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

Optimizing the two-step floating catchment area method for measuring spatial accessibility to medical clinics in Montreal

<p>Abstract</p> <p>Background</p> <p>Reducing spatial access disparities to healthcare services is a growing priority for healthcare planners especially among developed countries with aging populations. There is thus a pressing need to determine which populations do not enjoy access to healthcare, yet efforts to quantify such disparities in spatial accessibility have been hampered by a lack of satisfactory measurements and methods. This study compares an optimised and the conventional version of the two-step floating catchment area (2SFCA) method to assess spatial accessibility to medical clinics in Montreal.</p> <p>Methods</p> <p>We first computed catchments around existing medical clinics of Montreal Island based on the shortest network distance. Population nested in dissemination areas were used to determine potential users of a given medical clinic. To optimize the method, medical clinics (supply) were weighted by the number of physicians working in each clinic, while the previous year's medical clinic users were computed by ten years age group was used as weighting coefficient for potential users of each medical clinic (demand).</p> <p>Results</p> <p>The spatial accessibility score (SA) increased considerably with the optimisation method. Within a distance of 1 Km, for instance, the maximum clinic accessible for 1,000 persons is 2.4 when the conventional method is used, compared with 27.7 for the optimized method. The t-test indicates a significant difference between the conventional and the optimized 2SFCA methods. Also, results of the differences between the two methods reveal a clustering of residuals when distance increases. In other words, a low threshold would be associated with a lack of precision.</p> <p>Conclusion</p> <p>Results of this study suggest that a greater effort must be made ameliorate spatial accessibility to medical clinics in Montreal. To ensure that health resources are allocated in the interest of the population, health planners and the government should consider a strategy in the sitting of future clinics which would provide spatial access to the greatest number of people.</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

Fourier transform ion cyclotron resonance mass spectrometric detection of small Ca2+-induced conformational changes in the regulatory domain of human cardiac troponin C

AbstractTroponin C (TnC), a calcium-binding protein of the thin filament of muscle, plays a regulatory role in skeletal and cardiac muscle contraction. NMR reveals a small conformational change in the cardiac regulatory N-terminal domain of TnC (cNTnC) on binding of Ca2+ such that the total exposed hydrophobic surface area increases very slightly from 3090 ± 86 Å2 for apo-cNTnC to 3108 ± 71 Å2 for Ca2+-cNTnC. Here, we show that measurement of solvent accessibility for backbone amide protons by means of solution-phase hydrogen/deuterium (H/D) exchange followed by pepsin digestion, high-performance liquid chromatography, and electrospray ionization high-field (9.4 T) Fourier transform Ion cyclotron resonance mass spectrometry is sufficiently sensitive to detect such small ligand binding-induced conformational changes of that protein. The extent of deuterium incorporation increases significantly on binding of Ca2+ for each of four proteolytic segments derived from pepsin digestion of the apo- and Ca2+-saturated forms of cNTnC. The present results demonstrate that H/D exchange monitored by mass spectrometry can be sufficiently sensitive to detect and identify even very small conformational changes in proteins, and should therefore be especially informative for proteins too large (or too insoluble or otherwise intractable) for NMR analysis

Lower Use of Hospice by Cancer Patients who Live in Minority Versus White Areas

BACKGROUND: Although hospice care can alleviate suffering at the end of life for patients with cancer, it remains underutilized, particularly by African Americans and Hispanics. OBJECTIVE: To examine whether the racial composition of the census tract where an individual resides is associated with hospice use. DESIGN: Retrospective analysis of the Surveillance, Epidemiology, and End Results–Medicare file for individuals dying from breast, colorectal, lung, or prostate cancer (n = 70,669). MEASUREMENTS: Hospice use during the 12 months before death. RESULTS: Hospice was most commonly used by individuals who lived in areas with fewer African-American and Hispanic residents (47%), and was least commonly used by individuals who lived in areas with a high percentage of African-American and Hispanic residents (35%). Hispanics (odds ratio 0.51, 95% confidence interval 0.29–0.91) and African Americans (0.56, 0.44–0.71) were less likely to use hospice if they lived in a census tract with a high percentage of both African Americans and Hispanics than if they lived in a low minority tract. African Americans and whites were less likely to receive hospice care if they lived in a census tract with a high percentage of Hispanics than if they lived in a low minority area. CONCLUSIONS: Increasing hospice use may require interventions to improve the delivery of hospice care in minority communities