3,580 research outputs found

    The distribution of word matches between Markovian sequences with periodic boundary conditions

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    Word match counts have traditionally been proposed as an alignment-free measure of similarity for biological sequences. The D2 statistic, which simply counts the number of exact word matches between two sequences, is a useful test bed for developing rigorous mathematical results, which can then be extended to more biologically useful measures. The distributional properties of the D2 statistic under the null hypothesis of identically and independently distributed letters have been studied extensively, but no comprehensive study of the D2 distribution for biologically more realistic higher-order Markovian sequences exists. Here we derive exact formulas for the mean and variance of the D2 statistic for Markovian sequences of any order, and demonstrate through Monte Carlo simulations that the entire distribution is accurately characterized by a PĂłlya-Aeppli distribution for sequence lengths of biological interest. The approach is novel in that Markovian dependency is defined for sequences with periodic boundary conditions, and this enables exact analytic formulas for the mean and variance to be derived. We also carry out a preliminary comparison between the approximate D2 distribution computed with the theoretical mean and variance under a Markovian hypothesis and an empirical D2 distribution from the human genome

    Optimizing The Riparian Buffer: Harold Brook In The Skaneateles Lake Watershed, New York

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    The use of riparian land buffers to protect water quality for human consumption and wildlife habitat has become an important conservation tool of both government and non-government agencies. The funds available to acquire private lands for riparian buffers are limited, however, and not all land contributes to water quality goals in the same way. Conservation agencies must therefore identify effective ways to allocate their scarce budgets in heterogeneous landscapes. We demonstrate how the acquisition of land for a riparian buffer can be viewed as a binary optimization problem and we apply the resulting model to a case study in New York (JEL Q15, Q25). Working Paper # 2002-00

    Henri Temianka Correspondence; (conrad)

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    This collection contains material pertaining to the life, career, and activities of Henri Temianka, violin virtuoso, conductor, music teacher, and author. Materials include correspondence, concert programs and flyers, music scores, photographs, and books.https://digitalcommons.chapman.edu/temianka_correspondence/3470/thumbnail.jp

    Henri Temianka Correspondence; (conrad)

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    This collection contains material pertaining to the life, career, and activities of Henri Temianka, violin virtuoso, conductor, music teacher, and author. Materials include correspondence, concert programs and flyers, music scores, photographs, and books.https://digitalcommons.chapman.edu/temianka_correspondence/3471/thumbnail.jp

    Embryo culturing methodology and investigation of seed dormancy mechanisms in Mountain Silverbell (Halesia Carolina L.)

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    Desirable wood properties once made mountain silverbell (Halesia Carolina L.) a favored species among loggers in the southern Appalachians. Showy flowers, disease resistance, and handsome form continue to make it a desirable ornamental. Delayed and erratic germination over a one to two year period, plus a poorly understood dormancy mechanism, may be responsible for limiting its commercial availability. Prolonged warm and cold stratification has been recommended as a presowing treatment, but it is not clear whether such treatments relieve dormancy by overcoming hardseededness, inhibiting chemicals, or morphological and physiological impediments within the embryo itself. During the years 1982-84, a study was undertaken to find means of hastening germination, and to provide for a clearer understanding of dormancy. Various conventional sacrification procedures were used to quickly remove hard seed coverings, but these failed to induce germination. In vitro culturing of excised surface sterilized embryos, however, proved highly successful, yielding 100 percent germination within 7 days. Later experimentation showed that morphological and physiological dormancy factors were absent at the time of fruit abscision in mid autumn. Exogenously applied extracts from fruit and seed layers also did not inhibit germination. The primary impediments appeared to center on the hardened endocarp which physically restricted water availability to the quiescent embryo for several months, and then mechanically prevented embryo expansion once hydration occurred. Overwintering on the forest floor (or artificial stratification designed to mimic overwintering) gradually overcomes physical and mechanical barriers of hardseededness, especially under moist, non-sterile conditions. Embryo excision and culture expedites this process so that seedlings suitable for out-planting can be obtained within 1 year
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