Showing papers by "North Carolina State University published in 1994"

Precision mapping of quantitative trait loci.

Abstract: Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic markers in the statistical model as a control when performing interval mapping. Compared with the current QTL mapping method (i.e., the interval mapping method which uses a pair or two pairs of markers for mapping QTLs), this method has several advantages. (1) By confining the test to one region at a time, it reduces a multiple dimensional search problem (for multiple QTLs) to a one dimensional search problem. (2) By conditioning linked markers in the test, the sensitivity of the test statistic to the position of individual QTLs is increased, and the precision of QTL mapping can be improved. (3) By selectively and simultaneously using other markers in the analysis, the efficiency of QTL mapping can be also improved. The behavior of the test statistic under the null hypothesis and appropriate critical value of the test statistic for an overall test in a genome are discussed and analyzed. A simulation study of QTL mapping is also presented which illustrates the utility, properties, advantages and disadvantages of the method.

Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers

Abstract: We have used a "two-way pseudo-testcross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F1 progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, theta = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support > or = 1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organisms. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding.

Testing for a Unit Root in Time Series With Pretest Data-Based Model Selection

Abstract: In this article we examine the impact of data-based lag-length estimation on the behavior of the augmented Dickey–Fuller (ADF) test for a unit root We derive conditions under which the ADF test converges to the distribution tabulated by Dickey and Fuller and verify that these conditions are satisfied by several commonly employed lag-selection strategies Simulation evidence indicates that the performance of the ADF test is considerably improved when the lag length is selected from the data An application to inventory series illustrates that inference about a unit root can be very sensitive to the method of lag-length selection

GPS Meteorology: Mapping Zenith Wet Delays onto Precipitable Water

Abstract: Emerging networks of Global Positioning System (GPS) receivers can be used in the remote sensing of atmospheric water vapor. The time-varying zenith wet delay observed at each GPS receiver in a network can be transformed into an estimate of the precipitable water overlying that receiver. This transformation is achieved by multiplying the zenith wet delay by a factor whose magnitude is a function of certain constants related to the refractivity of moist air and of the weighted mean temperature of the atmosphere. The mean temperature varies in space and time and must be estimated a priori in order to transform an observed zenith wet delay into an estimate of precipitable water. We show that the relative error introduced during this transformation closely approximates the relative error in the predicted mean temperature. Numerical weather models can be used to predict the mean temperature with an rms relative error of less than 1%.

Network externality : an uncommon tragedy

Abstract: Economists have defined 'network externality' and have examined putative inframarginal market failures associated with it. This paper distinguishes between network effects and network externalities, where the latter are market failures. The authors argue that while network effects are important, network externalities are theoretically fragile and empirically undocumented. Some network externalities are merely pecuniary. Network ownership or transactions among network participants can internalize some network effects. The type of market failure that has been associated with these externalities is a transition problem that has little to do with externality.

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.

Abstract: A model of DNA sequence evolution applicable to coding regions is presented. This represents the first evolutionary model that accounts for dependencies among nucleotides within a codon. The model uses the codon, as opposed to the nucleotide, as the unit of evolution, and is parameterized in terms of synonymous and nonsynonymous nucleotide substitution rates. One of the model's advantages over those used in methods for estimating synonymous and nonsynonymous substitution rates is that it completely corrects for multiple hits at a codon, rather than taking a parsimony approach and considering only pathways of minimum change between homologous codons. Likelihood-ratio versions of the relative-rate test are constructed and applied to data from the complete chloroplast DNA sequences of Oryza sativa, Nicotiana tabacum, and Marchantia polymorpha. Results of these tests confirm previous findings that substitution rates in the chloroplast genome are subject to both lineage-specific and locus-specific effects. Additionally, the new tests suggest tha the rate heterogeneity is due primarily to differences in nonsynonymous substitution rates. Simulations help confirm previous suggestions that silent sites are saturated, leaving no evidence of heterogeneity in synonymous substitution rates.

Update on clinical significance of coagulase-negative staphylococci.

Abstract: The clinical significance of coagulase-negative Staphylococcus species (CNS) continues to increase as strategies in medical practice lead to more invasive procedures. Hospitalized patients that are immunocompromised and/or suffering from chronic diseases are the most vulnerable to infection. Since CNS are widespread on the human body and are capable of producing very large populations, distinguishing the etiologic agent(s) from contaminating flora is a serious challenge. For this reason, culture identification should proceed to the species and strain levels. A much stronger case can be made for the identification of a CNS etiologic agent if the same strain is repeatedly isolated from a series of specimens as opposed to the isolation of different strains of one or more species. Strain identity initially can be based on colony morphology, and then one or more molecular approaches can be used to gain information on the genotype. Many of the CNS species are commonly resistant to antibiotics that are being indicated for staphylococcal infections, with the exception of vancomycin. The widespread use of antibiotics in hospitals has provided a reservoir of antibiotic-resistant genes. The main focus on mechanisms of pathogenesis has been with foreign body infections and the role of specific adhesins and slime produced by Staphylococcus epidermidis. Slime can reduce the immune response and opsonophagocytosis, thereby interfering with host defense mechanisms. As we become more aware of the various strategies used by CNS, we will be in a better position to compromise their defense mechanisms and improve treatment.

On the use of non-stationary penalty functions to solve nonlinear constrained optimization problems with GA's

Abstract: We discuss the use of non-stationary penalty functions to solve general nonlinear programming problems (NP) using real-valued GAs. The non-stationary penalty is a function of the generation number; as the number of generations increases so does the penalty. Therefore, as the penalty increases it puts more and more selective pressure on the GA to find a feasible solution. The ideas presented in this paper come from two basic areas: calculus-based nonlinear programming and simulated annealing. The non-stationary penalty methods are tested on four NP test cases and the effectiveness of these methods are reported. >

Simulation-extrapolation estimation in parametric measurement error models

Abstract: We describe a simulation-based method of inference for parametric measurement error models in which the measurement error variance is known or at least well estimated. The method entails adding add...

Attachments to recreation settings: The case of rail‐trail users

Abstract: The authors explore the nature of place attachment (the extent to which an individual values or identifies with a particular environmental setting) and develop a model to help explain how such relationships with recreation settings form. This model is then tested with a sample of users of three “rail‐trails” (multiuse recreation trails constructed on unused railroad rights‐of‐way). Results support the literature, suggesting that place attachment has at least two dimensions: a place dependence, reflecting the importance of the place in facilitating a user's activity, and a more affective place identity, reflecting an individual's valuing of a setting for more symbolic or emotional reasons. Analysis reveals that place identity can best be predicted by how long users have been associated with the trail, the importance they ascribe to their trail activity, and their level of place dependence. Level of place dependence is best predicted by the distance between the trail and the user's home and users’ ...

On the Wave Theory in Heat Conduction

Abstract: This work contains three major components: a thorough review on the research emphasizing engineering applications of the thermal wave theory, special features in thermal wave propagation, and the thermal wave model in relation to the microscopic two-step model. For the sake of convenience, the research works are classified according to their individual emphases. Special features in thermal wave propagation include the sharp wavefront and rate effects, the thermal shock phenomenon, the thermal resonance phenomenon, and reflections and refractions of thermal waves across a material interface. By employing the dual-phase-lag concept, we show that the energy equation may be reduced to that governing the heat transport through the metal lattice in the microscopic two-step model

Gas separation using polymer membranes: an overview

Abstract: This overview article discusses fundamental principles of gas sorption and transport in rubbery and glassy polymers and material selection guidelines for gas separation membranes. Comparisons between the performance of membrane-based gas separation systems and more conventional technologies in key commercial applications are provided. Companion articles in this special edition focus on state-of-the-art reviews and descriptions of theoretical and experimental developments important in the technology of gas separations using polymeric membranes.

A comparison of unit root test criteria

Abstract: During the past 15 years, the ordinary least squares estimator and the corresponding pivotal statistic have been widely used for testing the unit-root hypothesis in autoregressive processes. Recently, several new criteria, based on maximum likelihood estimators and weighted symmetric estimators, have been proposed. In this article, we describe several different test criteria. Results from a Monte Carlo study that compares the power of the different criteria indicate that the new tests are more powerful against the stationary alternative. Of the procedures studied, the weighted symmetric estimator and the unconditional maximum likelihood estimator provide the most powerful tests against the stationary alternative. As an illustration, the weekly series of one-month treasury-bill rates is analyzed.

Surface circulation in the South China Sea

Abstract: A three-dimensional, primitive-equation model with a free surface is used to simulate the monthly circulation in the South China Sea. The model has a resolution of 0.4° in the horizontal and 21 layers in the vertical in a region from 2°N to 24°N and from 99°E to 124°E. Inflow and outflow in the Kuroshio, through the Taiwan Strait, and between the Sunda Shelf and the Java Sea are prescribed bimonthly. At the sea surface, the model is forced by monthly-averaged climatological winds and temperature and seasonally-averaged salinity. Several important features are reproduced in the model simulation. First, a strong coastal jet is present at the western boundary. The current is southward along the continental margin from China to southern Vietnam in winter. In summer, the current is northward and separates from the coast between 11°N and 14°N. The transition in September begins as a southward undercurrent, which is remotely forced by the northeast monsoon in the northern reaches of the South China Sea. The undercurrent extends to the surface in about a month. Second, inflow through the Luzon Strait from October to February transports the Kuroshio water in the top of 300 m of the water column westward along the continental slope south of China. In summer, eastward flow in the Luzon Strait transport surface water west of Luzon to the region east of Taiwan. Finally, a subsurface current, which is opposite to the surface current, exists over the Sunda Shelf and is driven by a pressure gradient set up by monsoon winds. These simulated currents are in qualitative agreement with the circulation inferred from the available observations.

Hydrologic and water quality impacts of agricultural drainage

Abstract: While some of the world's most productive agriculture is on artificially drained soils, drainage is increasingly perceived as a major contributor to detrimental off‐site environmental impacts. Howe...

State estimation for real-time monitoring of distribution systems

Abstract: Utilities currently use historical customer load data to forecast the loads in their distribution feeders for real-time feeder analysis and control. In this paper a three-phase state estimation method is developed to increase the accuracy of this load data. The method is based on the weighted least square approach and uses a three-phase node voltage formulation. The method can handle power, voltage, and current measurements. Test results indicate that state estimation can improve the forecasted load data by using real-time measurements. The effectiveness of branch current measurements were also tested. >

The Ribonuclease P database.

Abstract: The Ribonuclease P Sequence database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. In its initial form, the database contains information on RNase P RNA in bacteria and archaea, and RNase P protein in bacteria. The sequences themselves are presented phylogenetically ordered and aligned. The database also contains secondary structures of bacterial and archaeal RNAs, including specially annotated 'reference' secondary structures of Escherichia coli and Bacillus subtilis RNase P RNAs, a minimum phylogenetic consensus structure, and coordinates for models of three-dimensional structure.

Changes in Atmospheric Circulation and Ocean Ice Cover over the North Atlantic During the Last 41,000 Years

Abstract: High-resolution, continuous multivariate chemical records from a central Greenland ice core provide a sensitive measure of climate change and chemical composition of the atmosphere over the last 41,000 years. These chemical series reveal a record of change in the relative size and intensity of the circulation system that transported air masses to Greenland [defined here as the polar circulation index (PCI)] and in the extent of ocean ice cover. Massive iceberg discharge events previously defined from the marine record are correlated with notable expansions of ocean ice cover and increases in PCI. During stadials without discharge events, ocean ice cover appears to reach some common maximum level. The massive aerosol loadings and dramatic variations in ocean ice cover documented in ice cores should be included in climate modeling.

Measurement and Analysis of Object Reflectance Spectra

Abstract: Recent algorithms developed in the field of color vision make assumptions based on the spectral reflectance curves of Munsell chips and natural materials Some of them rely on data collected many years ago which is partially incomplete in the visible spectrum or contains many occurrences of the same material in it In this article we present a set of new measurements of different materials In particular we measured the spectral reflectance of Munsell chips, paints and various natural materials in the 390–730-nm range In addition, we have analyzed through principal-component analysis, the possibility of representing the data collected with a set of basis functions We show the implications of varying the number of principal components used (from 7 down to 3) on the errors introduced using this method

Role of overlapping generations in maintaining genetic variation in a fluctuating environment

Abstract: Population genetics theory suggests that temporally fluctuating selection on pheno- types can act to maintain genetic variance only under very restrictive conditions. However, this conclusion is based on models with discrete nonoverlapping generations. We propose here that temporally fluctuating selection can indeed contribute significantly to the maintenance of genetic variation when the effects of overlapping generations and age-specific or stage-specific selection are considered. We develop a simple model for a population with overlapping generations, experiencing stabilizing selection with a temporally fluctuating optimum, and subject to repeated invasions by mutants with alternative phenotypes. We find that an evolutionarily stable popula- tion must have positive genetic variance maintained by selection so long as the product (variance of fluctuations) times (amount of generation overlap) times (selection intensity) is sufficiently high. This result applies to haploid, diploid, single-locus, or multilocus inheritance, and it does not depend on any form of heterozygote advantage to maintain genetic variance. However, it depends on the map between genotype and phenotype being constrained. If a single genotype can produce an arbitrary distribution of phenotypes, then genetic variance is not maintained by selection.

Negative-electron-affinity effects on the diamond (100) surface

Abstract: A negative electron affinity (NEA) was found both experimentally by photoemission spectroscopy and theoretically by ab initio calculations for the 2\ifmmode\times\else\texttimes\fi{}1 reconstructed diamond (100) surface. This surface is the dominant growth surface for thin diamond films and can be obtained by chemical-vapor deposition. Various surface-preparation methods which result in a NEA are described. Theoretical results indicate that the observed NEA is associated with a monohydride-terminated surface, while the hydrogen-free surface exhibits a positive electron affinity.

Temperature, energy, and heat capacity of asymptotically anti-de Sitter black holes.

Abstract: We investigate the thermodynamical properties of black holes in (3+1)- and (2+1)-dimensional Einstein gravity with a negative cosmological constant. In each case, ther thermodynamic internal energy is computed for a finite spatial region that contains the black hole. The temperature at the boundary of this regoin is defined by differentiating the energy with respect to entropy, and is equal to the product of the surface gravity (divided by 2\ensuremath{\pi}) and the Tolman redshift factor for temperature in a stationary gravitational field. We also compute the thermodynamic surface pressure and, in the case of the 2+1 black hole, show that the chemical potential conjugate to angular momentum is equal to the proper angular velocity of the black hole with respect to observers who are at rest in the stationary time slices. In 3+1 dimensions, a calculation of the heat capacity reveals the existence of a thermodynamically stable black hole solution and a negative heat capacity instanton. This result holds in the limit that the spatial boundary tends to infinity only if the cosmological constant is negative; if the cosmological constant vanishes, the stable black hole solution is lost. In 2+1 dimensions, a calculation of the heat capacity reveals the existence of a thermodynamically stable black hole solution, but no negative heat capacity instanton.

P Values Maximized Over a Confidence Set for the Nuisance Parameter

Abstract: For testing problems of the form H 0: v = v 0 with unknown nuisance parameter θ, various methods are used to deal with θ. The simplest approach is exemplified by the t test where the unknown variance is replaced by the sample variance and the t distribution accounts for estimation of the variance. In other problems, such as the 2 × 2 contingency table, one conditions on a sufficient statistic for 0 and proceeds as in Fisher's exact test. Because neither of these standard methods is appropriate for all situations, this article suggests a new method for handling the unknown θ. This new method is a simple modification of the formal definition of a p value that involves taking a maximum over the nuisance parameter space of a p value obtained for the case when θ is known. The suggested modification is to restrict the maximization to a confidence set for the nuisance parameter. After giving a brief justification, we give various examples to show how this new method gives improved results for 2 × 2 tabl...

Factors involved in adherence of lactobacilli to human Caco-2 cells

Abstract: A quantitative assay performed with bacterial cells labelled with [3H]thymidine was used to investigate factors involved in the adherence of human isolates Lactobacillus acidophilus BG2FO4 and NCFM/N2 and Lactobacillus gasseri ADH to human Caco-2 intestinal cells. For all three strains, adherence was concentration dependent, greater at acidic pH values, and significantly greater than adherence of a control dairy isolate, Lactobacillus delbrueckii subsp. bulgaricus 1489. Adherence of L. acidophilus BG2FO4 and NCFM/N2 was decreased by protease treatment of the bacterial cells, whereas adherence of L. gasseri ADH either was not affected or was enhanced by protease treatment. Putative surface layer proteins were identified on L. acidophilus BG2FO4 and NCFM/N2 cells but were not involved in adherence. Periodate oxidation of bacterial cell surface carbohydrates significantly reduced adherence of L. gasseri ADH, moderately reduced adherence of L. acidophilus BG2FO4, and had no effect on adherence of L. acidophilus NCFM/N2. These results indicate that Lactobacillus species adhere to human intestinal cells via mechanisms which involve different combinations of carbohydrate and protein factors on the bacterial cell surface. The involvement of a secreted bridging protein, which has been proposed as the primary mediator of adherence of L. acidophilus BG2FO4 in spent culture supernatant (M.-H. Coconnier, T. R. Klaenhammer, S. Kerneis, M.-F. Bernet, and A. L. Servin, Appl. Environ. Microbiol. 58:2034-2039, 1992), was not confirmed in this study. Rather, a pH effect on Caco-2 cells contributed significantly to the adherence of this strain in spent culture supernatant.(ABSTRACT TRUNCATED AT 250 WORDS)

GAVaPS-a genetic algorithm with varying population size

Abstract: The size of the population can be critical in many applications of genetic algorithms. If the population size is too small, the genetic algorithm may converge too quickly; if it is too large, the genetic algorithm may waste computational resources; the waiting time for an improvement might be too long. We propose an adaptive method for maintaining variable population size, which grows and shrinks together according to some characteristic of the search. The first experimental results indicate some merits of the proposed method. >

Riparian wetlands and water quality

Abstract: Because of wet soils adjacent to the streams, riparian buffers are frequently present between farming and urban activities on the uplands and small streams. These riparian areas have been shown to be very valuable for the removal of nonpoint-source pollution from drainage water. Several researchers have measured >90% reductions in sediment and nitrate concentrations in water flowing through the riparian areas. The riparian buffers are less effective for P removal but may retain 50% of the surface-water P entering them. I consider riparian buffers to be the most important factor influencing nonpoint-source pollutants entering surface water in many areas of the USA and the most important wetlands for surface water quality protection.