HA-MRSA) isolates (from the University Hospital Birmingham, NHS Trust, UK) and 34 community-acquired MRSA (CA-MRSA) isolates (from general practitioners in Birmingham, UK). Strain relatedness was determined using Dice band-matching with UPGMA clustering and PCA. The results indicated that PCA revealed relationships between MRSA strains, which were more strongly correlated with known epidemiology, most likely because, unlike cluster analysis, PCA does not have the constraint of generating a hierarchic classification. In addition, PCA provides the opportunity for further analysis to identify key polymorphic bands within complex genotypic profiles, which is not always possible with dendrograms. Here we provide a detailed description of a PCA method for the analysis of PFGE profiles to complement further the epidemiological study of infectious disease. © 2005 Elsevier B.V. All rights reserved.

Does the neuropathology of human patients with variant Creutzfeldt-Jakob disease reflect haematogenous spread of the disease?

To test the hypothesis that the distribution of the pathology in variant Creutzfeldt-Jakob disease (vCJD) represents haematogenous spread of the disease, we studied the spatial correlation between the vacuolation, prion protein (PrP) deposits, and the blood vessel profiles in the cerebral cortex, hippocampus, dentate gyrus, and cerebellum of 11 cases of the disease. In the majority of areas, there were no significant spatial correlations between either the vacuolation or the diffuse type of PrP deposit and the blood vessels. By contrast, a consistent pattern of spatial correlation was observed between the florid PrP deposits and blood vessels mainly in the cerebral cortex. The frequency of positive spatial correlations was similar in different anatomical areas of the cerebral cortex and in the upper compared with the lower laminae. Hence, with the exception of the florid deposits, the data do not demonstrate a spatial relationship between the pathological features of vCJD and blood vessels. The spatial correlation of the florid deposits and blood vessels may be attributable to factors associated with the blood vessels that promote the aggregation of PrP to form a condensed core rather than reflecting the haematogenous spread of the disease. © 2003 Elsevier Ireland Ltd. All rights reserved.

Inhibition of transglutaminase 2 enzymatic activity ameliorates the anti-angiogenic effects of coeliac disease autoantibodies

Objective. Earlier work has demonstrated that serum autoantibodies from coeliac patients targeted against transglutaminase 2 (TG2) inhibit in vitro angiogenesis. The aim of this study was to establish whether coeliac patient-derived monoclonal TG2-targeted antibodies produced by recombination technology exert similar anti-angiogenic effects to serum-derived coeliac autoantibodies. In addition, we studied whether the monoclonal patient autoantibodies modulate endothelial cell TG2 activity and whether such modulation is related to the anti-angiogenic effects. Material and methods. The influence of coeliac patient-derived monoclonal TG2-targeted antibodies on endothelial cell tubule formation was studied using a three-dimensional angiogenic cell culture model. Endothelial cell TG2 enzymatic activity was determined by means of a live-cell enzyme-linked immunosorbent assay. Results. Coeliac patient-derived monoclonal TG2-targeted antibodies produced by recombination technology inhibited endothelial tubule formation and enhanced the crosslinking activity of TG2. When this enzymatic activity was inhibited using site-directed irreversible TG2 inhibitors in the presence of autoantibodies, in vitro angiogenesis reverted to the control level. Conclusions. Since we found a significant negative correlation between endothelial cell angiogenesis and TG2 activity, we suggest that the anti-angiogenic effects of coeliac patient-derived TG2-targeted autoantibodies are exerted by enhanced enzymatic activity of TG2.

Principal components analysis of Alzheimer’s disease based on neuropathological data: A study of 79 patients

A Principal Components Analysis of neuropathological data from 79 Alzheimer’s disease (AD) cases was performed to determine whether there was evidence for subtypes of the disease. Two principal components were extracted from the data which accounted for 72% and 12% of the total variance respectively. The results suggested that 1) AD was heterogeneous but subtypes could not be clearly defined; 2) the heterogeneity, in part, reflected disease onset; 3) familial cases did not constitute a distinct subtype of AD and 4) there were two forms of late onset AD, one of which was associated with less senile plaque and neurofibrillary tangle development but with a greater degree of brain atherosclerosis.

Adipokines have a role to play in the treatment of metabolic disease

Editorial

Does the neurodegeneration of Alzheimer’s disease spread between visual cortical regions B17 and B18 via the feedforward or feedback short cortico-cortical projections?

The laminar distribution of senile plaques (SP) and neurofibrillary tangles (NFT) was studied in areas B17 and B18 of the visual cortex in 18 cases of Alzheimer’s disease which varied in disease onset and duration. The objective was to test the hypothesis that SP and NFT could spread via either the feedforward or feedback short cortico-cortical projections. In area B17, the mean density of SP and NFT reached a maximum in lamina III and in laminae II and III respectively. In B18, mean SP density was maximal in laminae III and IV and NFT density in laminae II and III. No significant correlations were observed in any cortical lamina between the density of SP and patient age. However, the density of NFT in laminae III, IV and VI in B18 was negatively correlated with patient age. In addition, in B18, the density of SP in lamina II and lamina V was negatively correlated with disease duration and disease onset respectively. Although these results suggest that SP and NFT might spread between B17 and B18 via the feedforward short cortico-cortical projections, it is also possible that the longer cortico-cortical and cortico-subcortical connections may be involved.

AntigenDB:an immunoinformatics database of pathogen antigens

The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning pathogens, virulence factors and antigenic epitopes has resulted in many useful databases. However, most such immunological databases focus almost exclusively on antigens where epitopes are known and ignore those for which epitope information was unavailable. We have compiled more than 500 antigens into the AntigenDB database, making use of the literature and other immunological resources. These antigens come from 44 important pathogenic species. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases. We shall update AntigenDB on a rolling basis, regularly adding antigens from other organisms and extra data analysis tools. AntigenDB is available freely at http://www.imtech.res.in/raghava/antigendb and its mirror site http://www.bic.uams.edu/raghava/antigendb.

Genetics of ocular disease Part 1: Basic concepts: cells, chromosomes and inheritance

This series of articles describes the basic elements of genetics necessary to understand the new advances and the impact these advances will have on the study and treatment of ocular disease. The first article describes the patterns of inheritance of human characteristics, how they are transmitted between the generations and the structure of chromosomes.

Genetics of ocular disease Part 2: Basic concepts: DNA, proteins and genes

This article on the basic concepts of genetics concentrates on doeoxyribose nucleic acid (DNA), the chemical constituent of the genes. First, it will cover how DNA was discovered to be the substance of the genes. Second, the structure of DNA is revealed together with how DNA molecules can make copies of themselves. Third, the nature of the genetic code contained in DNA and how this code directs the manufacture of proteins is described. Finally, the effects of mutation of the genes and how the activities of genes are regulated will be discussed together with the relevance of these concepts to ocular disease.

Genetics of ocular disease Part 3: Patterns of inheritance of ocular disease

The objective of this article is to describe the patterns of inheritance exhibited in the human populations and to illustrate them with examples drawn from a variety of ocular diseases.

Genetics of ocular disease part 4: New developments in genetics

The objective of the final artcile in this series is to describe how recent developments in genetics are likely to imact the diagnosis, scientific understanding, and future treatment of ocular disease.

Characterization of Acanthamoeba-microsphere association by multiparameter flow cytometry and confocal microscopy

Background: Acanthamoebae, in common with other protozoa, readily endocytose particulate material, which in turn may lead to the spread of infectious disease. Methods: Evaluation and quantification of plain and carboxylate FITC-microsphere association with acanthamoebal trophzoites was undertaken using a combination of flow cytometry and confocal microscopy. Trophozoites from strains and species of Acanthamoeba were exposed to plain and carboxylate FITC-microspheres. Microsphere size and aspects such as trophozoite starvation, maturity, and exposure to metabolic inhibitors were assessed. Results: All species and strains of Acanthamoeba readily endocytosed plain and carboxylate microspheres. Starving trophozoites significantly increased binding and potential ingestion of microspheres, whereas trophozoites of increasing maturity lost such abilities. Trophozoites showed a significant preference for 2.0- and 3.0-μm-diameter microspheres when compared with other sizes, which in turn could occupy much of the cytoplasm. The physiological inhibitors sodium azide, 2,4-clinitrophenol, and cytochalasin B reduced microsphere association with trophozoites; however, some microspheres still bound and associated with trophozoites after inhibitor exposure, a manifestation of both active and inactive agent involvement in microsphere endocytosis. Conclusions: Even though the origins of microsphere binding by acanthamoebal trophozoite remains shrouded, the combination of flow cytometry and confocal microscopy supported synergistic quantification and qualification of trophozoite-microsphere endocytosis. © 2006 International Society for Analytical Cytology.

An examination of the UK community pharmacist's role in facilitating patient self-management of cardiovascular disease through lifestyle behaviours

The progression of cardiovascular disease (CVD) is largely modifiable through lifestyle behaviours. UK pharmacists are contractually obliged to facilitate patient self-management of chronic conditions such as CVD. Pharmacists are easily accessible health professionals who are well placed to identify “at risk” patients through medication regimes. Research has identified varying attitudes towards and levels of involvement in pharmacist-led health promotion activity. Given the diverse and exploratory nature of the work, a pragmatic, mixed methods approach was used to explore community pharmacists’ role in facilitating patient self-management of CVD. The thesis presents four studies: a qualitative study with pharmacists; a cross sectional questionnaire of community pharmacists; a systematic review and a qualitative study with patients with CVD. The qualitative study with pharmacists gave an insight into pharmacists’ experiences of giving patients with CVD lifestyle advice and the factors underpinning commonly cited barriers to providing public health services. This informed the development of the cross-sectional questionnaire which identified the predictors of pharmacists’ intentions to give two different types of advice to facilitate patient self-management. The systematic review identified a small number of interventions to prepare pharmacists to facilitate patient lifestyle behaviour change and evaluated the theories and behaviour change techniques used in successful interventions; however due to poor study quality and poor reporting of the interventions limited conclusions about the efficacy of the interventions could reliably be drawn. Finally, the qualitative study gave an insight into the experiences of patients with CVD using community pharmacy services and their expectations of the service they receive from community pharmacists. Recommendations about changes to pharmacy policy and practice in order to support pharmacists’ provision of CVD self-management advice are made.

High-accuracy discrimination of Parkinson’s Disease participants from healthy controls using smartphones

Objective: To test the practicality and effectiveness of cheap, ubiquitous, consumer-grade smartphones to discriminate Parkinson’s disease (PD) subjects from healthy controls, using self-administered tests of gait and postural sway. Background: Existing tests for the diagnosis of PD are based on subjective neurological examinations, performed in-clinic. Objective movement symptom severity data, collected using widely-accessible technologies such as smartphones, would enable the remote characterization of PD symptoms based on self-administered, behavioral tests. Smartphones, when backed up by interviews using web-based videoconferencing, could make it feasible for expert neurologists to perform diagnostic testing on large numbers of individuals at low cost. However, to date, the compliance rate of testing using smart-phones has not been assessed. Methods: We conducted a one-month controlled study with twenty participants, comprising 10 PD subjects and 10 controls. All participants were provided identical LG Optimus S smartphones, capable of recording tri-axial acceleration. Using these smartphones, patients conducted self-administered, short (less than 5 minute) controlled gait and postural sway tests. We analyzed a wide range of summary measures of gait and postural sway from the accelerometry data. Using statistical machine learning techniques, we identified discriminating patterns in the summary measures in order to distinguish PD subjects from controls. Results: Compliance was high all 20 participants performed an average of 3.1 tests per day for the duration of the study. Using this test data, we demonstrated cross-validated sensitivity of 98% and specificity of 98% in discriminating PD subjects from healthy controls. Conclusions: Using consumer-grade smartphone accelerometers, it is possible to distinguish PD from healthy controls with high accuracy. Since these smartphones are inexpensive (around $30 each) and easily available, and the tests are highly non-invasive and objective, we envisage that this kind of smartphone-based testing could radically increase the reach and effectiveness of experts in diagnosing PD.

Patients’ perceptions and experiences of cardiovascular disease and diabetes prevention programmes:a systematic review and framework synthesis using the Theoretical Domains Framework

Background - This review provides a worked example of ‘best fit’ framework synthesis using the Theoretical Domains Framework (TDF) of health psychology theories as an a priori framework in the synthesis of qualitative evidence. Framework synthesis works best with ‘policy urgent’ questions. Objective - The review question selected was: what are patients’ experiences of prevention programmes for cardiovascular disease (CVD) and diabetes? The significance of these conditions is clear: CVD claims more deaths worldwide than any other; diabetes is a risk factor for CVD and leading cause of death. Method - A systematic review and framework synthesis were conducted. This novel method for synthesizing qualitative evidence aims to make health psychology theory accessible to implementation science and advance the application of qualitative research findings in evidence-based healthcare. Results - Findings from 14 original studies were coded deductively into the TDF and subsequently an inductive thematic analysis was conducted. Synthesized findings produced six themes relating to: knowledge, beliefs, cues to (in)action, social influences, role and identity, and context. A conceptual model was generated illustrating combinations of factors that produce cues to (in)action. This model demonstrated interrelationships between individual (beliefs and knowledge) and societal (social influences, role and identity, context) factors. Conclusion - Several intervention points were highlighted where factors could be manipulated to produce favourable cues to action. However, a lack of transparency of behavioural components of published interventions needs to be corrected and further evaluations of acceptability in relation to patient experience are required. Further work is needed to test the comprehensiveness of the TDF as an a priori framework for ‘policy urgent’ questions using ‘best fit’ framework synthesis.