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Mapping Methods (mapping + methods)
Selected AbstractsCommentary: A Response to Reckase's Conceptual Framework and Examples for Evaluating Standard Setting MethodsEDUCATIONAL MEASUREMENT: ISSUES AND PRACTICE, Issue 3 2006E. Matthew Schulz A look at real data shows that Reckase's psychometric theory for standard setting is not applicable to bookmark and that his simulations cannot explain actual differences between methods. It is suggested that exclusively test-centered, criterion-referenced approaches are too idealized and that a psychophysics paradigm and a theory of group behavior could be more useful in thinking about the standard setting process. In this view, item mapping methods such as bookmark are reasonable adaptations to fundamental limitations in human judgments of item difficulty. They make item ratings unnecessary and have unique potential for integrating external validity data and student performance data more fully into the standard setting process. [source] Characterization of glyco isoforms in plasmaderived human antithrombin by on-line capillary zone electrophoresis-electrospray ionization-quadrupole ion trap-mass spectrometry of the intact glycoproteinsELECTROPHORESIS, Issue 13 2004Uwe M. Demelbauer Abstract The carbohydrate structures of five isoforms of ,-AT and two isoforms of ,-AT were determined by applying capillary zone electrophoresis (CZE) on-line coupled to electrospray ionization-mass spectrometry (ESI-MS) using an ion-trap analyzer. For the AT preparations gained from a plasma pool at least semiquantitative information on the isoform-distributions could be gained. Unlike to the commonly used approaches starting from enzymatically treated glycoproteins, this approach deals with intact proteins. The high accuracy of the molecular mass determination obtained by the ion-trap analyzer allows one to calculate and ascertain the carbohydrate composition assuming no variations in the protein moiety of AT and to exclude or confirm the presence of the potential post-translational or other modifications. Therefore, the direct coupling of CZE with ESI-MS does not only represent a fast alternative technique to two-dimensional electrophoresis (2-DE) but serves as a method which provides structural information complementary to that gained from peptide mapping methods. [source] Linkage mapping methods applied to the COGA data set: Presentation Group 4 of Genetic Analysis Workshop 14GENETIC EPIDEMIOLOGY, Issue S1 2005E. Warwick Daw Abstract Presentation Group 4 participants analyzed the Collaborative Study on the Genetics of Alcoholism data provided for Genetic Analysis Workshop 14. This group examined various aspects of linkage analysis and related issues. Seven papers included linkage analyses, while the eighth calculated identity-by-descent (IBD) probabilities. Six papers analyzed linkage to an alcoholism phenotype: ALDX1 (four papers), ALDX2 (one paper), or a combination both (one paper). Methods used included Bayesian variable selection coupled with Haseman-Elston regression, recursive partitioning to identify phenotype and covariate groupings that interact with evidence for linkage, nonparametric linkage regression modeling, affected sib-pair linkage analysis with discordant sib-pair controls, simulation-based homozygosity mapping in a single pedigree, and application of a propensity score to collapse covariates in a general conditional logistic model. Alcoholism linkage was found with ,2 of these approaches on chromosomes 2, 4, 6, 7, 9, 14, and 21. The remaining linkage paper compared the utility of several single-nucleotide polymorphism (SNP) and microsatellite marker maps for Monte Carlo Markov chain combined oligogenic segregation and linkage analysis, and analyzed one of the electrophysiological endophenotypes, ttth1, on chromosome 7. Linkage was found with all marker sets. The last paper compared the multipoint IBD information content of several SNP sets and the microsatellite set, and found that while all SNP sets examined contained more information than the microsatellite set, most of the information contained in the SNP sets was captured by a subset of the SNP markers with ,1-cM marker spacing. From these papers, we highlight three points: a 1-cM SNP map seems to capture most of the linkage information, so denser maps do not appear necessary; careful and appropriate use of covariates can aid linkage analysis; and sources of increased gene-sharing between relatives should be accounted for in analyses. Genet. Epidemiol. 29(Suppl. 1):S29,S34, 2005. © 2005 Wiley-Liss, Inc. [source] Fine mapping and detection of the causative mutation underlying Quantitative Trait LociJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2010E. Uleberg Summary The effect on power and precision of including the causative SNP amongst the investigated markers in Quantitative Trait Loci (QTL) mapping experiments was investigated. Three fine mapping methods were tested to see which was most efficient in finding the causative mutation: combined linkage and linkage disequilibrium mapping (LLD); association mapping (MARK); a combination of LLD and association mapping (LLDMARK). Two simulated data sets were analysed: in one set, the causative SNP was included amongst the markers, while in the other set the causative SNP was masked between markers. Including the causative SNP amongst the markers increased both precision and power in the analyses. For the LLD method the number of correctly positioned QTL increased from 17 for the analysis without the causative SNP to 77 for the analysis including the causative SNP. The likelihood of the data analysis increased from 3.4 to 13.3 likelihood units for the MARK method when the causative SNP was included. When the causative SNP was masked between the analysed markers, the LLD method was most efficient in detecting the correct QTL position, while the MARK method was most efficient when the causative SNP was included as a marker in the analysis. The LLDMARK method, combining association mapping and LLD, assumes a QTL as the null hypothesis (using LLD method) and tests whether the ,putative causative SNP' explains significantly more variance than a QTL in the region. Thus, if the putative causative SNP does not only give an Identical-By-Descent (IBD) signal, but also an Alike-In-State (AIS) signal, LLDMARK gives a positive likelihood ratio. LLDMARK detected less than half as many causative SNPs as the other methods, and also had a relatively high false discovery rate when the QTL effect was large. LLDMARK may however be more robust against spurious associations, because the regional IBD is largely corrected for by fitting a QTL effect in the null hypothesis model. [source] Fine mapping of a quantitative trait locus on chromosome 9 affecting non-return rate in Swedish dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2007M. Holmberg Summary We previously mapped a quantitative trait locus (QTL) affecting the trait non-return rate at 56 days in heifers to bovine chromosome 9. The purpose of this study was to confirm and refine the position of the QTL by using a denser marker map and fine mapping methods. Five families that previously showed segregation for the QTL were included in the study. The mapping population consisted of 139 bulls in a granddaughter design. All bulls were genotyped for 25 microsatellite markers surrounding the QTL on chromosome 9. We also analysed the correlated trait number of inseminations per service period in heifers. Both traits describe the heifer's ability to become pregnant after insemination. Linkage analysis, linkage disequilibrium and combined linkage and linkage disequilibrium analysis were used to analyse the data. Analysis of the families jointly by linkage analysis resulted in a significant but broad QTL peak for non-return rate. Results from the combined analysis gave a sharp QTL peak with a well-defined maximum in between markers BMS1724 and BM7209, at the same position as where the highest peak from the linkage disequilibrium analysis was found. One of the sire families segregated clearly at this position and the difference in effects between the two sire haplotypes was 2.9 percentage units in non-return rate. No significant results were found for the number of inseminations in the combined analysis. [source] Generalized marker regression and interval QTL mapping methods for binary traits in half-sib family designsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2001H. N. Kadarmideen A Generalized Marker Regression Mapping (GMR) approach was developed for mapping Quantitative Trait Loci (QTL) affecting binary polygenic traits in a single-family half-sib design. The GMR is based on threshold-liability model theory and regression of offspring phenotype on expected marker genotypes at flanking marker loci. Using simulation, statistical power and bias of QTL mapping for binary traits by GMR was compared with full QTL interval mapping based on a threshold model (GIM) and with a linear marker regression mapping method (LMR). Empirical significance threshold values, power and estimates of QTL location and effect were identical for GIM and GMR when QTL mapping was restricted to within the marker interval. These results show that the theory of the marker regression method for QTL mapping is also applicable to binary traits and possibly for traits with other non-normal distributions. The linear and threshold models based on marker regression (LMR and GMR) also resulted in similar estimates and power for large progeny group sizes, indicating that LMR can be used for binary data for balanced designs with large families, as this method is computationally simpler than GMR. GMR may have a greater potential than LMR for QTL mapping for binary traits in complex situations such as QTL mapping with complex pedigrees, random models and models with interactions. Generalisierte Marker Regression und Intervall QTL Kartierungsmethoden für binäre Merkmale in einem Halbgeschwisterdesign Es wurde ein Ansatz zur generalisierten Marker Regressions Kartierung (GMR) entwickelt, um quantitative Merkmalsloci (QTL) zu kartieren, die binäre polygenetische Merkmale in einem Einfamilien-Halbgeschwisterdesign beeinflussen. Das GMR basiert auf der Theorie eines Schwellenwertmodells und auf der Regression des Nachkommenphänotyps auf den erwarteten Markergenotyp der flankierenden Markerloci. Mittels Simulation wurde die statistische Power und Schiefe der QTL Kartierung für binäre Merkmale nach GMR verglichen mit vollständiger QTL Intervallkartierung, die auf einem Schwellenmodell (GIM) basiert, und mit einer Methode zur linearen Marker Regressions Kartierung (LMR). Empirische Signifikanzschwellenwerte, Power und Schätzer für die QTL Lokation und der Effekt waren für GIM und GMR identisch, so lange die QTL Kartierung innerhalb des Markerintervalls definiert war. Diese Ergebnisse zeigen, dass die Theorie der Marker Regressions-Methode zur QTL Kartierung auch für binäre Merkmale und möglicherweise auch für Merkmale, die keiner Normalverteilung folgen, geeignet ist. Die linearen und Schwellenmodelle, die auf Marker Regression (LMR und GMR) basieren, ergaben ebenfalls ähnliche Schätzer und Power bei großen Nachkommengruppen, was schlussfolgern lässt, dass LMR für binäre Daten in einem balancierten Design mit großen Familien genutzt werden kann. Schließlich ist diese Methode computertechnisch einfacher als GMR. GMR mag für die QTL Kartierung bei binären Merkmalen in komplexen Situationen ein größeres Potential haben als LMR. Ein Beispiel dafür ist die QTL Kartierung mit komplexen Pedigrees, zufälligen Modellen und Interaktionsmodellen. [source] Knowledge translation: An opportunity to reduce global health inequalitiesJOURNAL OF INTERNATIONAL DEVELOPMENT, Issue 8 2009Vivian Welch Abstract Knowledge translation represents an opportunity to redress global health inequalities. This paper first assesses models for how health inequalities are produced and sustained, including effects of catastrophic illness and globalisation. Secondly, this paper illustrates how methods for knowledge translation can be applied to reducing inequalities in health by ensuring the best evidence is applied when appropriate. Thirdly, the paper describes available databases and tools for monitoring effects of knowledge translation on global health inequalities. In particular, mapping methods for creating visual representations of changes in global health inequalities are useful for setting priorities for action and research. Copyright © 2009 John Wiley & Sons, Ltd. [source] Determination of mean free path for energy loss and surface oxide film thickness using convergent beam electron diffraction and thickness mapping: a case study using Si and P91 steelJOURNAL OF MICROSCOPY, Issue 2 2006D. R. G. MITCHELL Summary Determining transmission electron microscope specimen thickness is an essential prerequisite for carrying out quantitative microscopy. The convergent beam electron diffraction method is highly accurate but provides information only on the small region being probed and is only applicable to crystalline phases. Thickness mapping with an energy filter is rapid, maps an entire field of view and can be applied to both crystalline and amorphous phases. However, the thickness map is defined in terms of the mean free path for energy loss (,), which must be known in order to determine the thickness. Convergent beam electron diffraction and thickness mapping methods were used to determine , for two materials, Si and P91 steel. These represent best- and worst-case scenario materials, respectively, for this type of investigation, owing to their radically different microstructures. The effects of collection angle and the importance of dynamical diffraction contrast are also examined. By minimizing diffraction contrast effects in thickness maps, reasonably accurate (±15%) values of , were obtained for P91 and accuracies of ±5% were obtained for Si. The correlation between the convergent beam electron diffraction-derived thickness and the log intensity ratios from thickness maps also permits estimation of the thickness of amorphous layers on the upper and lower surfaces of transmission electron microscope specimens. These estimates were evaluated for both Si and P91 using cross-sectional transmission electron microscopy and were found to be quite accurate. [source] Do some enterprise zones create jobs?JOURNAL OF POLICY ANALYSIS AND MANAGEMENT, Issue 1 2010Jed Kolko We study how the employment effects of enterprise zones vary with their location, implementation, and administration, based on evidence from California. We use new establishment-level data and geographic mapping methods, coupled with a survey of enterprise zone administrators. Overall, the evidence indicates that enterprise zones do not increase employment. However, the evidence also suggests that the enterprise zone program has a more favorable effect on employment in zones that have a lower share of manufacturing and in zones where managers report doing more marketing and outreach activities. On the other hand, devoting more effort to helping firms get hiring tax credits reduces or eliminates any positive employment effects, which may be attributable to idiosyncrasies of California's enterprise zone program during the period we study. © 2010 by the Association for Public Policy Analysis and Management. [source] GEOSTATISTICAL ESTIMATION OF HORIZONTAL HYDRAULIC CONDUCTIVITY FOR THE KIRKWOOD-COHANSEY AQUIFER,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 1 2004Vikram M. Vyas ABSTRACT: The Kirkwood-Cohansey aquifer has been identified as a critical source for meeting existing and expected water supply needs for southern New Jersey. Several contaminated sites exist in the region; their impact on the aquifer has to be evaluated using ground water flow and transport models. Ground water modeling depends on availability of measured hydrogeologic data (e.g., hydraulic conductivity, for parameterization of the modeling runs). However, field measurements of such critical data have inadequate spatial density, and their locations are often clustered. The goal of this study was to research, compile, and geocode existing data, then use geostatistics and advanced mapping methods to develop a map of horizontal hydraulic conductivity for the Kirkwood-Cohansey aquifer. Spatial interpolation of horizontal hydraulic conductivity measurements was performed using the Bayesian Maximum Entropy (BME) Method implemented in the BMELib code library. This involved the integration of actual measurements with soft information on likely ranges of hydraulic conductivity at a given location to obtain estimate maps. The estimation error variance maps provide an insight into the uncertainty associated with the estimates, and indicate areas where more information on hydraulic conductivity is required. [source] Using aerial photography for identification of marine and coastal habitats under the EU's Habitats DirectiveAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 4 2003Jan Ekebom Abstract 1.Implementation of the E.U. Habitats Directive requires information on the distribution, abundance and area covered by the habitats listed in Annex I of the Directive. 2.In Finland, 21 of these habitats occur in marine and coastal areas. The demand for spatial information of these habitats is increasing, so rapid and relatively inexpensive mapping methods are needed. 3.This study examines the identification of 15 habitats using high altitude black and white aerial photographs. Our goal was to find out how well these habitats could be identified using these types of photographs. We used a test group of 34 persons who were given only brief instructions on how to identify the habitats prior to the test. Their results were compared to a set of field data from an archipelago area at the entrance of the Gulf of Finland, in August 1999 and autumn 2000. 4.The test group identified sandy beaches, lagoons, submerged sandbanks and cliffs with an accuracy of 82%, 71%, 66% and 65%, respectively. The main reasons for these high accuracy percentages were apparently the high contrast and/or easy delineation of the habitat from the surrounding areas. 5.Reefs, wooded dunes and submerged reefs were identified with an accuracy of 39%, 44% and 45%, respectively. The remaining habitats were less precisely identified, apparently due to their small size or poor contrast to the surrounding areas. 6.High altitude aerial photographs are shown to be a useful tool for identifying several of these habitats and can be used as a complement to field mapping methods, GIS methods and other remote sensing techniques. The use of high altitude photographs for monitoring change is discussed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Gaussian Process Based Bayesian Semiparametric Quantitative Trait Loci Interval MappingBIOMETRICS, Issue 1 2010Hanwen Huang Summary In linkage analysis, it is often necessary to include covariates such as age or weight to increase power or avoid spurious false positive findings. However, if a covariate term in the model is specified incorrectly (e.g., a quadratic term misspecified as a linear term), then the inclusion of the covariate may adversely affect power and accuracy of the identification of quantitative trait loci (QTL). Furthermore, some covariates may interact with each other in a complicated fashion. We implement semiparametric models for single and multiple QTL mapping. Both mapping methods include an unspecified function of any covariate found or suspected to have a more complex than linear but unknown relationship with the response variable. They also allow for interactions among different covariates. This analysis is performed in a Bayesian inference framework using Markov chain Monte Carlo. The advantages of our methods are demonstrated via extensive simulations and real data analysis. [source] Refinement of 2q and 7p loci in a large multiplex NTD family,BIRTH DEFECTS RESEARCH, Issue 6 2008Demetra S. Stamm Abstract BACKGROUND: NTDs are considered complex disorders that arise from an interaction between genetic and environmental factors. NTD family 8776 is a large multigenerational Caucasian family that provides a unique resource for the genetic analysis of NTDs. Previous linkage analysis using a genome-wide SNP screen in family 8776 with multipoint nonparametric mapping methods identified maximum LOD* scores of ,3.0 mapping to 2q33.1,q35 and 7p21.1,pter. METHODS: We ascertained an additional nuclear branch of 8776 and conducted additional linkage analysis, fine mapping, and haplotyping. Expression data from lymphoblast cell lines were used to prioritize candidate genes within the minimum candidate intervals. Genomic copy number changes were evaluated using BAC tiling arrays and subtelomeric fluorescent in situ hybridization probes. RESULTS: Increased evidence for linkage was observed with LOD* scores of ,3.3 for both regions. Haplotype analyses narrowed the minimum candidate intervals to a 20.3 Mb region in 2q33.1,q35 between markers rs1050347 and D2S434, and an 8.3 Mb region in 7p21.1,21.3 between a novel marker 7M0547 and rs28177. Within these candidate regions, 16 genes were screened for mutations; however, no obvious causative NTD mutation was identified. Evaluation of chromosomal aberrations using comparative genomic hybridization arrays, subtelomeric fluorescent in situ hybridization, and copy number variant detection techniques within the 2q and 7p regions did not detect any chromosomal abnormalities. CONCLUSIONS: This large NTD family has identified two genomic regions that may harbor NTD susceptibility genes. Ascertainment of another branch of family 8776 and additional fine mapping permitted a 9.1 Mb reduction of the NTD candidate interval on chromosome 7 and 37.3 Mb on chromosome 2 from previously published data. Identification of one or more NTD susceptibility genes in this family could provide insight into genes that may affect other NTD families. Birth Defects Research (Part A), 2008. © 2008 Wiley-Liss, Inc. [source] | |||||||||||||