On epidemiology and geographic information systems: a review and discussion of future directions

Geographic information systems are powerful automated systems for the capture, storage, retrieval, analysis, and display of spatial data. While the systems have been in development for more than 20 years, recent software has made them substantially easier to use for those outside the field. The systems offer new and expanding opportunities for epidemiology because they allow an informed user to choose between options when geographic distributions are part of the problem. Even when used minimally, these systems allow a spatial perspective on disease. Used to their optimum level, as tools for analysis and decision making, they are indeed a new information management vehicle with a rich potential for public health and epidemiology

Foot health education for people with rheumatoid arthritis : the practitioner's perspective

Background: Patient education is considered to be a key role for podiatrists in the management of patients with rheumatoid arthritis (RA). Patient education has undoubtedly led to improved clinical outcomes, however no attempts have been made to optimise its content or delivery to maximise benefits within the context of the foot affected by rheumatoid arthritis. The aim of this study was to identify the nature and content of podiatrists' foot health education for people with RA. Any potential barriers to its provision were also explored. Methods: A focus group was conducted. The audio dialogue was recorded digitally, transcribed verbatim and analysed using a structured, thematic approach. The full transcription was verified by the focus group as an accurate account of what was said. The thematic analysis framework was verified by members of the research team to ensure validity of the data. Results: Twelve members (all female) of the north west Podiatry Clinical Effectiveness Group for Rheumatology participated. Six overarching themes emerged: (i) the essence of patient education; (ii) the content; (iii) patient-centred approach to content and timing; (iv) barriers to provision; (v) the therapeutic relationship; and (vi) tools of the trade. Conclusion: The study identified aspects of patient education that this group of podiatrists consider most important in relation to its: content, timing, delivery and barriers to its provision. General disease and foot health information in relation to RA together with a potential prognosis for foot health, the role of the podiatrist in management of foot health, and appropriate self-management strategies were considered to be key aspects of content, delivered according to the needs of the individual. Barriers to foot health education provision, including financial constraints and difficulties in establishing effective therapeutic relationships, were viewed as factors that strongly influenced foot health education provision. These data will contribute to the development of a patient-centred, negotiated approach to the provision of foot health education for people with RA

Liquid Chromatography Electron Capture Dissociation Tandem Mass Spectrometry (LC-ECD-MS/MS) versus Liquid Chromatography Collision-induced Dissociation Tandem Mass Spectrometry (LC-CID-MS/MS) for the Identification of Proteins

Electron capture dissociation (ECD) offers many advantages over the more traditional fragmentation techniques for the analysis of peptides and proteins, although the question remains: How suitable is ECD for incorporation within proteomic strategies for the identification of proteins? Here, we compare LC-ECD-MS/MS and LC-CID-MS/MS as techniques for the identification of proteins.Experiments were performed on a hybrid linear ion trap–Fourier transform ion cyclotron resonance mass spectrometer. Replicate analyses of a six-protein (bovine serum albumin, apo-transferrin,lysozyme, cytochrome c, alcohol dehydrogenase, and β-galactosidase) tryptic digest were performed and the results analyzed on the basis of overall protein sequence coverage and sequence tag lengths within individual peptides. The results show that although protein coverage was lower for LC-ECDMS/MS than for LC-CID-MS/MS, LC-ECD-MS/MS resulted in longer peptide sequence tags,providing greater confidence in protein assignment

Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis and brings more accurate information about compound retention times and mass spectra. Despite these advantages, the retention times of the resolved peaks on the two-dimensional gas chromatographic columns are always shifted due to experimental variations, introducing difficulty in the data processing for metabolomics analysis. Therefore, the retention time variation must be adjusted in order to compare multiple metabolic profiles obtained from different conditions.</p> <p>Results</p> <p>We developed novel peak alignment algorithms for both homogeneous (acquired under the identical experimental conditions) and heterogeneous (acquired under the different experimental conditions) GC × GC-MS data using modified Smith-Waterman local alignment algorithms along with mass spectral similarity. Compared with literature reported algorithms, the proposed algorithms eliminated the detection of landmark peaks and the usage of retention time transformation. Furthermore, an automated peak alignment software package was established by implementing a likelihood function for optimal peak alignment.</p> <p>Conclusions</p> <p>The proposed Smith-Waterman local alignment-based algorithms are capable of aligning both the homogeneous and heterogeneous data of multiple GC × GC-MS experiments without the transformation of retention times and the selection of landmark peaks. An optimal version of the SW-based algorithms was also established based on the associated likelihood function for the automatic peak alignment. The proposed alignment algorithms outperform the literature reported alignment method by analyzing the experiment data of a mixture of compound standards and a metabolite extract of mouse plasma with spiked-in compound standards.</p

Improvements in Modeling 90 degree Bleed Holes for Supersonic Inlets

The modeling of porous bleed regions as boundary conditions in computational fluid dynamics (CFD) simulations of supersonic inlet flows has been improved through a scaling of sonic flow coefficient data for 90deg bleed holes. The scaling removed the Mach number as a factor in computing the sonic flow coefficient and allowed the data to be fitted with a quadratic equation, with the only factor being the ratio of the plenum static pressure to the surface static pressure. The implementation of the bleed model into the Wind-US CFD flow solver was simplified by no longer requiring the evaluation of the flow properties at the boundary-layer edge. The quadratic equation can be extrapolated to allow the modeling of small amounts of blowing, which can exist when recirculation of the bleed flow occurs within the bleed region. The improved accuracy of the bleed model was demonstrated through CFD simulations of bleed regions on a flat plate in supersonic flow with and without an impinging oblique shock. The bleed model demonstrated good agreement with experimental data and three-dimensional CFD simulations of bleed holes

Mapping as a knowledge translation tool for Ontario Early Years Centres: views from data analysts and managers

<p>Abstract</p> <p>Background</p> <p>Local Ontario Early Years Centres (OEYCs) collect timely and relevant local data, but knowledge translation is needed for the data to be useful. Maps represent an ideal tool to interpret local data. While geographic information system (GIS) technology is available, it is less clear what users require from this technology for evidence-informed program planning. We highlight initial challenges and opportunities encountered in implementing a mapping innovation (software and managerial decision-support) as a knowledge translation strategy.</p> <p>Methods</p> <p>Using focus groups, individual interviews and interactive software development events, we taped and transcribed verbatim our interactions with nine OEYCs in Ontario, Canada. Research participants were composed of data analysts and their managers. Deductive analysis of the data was based on the Ottawa Model of Research Use, focusing on the innovation (the mapping tool and maps), the potential adopters, and the environment.</p> <p>Results</p> <p>Challenges associated with the innovation included preconceived perceptions of a steep learning curve with GIS software. Challenges related to the potential adopters included conflicting ideas about tool integration into the organization and difficulty with map interpretation. Lack of funds, lack of availability of accurate data, and unrealistic reporting requirements represent environmental challenges.</p> <p>Conclusion</p> <p>Despite the clear need for mapping software and maps, there remain several challenges to their effective implementation. Some can be modified, while other challenges might require attention at the systemic level. Future research is needed to identify barriers and facilitators related to using mapping software and maps for decision-making by other users, and to subsequently develop mapping best practices guidelines to assist community-based agencies in circumventing some challenges, and support information equity across a region.</p

Effects of Charge State and Cationizing Agent on the Electron Capture Dissociation of a Peptide

Electron capture dissociation (ECD) is a promising method for de novo sequencing proteins and peptides and for locating the positions of labile posttranslational modifications and binding sites of noncovalently bound species. We report the ECD of a synthetic peptide containing 10 alanine residues and 6 lysine residues uniformly distributed across the sequence. ECD of the (M + 2H) 2+ produces a limited range of c (c 7 -c 15 ) and z (z 9 -z 15 ) fragment ions, but ECD of higher charge states produces a wider range of c (c 2 -c 15 ) and z (z 2 -z 6 , z 9 -z 15 ) ions. Although mass spectrometry (MS) and tandem mass spectrometry (MS/MS) have been used to characterize peptides for more than three decades, 1,2 the developments of electrospray ionization (ESI) 3 and matrix-assisted laser desorption/ionization 4 have dramatically expanded the size and type of molecules amenable to characterization by MS/MS. For example, ESI has been used to form intact gas-phase ions from virus particles (4.0 × 10 7 Da) 5 and DNA molecules as large as 1.2 × 10 8 Da. 6 ESI-MS and ESI-MS/MS experiments can be performed using as little as 10 -18 mol of sample. 7 For these measurements, Fourier transform (FT) MS has the advantages of ultrahigh resolution, multichannel detection, and MS n capabilities. 8,9 Dissociation methods in FTMS, including collisionally activated dissociation (CAD), 10 surface-induced dissociation, 11,12 infrared multiphoton dissociation, 13 and blackbody infrared radiative dissociation, 14,15 have been used to obtain sequence information and locations of posttranslational modifications (PTMs) in biomolecules. With these activation methods, the most labile bonds within an ion are typically cleaved. This often produces incomplete sequence coverage, the loss of PTMs, and a lack of backbone cleavages within regions enclosed by disulfide bridges. The recently developed method of electron capture dissociation (ECD), [16][17][18][19][20][21][22][23][24][25