Optimization of a Non-traditional Unsupervised Classification Approach for Land Cover Analysis

The conditions under which a hybrid of clustering and canonical analysis for image classification produce optimum results were analyzed. The approach involves generation of classes by clustering for input to canonical analysis. The importance of the number of clusters input and the effect of other parameters of the clustering algorithm (ISOCLS) were examined. The approach derives its final result by clustering the canonically transformed data. Therefore the importance of number of clusters requested in this final stage was also examined. The effect of these variables were studied in terms of the average separability (as measured by transformed divergence) of the final clusters, the transformation matrices resulting from different numbers of input classes, and the accuracy of the final classifications. The research was performed with LANDSAT MSS data over the Hazleton/Berwick Pennsylvania area. Final classifications were compared pixel by pixel with an existing geographic information system to provide an indication of their accuracy

A theoretical/experimental program to develop active optical pollution sensors: Quantitative remote Raman lidar measurements of pollutants from stationary sources

Typical pollutant gas concentrations at the stack exits of stationary sources can be estimated to be about 500 ppm under the present emission standards. Raman lidar has a number of advantages which makes it a valuable tool for remote measurements of these stack emissions. Tests of the Langley Research Center Raman lidar at a calibration tank indicate that night measurements of SO2 concentrations and stack opacity are possible. Accuracies of 10 percent are shown to be achievable from a distance of 300 m within 30 min integration times for 500 ppm SO2 at the stack exits. All possible interferences were examined quantitatively (except for the fluorescence of aerosols in actual stack emissions) and found to have negligible effect on the measurements. An early test at an instrumented stack is strongly recommended

Estimating species trees using multiple-allele DNA sequence data

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets - yeast (Saccharomyces) and birds (Manacus - manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics. © 2008 The Author(s)

Andean Land Use And Biodiversity: Humanized Landscapes In A Time Of Change

Some landscapes Cannot be understood without reference., to the kinds. degrees, kinds, degrees, and history of human-caused modifications to the Earth's surface. The tropical latitudes of the Andes represent one such place, with agricultural land-use systems appearing in the Early Holocene. Current land use includes both intensive and extensive grazing and crop- or tree-based agricultural systems found across virtually the, entire range of possible elevations and humidity regimes. Biodiversity found in or adjacent to such humanized landscapes will have been altered in abundance. composition, and distribution in relation to the resiliency of the native Species to harvest, hold cover modifications, and other deliberate or inadvertent human land uses. In addition, the geometries of land cover, resulting flout difference among the shapes, sizes, connectivities, and physical structures of the patches, corridors, and matrices that compose landscape mosaics, will constrain biodiversity, often in predictable ways. This article proposes a conceptual model that alter ins that the Continued persistence of native species may depend as much oil the shifting Of Andean landscape mosaics as on species characteristics, themselves. Furthermore, mountains such as the Andes display long gradients of environmental Conditions that after in relation to latitude, soil moisture, aspect, and elevation. Global environmental change will shift these, especially temperature and humidity regimes along elevational gradients, causing Changes outside the historical range of variation for some species. Both land-use systems and Conservation efforts will need to respond spatially to these shifts in the future, at both landscape and regional scales.Geography and the Environmen

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte

Information Needs of Hong Kong Chinese Patients Undergoing Surgery

BACKGROUND: The provision of information to patients is an important aspect of contemporary health care. Limitations in health resources necessitates that the provision of information is carefully planned and culturally specific to maximize the benefits to patients from the resources available. AIM AND OBJECTIVES: The purposes of the study were to recognize Chinese surgical patients' information needs on admission and ascertain why the information is important to assist in understanding how it is used and, therefore, its potential impact. METHODS: A descriptive study design was used. A convenience sample of 83 surgical patients took part comprising 51 men and 32 women. An eight-item questionnaire based on the right of patients to information as listed in the Patients' Charter in Hong Kong using a 5-point Likert scale and one open-ended question to comment on why the information was important to them was completed by patients on the day of admission. RESULTS: Patients rated highly the need for all types of information. They rated most highly the need for information about the signs and symptoms indicating postoperative complications and when to seek medical help. Patients did not rate as highly, information regarding why the doctor believes the surgery is important, treatment alternatives and explanation of the procedure. CONCLUSIONS: These findings indicate that Chinese patients are desirous of a range of relevant information. RELEVANCE TO PRACTICE: Nursing staff, in particular, need to consider the 'timeliness' of information and the cultural appropriateness of how information is delivered

Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay

Single nucleotide polymorphisms (SNPs) are indispensable in such applications as association mapping and construction of high-density genetic maps. These applications usually require genotyping of thousands of SNPs in a large number of individuals. Although a number of SNP genotyping assays are available, most of them are designed for SNP genotyping in diploid individuals. Here, we demonstrate that the Illumina GoldenGate assay could be used for SNP genotyping of homozygous tetraploid and hexaploid wheat lines. Genotyping reactions could be carried out directly on genomic DNA without the necessity of preliminary PCR amplification. A total of 53 tetraploid and 38 hexaploid homozygous wheat lines were genotyped at 96 SNP loci. The genotyping error rate estimated after removal of low-quality data was 0 and 1% for tetraploid and hexaploid wheat, respectively. Developed SNP genotyping assays were shown to be useful for genotyping wheat cultivars. This study demonstrated that the GoldenGate assay is a very efficient tool for high-throughput genotyping of polyploid wheat, opening new possibilities for the analysis of genetic variation in wheat and dissection of genetic basis of complex traits using association mapping approach

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog

On species delimitation: Yet another lemur species or just genetic variation?

<p>Abstract</p> <p>Background</p> <p>Although most taxonomists agree that species are independently evolving metapopulation lineages that should be delimited with several kinds of data, the taxonomic practice in Malagasy primates (Lemuriformes) looks quite different. Several recently described lemur species are based solely on evidence of genetic distance and diagnostic characters of mitochondrial DNA sequences sampled from a few individuals per location. Here we explore the validity of this procedure for species delimitation in lemurs using published sequence data.</p> <p>Results</p> <p>We show that genetic distance estimates and <it>Population Aggregation Analysis </it>(PAA) are inappropriate for species delimitation in this group of primates. Intra- and interspecific genetic distances overlapped in 14 of 17 cases independent of the genetic marker used. A simulation of a fictive taxonomic study indicated that for the mitochondrial D-loop the minimum required number of individuals sampled per location is 10 in order to avoid false positives via PAA.</p> <p>Conclusions</p> <p>Genetic distances estimates and PAA alone should not be used for species delimitation in lemurs. Instead, several nuclear and sex-specific loci should be considered and combined with other data sets from morphology, ecology or behavior. Independent of the data source, sampling should be done in a way to ensure a quantitative comparison of intra- and interspecific variation of the taxa in question. The results of our study also indicate that several of the recently described lemur species should be reevaluated with additional data and that the number of good species among the currently known taxa is probably lower than currently assumed.</p

DNA Barcode Detects High Genetic Structure within Neotropical Bird Species

BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods