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Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.
genotyping by sequencing (GBS), microsatellite development, next-generation sequencing (NGS), restriction site associated DNA sequencing (RAD-Seq), simple sequence repeats (SSR), transcriptomes
The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century1
Richard G. J. Hodel,2,3,7 M. Claudia Segovia-Salcedo,4 Jacob B. Landis,2,3 Andrew A. Crowl,2,3 Miao Sun,3 Xiaoxian Liu,2,3 Matthew A. Gitzendanner,2 Norman A. Douglas,2 Charlotte C. Germain-Aubrey,3 Shichao Chen,5 Douglas E. Soltis,2,3,6 and Pamela S. Soltis3,6
To propose a simplified method of correcting vital information and estimating the coefficient of infant mortality in Brazil.
Vital data in the information systems on mortality and live births were corrected using correction factors, estimated based on events not reported to the Brazilian Ministry of Health and obtained by active search. This simplified method for correcting vital information for the period 2000-2009 for Brazil and its federal units establishes the level of adequacy of information on deaths and live births by calculating the overall coefficient of mortality standardized by age and the ratio between reported and expected live births, respectively, in each Brazilian municipality. By applying correction factors to the number of deaths and live births reported in each county, the vital statistics were corrected, making it possible to estimate the coefficient of infant mortality.
The highest correction factors were related to infant deaths, reaching values higher than 7 for municipalities with very precarious mortality information. For deaths and live births, the correction factors exhibit a decreasing gradient as indicators of adequacy of the vital information improve. For the year 2008, the vital information corrected by the simplified method per state were similar to those obtained in the research of active search. Both the birth rate and the infant mortality rate decreased in the period in all Brazilian regions. In the Northeast, the annual rate of decline was 6.0%, the highest in Brazil (4.7%).
The active search of deaths and births allowed correction factors to be calculated by level of adequacy of mortality information and live births. The simplified method proposed here allowed vital information to be corrected per state for the period 2000-2009 and the progress of the coefficient of infant mortality in Brazil, its regions and states to be assessed.
Infant Mortality, Vital Statistics, Birth Registration, Mortality Registries, Underregistration, Information Systems
Correcting vital information: estimating infant mortality, Brazil, 2000-2009
Paulo Germano de Frias,I,II Celia Landmann Szwarcwald,III Paulo Roberto Borges de Souza, Junior,III Wanessa da Silva de Almeida,III and Pedro Israel Cabral LiraIV
The present study proposes a workflow to extract vegetation height for urban areas from Pleiades stereo and tri-stereo satellite imagery. The workflow was applied on a stereo image pair for Szeged, Hungary and on tri-stereo imagery for Salzburg, Austria. Digital surface models (DSMs) of the study areas were computed using the semi-global matching algorithm. Normalised digital surface models (nDSMs) were then generated. Objects of vegetation and non-vegetation were delineated based on the spectral information of the multispectral images by applying multi-resolution segmentation and support vector machine classifier. Mean object height values were then computed from the overlaid pixels of the nDSMs and assigned to the objects. Finally, the delineated vegetation was classified into six vegetation height classes based on their assigned height values by using hierarchical classification. The vegetation discrimination resulted in very high accuracy, while the vegetation height extraction was moderately accurate. The results of the vegetation height extraction provided a vertical stratification of the vegetation in the two study areas which is readily applicable for decision support purposes. The elaborated workflow will contribute to a green monitoring and valuation strategy and provide input data for an urban green accessibility study.
3D extraction of urban vegetation, Pleiades (tri-)stereo imagery, semi-global matching, digital surface model, support vector machine
Urban vegetation extraction from VHR (tri-)stereo imagery - a comparative study in two central European cities
Gyula Kothencz, a Kerstin Kulessa, b Aynabat Anyyeva, a and Stefan Lang a