Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

PubMed

Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

2015-08-18

Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.

Global Ionospheric Perturbations Monitored by the Worldwide GPS Network

NASA Technical Reports Server (NTRS)

Ho, C. M.; Mannucci, A. T.; Lindqwister, U. J.; Pi, X. Q.

1996-01-01

Based on the delays of these (Global Positioning System-GPS)signals, we have generated high resolution global ionospheric TEC (Total Electronic Changes) maps at 15-minute intervals. Using a differential method comparing storm time maps with quiet time maps, we find that the ionopshere during this time storm has increased significantly (the percentage change relative to quiet times is greater than 150 percent) ...These preliminary results (those mentioned above plus other in the paper)indicate that the differential maping method, which is based on GPS network measurements appears to be a useful tool for studying the global pattern and evolution process of the entire ionospheric perturbation.

Assessment of the Thematic Accuracy of Land Cover Maps

NASA Astrophysics Data System (ADS)

Höhle, J.

2015-08-01

Several land cover maps are generated from aerial imagery and assessed by different approaches. The test site is an urban area in Europe for which six classes (`building', `hedge and bush', `grass', `road and parking lot', `tree', `wall and car port') had to be derived. Two classification methods were applied (`Decision Tree' and `Support Vector Machine') using only two attributes (height above ground and normalized difference vegetation index) which both are derived from the images. The assessment of the thematic accuracy applied a stratified design and was based on accuracy measures such as user's and producer's accuracy, and kappa coefficient. In addition, confidence intervals were computed for several accuracy measures. The achieved accuracies and confidence intervals are thoroughly analysed and recommendations are derived from the gained experiences. Reliable reference values are obtained using stereovision, false-colour image pairs, and positioning to the checkpoints with 3D coordinates. The influence of the training areas on the results is studied. Cross validation has been tested with a few reference points in order to derive approximate accuracy measures. The two classification methods perform equally for five classes. Trees are classified with a much better accuracy and a smaller confidence interval by means of the decision tree method. Buildings are classified by both methods with an accuracy of 99% (95% CI: 95%-100%) using independent 3D checkpoints. The average width of the confidence interval of six classes was 14% of the user's accuracy.

Algorithms and Complexity Results for Genome Mapping Problems.

PubMed

Rajaraman, Ashok; Zanetti, Joao Paulo Pereira; Manuch, Jan; Chauve, Cedric

2017-01-01

Genome mapping algorithms aim at computing an ordering of a set of genomic markers based on local ordering information such as adjacencies and intervals of markers. In most genome mapping models, markers are assumed to occur uniquely in the resulting map. We introduce algorithmic questions that consider repeats, i.e., markers that can have several occurrences in the resulting map. We show that, provided with an upper bound on the copy number of repeated markers and with intervals that span full repeat copies, called repeat spanning intervals, the problem of deciding if a set of adjacencies and repeat spanning intervals admits a genome representation is tractable if the target genome can contain linear and/or circular chromosomal fragments. We also show that extracting a maximum cardinality or weight subset of repeat spanning intervals given a set of adjacencies that admits a genome realization is NP-hard but fixed-parameter tractable in the maximum copy number and the number of adjacent repeats, and tractable if intervals contain a single repeated marker.

Zero entropy continuous interval maps and MMLS-MMA property

NASA Astrophysics Data System (ADS)

Jiang, Yunping

2018-06-01

We prove that the flow generated by any continuous interval map with zero topological entropy is minimally mean-attractable and minimally mean-L-stable. One of the consequences is that any oscillating sequence is linearly disjoint from all flows generated by all continuous interval maps with zero topological entropy. In particular, the Möbius function is linearly disjoint from all flows generated by all continuous interval maps with zero topological entropy (Sarnak’s conjecture for continuous interval maps). Another consequence is a non-trivial example of a flow having discrete spectrum. We also define a log-uniform oscillating sequence and show a result in ergodic theory for comparison. This material is based upon work supported by the National Science Foundation. It is also partially supported by a collaboration grant from the Simons Foundation (grant number 523341) and PSC-CUNY awards and a grant from NSFC (grant number 11571122).

Considerations of solar wind dynamics in mapping of Jupiter's auroral features to magnetospheric sources

NASA Astrophysics Data System (ADS)

Gyalay, S.; Vogt, M.; Withers, P.

2015-12-01

Previous studies have mapped locations from the magnetic equator to the ionosphere in order to understand how auroral features relate to magnetospheric sources. Vogt et al. (2011) in particular mapped equatorial regions to the ionosphere by using a method of flux equivalence—requiring that the magnetic flux in a specified region at the equator is equal to the magnetic flux in the region to which it maps in the ionosphere. This is preferred to methods relying on tracing field lines from global Jovian magnetic field models, which are inaccurate beyond 30 Jupiter radii from the planet. That previous study produced a two-dimensional model—accounting for changes with radial distance and local time—of the normal component of the magnetic field in the equatorial region. However, this two-dimensional fit—which aggregated all equatorial data from Pioneer 10, Pioneer 11, Voyager 1, Voyager 2, Ulysses, and Galileo—did not account for temporal variability resulting from changing solar wind conditions. Building off of that project, this study aims to map the Jovian aurora to the magnetosphere for two separate cases: with a nominal magnetosphere, and with a magnetosphere compressed by high solar wind dynamic pressure. Using the Michigan Solar Wind Model (mSWiM) to predict the solar wind conditions upstream of Jupiter, intervals of high solar wind dynamic pressure were separated from intervals of low solar wind dynamic pressure—thus creating two datasets of magnetometer measurements to be used for two separate 2D fits, and two separate mappings.

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses

PubMed Central

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-01-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population. PMID:28722705

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses.

PubMed

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-10-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population.

Orthogonal on-off control of radar pulses for the suppression of mutual interference

NASA Astrophysics Data System (ADS)

Kim, Yong Cheol

1998-10-01

Intelligent vehicles of the future will be guided by radars and other sensors to avoid obstacles. When multiple vehicles move simultaneously in autonomous navigational mode, mutual interference among car radars becomes a serious problem. An obstacle is illuminated with electromagnetic pulses from several radars. The signal at a radar receiver is actually a mixture of the self-reflection and the reflection of interfering pulses emitted by others. When standardized pulse- type radars are employed on vehicles for obstacle avoidance and so self-pulse and interfering pulses have identical pulse repetition interval, this SI (synchronous Interference) is very difficult to separate from the true reflection. We present a method of suppressing such a synchronous interference. By controlling the pulse emission of a radar in a binary orthogonal ON, OFF pattern, the true self-reflection can be separated from the false one. Two range maps are generated, TRM (true-reflection map) and SIM (synchronous- interference map). TRM is updated for every ON interval and SIM is updated for every OFF interval of the self-radar. SIM represents the SI of interfering radars while TRM keeps a record of a mixture of the true self-reflection and SI. Hence the true obstacles can be identified by the set subtraction operation. The performance of the proposed method is compared with that of the conventional M of N method. Bayesian analysis shows that the probability of false alarm is improved by order of 103 to approximately 106 while the deterioration in the probability of detection is negligible.

Large-extent digital soil mapping approaches for total soil depth

NASA Astrophysics Data System (ADS)

Mulder, Titia; Lacoste, Marine; Saby, Nicolas P. A.; Arrouays, Dominique

2015-04-01

Total soil depth (SDt) plays a key role in supporting various ecosystem services and properties, including plant growth, water availability and carbon stocks. Therefore, predictive mapping of SDt has been included as one of the deliverables within the GlobalSoilMap project. In this work SDt was predicted for France following the directions of GlobalSoilMap, which requires modelling at 90m resolution. This first method, further referred to as DM, consisted of modelling the deterministic trend in SDt using data mining, followed by a bias correction and ordinary kriging of the residuals. Considering the total surface area of France, being about 540K km2, employed methods may need to be able dealing with large data sets. Therefore, a second method, multi-resolution kriging (MrK) for large datasets, was implemented. This method consisted of modelling the deterministic trend by a linear model, followed by interpolation of the residuals. For the two methods, the general trend was assumed to be explained by the biotic and abiotic environmental conditions, as described by the Soil-Landscape paradigm. The mapping accuracy was evaluated by an internal validation and its concordance with previous soil maps. In addition, the prediction interval for DM and the confidence interval for MrK were determined. Finally, the opportunities and limitations of both approaches were evaluated. The results showed consistency in mapped spatial patterns and a good prediction of the mean values. DM was better capable in predicting extreme values due to the bias correction. Also, DM was more powerful in capturing the deterministic trend than the linear model of the MrK approach. However, MrK was found to be more straightforward and flexible in delivering spatial explicit uncertainty measures. The validation indicated that DM was more accurate than MrK. Improvements for DM may be expected by predicting soil depth classes. MrK shows potential for modelling beyond the country level, at high resolution. Large-extent digital soil mapping approaches for SDt may be improved by (1) taking into account SDt observations which are censored and (2) using high-resolution biotic and abiotic environmental data. The latter may improve modelling the soil-landscape interactions influencing soil pedogenesis. Concluding, this work provided a robust and reproducible method (DM) for high-resolution soil property modelling, in accordance with the GlobalSoilMap requirements and an efficient alternative for large-extent digital soil mapping (MrK).

A comparison between univariate probabilistic and multivariate (logistic regression) methods for landslide susceptibility analysis: the example of the Febbraro valley (Northern Alps, Italy)

NASA Astrophysics Data System (ADS)

Rossi, M.; Apuani, T.; Felletti, F.

2009-04-01

The aim of this paper is to compare the results of two statistical methods for landslide susceptibility analysis: 1) univariate probabilistic method based on landslide susceptibility index, 2) multivariate method (logistic regression). The study area is the Febbraro valley, located in the central Italian Alps, where different types of metamorphic rocks croup out. On the eastern part of the studied basin a quaternary cover represented by colluvial and secondarily, by glacial deposits, is dominant. In this study 110 earth flows, mainly located toward NE portion of the catchment, were analyzed. They involve only the colluvial deposits and their extension mainly ranges from 36 to 3173 m2. Both statistical methods require to establish a spatial database, in which each landslide is described by several parameters that can be assigned using a main scarp central point of landslide. The spatial database is constructed using a Geographical Information System (GIS). Each landslide is described by several parameters corresponding to the value of main scarp central point of the landslide. Based on bibliographic review a total of 15 predisposing factors were utilized. The width of the intervals, in which the maps of the predisposing factors have to be reclassified, has been defined assuming constant intervals to: elevation (100 m), slope (5 °), solar radiation (0.1 MJ/cm2/year), profile curvature (1.2 1/m), tangential curvature (2.2 1/m), drainage density (0.5), lineament density (0.00126). For the other parameters have been used the results of the probability-probability plots analysis and the statistical indexes of landslides site. In particular slope length (0 ÷ 2, 2 ÷ 5, 5 ÷ 10, 10 ÷ 20, 20 ÷ 35, 35 ÷ 260), accumulation flow (0 ÷ 1, 1 ÷ 2, 2 ÷ 5, 5 ÷ 12, 12 ÷ 60, 60 ÷27265), Topographic Wetness Index 0 ÷ 0.74, 0.74 ÷ 1.94, 1.94 ÷ 2.62, 2.62 ÷ 3.48, 3.48 ÷ 6,00, 6.00 ÷ 9.44), Stream Power Index (0 ÷ 0.64, 0.64 ÷ 1.28, 1.28 ÷ 1.81, 1.81 ÷ 4.20, 4.20 ÷ 9.40). Geological map and land use map were also used, considering geological and land use properties as categorical variables. Appling the univariate probabilistic method the Landslide Susceptibility Index (LSI) is defined as the sum of the ratio Ra/Rb calculated for each predisposing factor, where Ra is the ratio between number of pixel of class and the total number of pixel of the study area, and Rb is the ratio between number of landslides respect to the pixel number of the interval area. From the analysis of the Ra/Rb ratio the relationship between landslide occurrence and predisposing factors were defined. Then the equation of LSI was used in GIS to trace the landslide susceptibility maps. The multivariate method for landslide susceptibility analysis, based on logistic regression, was performed starting from the density maps of the predisposing factors, calculated with the intervals defined above using the equation Rb/Rbtot, where Rbtot is a sum of all Rb values. Using stepwise forward algorithms the logistic regression was performed in two successive steps: first a univariate logistic regression is used to choose the most significant predisposing factors, then the multivariate logistic regression can be performed. The univariate regression highlighted the importance of the following factors: elevation, accumulation flow, drainage density, lineament density, geology and land use. When the multivariate regression was applied the number of controlling factors was reduced neglecting the geological properties. The resulting final susceptibility equation is: P = 1 / (1 + exp-(6.46-22.34*elevation-5.33*accumulation flow-7.99* drainage density-4.47*lineament density-17.31*land use)) and using this equation the susceptibility maps were obtained. To easy compare the results of the two methodologies, the susceptibility maps were reclassified in five susceptibility intervals (very high, high, moderate, low and very low) using natural breaks. Then the maps were validated using two cumulative distribution curves, one related to the landslides (number of landslides in each susceptibility class) and one to the basin (number of pixel covering each class). Comparing the curves for each method, it results that the two approaches (univariate and multivariate) are appropriate, providing acceptable results. In both maps the distribution of high susceptibility condition is mainly localized on the left slope of the catchment in agreement with the field evidences. The comparison between the methods was obtained by subtraction of the two maps. This operation shows that about 40% of the basin is classified by the same class of susceptibility. In general the univariate probabilistic method tends to overestimate the areal extension of the high susceptibility class with respect to the maps obtained by the logistic regression method.

[Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

PubMed

Gao, Yong-Ming; Wan, Ping

2002-06-01

Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x environments could enhance marker screening power, the former had a greater influence on QTLs with larger main and/or epistatic effects, while the later on QTLs with small main and/or epistatic effects. The simulation of 100 times was also conducted to study the influence of different marker number and density on marker screening power. It is indicated that the marker screening power would decrease if there were too many markers, especially with high density in a mapping population, which suggested that a mapping population with definite individuals could only hold limited markers. According to the simulation study, the reasonable number of markers should not be more than individuals. The simulation study of marker screening under multiple environments showed high total power of marker screening. In order to relieve the problem that marker screening power restricted the efficiency of QTL mapping, markers identified in multiple environments could be used to construct two search intervals.

Interval mapping of high growth (hg), a major locus that increases weight gain in mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horvat, S.; Medrano, J.F.

1995-04-01

The high growth locus (hg) causes a major increase in weight gain and body size in mice. As a first step to map-based cloning of hg, we developed a genetic map of the hg-containing region using interval mapping of 403 F{sub 2} from a C57BL/6J-hghg x CAST/EiJ cross. The maximum likelihood position of hg was at the chromosome 10 marker D10Mit41 (LOD = 24.8) in the F{sub 2} females and 1.5 cM distal to D10Mit41 (LOD = 9.56) in the F{sub 2} males with corresponding LOD 2 support intervals of 3.7 and 5.4 cM, respectively. The peak LOD scores weremore » significantly higher than the estimated empirical threshold LOD values. The localization of hg by interval mapping was supported by a test cross of F{sub 2} mice recombinant between the LOD 2 support interval and the flanking marker. The interval mapping and test-cross indicate that hg is not allelic with candidate genes Igf1 or decorin (Dcn), a gene that was mapped close to hg in this study. The hg inheritance was recessive in females, although we could not reject recessive or additive inheritance in males. Possible causes for sex differences in peak LOD scores and for the distortion of transmission ratios observed in F{sub 2} males are discussed. The genetic map of the hg region will facilitate further fine mapping and cloning of hg, and allow searches for a homologous quantitative trait locus affecting growth in humans and domestic animals. 48 refs., 3 figs., 3 tabs.« less

A new method for determining a sector alert

DOT National Transportation Integrated Search

2008-09-29

The Traffic Flow Management System (TFMS) currently declares an alert for any 15-minute interval in which the predicted demand exceeds the Monitor/Alert Parameter (MAP) for any airport, sector, or fix. For a sector, TFMS predicts the demand for each ...

U.S. Geological Survey groundwater toolbox, a graphical and mapping interface for analysis of hydrologic data (version 1.0): user guide for estimation of base flow, runoff, and groundwater recharge from streamflow data

USGS Publications Warehouse

Barlow, Paul M.; Cunningham, William L.; Zhai, Tong; Gray, Mark

2015-01-01

This report is a user guide for the streamflow-hydrograph analysis methods provided with version 1.0 of the U.S. Geological Survey (USGS) Groundwater Toolbox computer program. These include six hydrograph-separation methods to determine the groundwater-discharge (base-flow) and surface-runoff components of streamflow—the Base-Flow Index (BFI; Standard and Modified), HYSEP (Fixed Interval, Sliding Interval, and Local Minimum), and PART methods—and the RORA recession-curve displacement method and associated RECESS program to estimate groundwater recharge from streamflow data. The Groundwater Toolbox is a customized interface built on the nonproprietary, open source MapWindow geographic information system software. The program provides graphing, mapping, and analysis capabilities in a Microsoft Windows computing environment. In addition to the four hydrograph-analysis methods, the Groundwater Toolbox allows for the retrieval of hydrologic time-series data (streamflow, groundwater levels, and precipitation) from the USGS National Water Information System, downloading of a suite of preprocessed geographic information system coverages and meteorological data from the National Oceanic and Atmospheric Administration National Climatic Data Center, and analysis of data with several preprocessing and postprocessing utilities. With its data retrieval and analysis tools, the Groundwater Toolbox provides methods to estimate many of the components of the water budget for a hydrologic basin, including precipitation; streamflow; base flow; runoff; groundwater recharge; and total, groundwater, and near-surface evapotranspiration.

Exploring nonlinear feature space dimension reduction and data representation in breast Cadx with Laplacian eigenmaps and t-SNE.

PubMed

Jamieson, Andrew R; Giger, Maryellen L; Drukker, Karen; Li, Hui; Yuan, Yading; Bhooshan, Neha

2010-01-01

In this preliminary study, recently developed unsupervised nonlinear dimension reduction (DR) and data representation techniques were applied to computer-extracted breast lesion feature spaces across three separate imaging modalities: Ultrasound (U.S.) with 1126 cases, dynamic contrast enhanced magnetic resonance imaging with 356 cases, and full-field digital mammography with 245 cases. Two methods for nonlinear DR were explored: Laplacian eigenmaps [M. Belkin and P. Niyogi, "Laplacian eigenmaps for dimensionality reduction and data representation," Neural Comput. 15, 1373-1396 (2003)] and t-distributed stochastic neighbor embedding (t-SNE) [L. van der Maaten and G. Hinton, "Visualizing data using t-SNE," J. Mach. Learn. Res. 9, 2579-2605 (2008)]. These methods attempt to map originally high dimensional feature spaces to more human interpretable lower dimensional spaces while preserving both local and global information. The properties of these methods as applied to breast computer-aided diagnosis (CADx) were evaluated in the context of malignancy classification performance as well as in the visual inspection of the sparseness within the two-dimensional and three-dimensional mappings. Classification performance was estimated by using the reduced dimension mapped feature output as input into both linear and nonlinear classifiers: Markov chain Monte Carlo based Bayesian artificial neural network (MCMC-BANN) and linear discriminant analysis. The new techniques were compared to previously developed breast CADx methodologies, including automatic relevance determination and linear stepwise (LSW) feature selection, as well as a linear DR method based on principal component analysis. Using ROC analysis and 0.632+bootstrap validation, 95% empirical confidence intervals were computed for the each classifier's AUC performance. In the large U.S. data set, sample high performance results include, AUC0.632+ = 0.88 with 95% empirical bootstrap interval [0.787;0.895] for 13 ARD selected features and AUC0.632+ = 0.87 with interval [0.817;0.906] for four LSW selected features compared to 4D t-SNE mapping (from the original 81D feature space) giving AUC0.632+ = 0.90 with interval [0.847;0.919], all using the MCMC-BANN. Preliminary results appear to indicate capability for the new methods to match or exceed classification performance of current advanced breast lesion CADx algorithms. While not appropriate as a complete replacement of feature selection in CADx problems, DR techniques offer a complementary approach, which can aid elucidation of additional properties associated with the data. Specifically, the new techniques were shown to possess the added benefit of delivering sparse lower dimensional representations for visual interpretation, revealing intricate data structure of the feature space.

Automated mapping of the ocean floor using the theory of intrinsic random functions of order k

USGS Publications Warehouse

David, M.; Crozel, D.; Robb, James M.

1986-01-01

High-quality contour maps can be computer drawn from single track echo-sounding data by combining Universal Kriging and the theory of intrinsic random function of order K (IRFK). These methods interpolate values among the closely spaced points that lie along relatively widely spaced lines. The technique provides a variance which can be contoured as a quantitative measure of map precision. The technique can be used to evaluate alternative survey trackline configurations and data collection intervals, and can be applied to other types of oceanographic data. ?? 1986 D. Reidel Publishing Company.

Targeted Recombinant Progeny: a design for ultra-high resolution mapping of Quantitative Trait Loci in crosses between inbred or pure lines.

PubMed

Heifetz, Eliyahu M; Soller, Morris

2015-07-07

High-resolution mapping of the loci (QTN) responsible for genetic variation in quantitative traits is essential for positional cloning of candidate genes, and for effective marker assisted selection. The confidence interval (QTL) flanking the point estimate of QTN-location is proportional to the number of individuals in the mapping population carrying chromosomes recombinant in the given interval. Consequently, many designs for high resolution QTN mapping are based on increasing the proportion of recombinants in the mapping population. The "Targeted Recombinant Progeny" (TRP) design is a new design for high resolution mapping of a target QTN in crosses between pure, or inbred lines. It is a three-generation procedure generating a large number of recombinant individuals within a QTL previously shown to contain a QTN. This is achieved by having individuals that carry chromosomes recombinant across the target QTL interval as parents of a large mapping population; most of whom will therefore carry recombinant chromosomes targeted to the given QTL. The TRP design is particularly useful for high resolution mapping of QTN that differentiate inbred or pure lines, and hence are not amenable to high resolution mapping by genome-wide association tests. In the absence of residual polygenic variation, population sizes required for achieving given mapping resolution by the TRP-F2 design relative to a standard F2 design ranged from 0.289 for a QTN with standardized allele substitution effect = 0.2, mapped to an initial QTL of 0.2 Morgan to 0.041 for equivalent QTN mapped to an initial QTL of 0.02 M. In the presence of residual polygenic variation, the relative effectiveness of the TRP design ranges from 1.068 to 0.151 for the same initial QTL intervals and QTN effect. Thus even in the presence of polygenic variation, the TRP can still provide major savings. Simulation showed that mapping by TRP should be based on 30-50 markers spanning the initial interval; and on at least 50 or more G2 families representing this number of recombination points,. The TRP design can be an effective procedure for achieving high and ultra-high mapping resolution of a target QTN previously mapped to a known confidence interval (QTL).

Procedural Documentation and Accuracy Assessment of Bathymetric Maps and Area/Capacity Tables for Small Reservoirs

USGS Publications Warehouse

Wilson, Gary L.; Richards, Joseph M.

2006-01-01

Because of the increasing use and importance of lakes for water supply to communities, a repeatable and reliable procedure to determine lake bathymetry and capacity is needed. A method to determine the accuracy of the procedure will help ensure proper collection and use of the data and resulting products. It is important to clearly define the intended products and desired accuracy before conducting the bathymetric survey to ensure proper data collection. A survey-grade echo sounder and differential global positioning system receivers were used to collect water-depth and position data in December 2003 at Sugar Creek Lake near Moberly, Missouri. Data were collected along planned transects, with an additional set of quality-assurance data collected for use in accuracy computations. All collected data were imported into a geographic information system database. A bathymetric surface model, contour map, and area/capacity tables were created from the geographic information system database. An accuracy assessment was completed on the collected data, bathymetric surface model, area/capacity table, and contour map products. Using established vertical accuracy standards, the accuracy of the collected data, bathymetric surface model, and contour map product was 0.67 foot, 0.91 foot, and 1.51 feet at the 95 percent confidence level. By comparing results from different transect intervals with the quality-assurance transect data, it was determined that a transect interval of 1 percent of the longitudinal length of Sugar Creek Lake produced nearly as good results as 0.5 percent transect interval for the bathymetric surface model, area/capacity table, and contour map products.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes.

PubMed

Mok, Calvin A; Au, Vinci; Thompson, Owen A; Edgley, Mark L; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G; Waterston, Robert H

2017-10-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C . elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2 We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. Copyright © 2017 by the Genetics Society of America.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes

PubMed Central

Mok, Calvin A.; Au, Vinci; Thompson, Owen A.; Edgley, Mark L.; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R.; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G.; Waterston, Robert H.

2017-01-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. PMID:28827289

Quantile rank maps: a new tool for understanding individual brain development.

PubMed

Chen, Huaihou; Kelly, Clare; Castellanos, F Xavier; He, Ye; Zuo, Xi-Nian; Reiss, Philip T

2015-05-01

We propose a novel method for neurodevelopmental brain mapping that displays how an individual's values for a quantity of interest compare with age-specific norms. By estimating smoothly age-varying distributions at a set of brain regions of interest, we derive age-dependent region-wise quantile ranks for a given individual, which can be presented in the form of a brain map. Such quantile rank maps could potentially be used for clinical screening. Bootstrap-based confidence intervals are proposed for the quantile rank estimates. We also propose a recalibrated Kolmogorov-Smirnov test for detecting group differences in the age-varying distribution. This test is shown to be more robust to model misspecification than a linear regression-based test. The proposed methods are applied to brain imaging data from the Nathan Kline Institute Rockland Sample and from the Autism Brain Imaging Data Exchange (ABIDE) sample. Copyright © 2015 Elsevier Inc. All rights reserved.

A Control Algorithm for Chaotic Physical Systems

DTIC Science & Technology

1991-10-01

revision expands the grid to cover the entire area of any attractor that is present. 5 Map Selection The final choices of the state- space mapping process...interval h?; overrange R0 ; control parameter interval AkO and range [kbro, khigh]; iteration depth. "* State- space mapping : 1. Set up grid by expanding

An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

PubMed

Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

2006-08-01

Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

Exploring nonlinear feature space dimension reduction and data representation in breast CADx with Laplacian eigenmaps and t-SNE

PubMed Central

Jamieson, Andrew R.; Giger, Maryellen L.; Drukker, Karen; Li, Hui; Yuan, Yading; Bhooshan, Neha

2010-01-01

Purpose: In this preliminary study, recently developed unsupervised nonlinear dimension reduction (DR) and data representation techniques were applied to computer-extracted breast lesion feature spaces across three separate imaging modalities: Ultrasound (U.S.) with 1126 cases, dynamic contrast enhanced magnetic resonance imaging with 356 cases, and full-field digital mammography with 245 cases. Two methods for nonlinear DR were explored: Laplacian eigenmaps [M. Belkin and P. Niyogi, “Laplacian eigenmaps for dimensionality reduction and data representation,” Neural Comput. 15, 1373–1396 (2003)] and t-distributed stochastic neighbor embedding (t-SNE) [L. van der Maaten and G. Hinton, “Visualizing data using t-SNE,” J. Mach. Learn. Res. 9, 2579–2605 (2008)]. Methods: These methods attempt to map originally high dimensional feature spaces to more human interpretable lower dimensional spaces while preserving both local and global information. The properties of these methods as applied to breast computer-aided diagnosis (CADx) were evaluated in the context of malignancy classification performance as well as in the visual inspection of the sparseness within the two-dimensional and three-dimensional mappings. Classification performance was estimated by using the reduced dimension mapped feature output as input into both linear and nonlinear classifiers: Markov chain Monte Carlo based Bayesian artificial neural network (MCMC-BANN) and linear discriminant analysis. The new techniques were compared to previously developed breast CADx methodologies, including automatic relevance determination and linear stepwise (LSW) feature selection, as well as a linear DR method based on principal component analysis. Using ROC analysis and 0.632+bootstrap validation, 95% empirical confidence intervals were computed for the each classifier’s AUC performance. Results: In the large U.S. data set, sample high performance results include, AUC0.632+=0.88 with 95% empirical bootstrap interval [0.787;0.895] for 13 ARD selected features and AUC0.632+=0.87 with interval [0.817;0.906] for four LSW selected features compared to 4D t-SNE mapping (from the original 81D feature space) giving AUC0.632+=0.90 with interval [0.847;0.919], all using the MCMC-BANN. Conclusions: Preliminary results appear to indicate capability for the new methods to match or exceed classification performance of current advanced breast lesion CADx algorithms. While not appropriate as a complete replacement of feature selection in CADx problems, DR techniques offer a complementary approach, which can aid elucidation of additional properties associated with the data. Specifically, the new techniques were shown to possess the added benefit of delivering sparse lower dimensional representations for visual interpretation, revealing intricate data structure of the feature space. PMID:20175497

Pseudorandom number generation using chaotic true orbits of the Bernoulli map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saito, Asaki, E-mail: saito@fun.ac.jp; Yamaguchi, Akihiro

We devise a pseudorandom number generator that exactly computes chaotic true orbits of the Bernoulli map on quadratic algebraic integers. Moreover, we describe a way to select the initial points (seeds) for generating multiple pseudorandom binary sequences. This selection method distributes the initial points almost uniformly (equidistantly) in the unit interval, and latter parts of the generated sequences are guaranteed not to coincide. We also demonstrate through statistical testing that the generated sequences possess good randomness properties.

Fast-dynamo action in unsteady flows and maps in three dimensions

NASA Technical Reports Server (NTRS)

Bayly, B. J.; Childress, S.

1987-01-01

Unsteady fast-dynamo action is obtained in a family of stretch-fold-shear maps applied to a spatially periodic magnetic field in three dimensions. Exponential growth of a mean field in the limit of vanishing diffusivity is demonstrated by a numerical method which alternates instantaneous deformations with molecular diffusion over a finite time interval. Analysis indicates that the dynamo is a coherent feature of the large scales, essentially independent of the cascade of structure to small scales.

Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus.

PubMed

Sun, Fengming; Liu, Jing; Hua, Wei; Sun, Xingchao; Wang, Xinfa; Wang, Hanzhong

2016-11-01

Seed oil content is an important agricultural trait in rapeseed breeding. Although numerous quantitative trait locus (QTL) have been identified, most of them cannot be applied in practical breeding mainly due to environmental instability or large confidence intervals. The purpose of this study was to identify and validate high quality and more stable QTLs by combining linkage mapping and genome-wide association study (GWAS). For linkage mapping, we constructed two F 2 populations from crosses of high-oil content (∼50%) lines 6F313 and 61616 with a low-oil content (∼40%) line 51070. Two high density linkage maps spanned 1987cM (1659 bins) and 1856cM (1746 bins), respectively. For GWAS, we developed more than 34,000 high-quality SNP markers based on 227 accessions. Finally, 40 QTLs and 29 associations were established by linkage and association mapping in different environments. After merging the results, 32 consensus QTLs were obtained and 7 of them were identified by both mapping methods. Seven overlapping QTLs covered an average confidence interval of 183kb and explained the phenotypic variation of 10.23 to 24.45%. We further developed allele-specific PCR primers to identify each of the seven QTLs. These stable QTLs should be useful in gene cloning and practical breeding application. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

PubMed Central

2014-01-01

Background Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (“D3-Map” technique) that provides an animated representation of a system’s dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincaré plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n + 1). First, we divide the original time series, x(n) (n = 1,…, N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincaré surface plot of x(n), x(n + 1), h[x(n),x(n + 1)] is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n + 1)) point. This 3D Poincaré surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincaré surface. Finally, the original time series graph, the colourised 3D Poincaré surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full “D3-Map.” Results We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions Animations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincaré plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration. PMID:24438439

Magnetic Resonance Fingerprinting with short relaxation intervals.

PubMed

Amthor, Thomas; Doneva, Mariya; Koken, Peter; Sommer, Karsten; Meineke, Jakob; Börnert, Peter

2017-09-01

The aim of this study was to investigate a technique for improving the performance of Magnetic Resonance Fingerprinting (MRF) in repetitive sampling schemes, in particular for 3D MRF acquisition, by shortening relaxation intervals between MRF pulse train repetitions. A calculation method for MRF dictionaries adapted to short relaxation intervals and non-relaxed initial spin states is presented, based on the concept of stationary fingerprints. The method is applicable to many different k-space sampling schemes in 2D and 3D. For accuracy analysis, T 1 and T 2 values of a phantom are determined by single-slice Cartesian MRF for different relaxation intervals and are compared with quantitative reference measurements. The relevance of slice profile effects is also investigated in this case. To further illustrate the capabilities of the method, an application to in-vivo spiral 3D MRF measurements is demonstrated. The proposed computation method enables accurate parameter estimation even for the shortest relaxation intervals, as investigated for different sampling patterns in 2D and 3D. In 2D Cartesian measurements, we achieved a scan acceleration of more than a factor of two, while maintaining acceptable accuracy: The largest T 1 values of a sample set deviated from their reference values by 0.3% (longest relaxation interval) and 2.4% (shortest relaxation interval). The largest T 2 values showed systematic deviations of up to 10% for all relaxation intervals, which is discussed. The influence of slice profile effects for multislice acquisition is shown to become increasingly relevant for short relaxation intervals. In 3D spiral measurements, a scan time reduction of 36% was achieved, maintaining the quality of in-vivo T1 and T2 maps. Reducing the relaxation interval between MRF sequence repetitions using stationary fingerprint dictionaries is a feasible method to improve the scan efficiency of MRF sequences. The method enables fast implementations of 3D spatially resolved MRF. Copyright © 2017 Elsevier Inc. All rights reserved.

Generation and Validation of Spatial Distribution of Hourly Wind Speed Time-Series using Machine Learning

NASA Astrophysics Data System (ADS)

Veronesi, F.; Grassi, S.

2016-09-01

Wind resource assessment is a key aspect of wind farm planning since it allows to estimate the long term electricity production. Moreover, wind speed time-series at high resolution are helpful to estimate the temporal changes of the electricity generation and indispensable to design stand-alone systems, which are affected by the mismatch of supply and demand. In this work, we present a new generalized statistical methodology to generate the spatial distribution of wind speed time-series, using Switzerland as a case study. This research is based upon a machine learning model and demonstrates that statistical wind resource assessment can successfully be used for estimating wind speed time-series. In fact, this method is able to obtain reliable wind speed estimates and propagate all the sources of uncertainty (from the measurements to the mapping process) in an efficient way, i.e. minimizing computational time and load. This allows not only an accurate estimation, but the creation of precise confidence intervals to map the stochasticity of the wind resource for a particular site. The validation shows that machine learning can minimize the bias of the wind speed hourly estimates. Moreover, for each mapped location this method delivers not only the mean wind speed, but also its confidence interval, which are crucial data for planners.

Volume II: Compendium Abstracts

DTIC Science & Technology

2008-08-01

project developed a fast and simple method of characterization for ceramic , polymer composite, and ceramic -composite materials systems. Current methods...incrementally at 1-inch intervals and displayed as a false-color image map of the sample. This experimental setup can be easily scaled from single ceramic ...low-power, high-force characteristics of lead zirconate titanate ( PZT ) and an offset-beam design to achieve rotational or near-linear translational

The gene for autosomal dominant cerebellar ataxia with pigmentary macular dystrophy maps to chromosome 3p12-p21.1.

PubMed

Benomar, A; Krols, L; Stevanin, G; Cancel, G; LeGuern, E; David, G; Ouhabi, H; Martin, J J; Dürr, A; Zaim, A

1995-05-01

Autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) is a rare neurodegenerative disorder with marked anticipation. We have mapped the ADCA type II locus to chromosome 3 by linkage analysis in a genome-wide search and found no evidence for genetic heterogeneity among four families of different geographic origins. Haplotype reconstruction initially restricted the locus to the 33 cM interval flanked by D3S1300 and D3S1276 located at 3p12-p21.1. Combined multipoint analysis, using the Zmax-1 method, further reduced the candidate interval to an 8 cM region around D3S1285. Our results show that ADCA type II is a genetically homogenous disorder, independent of the heterogeneous group of type I cerebellar ataxias.

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng

2014-06-04

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

PubMed Central

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the ‘Mantianhong’ and ‘Hongxiangsu’ red-skinned cultivars. The ‘Dangshansuli’ cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit. PMID:29118994

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

PubMed

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

Enface Thickness Mapping and Reflectance Imaging of Retinal Layers in Diabetic Retinopathy

PubMed Central

Francis, Andrew W.; Wanek, Justin; Lim, Jennifer I.; Shahidi, Mahnaz

2015-01-01

Purpose To present a method for image segmentation and generation of enface thickness maps and reflectance images of retinal layers in healthy and diabetic retinopathy (DR) subjects. Methods High density spectral domain optical coherence tomography (SDOCT) images were acquired in 10 healthy and 4 DR subjects. Customized image analysis software identified 5 retinal cell layer interfaces and generated thickness maps and reflectance images of the total retina (TR), inner retina (IR), outer retina (OR), and the inner segment ellipsoid (ISe) band. Thickness maps in DR subjects were compared to those of healthy subjects by generating deviation maps which displayed retinal locations with thickness below, within, and above the normal 95% confidence interval. Results In healthy subjects, TR and IR thickness maps displayed the foveal depression and increased thickness in the parafoveal region. OR and ISe thickness maps showed increased thickness at the fovea, consistent with normal retinal anatomy. In DR subjects, thickening and thinning in localized regions were demonstrated on TR, IR, OR, and ISe thickness maps, corresponding to retinal edema and atrophy, respectively. TR and OR reflectance images showed reduced reflectivity in regions of increased thickness. Hard exudates appeared as hyper-reflective spots in IR reflectance images and casted shadows on the deeper OR and ISe reflectance images. The ISe reflectance image clearly showed the presence of focal laser scars. Conclusions Enface thickness mapping and reflectance imaging of retinal layers is a potentially useful method for quantifying the spatial and axial extent of pathologies due to DR. PMID:26699878

Simultaneous mapping of water shift and B1 (WASABI)-Application to field-Inhomogeneity correction of CEST MRI data.

PubMed

Schuenke, Patrick; Windschuh, Johannes; Roeloffs, Volkert; Ladd, Mark E; Bachert, Peter; Zaiss, Moritz

2017-02-01

Together with the development of MRI contrasts that are inherently small in their magnitude, increased magnetic field accuracy is also required. Hence, mapping of the static magnetic field (B 0 ) and the excitation field (B 1 ) is not only important to feedback shim algorithms, but also for postprocess contrast-correction procedures. A novel field-inhomogeneity mapping method is presented that allows simultaneous mapping of the water shift and B 1 (WASABI) using an off-resonant rectangular preparation pulse. The induced Rabi oscillations lead to a sinc-like spectrum in the frequency-offset dimension and allow for determination of B 0 by its symmetry axis and of B 1 by its oscillation frequency. Stability of the WASABI method with regard to the influences of T 1 , T 2 , magnetization transfer, and repetition time was investigated and its convergence interval was verified. B 0 and B 1 maps obtained simultaneously by means of WASABI in the human brain at 3 T and 7 T can compete well with maps obtained by standard methods. Finally, the method was applied successfully for B 0 and B 1 correction of chemical exchange saturation transfer MRI (CEST-MRI) data of the human brain. The proposed WASABI method yields a novel simultaneous B 0 and B 1 mapping within 1 min that is robust and easy to implement. Magn Reson Med 77:571-580, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Anatomo-clinical overlapping maps (AnaCOM): a new method to create anatomo-functional maps from neuropsychological tests and structural MRI scan of subjects with brain lesions

NASA Astrophysics Data System (ADS)

Kinkingnehun, Serge R. J.; du Boisgueheneuc, Foucaud; Golmard, Jean-Louis; Zhang, Sandy X.; Levy, Richard; Dubois, Bruno

2004-04-01

We have developed a new technique to analyze correlations between brain anatomy and its neurological functions. The technique is based on the anatomic MRI of patients with brain lesions who are administered neuropsychological tests. Brain lesions of the MRI scans are first manually segmented. The MRI volumes are then normalized to a reference map, using the segmented area as a mask. After normalization, the brain lesions of the MRI are segmented again in order to redefine the border of the lesions in the context of the normalized brain. Once the MRI is segmented, the patient's score on the neuropsychological test is assigned to each voxel in the lesioned area, while the rest of the voxels of the image are set to 0. Subsequently, the individual patient's MRI images are superimposed, and each voxel is reassigned the average score of the patients who have a lesion at that voxel. A threshold is applied to remove regions having less than three overlaps. This process leads to an anatomo-functional map that links brain areas to functional loss. Other maps can be created to aid in analyzing the functional maps, such as one that indicates the 95% confidence interval of the averaged scores for each area. This anatomo-clinical overlapping map (AnaCOM) method was used to obtain functional maps from patients with lesions in the superior frontal gyrus. By finding particular subregions more responsible for a particular deficit, this method can generate new hypotheses to be tested by conventional group methods.

Correlation of physical and genetic maps of human chromosome 16

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutherland, G.R.

1991-01-01

This project aimed to divide chromosome 16 into approximately 50 intervals of {approximately}2Mb in size by constructing a series of mouse/human somatic cell hybrids each containing a rearranged chromosome 16. Using these hybrids, DNA probes would be regionally mapped by Southern blot or PCR analysis. Preference would be given to mapping probes which demonstrated polymorphisms for which the CEPH panel of families had been typed. This would allow a correlation of the physical and linkage maps of this chromosome. The aims have been substantially achieved. 49 somatic cell hybrids have been constructed which have allowed definition of 46, and potentiallymore » 57, different physical intervals on the chromosome. 164 loci have been fully mapped into these intervals. A correlation of the physical and genetic maps of the chromosome is in an advanced stage of preparation. The somatic cell hybrids constructed have been widely distributed to groups working on chromosome 16 and other genome projects.« less

Correlation of physical and genetic maps of human chromosome 16. Annual progress report, October 1, 1990--July 31, 1991

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutherland, G.R.

1991-12-31

This project aimed to divide chromosome 16 into approximately 50 intervals of {approximately}2Mb in size by constructing a series of mouse/human somatic cell hybrids each containing a rearranged chromosome 16. Using these hybrids, DNA probes would be regionally mapped by Southern blot or PCR analysis. Preference would be given to mapping probes which demonstrated polymorphisms for which the CEPH panel of families had been typed. This would allow a correlation of the physical and linkage maps of this chromosome. The aims have been substantially achieved. 49 somatic cell hybrids have been constructed which have allowed definition of 46, and potentiallymore » 57, different physical intervals on the chromosome. 164 loci have been fully mapped into these intervals. A correlation of the physical and genetic maps of the chromosome is in an advanced stage of preparation. The somatic cell hybrids constructed have been widely distributed to groups working on chromosome 16 and other genome projects.« less

Photogrammetric portrayal of Mars topography.

USGS Publications Warehouse

Wu, S.S.C.

1979-01-01

Special photogrammetric techniques have been developed to portray Mars topography, using Mariner and Viking imaging and nonimaging topographic information and earth-based radar data. Topography is represented by the compilation of maps at three scales: global, intermediate, and very large scale. The global map is a synthesis of topographic information obtained from Mariner 9 and earth-based radar, compiled at a scale of 1:25,000,000 with a contour interval of 1 km; it gives a broad quantitative view of the planet. At intermediate scales, Viking Orbiter photographs of various resolutions are used to compile detailed contour maps of a broad spectrum of prominent geologic features; a contour interval as small as 20 m has been obtained from very high resolution orbital photography. Imagery from the Viking lander facsimile cameras permits construction of detailed, very large scale (1:10) topographic maps of the terrain surrounding the two landers; these maps have a contour interval of 1 cm. This paper presents several new detailed topographic maps of Mars.-Author

Photogrammetric portrayal of Mars topography

NASA Technical Reports Server (NTRS)

Wu, S. S. C.

1979-01-01

Special photogrammetric techniques have been developed to portray Mars topography, using Mariner and Viking imaging and nonimaging topographic information and earth-based radar data. Topography is represented by the compilation of maps at three scales: global, intermediate, and very large scale. The global map is a synthesis of topographic information obtained from Mariner 9 and earth-based radar, compiled at a scale of 1:25,000,000 with a contour interval of 1 km; it gives a broad quantitative view of the planet. At intermediate scales, Viking Orbiter photographs of various resolutions are used to compile detailed contour maps of a broad spectrum of prominent geologic features; a contour interval as small as 20 m has been obtained from very high resolution orbital photography. Imagery from the Viking lander facsimile cameras permits construction of detailed, very large scale (1:10) topographic maps of the terrain surrounding the two landers; these maps have a contour interval of 1 cm. This paper presents several new detailed topographic maps of Mars.

History of ozone injury monitoring methods and the development of a recommended protocol

Treesearch

Daniel Duriscoe; Kenneth Stolte; John Pronos

1996-01-01

The minimum requirement for long–term monitoring of air pollution effects on forest stands is to develop methods for observers to locate, evaluate, and re–evaluate individual trees at intervals of one or more years. Studies of this nature have used permanent quadrats or "plots" in which individual plants are tagged or mapped. Multiple levels of information...

Global Ionosphere Perturbations Monitored by the Worldwide GPS Network

NASA Technical Reports Server (NTRS)

Ho, C. M.; Manucci, A. T.; Lindqwister, U. J.; Pi, X.

1996-01-01

For the first time, measurements from the Global Positioning System (GPS) worldwide network are employed to study the global ionospheric total electron content(TEC) changes during a magnetic storm (November 26, 1994). These measurements are obtained from more than 60 world-wide GPS stations which continuously receive dual-frequency signals. Based on the delays of the signals, we have generated high resolution global ionospheric maps (GIM) of TEC at 15 minute intervals. Using a differential method comparing storm time maps with quiet time maps, we find that significant TEC increases (the positive effect ) are the major feature in the winter hemisphere during this storm (the maximum percent change relative to quiet times is about 150 percent).

A maximum likelihood algorithm for genome mapping of cytogenetic loci from meiotic configuration data.

PubMed Central

Reyes-Valdés, M H; Stelly, D M

1995-01-01

Frequencies of meiotic configurations in cytogenetic stocks are dependent on chiasma frequencies in segments defined by centromeres, breakpoints, and telomeres. The expectation maximization algorithm is proposed as a general method to perform maximum likelihood estimations of the chiasma frequencies in the intervals between such locations. The estimates can be translated via mapping functions into genetic maps of cytogenetic landmarks. One set of observational data was analyzed to exemplify application of these methods, results of which were largely concordant with other comparable data. The method was also tested by Monte Carlo simulation of frequencies of meiotic configurations from a monotelodisomic translocation heterozygote, assuming six different sample sizes. The estimate averages were always close to the values given initially to the parameters. The maximum likelihood estimation procedures can be extended readily to other kinds of cytogenetic stocks and allow the pooling of diverse cytogenetic data to collectively estimate lengths of segments, arms, and chromosomes. Images Fig. 1 PMID:7568226

A multifractal analysis of equilibrium measures for conformal expanding maps and Moran-like geometric constructions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pesin, Y.; Weiss, H.

1997-01-01

In this paper we establish the complete multifractal formalism for equilibrium measures for Holder continuous conformal expanding maps and expanding Markov Moran-like geometric constructions. Examples include Markov maps of an interval, beta transformations of an interval, rational maps with hyperbolic Julia sets, and conformal total endomorphisms. We also construct a Holder continuous homeomorphism of a compact metric space with an ergodic invariant measure of positive entropy for which the dimension spectrum is not convex, and hence the multifractal formalism fails.

Topographic mapping of the Moon

USGS Publications Warehouse

Wu, S.S.C.

1985-01-01

Contour maps of the Moon have been compiled by photogrammetric methods that use stereoscopic combinations of all available metric photographs from the Apollo 15, 16, and 17 missions. The maps utilize the same format as the existing NASA shaded-relief Lunar Planning Charts (LOC-1, -2, -3, and -4), which have a scale of 1:2 750 000. The map contour interval is 500m. A control net derived from Apollo photographs by Doyle and others was used for the compilation. Contour lines and elevations are referred to the new topographic datum of the Moon, which is defined in terms of spherical harmonics from the lunar gravity field. Compilation of all four LOC charts was completed on analytical plotters from 566 stereo models of Apollo metric photographs that cover approximately 20% of the Moon. This is the first step toward compiling a global topographic map of the Moon at a scale of 1:5 000 000. ?? 1985 D. Reidel Publishing Company.

Genetic dissection of quantitative trait locus for ethanol sensitivity in long- and short-sleep mice.

PubMed

Bennett, B; Carosone-Link, P; Beeson, M; Gordon, L; Phares-Zook, N; Johnson, T E

2008-08-01

Interval-specific congenic strains (ISCS) allow fine mapping of a quantitative trait locus (QTL), narrowing its confidence interval by an order of magnitude or more. In earlier work, we mapped four QTL specifying differential ethanol sensitivity, assessed by loss of righting reflex because of ethanol (LORE), in the inbred long-sleep (ILS) and inbred short-sleep (ISS) strains, accounting for approximately 50% of the genetic variance for this trait. Subsequently, we generated reciprocal congenic strains in which each full QTL interval from ILS was bred onto the ISS background and vice versa. An earlier paper reported construction and results of the ISCS on the ISS background; here, we describe this process and report results on the ILS background. We developed multiple ISCS for each Lore QTL in which the QTL interval was broken into a number of smaller intervals. For each of the four QTL regions (chromosomes 1, 2, 11 and 15), we were successful in reducing the intervals significantly. Multiple, positive strains were overlapped to generate a single, reduced interval. Subsequently, this reduced region was overlaid on previous reductions from the ISS background congenics, resulting in substantial reductions in all QTL regions by approximately 75% from the initial mapping study. Genes with sequence or expression polymorphisms in the reduced intervals are potential candidates; evidence for these is presented. Genetic background effects can be important in detection of single QTL; combining this information with the generation of congenics on both backgrounds, as described here, is a powerful approach for fine mapping QTL.

Spatiotemporal Modeling for Fine-Scale Maps of Regional Malaria Endemicity and Its Implications for Transitional Complexities in a Routine Surveillance Network in Western Cambodia

PubMed Central

Okami, Suguru; Kohtake, Naohiko

2017-01-01

Due to the associated and substantial efforts of many stakeholders involved in malaria containment, the disease burden of malaria has dramatically decreased in many malaria-endemic countries in recent years. Some decades after the past efforts of the global malaria eradication program, malaria elimination has again featured on the global health agenda. While risk distribution modeling and a mapping approach are effective tools to assist with the efficient allocation of limited health-care resources, these methods need some adjustment and reexamination in accordance with changes occurring in relation to malaria elimination. Limited available data, fine-scale data inaccessibility (for example, household or individual case data), and the lack of reliable data due to inefficiencies within the routine surveillance system, make it difficult to create reliable risk maps for decision-makers or health-care practitioners in the field. Furthermore, the risk of malaria may dynamically change due to various factors such as the progress of containment interventions and environmental changes. To address the complex and dynamic nature of situations in low-to-moderate malaria transmission settings, we built a spatiotemporal model of a standardized morbidity ratio (SMR) of malaria incidence, calculated through annual parasite incidence, using routinely reported surveillance data in combination with environmental indices such as remote sensing data, and the non-environmental regional containment status, to create fine-scale risk maps. A hierarchical Bayesian frame was employed to fit the transitioning malaria risk data onto the map. The model was set to estimate the SMRs of every study location at specific time intervals within its uncertainty range. Using the spatial interpolation of estimated SMRs at village level, we created fine-scale maps of two provinces in western Cambodia at specific time intervals. The maps presented different patterns of malaria risk distribution at specific time intervals. Moreover, the visualized weights estimated using the risk model, and the structure of the routine surveillance network, represent the transitional complexities emerging from ever-changing regional endemic situations. PMID:29034229

The Regional Land Cover Monitoring System: Building regional capacity through innovative land cover mapping approaches

NASA Astrophysics Data System (ADS)

Saah, D.; Tenneson, K.; Hanh, Q. N.; Aekakkararungroj, A.; Aung, K. S.; Goldstein, J.; Cutter, P. G.; Maus, P.; Markert, K. N.; Anderson, E.; Ellenburg, W. L.; Ate, P.; Flores Cordova, A. I.; Vadrevu, K.; Potapov, P.; Phongsapan, K.; Chishtie, F.; Clinton, N.; Ganz, D.

2017-12-01

Earth observation and Geographic Information System (GIS) tools, products, and services are vital to support the environmental decision making by governmental institutions, non-governmental agencies, and the general public. At the heart of environmental decision making is the monitoring land cover and land use change (LCLUC) for land resource planning and for ecosystem services, including biodiversity conservation and resilience to climate change. A major challenge for monitoring LCLUC in developing regions, such as Southeast Asia, is inconsistent data products at inconsistent intervals that have different typologies across the region and are typically made in without stakeholder engagement or input. Here we present the Regional Land Cover Monitoring System (RLCMS), a novel land cover mapping effort for Southeast Asia, implemented by SERVIR-Mekong, a joint NASA-USAID initiative that brings Earth observations to improve environmental decision making in developing countries. The RLCMS focuses on mapping biophysical variables (e.g. canopy cover, tree height, or percent surface water) at an annual interval and in turn using those biophysical variables to develop land cover maps based on stakeholder definitions of land cover classes. This allows for flexible and consistent land cover classifications that can meet the needs of different institutions across the region. Another component of the RLCMS production is the stake-holder engagement through co-development. Institutions that directly benefit from this system have helped drive the development for regional needs leading to services for their specific uses. Examples of services for regional stakeholders include using the RLCMS to develop maps using the IPCC classification scheme for GHG emission reporting and developing custom annual maps as an input to hydrologic modeling/flood forecasting systems. In addition to the implementation of this system and the service stemming from the RLCMS in Southeast Asia, it is planned to replicate the methods presented at the SERVIR-Hindu Kush Himalaya hub serving South Asia. Enhancements to the system will include change detection methods, enhanced biophysical models, and delivery systems.

GlobalSoilMap France: High-resolution spatial modelling the soils of France up to two meter depth.

PubMed

Mulder, V L; Lacoste, M; Richer-de-Forges, A C; Arrouays, D

2016-12-15

This work presents the first GlobalSoilMap (GSM) products for France. We developed an automatic procedure for mapping the primary soil properties (clay, silt, sand, coarse elements, pH, soil organic carbon (SOC), cation exchange capacity (CEC) and soil depth). The procedure employed a data-mining technique and a straightforward method for estimating the 90% confidence intervals (CIs). The most accurate models were obtained for pH, sand and silt. Next, CEC, clay and SOC were found reasonably accurate predicted. Coarse elements and soil depth were the least accurate of all models. Overall, all models were considered robust; important indicators for this were 1) the small difference in model diagnostics between the calibration and cross-validation set, 2) the unbiased mean predictions, 3) the smaller spatial structure of the prediction residuals in comparison to the observations and 4) the similar performance compared to other developed GlobalSoilMap products. Nevertheless, the confidence intervals (CIs) were rather wide for all soil properties. The median predictions became less reliable with increasing depth, as indicated by the increase of CIs with depth. In addition, model accuracy and the corresponding CIs varied depending on the soil variable of interest, soil depth and geographic location. These findings indicated that the CIs are as informative as the model diagnostics. In conclusion, the presented method resulted in reasonably accurate predictions for the majority of the soil properties. End users can employ the products for different purposes, as was demonstrated with some practical examples. The mapping routine is flexible for cloud-computing and provides ample opportunity to be further developed when desired by its users. This allows regional and international GSM partners with fewer resources to develop their own products or, otherwise, to improve the current routine and work together towards a robust high-resolution digital soil map of the world. Copyright © 2016 Elsevier B.V. All rights reserved.

Cathepsin B is a novel gender-dependent determinant of cholesterol absorption from the intestine[S

PubMed Central

Wong, Winifred P. S.; Altemus, Jessica B.; Hester, James F.; Chan, Ernest R.; Côté, Jean-François; Serre, David; Sehayek, Ephraim

2013-01-01

We used a mouse C57BL/6J×CASA/Rk intercross to map a locus on chromosome 14 that displayed a gender-dependent effect on cholesterol absorption from the intestine. Studies in congenic animals revealed a complex locus with multiple operating genetic determinants resulting in alternating gender-dependent phenotypic effects. Fine-mapping narrowed the locus to a critical 6.3 Mb interval. Female subcongenics, but not males, of the critical interval displayed a decrease of 33% in cholesterol absorption. RNA-Seq analysis of female subcongenic jejunum revealed that cysteine protease cathepsin B (Ctsb) is a candidate to explain the interval effect. Consistent with the phenotype in critical interval subcongenics, female Ctsb knockout mice, but not males, displayed a decrease of 31% in cholesterol absorption. Although studies in Ctsb knockouts revealed a gender-dependent effect on cholesterol absorption, further fine-mapping dismissed a role for Ctsb in determining the effect of the critical 6.3 Mb interval on cholesterol absorption. PMID:23248330

Four-dimensional optoacoustic temperature mapping in laser-induced thermotherapy

NASA Astrophysics Data System (ADS)

Oyaga Landa, Francisco Javier; Deán-Ben, Xosé Luís.; Sroka, Ronald; Razansky, Daniel

2018-02-01

Photoablative laser therapy is in common use for selective destruction of malignant masses, vascular and brain abnormalities. Tissue ablation and coagulation are irreversible processes occurring shortly after crossing a certain thermal exposure threshold. As a result, accurate mapping of the temperature field is essential for optimizing the outcome of these clinical interventions. Here we demonstrate four-dimensional optoacoustic temperature mapping of the entire photoablated region. Accuracy of the method is investigated in tissue-mimicking phantom experiments. Deviations of the volumetric optoacoustic temperature readings provided at 40ms intervals remained below 10% for temperature elevations above 3°C, as validated by simultaneous thermocouple measurements. The excellent spatio-temporal resolution of the new temperature monitoring approach aims at improving safety and efficacy of laser-based photothermal procedures.

Mapping hurricane rita inland storm tide

USGS Publications Warehouse

Berenbrock, C.; Mason, R.R.; Blanchard, S.F.

2009-01-01

Flood-inundation data are most useful for decision makers when presented in the context of maps of affected communities and (or) areas. But because the data are scarce and rarely cover the full extent of the flooding, interpolation and extrapolation of the information are needed. Many geographic information systems provide various interpolation tools, but these tools often ignore the effects of the topographic and hydraulic features that influence flooding. A barrier mapping method was developed to improve maps of storm tide produced by Hurricane Rita. Maps were developed for the maximum storm tide and at 3-h intervals from midnight (00:00 hours) through noon (12:00 hours) on 24 September 2005. The improved maps depict storm-tide elevations and the extent of flooding. The extent of storm-tide inundation from the improved maximum storm-tide map was compared with the extent of flood inundation from a map prepared by the Federal Emergency Management Agency (FEMA). The boundaries from these two maps generally compared quite well especially along the Calcasieu River. Also a cross-section profile that parallels the Louisiana coast was developed from the maximum storm-tide map and included FEMA high-water marks. ?? 2009 Blackwell Publishing Ltd.

Mapping Hurricane Rita inland storm tide

USGS Publications Warehouse

Berenbrock, Charles; Mason, Jr., Robert R.; Blanchard, Stephen F.; Simonovic, Slobodan P.

2009-01-01

Flood-inundation data are most useful for decision makers when presented in the context of maps of effected communities and (or) areas. But because the data are scarce and rarely cover the full extent of the flooding, interpolation and extrapolation of the information are needed. Many geographic information systems (GIS) provide various interpolation tools, but these tools often ignore the effects of the topographic and hydraulic features that influence flooding. A barrier mapping method was developed to improve maps of storm tide produced by Hurricane Rita. Maps were developed for the maximum storm tide and at 3-hour intervals from midnight (0000 hour) through noon (1200 hour) on September 24, 2005. The improved maps depict storm-tide elevations and the extent of flooding. The extent of storm-tide inundation from the improved maximum storm-tide map was compared to the extent of flood-inundation from a map prepared by the Federal Emergency Management Agency (FEMA). The boundaries from these two maps generally compared quite well especially along the Calcasieu River. Also a cross-section profile that parallels the Louisiana coast was developed from the maximum storm-tide map and included FEMA high-water marks.

Map based navigation for autonomous underwater vehicles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuohy, S.T.; Leonard, J.J.; Bellingham, J.G.

1995-12-31

In this work, a map based navigation algorithm is developed wherein measured geophysical properties are matched to a priori maps. The objectives is a complete algorithm applicable to a small, power-limited AUV which performs in real time to a required resolution with bounded position error. Interval B-Splines are introduced for the non-linear representation of two-dimensional geophysical parameters that have measurement uncertainty. Fine-scale position determination involves the solution of a system of nonlinear polynomial equations with interval coefficients. This system represents the complete set of possible vehicle locations and is formulated as the intersection of contours established on each map frommore » the simultaneous measurement of associated geophysical parameters. A standard filter mechanisms, based on a bounded interval error model, predicts the position of the vehicle and, therefore, screens extraneous solutions. When multiple solutions are found, a tracking mechanisms is applied until a unique vehicle location is determined.« less

Convergence of Newton's method for a single real equation

NASA Technical Reports Server (NTRS)

Campbell, C. W.

1985-01-01

Newton's method for finding the zeroes of a single real function is investigated in some detail. Convergence is generally checked using the Contraction Mapping Theorem which yields sufficient but not necessary conditions for convergence of the general single point iteration method. The resulting convergence intervals are frequently considerably smaller than actual convergence zones. For a specific single point iteration method, such as Newton's method, better estimates of regions of convergence should be possible. A technique is described which, under certain conditions (frequently satisfied by well behaved functions) gives much larger zones where convergence is guaranteed.

Dynamics of Stability of Orientation Maps Recorded with Optical Imaging.

PubMed

Shumikhina, S I; Bondar, I V; Svinov, M M

2018-03-15

Orientation selectivity is an important feature of visual cortical neurons. Optical imaging of the visual cortex allows for the generation of maps of orientation selectivity that reflect the activity of large populations of neurons. To estimate the statistical significance of effects of experimental manipulations, evaluation of the stability of cortical maps over time is required. Here, we performed optical imaging recordings of the visual cortex of anesthetized adult cats. Monocular stimulation with moving clockwise square-wave gratings that continuously changed orientation and direction was used as the mapping stimulus. Recordings were repeated at various time intervals, from 15 min to 16 h. Quantification of map stability was performed on a pixel-by-pixel basis using several techniques. Map reproducibility showed clear dynamics over time. The highest degree of stability was seen in maps recorded 15-45 min apart. Averaging across all time intervals and all stimulus orientations revealed a mean shift of 2.2 ± 0.1°. There was a significant tendency for larger shifts to occur at longer time intervals. Shifts between 2.8° (mean ± 2SD) and 5° were observed more frequently at oblique orientations, while shifts greater than 5° appeared more frequently at cardinal orientations. Shifts greater than 5° occurred rarely overall (5.4% of cases) and never exceeded 11°. Shifts of 10-10.6° (0.7%) were seen occasionally at time intervals of more than 4 h. Our findings should be considered when evaluating the potential effect of experimental manipulations on orientation selectivity mapping studies. Copyright © 2018 IBRO. Published by Elsevier Ltd. All rights reserved.

Enface Thickness Mapping and Reflectance Imaging of Retinal Layers in Diabetic Retinopathy.

PubMed

Francis, Andrew W; Wanek, Justin; Lim, Jennifer I; Shahidi, Mahnaz

2015-01-01

To present a method for image segmentation and generation of enface thickness maps and reflectance images of retinal layers in healthy and diabetic retinopathy (DR) subjects. High density spectral domain optical coherence tomography (SDOCT) images were acquired in 10 healthy and 4 DR subjects. Customized image analysis software identified 5 retinal cell layer interfaces and generated thickness maps and reflectance images of the total retina (TR), inner retina (IR), outer retina (OR), and the inner segment ellipsoid (ISe) band. Thickness maps in DR subjects were compared to those of healthy subjects by generating deviation maps which displayed retinal locations with thickness below, within, and above the normal 95% confidence interval. In healthy subjects, TR and IR thickness maps displayed the foveal depression and increased thickness in the parafoveal region. OR and ISe thickness maps showed increased thickness at the fovea, consistent with normal retinal anatomy. In DR subjects, thickening and thinning in localized regions were demonstrated on TR, IR, OR, and ISe thickness maps, corresponding to retinal edema and atrophy, respectively. TR and OR reflectance images showed reduced reflectivity in regions of increased thickness. Hard exudates appeared as hyper-reflective spots in IR reflectance images and casted shadows on the deeper OR and ISe reflectance images. The ISe reflectance image clearly showed the presence of focal laser scars. Enface thickness mapping and reflectance imaging of retinal layers is a potentially useful method for quantifying the spatial and axial extent of pathologies due to DR.

Exploiting the extraordinary genetic polymorphism of ciona for developmental genetics with whole genome sequencing.

PubMed

Abdul-Wajid, Sarah; Veeman, Michael T; Chiba, Shota; Turner, Thomas L; Smith, William C

2014-05-01

Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca(2+) channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.

Characterization of minimal sequences associated with self-similar interval exchange maps

NASA Astrophysics Data System (ADS)

Cobo, Milton; Gutiérrez-Romo, Rodolfo; Maass, Alejandro

2018-04-01

The construction of affine interval exchange maps (IEMs) with wandering intervals that are semi-conjugate to a given self-similar IEM is strongly related to the existence of the so-called minimal sequences associated with local potentials, which are certain elements of the substitution subshift arising from the given IEM. In this article, under the condition called unique representation property, we characterize such minimal sequences for potentials coming from non-real eigenvalues of the substitution matrix. We also give conditions on the slopes of the affine extensions of a self-similar IEM that determine whether it exhibits a wandering interval or not.

Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

PubMed Central

2012-01-01

Background Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker. Conclusions Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions. PMID:22520935

Bayesian B-spline mapping for dynamic quantitative traits.

PubMed

Xing, Jun; Li, Jiahan; Yang, Runqing; Zhou, Xiaojing; Xu, Shizhong

2012-04-01

Owing to their ability and flexibility to describe individual gene expression at different time points, random regression (RR) analyses have become a popular procedure for the genetic analysis of dynamic traits whose phenotypes are collected over time. Specifically, when modelling the dynamic patterns of gene expressions in the RR framework, B-splines have been proved successful as an alternative to orthogonal polynomials. In the so-called Bayesian B-spline quantitative trait locus (QTL) mapping, B-splines are used to characterize the patterns of QTL effects and individual-specific time-dependent environmental errors over time, and the Bayesian shrinkage estimation method is employed to estimate model parameters. Extensive simulations demonstrate that (1) in terms of statistical power, Bayesian B-spline mapping outperforms the interval mapping based on the maximum likelihood; (2) for the simulated dataset with complicated growth curve simulated by B-splines, Legendre polynomial-based Bayesian mapping is not capable of identifying the designed QTLs accurately, even when higher-order Legendre polynomials are considered and (3) for the simulated dataset using Legendre polynomials, the Bayesian B-spline mapping can find the same QTLs as those identified by Legendre polynomial analysis. All simulation results support the necessity and flexibility of B-spline in Bayesian mapping of dynamic traits. The proposed method is also applied to a real dataset, where QTLs controlling the growth trajectory of stem diameters in Populus are located.

USGS Maps

USGS Publications Warehouse

,

1994-01-01

Most USGS topographic maps use brown contours to show the shape and elevation of the terrain. Elevations are usually shown in feet, but on some maps they are in meters. Contour intervals vary, depending mainly on the scale of the map and the type of terrain.

High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology

PubMed Central

Su, Chengfu; Wang, Wei; Gong, Shunliang; Zuo, Jinghui; Li, Shujiang; Xu, Shizhong

2017-01-01

Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and one gene (GRMZM2G019183) encoding the UDP-Glycosyltransferase. The work will not only help to understand the mechanisms that control yield traits of maize, but also provide a basis for marker-assisted selection and map-based cloning in further studies. PMID:28533786

Modeling stream fish distributions using interval-censored detection times.

PubMed

Ferreira, Mário; Filipe, Ana Filipa; Bardos, David C; Magalhães, Maria Filomena; Beja, Pedro

2016-08-01

Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time-to-detection model provided unbiased parameter estimates despite interval-censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P-values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval-censored time-to-detection model provides a practical solution to model occupancy-detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.

Multitemporal Snow Cover Mapping in Mountainous Terrain for Landsat Climate Data Record Development

NASA Technical Reports Server (NTRS)

Crawford, Christopher J.; Manson, Steven M.; Bauer, Marvin E.; Hall, Dorothy K.

2013-01-01

A multitemporal method to map snow cover in mountainous terrain is proposed to guide Landsat climate data record (CDR) development. The Landsat image archive including MSS, TM, and ETM+ imagery was used to construct a prototype Landsat snow cover CDR for the interior northwestern United States. Landsat snow cover CDRs are designed to capture snow-covered area (SCA) variability at discrete bi-monthly intervals that correspond to ground-based snow telemetry (SNOTEL) snow-water-equivalent (SWE) measurements. The June 1 bi-monthly interval was selected for initial CDR development, and was based on peak snowmelt timing for this mountainous region. Fifty-four Landsat images from 1975 to 2011 were preprocessed that included image registration, top-of-the-atmosphere (TOA) reflectance conversion, cloud and shadow masking, and topographic normalization. Snow covered pixels were retrieved using the normalized difference snow index (NDSI) and unsupervised classification, and pixels having greater (less) than 50% snow cover were classified presence (absence). A normalized SCA equation was derived to independently estimate SCA given missing image coverage and cloud-shadow contamination. Relative frequency maps of missing pixels were assembled to assess whether systematic biases were embedded within this Landsat CDR. Our results suggest that it is possible to confidently estimate historical bi-monthly SCA from partially cloudy Landsat images. This multitemporal method is intended to guide Landsat CDR development for freshwaterscarce regions of the western US to monitor climate-driven changes in mountain snowpack extent.

Genetic organization of the unc-22 IV gene and the adjacent region in Caenorhabditis elegans.

PubMed

Rogalski, T M; Baillie, D L

1985-01-01

The genetic organization of the region immediately adjacent to the unc-22 IV gene in Caenorhabditis elegans has been studied. We have identified twenty essential genes in this interval of approximately 1.5-map units on Linkage Group IV. The mutations that define these genes were positioned by recombination mapping and complementation with several deficiencies. With few exceptions, the positions obtained by these two methods agreed. Eight of the twenty essential genes identified are represented by more than one allele. Three possible internal deletions of the unc-22 gene have been located by intra-genic mapping. In addition, the right end point of a deficiency or an inversion affecting the adjacent genes let-56 and unc-22 has been positioned inside the unc-22 gene.

Prediction of fracture profile using digital image correlation

NASA Astrophysics Data System (ADS)

Chaitanya, G. M. S. K.; Sasi, B.; Kumar, Anish; Babu Rao, C.; Purnachandra Rao, B.; Jayakumar, T.

2015-04-01

Digital Image Correlation (DIC) based full field strain mapping methodology is used for mapping strain on an aluminum sample subjected to tensile deformation. The local strains on the surface of the specimen are calculated at different strain intervals. Early localization of strain is observed at a total strain of 0.050ɛ; itself, whereas a visually apparent localization of strain is observed at a total strain of 0.088ɛ;. Orientation of the line of fracture (12.0°) is very close to the orientation of locus of strain maxima (11.6°) computed from the strain mapping at 0.063ɛ itself. These results show the efficacy of the DIC based method to predict the location as well as the profile of the fracture, at an early stage.

IMPROVEMENT OF EFFICIENCY OF CUT AND OVERLAY ASPHALT WORKS BY USING MOBILE MAPPING SYSTEM

NASA Astrophysics Data System (ADS)

Yabuki, Nobuyoshi; Nakaniwa, Kazuhide; Kidera, Hiroki; Nishi, Daisuke

When the cut-and-overlay asphalt work is done for improving road pavement, conventional road surface elevation survey with levels often requires traffic regulation and takes much time and effort. Recently, although new surveying methods using non-prismatic total stations or fixed 3D laser scanners have been proposed in industry, they have not been adopted much due to their high cost. In this research, we propose a new method using Mobile Mapping Systems (MMS) in order to increase the efficiency and to reduce the cost. In this method, small white marks are painted at the intervals of 10m along the road to identify cross sections and to modify the elevations of the white marks with accurate survey data. To verify this proposed method, we executed an experiment and compared this method with the conventional level survey method and the fixed 3D laser scanning method at a road of Osaka University. The result showed that the proposed method had a similar accuracy with other methods and it was more efficient.

Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.).

PubMed

Yang, Cong; Tang, Dengguo; Qu, Jingtao; Zhang, Ling; Zhang, Lei; Chen, Zhengjie; Liu, Jian

2016-11-01

A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis. A total of 171 and 159 putative QTLs were detected through these two mapping methods, respectively. Single-environment mapping revealed that 39 stable QTLs explained more than 10 % of the phenotypic variance, and 35 of the 39 QTLs were also detected by joint analysis. In addition, joint analysis showed that nine of the 159 QTLs exhibited significant QTL × environment interaction and 15 significant epistatic interactions were identified. Approximately 47.17 % of the QTLs for leaf architectural traits in joint analysis were concentrated in ten main chromosomal regions, namely, bins 1.07, 2.02, 3.06, 4.09, 5.01, 5.02, 5.03-5.04, 5.07, 6.07, and 8.05. This study should provide a basis for further fine-mapping of these main genetic regions and improvement of maize leaf architecture.

Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12.

PubMed

Zhang, Kun; Lott, Steven T; Jin, Li; Killary, Ann McNeill

2007-08-31

Identification of tumor suppressor genes based on physical mapping exercises has proven to be a challenging endeavor, due to the difficulty of narrowing regions of loss of heterozygosity (LOH), infrequency of homozygous deletions, and the labor-intensive characterization process for screening candidates in a given genomic interval. We previously defined a chromosome 3p12 tumor suppressor locus NRC-1 (Nonpapillary Renal Carcinoma-1) by functional complementation experiments in which renal cell carcinoma microcell hybrids containing introduced normal chromosome 3p fragments were either suppressed or unsuppressed for tumorigenicity following injection into athymic nude mice. We now present the fine-scale physical mapping of NRC-1 using a QPCR-based approach for measuring copy number at sequence tagged sites (STS) which allowed a sub-exon mapping resolution. Using STS-QPCR and a novel statistical algorithm, the NRC-1 locus was narrowed to 4.615-Mb with the distal boundary mapping within a 38-Kb interval between exon 3 and exon 4 of the DUTT1/Robo1 gene, currently the only candidate tumor suppressor gene in the interval. Further mutational screening and gene expression analyses indicate that DUTT1/ROBO1 is not involved in the tumor suppressor activity of NRC-1, suggesting that there are at least two important tumor suppressor genes within the chromosome 3p12 interval.

Chaotic orbits obeying one isolating integral in a four-dimensional map

NASA Astrophysics Data System (ADS)

Muzzio, J. C.

2018-02-01

We have recently presented strong evidence that chaotic orbits that obey one isolating integral besides energy exist in a toy Hamiltonian model with three degrees of freedom and are bounded by regular orbits that isolate them from the Arnold web. The interval covered by those numerical experiments was equivalent to about one million Hubble times in a galactic context. Here, we use a four-dimensional map to confirm our previous results and to extend that interval 50 times. We show that, at least within that interval, features found in lower dimension Hamiltonian systems and maps are also present in our study, e.g. within the phase space occupied by a chaotic orbit that obeys one integral there are subspaces where that orbit does not enter and are, instead, occupied by regular orbits that, if tori, bound other chaotic orbits obeying one integral and, if cantori, produce stickiness. We argue that the validity of our results might exceed the time intervals covered by the numerical experiments.

Flood Mapping in the Lower Mekong River Basin Using Daily MODIS Observations

NASA Technical Reports Server (NTRS)

Fayne, Jessica V.; Bolten, John D.; Doyle, Colin S.; Fuhrmann, Sven; Rice, Matthew T.; Houser, Paul R.; Lakshmi, Venkat

2017-01-01

In flat homogenous terrain such as in Cambodia and Vietnam, the monsoon season brings significant and consistent flooding between May and November. To monitor flooding in the Lower Mekong region, the near real-time NASA Flood Extent Product (NASA-FEP) was developed using seasonal normalized difference vegetation index (NDVI) differences from the 250 m resolution Moderate Resolution Imaging Spectroradiometer (MODIS) sensor compared to daily observations. The use of a percentage change interval classification relating to various stages of flooding reduces might be confusing to viewers or potential users, and therefore reducing the product usage. To increase the product usability through simplification, the classification intervals were compared with other commonly used change detection schemes to identify the change classification scheme that best delineates flooded areas. The percentage change method used in the NASA-FEP proved to be helpful in delineating flood boundaries compared to other change detection methods. The results of the accuracy assessments indicate that the -75% NDVI change interval can be reclassified to a descriptive 'flood' classification. A binary system was used to simplify the interpretation of the NASA-FEP by removing extraneous information from lower interval change classes.

Rigorous high-precision enclosures of fixed points and their invariant manifolds

NASA Astrophysics Data System (ADS)

Wittig, Alexander N.

The well established concept of Taylor Models is introduced, which offer highly accurate C0 enclosures of functional dependencies, combining high-order polynomial approximation of functions and rigorous estimates of the truncation error, performed using verified arithmetic. The focus of this work is on the application of Taylor Models in algorithms for strongly non-linear dynamical systems. A method is proposed to extend the existing implementation of Taylor Models in COSY INFINITY from double precision coefficients to arbitrary precision coefficients. Great care is taken to maintain the highest efficiency possible by adaptively adjusting the precision of higher order coefficients in the polynomial expansion. High precision operations are based on clever combinations of elementary floating point operations yielding exact values for round-off errors. An experimental high precision interval data type is developed and implemented. Algorithms for the verified computation of intrinsic functions based on the High Precision Interval datatype are developed and described in detail. The application of these operations in the implementation of High Precision Taylor Models is discussed. An application of Taylor Model methods to the verification of fixed points is presented by verifying the existence of a period 15 fixed point in a near standard Henon map. Verification is performed using different verified methods such as double precision Taylor Models, High Precision intervals and High Precision Taylor Models. Results and performance of each method are compared. An automated rigorous fixed point finder is implemented, allowing the fully automated search for all fixed points of a function within a given domain. It returns a list of verified enclosures of each fixed point, optionally verifying uniqueness within these enclosures. An application of the fixed point finder to the rigorous analysis of beam transfer maps in accelerator physics is presented. Previous work done by Johannes Grote is extended to compute very accurate polynomial approximations to invariant manifolds of discrete maps of arbitrary dimension around hyperbolic fixed points. The algorithm presented allows for automatic removal of resonances occurring during construction. A method for the rigorous enclosure of invariant manifolds of continuous systems is introduced. Using methods developed for discrete maps, polynomial approximations of invariant manifolds of hyperbolic fixed points of ODEs are obtained. These approximations are outfit with a sharp error bound which is verified to rigorously contain the manifolds. While we focus on the three dimensional case, verification in higher dimensions is possible using similar techniques. Integrating the resulting enclosures using the verified COSY VI integrator, the initial manifold enclosures are expanded to yield sharp enclosures of large parts of the stable and unstable manifolds. To demonstrate the effectiveness of this method, we construct enclosures of the invariant manifolds of the Lorenz system and show pictures of the resulting manifold enclosures. To the best of our knowledge, these enclosures are the largest verified enclosures of manifolds in the Lorenz system in existence.

Random Forests (RFs) for Estimation, Uncertainty Prediction and Interpretation of Monthly Solar Potential

NASA Astrophysics Data System (ADS)

Assouline, Dan; Mohajeri, Nahid; Scartezzini, Jean-Louis

2017-04-01

Solar energy is clean, widely available, and arguably the most promising renewable energy resource. Taking full advantage of solar power, however, requires a deep understanding of its patterns and dependencies in space and time. The recent advances in Machine Learning brought powerful algorithms to estimate the spatio-temporal variations of solar irradiance (the power per unit area received from the Sun, W/m2), using local weather and terrain information. Such algorithms include Deep Learning (e.g. Artificial Neural Networks), or kernel methods (e.g. Support Vector Machines). However, most of these methods have some disadvantages, as they: (i) are complex to tune, (ii) are mainly used as a black box and offering no interpretation on the variables contributions, (iii) often do not provide uncertainty predictions (Assouline et al., 2016). To provide a reasonable solar mapping with good accuracy, these gaps would ideally need to be filled. We present here simple steps using one ensemble learning algorithm namely, Random Forests (Breiman, 2001) to (i) estimate monthly solar potential with good accuracy, (ii) provide information on the contribution of each feature in the estimation, and (iii) offer prediction intervals for each point estimate. We have selected Switzerland as an example. Using a Digital Elevation Model (DEM) along with monthly solar irradiance time series and weather data, we build monthly solar maps for Global Horizontal Irradiance (GHI), Diffuse Horizontal Irradiance (GHI), and Extraterrestrial Irradiance (EI). The weather data include monthly values for temperature, precipitation, sunshine duration, and cloud cover. In order to explain the impact of each feature on the solar irradiance of each point estimate, we extend the contribution method (Kuz'min et al., 2011) to a regression setting. Contribution maps for all features can then be computed for each solar map. This provides precious information on the spatial variation of the features impact all across Switzerland maps. Finally, as RFs are based on bootstrap samples of the training data, they can produce prediction intervals by looking at the trees estimates distribution, instead of taking the mean estimate. To do so, a simple idea is to grow all trees fully so that each leaf has exactly one value, that is, a training sample value. Then, for each point estimate, we compute percentiles of the trees estimates data to build a prediction interval. Two issues arise from this process: (i) growing the trees fully is not always possible, and (ii) there is a risk of over-fitting. We show how to solve them. These steps can be used for any type of environmental mapping so as to extract useful information on uncertainty and feature impact interpretation. References -Assouline, D., Mohajeri, N., & Scartezzini, J. L. (2017). Quantifying rooftop photovoltaic solar energy potential: A machine learning approach. Solar Energy, 141, 278-296. -Breiman, L. (2001). Random forests. Machine learning, 45(1), 5-32. -Kuz'min, V. E., Polishchuk, P. G., Artemenko, A. G., & Andronati, S. A. (2011). Interpretation of QSAR models based on random forest methods. Molecular Informatics, 30(6-7), 593-603.

Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach.

PubMed

Wang, Yankun; Chen, Wenjing; Chu, Pu; Wan, Shubei; Yang, Mao; Wang, Mingming; Guan, Rongzhan

2016-08-18

Key genes related to plant type traits have played very important roles in the "green revolution" by increasing lodging resistance and elevating the harvest indices of crop cultivars. Although there have been numerous achievements in the development of dwarfism and plant type in Brassica napus breeding, exploring new materials conferring oilseed rape with efficient plant types that provide higher yields is still of significance in breeding, as well as in elucidating the mechanisms underlying plant development. Here, we report a new dwarf architecture with down-curved leaf mutant (Bndwf/dcl1) isolated from an ethyl methanesulphonate (EMS)-mutagenized B. napus line, together with its inheritance and gene mapping, and pleiotropic effects of the mapped locus on plant-type traits. We constructed a high-density single-nucleotide polymorphism (SNP) map using a backcross population derived from the Bndwf/dcl1 mutant and the canola cultivar 'zhongshuang11' ('ZS11') and mapped the dwarf architecture with the down-curved leaf dominant locus, BnDWF/DCL1, in a 6.58-cM interval between SNP marker bins M46180 and M49962 on the linkage group (LG) C05 of B. napus. Further mapping with other materials derived from Bndwf/dcl1 narrowed the interval harbouring BnDWF/DCL1 to 175 kb in length and this interval contained 16 annotated genes. Quantitative trait locus (QTL) mappings with the backcross population for plant type traits, including plant height, branching height, main raceme length and average branching interval, indicated that the mapped QTLs for plant type traits were located at the same position as the BnDWF/DCL1 locus. This study suggests that the BnDWF/DCL1 locus is a major pleiotropic locus/QTL in B. napus, which may reduce plant height, alter plant type traits and change leaf shape, and thus may lead to compact plant architecture. Accordingly, this locus may have substantial breeding potential for increasing planting density.

Response Surface Methods for Spatially-Resolved Optical Measurement Techniques

NASA Technical Reports Server (NTRS)

Danehy, P. M.; Dorrington, A. A.; Cutler, A. D.; DeLoach, R.

2003-01-01

Response surface methods (or methodology), RSM, have been applied to improve data quality for two vastly different spatial ly-re solved optical measurement techniques. In the first application, modern design of experiments (MDOE) methods, including RSM, are employed to map the temperature field in a direct-connect supersonic combustion test facility at NASA Langley Research Center. The laser-based measurement technique known as coherent anti-Stokes Raman spectroscopy (CARS) is used to measure temperature at various locations in the combustor. RSM is then used to develop temperature maps of the flow. Even though the temperature fluctuations at a single point in the flowfield have a standard deviation on the order of 300 K, RSM provides analytic fits to the data having 95% confidence interval half width uncertainties in the fit as low as +/-30 K. Methods of optimizing future CARS experiments are explored. The second application of RSM is to quantify the shape of a 5-meter diameter, ultra-light, inflatable space antenna at NASA Langley Research Center.

Urban-scale mapping of PM2.5 distribution via data fusion between high-density sensor network and MODIS Aerosol Optical Depth

NASA Astrophysics Data System (ADS)

Ba, Yu Tao; xian Liu, Bao; Sun, Feng; Wang, Li hua; Tang, Yu jia; Zhang, Da wei

2017-04-01

High-resolution mapping of PM2.5 is the prerequisite for precise analytics and subsequent anti-pollution interventions. Considering the large variances of particulate distribution, urban-scale mapping is challenging either with ground-based fixed stations, with satellites or via models. In this study, a dynamic fusion method between high-density sensor network and MODIS Aerosol Optical Depth (AOD) was introduced. The sensor network was deployed in Beijing ( > 1000 fixed monitors across 16000 km2 area) to provide raw observations with high temporal resolution (sampling interval < 1 hour), high spatial resolution in flat areas ( < 1 km), and low spatial resolution in mountainous areas ( > 5 km). The MODIS AOD was calibrated to provide distribution map with low temporal resolution (daily) and moderate spatial resolution ( = 3 km). By encoding the data quality and defects (e.g. could, reflectance, abnormal), a hybrid interpolation procedure with cross-validation generated PM2.5 distribution with both high temporal and spatial resolution. Several no-pollutant and high-pollution periods were tested to validate the proposed fusion method for capturing the instantaneous patterns of PM2.5 emission.

Statistical parametric mapping of LORETA using high density EEG and individual MRI: application to mismatch negativities in schizophrenia.

PubMed

Park, Hae-Jeong; Kwon, Jun Soo; Youn, Tak; Pae, Ji Soo; Kim, Jae-Jin; Kim, Myung-Sun; Ha, Kyoo-Seob

2002-11-01

We describe a method for the statistical parametric mapping of low resolution electromagnetic tomography (LORETA) using high-density electroencephalography (EEG) and individual magnetic resonance images (MRI) to investigate the characteristics of the mismatch negativity (MMN) generators in schizophrenia. LORETA, using a realistic head model of the boundary element method derived from the individual anatomy, estimated the current density maps from the scalp topography of the 128-channel EEG. From the current density maps that covered the whole cortical gray matter (up to 20,000 points), volumetric current density images were reconstructed. Intensity normalization of the smoothed current density images was used to reduce the confounding effect of subject specific global activity. After transforming each image into a standard stereotaxic space, we carried out statistical parametric mapping of the normalized current density images. We applied this method to the source localization of MMN in schizophrenia. The MMN generators, produced by a deviant tone of 1,200 Hz (5% of 1,600 trials) under the standard tone of 1,000 Hz, 80 dB binaural stimuli with 300 msec of inter-stimulus interval, were measured in 14 right-handed schizophrenic subjects and 14 age-, gender-, and handedness-matched controls. We found that the schizophrenic group exhibited significant current density reductions of MMN in the left superior temporal gyrus and the left inferior parietal gyrus (P < 0. 0005). This study is the first voxel-by-voxel statistical mapping of current density using individual MRI and high-density EEG. Copyright 2002 Wiley-Liss, Inc.

Graded-threshold parametric response maps: towards a strategy for adaptive dose painting

NASA Astrophysics Data System (ADS)

Lausch, A.; Jensen, N.; Chen, J.; Lee, T. Y.; Lock, M.; Wong, E.

2014-03-01

Purpose: To modify the single-threshold parametric response map (ST-PRM) method for predicting treatment outcomes in order to facilitate its use for guidance of adaptive dose painting in intensity-modulated radiotherapy. Methods: Multiple graded thresholds were used to extend the ST-PRM method (Nat. Med. 2009;15(5):572-576) such that the full functional change distribution within tumours could be represented with respect to multiple confidence interval estimates for functional changes in similar healthy tissue. The ST-PRM and graded-threshold PRM (GT-PRM) methods were applied to functional imaging scans of 5 patients treated for hepatocellular carcinoma. Pre and post-radiotherapy arterial blood flow maps (ABF) were generated from CT-perfusion scans of each patient. ABF maps were rigidly registered based on aligning tumour centres of mass. ST-PRM and GT-PRM analyses were then performed on overlapping tumour regions within the registered ABF maps. Main findings: The ST-PRMs contained many disconnected clusters of voxels classified as having a significant change in function. While this may be useful to predict treatment response, it may pose challenges for identifying boost volumes or for informing dose-painting by numbers strategies. The GT-PRMs included all of the same information as ST-PRMs but also visualized the full tumour functional change distribution. Heterogeneous clusters in the ST-PRMs often became more connected in the GT-PRMs by voxels with similar functional changes. Conclusions: GT-PRMs provided additional information which helped to visualize relationships between significant functional changes identified by ST-PRMs. This may enhance ST-PRM utility for guiding adaptive dose painting.

Psychophysical Map Stability in Bilateral Sequential Cochlear Implantation: Comparing Current Audiology Methods to a New Statistical Definition.

PubMed

Domville-Lewis, Chloe; Santa Maria, Peter L; Upson, Gemma; Chester-Browne, Ronel; Atlas, Marcus D

2015-01-01

The purpose of this study was to establish a statistical definition for stability in cochlear implant maps. Once defined, this study aimed to compare the duration taken to achieve a stable map in first and second implants in patients who underwent sequential bilateral cochlear implantation. This article also sought to evaluate a number of factors that potentially affect map stability. A retrospective cohort study of 33 patients with sensorineural hearing loss who received sequential bilateral cochlear implantation (Cochlear, Sydney, Australia), performed by the senior author. Psychophysical parameters of hearing threshold scores, comfort scores, and the dynamic range were measured for the apical, medial, and basal portions of the cochlear implant electrode at a range of intervals postimplantation. Stability was defined statistically as a less than 10% difference in threshold, comfort, and dynamic range scores over three consecutive mapping sessions. A senior cochlear implant audiologist, blinded to implant order and the statistical results, separately analyzed these psychophysical map parameters using current assessment methods. First and second implants were compared for duration to achieve stability, age, gender, the duration of deafness, etiology of deafness, time between the insertion of the first and second implant, and the presence or absence of preoperative hearing aids were evaluated and its relationship to stability. Statistical analysis included performing a two-tailed Student's t tests and least squares regression analysis, with a statistical significance set at p ≤ 0.05. There was a significant positive correlation between the devised statistical definition and the current audiology methods for assessing stability, with a Pearson correlation coefficient r = 0.36 and a least squares regression slope (b) of 0.41, df(58), 95% confidence interval 0.07 to 0.55 (p = 0.004). The average duration from device switch on to stability in the first implant was 87 days using current audiology methods and 81 days using the statistical definition, with no statistically significant difference between assessment methods (p = 0.2). The duration to achieve stability in the second implant was 51 days using current audiology methods and 60 days using the statistical method, and again no difference between the two assessment methods (p = 0.13). There was a significant reduction in the time to achieve stability in second implants for both audiology and statistical methods (p < 0.001 and p = 0.02, respectively). There was a difference in duration to achieve stability based on electrode array region, with basal portions taking longer to stabilize than apical in the first implant (p = 0.02) and both apical and medial segments in second implants (p = 0.004 and p = 0.01, respectively). No factors that were evaluated in this study, including gender, age, etiology of deafness, duration of deafness, time between implant insertion, and the preoperative hearing aid status, were correlated with stability duration in either stability assessment method. Our statistical definition can accurately predict cochlear implant map stability when compared with current audiology practices. Cochlear implants that are implanted second tend to stabilize sooner than the first, which has a significant impact on counseling before a second implant. No factors evaluated affected the duration required to achieve stability in this study.

Effect of increasing the sampling interval to 2 seconds on the radiation dose and accuracy of CT perfusion of the head and neck.

PubMed

Tawfik, Ahmed M; Razek, Ahmed A; Elhawary, Galal; Batouty, Nihal M

2014-01-01

To evaluate the effect of increasing the sampling interval from 1 second (1 image per second) to 2 seconds (1 image every 2 seconds) on computed tomographic (CT) perfusion (CTP) of head and neck tumors. Twenty patients underwent CTP studies of head and neck tumors with images acquired in cine mode for 50 seconds using sampling interval of 1 second. Using deconvolution-based software, analysis of CTP was done with sampling interval of 1 second and then 2 seconds. Perfusion maps representing blood flow, blood volume, mean transit time, and permeability surface area product (PS) were obtained. Quantitative tumor CTP values were compared between the 2 sampling intervals. Two blinded radiologists compared the subjective quality of CTP maps using a 3-point scale between the 2 sampling intervals. Radiation dose parameters were recorded for the 2 sampling interval rates. No significant differences were observed between the means of the 4 perfusion parameters generated using both sampling intervals; all P >0.05. The 95% limits of agreement between the 2 sampling intervals were -65.9 to 48.1) mL/min per 100 g for blood flow, -3.6 to 3.1 mL/100 g for blood volume, -2.9 to 3.8 seconds for mean transit time, and -10.0 to 12.5 mL/min per 100 g for PS. There was no significant difference between the subjective quality scores of CTP maps obtained using the 2 sampling intervals; all P > 0.05. Radiation dose was halved when sampling interval increased from 1 to 2 seconds. Increasing the sampling interval rate to 1 image every 2 seconds does not compromise the image quality and has no significant effect on quantitative perfusion parameters of head and neck tumors. The radiation dose is halved.

Cuntz-Krieger algebras representations from orbits of interval maps

NASA Astrophysics Data System (ADS)

Correia Ramos, C.; Martins, Nuno; Pinto, Paulo R.; Sousa Ramos, J.

2008-05-01

Let f be an expansive Markov interval map with finite transition matrix Af. Then for every point, we yield an irreducible representation of the Cuntz-Krieger algebra and show that two such representations are unitarily equivalent if and only if the points belong to the same generalized orbit. The restriction of each representation to the gauge part of is decomposed into irreducible representations, according to the decomposition of the orbit.

Simulating the Effects of Spread of Electric Excitation on Musical Tuning and Melody Identification with a Cochlear Implant

ERIC Educational Resources Information Center

Spahr, Anthony J.; Litvak, Leonid M.; Dorman, Michael F.; Bohanan, Ashley R.; Mishra, Lakshmi N.

2008-01-01

Purpose: To determine why, in a pilot study, only 1 of 11 cochlear implant listeners was able to reliably identify a frequency-to-electrode map where the intervals of a familiar melody were played on the correct musical scale. The authors sought to validate their method and to assess the effect of pitch strength on musical scale recognition in…

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

PubMed

Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

2017-07-14

Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

Boundedness and global robust stability analysis of delayed complex-valued neural networks with interval parameter uncertainties.

PubMed

Song, Qiankun; Yu, Qinqin; Zhao, Zhenjiang; Liu, Yurong; Alsaadi, Fuad E

2018-07-01

In this paper, the boundedness and robust stability for a class of delayed complex-valued neural networks with interval parameter uncertainties are investigated. By using Homomorphic mapping theorem, Lyapunov method and inequality techniques, sufficient condition to guarantee the boundedness of networks and the existence, uniqueness and global robust stability of equilibrium point is derived for the considered uncertain neural networks. The obtained robust stability criterion is expressed in complex-valued LMI, which can be calculated numerically using YALMIP with solver of SDPT3 in MATLAB. An example with simulations is supplied to show the applicability and advantages of the acquired result. Copyright © 2018 Elsevier Ltd. All rights reserved.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Preliminary Mapping of the Western Corn Rootworm (Diabrotica virgifera virgifera) Genome and Quantitative Trait Locus (QTL) Interval Mapping for Growth

USDA-ARS?s Scientific Manuscript database

Preliminary investigations into the organization of the western corn rootworm (Diabrotica virgifera virgifera; WCR) genome have resulted in low to moderate density gender-specific maps constructed from progeny of a backcrossed, short-diapause WCR family. Maps were based upon variation at microsatel...

Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.).

PubMed

Mondal, Suvendu; Badigannavar, Anand M

2018-05-09

A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance. A fine mapping approach towards the development of closely linked markers for rust resistance gene was undertaken in this study. Phenotyping of an RIL population at five environments for field rust score and subsequent QTL analysis has identified a 1.25 cM map interval that harbored a consensus major Rust_QTL in A03 chromosome. This Rust_QTL is flanked by two SSR markers: FRS72 and SSR_GO340445. Both the markers clearly identified strong association of the mapped region with rust reaction in both resistant and susceptible genotypes from a collection of 95 cultivated peanut germplasm. This 1.25 cM map interval contained 331.7 kb in the physical map of A. duranensis and had a TIR-NB-LRR category R gene (Aradu.Z87JB) and four glucan endo-1,3 β glucosidase genes (Aradu.RKA6 M, Aradu.T44NR, Aradu.IWV86 and Aradu.VG51Q). Another resistance gene analog was also found in the vicinity of mapped Rust_QTL. The sequence between SSR markers, FRS72 and FRS49, contains an LRR-PK (Aradu.JG217) which is equivalent to RHG4 in soybean. Probably, the protein kinase domain in AhRHG4 acts as an integrated decoy for the cognate AVR from Puccinia arachidis and helps the TIR-NB-LRR R-protein to initiate a controlled program cell death in resistant peanut plants.

Mapped Chebyshev Pseudo-Spectral Method for Dynamic Aero-Elastic Problem of Limit Cycle Oscillation

NASA Astrophysics Data System (ADS)

Im, Dong Kyun; Kim, Hyun Soon; Choi, Seongim

2018-05-01

A mapped Chebyshev pseudo-spectral method is developed as one of the Fourier-spectral approaches and solves nonlinear PDE systems for unsteady flows and dynamic aero-elastic problem in a given time interval, where the flows or elastic motions can be periodic, nonperiodic, or periodic with an unknown frequency. The method uses the Chebyshev polynomials of the first kind for the basis function and redistributes the standard Chebyshev-Gauss-Lobatto collocation points more evenly by a conformal mapping function for improved numerical stability. Contributions of the method are several. It can be an order of magnitude more efficient than the conventional finite difference-based, time-accurate computation, depending on the complexity of solutions and the number of collocation points. The method reformulates the dynamic aero-elastic problem in spectral form for coupled analysis of aerodynamics and structures, which can be effective for design optimization of unsteady and dynamic problems. A limit cycle oscillation (LCO) is chosen for the validation and a new method to determine the LCO frequency is introduced based on the minimization of a second derivative of the aero-elastic formulation. Two examples of the limit cycle oscillation are tested: nonlinear, one degree-of-freedom mass-spring-damper system and two degrees-of-freedom oscillating airfoil under pitch and plunge motions. Results show good agreements with those of the conventional time-accurate simulations and wind tunnel experiments.

Mapping of the locus for autosomal dominant amelogenesis imperfecta (AIH2) to a 4-Mb YAC contig on chromosome 4q11-q21

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaerrman, C.; Holmgren, G.; Forsman, K.

1997-01-15

Amelogenesis imperfecta (Al) is a clinically and genetically heterogeneous group of inherited enamel defects. We recently mapped a locus for autosomal dominant local hypoplastic amelogenesis imperfecta (AIH2) to the long arm of chromosome 4. The disease gene was localized to a 17.6-cM region between the markers D4S392 and D4S395. The albumin gene (ALB), located in the same interval, was a candidate gene for autosomal dominant AI (ADAI) since albumin has a potential role in enamel maturation. Here we describe refined mapping of the AIH2 locus and the construction of marker maps by radiation hybrid mapping and yeast artificial chromosome (YAC)-basedmore » sequence tagged site-content mapping. A radiation hybrid map consisting of 11 microsatellite markers in the 5-cM interval between D4S409 and D4S1558 was constructed. Recombinant haplotypes in six Swedish ADAI families suggest that the disease gene is located in the interval between D4S2421 and ALB. ALB is therefore not likely to be the disease-causing gene. Affected members in all six families share the same allele haplotypes, indicating a common ancestral mutation in all families. The AIH2 critical region is less than 4 cM and spans a physical distance of approximately 4 Mb as judged from radiation hybrid maps. A YAC contig over the AIH2 critical region including several potential candidate genes was constructed. 35 refs., 4 figs., 1 tab.« less

Molecular mapping of chromosomes 17 and X

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barker, D.F.

1991-01-15

Progress toward the construction of high density genetic maps of chromosomes 17 and X has been made by isolating and characterizing a relatively large set of polymorphic probes for each chromosome and using these probes to construct genetic maps. We have mapped the same polymorphic probes against a series of chromosome breakpoints on X and 17. The probes could be assigned to over 30 physical intervals on the X chromosome and 7 intervals on 17. In many cases, this process resulted in improved characterization of the relative locations of the breakpoints with respect to each other and the definition ofmore » new physical intervals. The strategy for isolation of the polymorphic clones utilized chromosome specific libraries of 1--15 kb segments from each of the two chromosomes. From these libraries, clones were screened for those detecting restriction fragment length polymorphisms. The markers were further characterized, the chromosomal assignments confirmed and in most cases segments of the original probes were subcloned into plasmids to produce probes with improved signal to noise ratios for use in the genetic marker studies. The linkage studies utilize the CEPH reference families and other well-characterized families in our collection which have been used for genetic disease linkage work. Preliminary maps and maps of portions of specific regions of 17 and X are provided. We have nearly completed a map of the 1 megabase Mycoplasma arthritidis genome by applying these techniques to a lambda phage library of its genome. We have found bit mapping to be an efficient means to organize a contiguous set of overlapping clones from a larger genome.« less

Molecular mapping of chromosomes 17 and X. Progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barker, D.F.

1991-01-15

Progress toward the construction of high density genetic maps of chromosomes 17 and X has been made by isolating and characterizing a relatively large set of polymorphic probes for each chromosome and using these probes to construct genetic maps. We have mapped the same polymorphic probes against a series of chromosome breakpoints on X and 17. The probes could be assigned to over 30 physical intervals on the X chromosome and 7 intervals on 17. In many cases, this process resulted in improved characterization of the relative locations of the breakpoints with respect to each other and the definition ofmore » new physical intervals. The strategy for isolation of the polymorphic clones utilized chromosome specific libraries of 1--15 kb segments from each of the two chromosomes. From these libraries, clones were screened for those detecting restriction fragment length polymorphisms. The markers were further characterized, the chromosomal assignments confirmed and in most cases segments of the original probes were subcloned into plasmids to produce probes with improved signal to noise ratios for use in the genetic marker studies. The linkage studies utilize the CEPH reference families and other well-characterized families in our collection which have been used for genetic disease linkage work. Preliminary maps and maps of portions of specific regions of 17 and X are provided. We have nearly completed a map of the 1 megabase Mycoplasma arthritidis genome by applying these techniques to a lambda phage library of its genome. We have found bit mapping to be an efficient means to organize a contiguous set of overlapping@ clones from a larger genome.« less

Active, capable, and potentially active faults - a paleoseismic perspective

USGS Publications Warehouse

Machette, M.N.

2000-01-01

Maps of faults (geologically defined source zones) may portray seismic hazards in a wide range of completeness depending on which types of faults are shown. Three fault terms - active, capable, and potential - are used in a variety of ways for different reasons or applications. Nevertheless, to be useful for seismic-hazards analysis, fault maps should encompass a time interval that includes several earthquake cycles. For example, if the common recurrence in an area is 20,000-50,000 years, then maps should include faults that are 50,000-100,000 years old (two to five typical earthquake cycles), thus allowing for temporal variability in slip rate and recurrence intervals. Conversely, in more active areas such as plate boundaries, maps showing faults that are <10,000 years old should include those with at least 2 to as many as 20 paleoearthquakes. For the International Lithosphere Programs' Task Group II-2 Project on Major Active Faults of the World our maps and database will show five age categories and four slip rate categories that allow one to select differing time spans and activity rates for seismic-hazard analysis depending on tectonic regime. The maps are accompanied by a database that describes evidence for Quaternary faulting, geomorphic expression, and paleoseismic parameters (slip rate, recurrence interval and time of most recent surface faulting). These maps and databases provide an inventory of faults that would be defined as active, capable, and potentially active for seismic-hazard assessments.

Accuracy assessment, using stratified plurality sampling, of portions of a LANDSAT classification of the Arctic National Wildlife Refuge Coastal Plain

NASA Technical Reports Server (NTRS)

Card, Don H.; Strong, Laurence L.

1989-01-01

An application of a classification accuracy assessment procedure is described for a vegetation and land cover map prepared by digital image processing of LANDSAT multispectral scanner data. A statistical sampling procedure called Stratified Plurality Sampling was used to assess the accuracy of portions of a map of the Arctic National Wildlife Refuge coastal plain. Results are tabulated as percent correct classification overall as well as per category with associated confidence intervals. Although values of percent correct were disappointingly low for most categories, the study was useful in highlighting sources of classification error and demonstrating shortcomings of the plurality sampling method.

Mapping hard magnetic recording disks by TOF-SIMS

NASA Astrophysics Data System (ADS)

Spool, A.; Forrest, J.

2008-12-01

Mapping of hard magnetic recording disks by TOF-SIMS was performed both to produce significant analytical results for the understanding of the disk surface and the head disk interface in hard disk drives, and as an example of a macroscopic non-rectangular mapping problem for the technique. In this study, maps were obtained by taking discrete samples of the disk surface at set intervals in R and Θ. Because both in manufacturing, and in the disk drive, processes that may affect the disk surface are typically circumferential in nature, changes in the surface are likely to be blurred in the Θ direction. An algorithm was developed to determine the optimum relative sampling ratio in R and Θ. The results confirm what the experience of the analysts suggested, that changes occur more rapidly on disks in the radial direction, and that more sampling in the radial direction is desired. The subsequent use of statistical methods principle component analysis (PCA), maximum auto-correlation factors (MAF), and the algorithm inverse distance weighting (IDW) are explored.

Atlas of interoccurrence intervals for selected thresholds of daily precipitation in Texas

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.

2003-01-01

A Poisson process model is used to define the distribution of interoccurrence intervals of daily precipitation in Texas. A precipitation interoccurrence interval is the time period between two successive rainfall events. Rainfall events are defined as daily precipitation equaling or exceeding a specified depth threshold. Ten precipitation thresholds are considered: 0.05, 0.10, 0.25, 0.50, 0.75, 1.0, 1.5, 2.0, 2.5, and 3.0 inches. Site-specific mean interoccurrence interval and ancillary statistics are presented for each threshold and for each of 1,306 National Weather Service daily precipitation gages. Maps depicting the spatial variation across Texas of the mean interoccurrence interval for each threshold are presented. The percent change from the statewide standard deviation of the interoccurrence intervals to the root-mean-square error ranges from a magnitude minimum of (negative) -24 to a magnitude maximum of -60 percent for the 0.05- and 2.0-inch thresholds, respectively. Because of the substantial negative percent change, the maps are considered more reliable estimators of the mean interoccurrence interval for most locations in Texas than the statewide mean values.

Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice

PubMed Central

Zeng, Yuxiang; Ji, Zhijuan; Wen, Zhihua; Liang, Yan; Yang, Changdeng

2016-01-01

Grain length is an important quantitative trait in rice (Oryza sativa L.) that influences both grain yield and exterior quality. Although many quantitative trait loci (QTLs) for grain length have been identified, it is still unclear how different alleles from different QTLs regulate grain length coordinately. To explore the mechanisms of QTL combination in the determination of grain length, five mapping populations, including two F2 populations, an F3 population, an F7 recombinant inbred line (RIL) population, and an F8 RIL population, were developed from the cross between the U.S. tropical japonica variety ‘Lemont’ and the Chinese indica variety ‘Yangdao 4’ and grown under different environmental conditions. Four QTLs (qGL-3-1, qGL-3-2, qGL-4, and qGL-7) for grain length were detected using both composite interval mapping and multiple interval mapping methods in the mapping populations. In each locus, there was an allele from one parent that increased grain length and another allele from another parent that decreased it. The eight alleles in the four QTLs were analyzed to determine whether these alleles act additively across loci, and lead to a linear relationship between the predicted breeding value of QTLs and phenotype. Linear regression analysis suggested that the combination of eight alleles determined grain length. Plants carrying more grain length-increasing alleles had longer grain length than those carrying more grain length-decreasing alleles. This trend was consistent in all five mapping populations and demonstrated the regulation of grain length by the four QTLs. Thus, these QTLs are ideal resources for modifying grain length in rice. PMID:26942914

The role of human and mouse Y chromosome genes in male infertility.

PubMed

Affara, N A; Mitchell, M J

2000-11-01

It was suggested by Ronald Fisher in 1931 that genes involved in benefit to the male (including spermatogenesis genes) would accumulate on the Y chromosome. The analysis of mouse Y chromosome deletions and the discovery of microdeletions of the human Y chromosome associated with diverse defective spermatogenic phenotypes has revealed the presence of intervals containing one or more genes controlling male germ cell differentiation. These intervals have been mapped, cloned and examined in detail for functional genes. This review discusses the genes mapping to critical spermatogenesis intervals and the evidence indicating which are the most likely candidates underlying Y-linked male infertility.

Genetic mapping and QTL analysis for body weight in Jian carp ( Cyprinus carpio var. Jian) compared with mirror carp ( Cyprinus carpio L.)

NASA Astrophysics Data System (ADS)

Gu, Ying; Lu, Cuiyun; Zhang, Xiaofeng; Li, Chao; Yu, Juhua; Sun, Xiaowen

2015-05-01

We report the genetic linkage map of Jian carp ( Cyprinus carpio var. Jian). An F1 population comprising 94 Jian carp individuals was mapped using 254 microsatellite markers. The genetic map spanned 1 381.592 cM and comprised 44 linkage groups, with an average marker distance of 6.58 cM. We identified eight quantitative trait loci (QTLs) for body weight (BW) in seven linkage groups, explaining 12.6% to 17.3% of the phenotypic variance. Comparative mapping was performed between Jian carp and mirror carp ( Cyprinus carpio L.), which both have 50 chromosomes. One hundred and ninety-eight Jian carp marker loci were found in common with the mirror carp map, with 186 (93.94%) showing synteny. All 44 Jian carp linkage groups could be one-to-one aligned to the 44 mirror carp linkage groups, mostly sharing two or more common loci. Three QTLs for BW in Jian carp were conserved in mirror carp. QTL comparison suggested that the QTL confidence interval in mirror carp was more precise than the homologous interval in Jian carp, which was contained within the QTL interval in Jian carp. The syntenic relationship and consensus QTLs between the two varieties provide a foundation for genomic research and genetic breeding in common carp.

[Comparative analysis of parameters of corrected and uncorrected QT-interval dispersion of magneto-, electrocardiography and isomagnetic maps in patients with ischemic heart disease].

PubMed

Shabalin, A V; Tret'iakova, T V; Kuznetsov, A A; Motorin, S V; Golyshev, N V

2002-01-01

To compare possibilities of magnetocardiography (MCG) and electrocardiography for assessment of regional dispersion of ventricular recovery time using parameters of corrected and uncorrected QT-interval dispersion (DQTs and DQT). Twenty three patients with class II angina pectoris including 11 patients with history of myocardial infarction (MI) and 13 practically healthy subjects. Mean DQT and DQTc were significantly higher (p<0.005) in patients than in healthy subjects according to both techniques. Values of DQT and DQTc obtained by MCG were higher in patients with history of MI compared with those without MI (p=0.006 and 0.02, respectively). There was a significant positive correlation between age and DQT and DQTc determined by electrocardiography. Mean number of T-wave dipoles was significantly higher in patients than in healthy subjects. Substantial positive correlation was found between number of T-wave dipoles on isomagnetic maps and age in both patients and healthy people. The method of MCG gave supplementary information on the state of ventricular depolarization in patients with ischemic heart disease.

A comparison of turtle sampling methods in a small lake in Standing Stone State Park, Overton County, Tennessee

USGS Publications Warehouse

Weber, A.; Layzer, James B.

2011-01-01

We used basking traps and hoop nets to sample turtles in Standing Stone Lake at 2-week intervals from May to November 2006. In alternate weeks, we conducted visual basking surveys. We collected and observed four species of turtles: spiny softshell (Apalone spinifera), northern map turtle (Graptemys geographica), pond slider (Trachernys scripta), and snapping turtle (Chelydra serpentina). Relative abundances varied greatly among sampling methods. To varying degrees, all methods were species selective. Population estimates from mark and recaptures of three species, basking counts, and hoop net catches indicated that pond sliders were the most abundant species, but northern map turtles were 8× more abundant than pond sliders in basking trap catches. We saw relatively few snapping turtles basking even though population estimates indicated they were the second most abundant species. Populations of all species were dominated by adult individuals. Sex ratios of three species differed significantly from 1:1. Visual surveys were the most efficient method for determining the presence of species, but capture methods were necessary to obtain size and sex data.

The Wavelet Element Method. Part 2; Realization and Additional Features in 2D and 3D

NASA Technical Reports Server (NTRS)

Canuto, Claudio; Tabacco, Anita; Urban, Karsten

1998-01-01

The Wavelet Element Method (WEM) provides a construction of multiresolution systems and biorthogonal wavelets on fairly general domains. These are split into subdomains that are mapped to a single reference hypercube. Tensor products of scaling functions and wavelets defined on the unit interval are used on the reference domain. By introducing appropriate matching conditions across the interelement boundaries, a globally continuous biorthogonal wavelet basis on the general domain is obtained. This construction does not uniquely define the basis functions but rather leaves some freedom for fulfilling additional features. In this paper we detail the general construction principle of the WEM to the 1D, 2D and 3D cases. We address additional features such as symmetry, vanishing moments and minimal support of the wavelet functions in each particular dimension. The construction is illustrated by using biorthogonal spline wavelets on the interval.

Correlation of Geophysical and Geotechnical Methods for Sediment Mapping in Sungai Batu, Kedah

NASA Astrophysics Data System (ADS)

Zakaria, M. T.; Taib, A.; Saidin, M. M.; Saad, R.; Muztaza, N. M.; Masnan, S. S. K.

2018-04-01

Exploration geophysics is widely used to map the subsurface characteristics of a region, to understand the underlying rock structures and spatial distribution of rock units. 2-D resistivity and seismic refraction methods were conducted in Sungai Batu locality with objective to identify and map the sediment deposit with correlation of borehole record. 2-D resistivity data was acquire using ABEM SAS4000 system with Pole-dipole array and 2.5 m minimum electrode spacing while for seismic refraction ABEM MK8 seismograph was used to record the seismic data and 5 kg sledgehammer used as a seismic source with geophones interval of 5 m spacing. The inversion model of 2-D resistivity result shows that, the resistivity values <100 Ωm was interpreted as saturated zone with while high resistivity values >500 Ωm as the hard layer for this study area. The seismic result indicates that the velocity values <2000 m/s represent as the highly-weathered soil consists of clay and sand while high velocity values >3600 m/s interpreted as the hard layer in this locality.

Association Between Serum 25-Hydroxy Vitamin D Levels and Blood Pressure Among Adolescents in Two Resource-Limited Settings in Peru

PubMed Central

Tomaino, Katherine; Romero, Karina M.; Robinson, Colin L.; Baumann, Lauren M.; Hansel, Nadia N.; Pollard, Suzanne L.; Gilman, Robert H.; Mougey, Edward; Lima, John J.

2015-01-01

INTRODUCTION Serum 25-hydroxyvitamin D (25OHD) deficiency (<50 nmol/l or 20ng/ml) has been associated with increased blood pressure (BP) in observational studies. A paucity of data on this relationship is available in Latin American or child populations. This study investigates the association between 25OHD levels and BP in adolescents at risk for vitamin D deficiency in 2 Peruvian settings. METHODS In a population-based study of 1,441 Peruvian adolescents aged 13–15 years, 1,074 (75%) provided a serum blood sample for 25OHD analysis and BP measurements. Relationships between 25OHD and BP metrics were assessed using multiple linear regressions, adjusted for anthropometrics and sociodemographic factors. RESULTS 25OHD deficiency was associated with an elevated diastolic BP (DBP) (1.09mm Hg increase, 95% confidence interval: 0.04 to 2.14; P = 0.04) compared to nondeficient adolescents. Systolic BP (SBP) trended to increase with vitamin D deficiency (1.30mm Hg increase, 95% confidence interval: −0.13 to 2.72; P = 0.08). Mean arterial pressure (MAP) was also greater in adolescents with 25OHD (1.16mm Hg increase, 95% confidence interval: 0.10 to 2.22; P = 0.03). SBP was found to demonstrate a U-shaped relationship with 25OHD, while DBP and MAP demonstrated inverse J-shaped relationships with serum 25OHD status. The association between 25OHD deficiency and BP was not different across study sites (all P ≥ 0.19). DISCUSSION Adolescents deficient in 25OHD demonstrated increased DBP and MAP and a trend toward increased SBP, when compared to nondeficient subjects. 25OHD deficiency early in life was associated with elevated BP metrics, which may predispose risk of hypertension later in adulthood. PMID:25600222

Updating flood maps efficiently using existing hydraulic models, very-high-accuracy elevation data, and a geographic information system; a pilot study on the Nisqually River, Washington

USGS Publications Warehouse

Jones, Joseph L.; Haluska, Tana L.; Kresch, David L.

2001-01-01

A method of updating flood inundation maps at a fraction of the expense of using traditional methods was piloted in Washington State as part of the U.S. Geological Survey Urban Geologic and Hydrologic Hazards Initiative. Large savings in expense may be achieved by building upon previous Flood Insurance Studies and automating the process of flood delineation with a Geographic Information System (GIS); increases in accuracy and detail result from the use of very-high-accuracy elevation data and automated delineation; and the resulting digital data sets contain valuable ancillary information such as flood depth, as well as greatly facilitating map storage and utility. The method consists of creating stage-discharge relations from the archived output of the existing hydraulic model, using these relations to create updated flood stages for recalculated flood discharges, and using a GIS to automate the map generation process. Many of the effective flood maps were created in the late 1970?s and early 1980?s, and suffer from a number of well recognized deficiencies such as out-of-date or inaccurate estimates of discharges for selected recurrence intervals, changes in basin characteristics, and relatively low quality elevation data used for flood delineation. FEMA estimates that 45 percent of effective maps are over 10 years old (FEMA, 1997). Consequently, Congress has mandated the updating and periodic review of existing maps, which have cost the Nation almost 3 billion (1997) dollars. The need to update maps and the cost of doing so were the primary motivations for piloting a more cost-effective and efficient updating method. New technologies such as Geographic Information Systems and LIDAR (Light Detection and Ranging) elevation mapping are key to improving the efficiency of flood map updating, but they also improve the accuracy, detail, and usefulness of the resulting digital flood maps. GISs produce digital maps without manual estimation of inundated areas between cross sections, and can generate working maps across a broad range of scales, for any selected area, and overlayed with easily updated cultural features. Local governments are aggressively collecting very-high-accuracy elevation data for numerous reasons; this not only lowers the cost and increases accuracy of flood maps, but also inherently boosts the level of community involvement in the mapping process. These elevation data are also ideal for hydraulic modeling, should an existing model be judged inadequate.

Analysis on bilateral hindlimb mapping in motor cortex of the rat by an intracortical microstimulation method.

PubMed

Seong, Han Yu; Cho, Ji Young; Choi, Byeong Sam; Min, Joong Kee; Kim, Yong Hwan; Roh, Sung Woo; Kim, Jeong Hoon; Jeon, Sang Ryong

2014-04-01

Intracortical microstimulation (ICMS) is a technique that was developed to derive movement representation of the motor cortex. Although rats are now commonly used in motor mapping studies, the precise characteristics of rat motor map, including symmetry and consistency across animals, and the possibility of repeated stimulation have not yet been established. We performed bilateral hindlimb mapping of motor cortex in six Sprague-Dawley rats using ICMS. ICMS was applied to the left and the right cerebral hemisphere at 0.3 mm intervals vertically and horizontally from the bregma, and any movement of the hindlimbs was noted. The majority (80%± 11%) of responses were not restricted to a single joint, which occurred simultaneously at two or three hindlimb joints. The size and shape of hindlimb motor cortex was variable among rats, but existed on the convex side of the cerebral hemisphere in all rats. The results did not show symmetry according to specific joints in each rats. Conclusively, the hindlimb representation in the rat motor cortex was conveniently mapped using ICMS, but the characteristics and inter-individual variability suggest that precise individual mapping is needed to clarify motor distribution in rats.

In Silico Genome Mismatch Scanning to Map Breast Cancer Genes in Extended Pedigrees

DTIC Science & Technology

2009-07-01

contiguous window of loci. The current graphical model is applied to both the paternal and maternal haplotypes for each observed individual. The values at... paternal and maternal haplotypes of each individual in the sample in parallel. These affect the observed genotypes shown as white squares. The states...individuals, but also, by listing the parents as zero, allows for samples of unrelated individuals as required by these methods. IntervalLDwill treat

Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

PubMed Central

Niu, Yuze; Gao, Fengtao; Zhao, Yongwei; Zhang, Jing; Sun, Jian; Shao, Changwei; Liao, Xiaolin; Wang, Lei; Tian, Yongsheng; Chen, Songlin

2012-01-01

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS. PMID:23209734

A novel candidate gene for mouse and human preaxial polydactyly with altered expression in limbs of Hemimelic extra-toes mutant mice.

PubMed

Clark, R M; Marker, P C; Kingsley, D M

2000-07-01

Polydactyly is a common malformation of vertebrate limbs. In humans a major locus for nonsyndromic pre-axial polydactyly (PPD) has been mapped previously to 7q36. The mouse Hemimelic extra-toes (Hx) mutation maps to a homologous chromosome segment and has been proposed to affect a homologous gene. To understand the molecular changes underlying PPD, we used a positional cloning approach to identify the gene or genes disrupted by the Hx mutation and a closely linked limb mutation, Hammertoe (Hm). High resolution genetic mapping identified a small candidate interval for the mouse mutations located 1.2 cM distal to the Shh locus. The nonrecombinant interval was completely cloned in bacterial artificial chromosomes and searched for genes using a combination of exon trapping, sample sequencing, and mapping of known genes. Two novel genes, Lmbr1 and Lmbr2, are entirely within the candidate interval we defined genetically. The open reading frame of both genes is intact in mutant mice, but the expression of the Lmbr1 gene is dramatically altered in developing limbs of Hx mutant mice. The correspondence between the spatial and temporal changes in Lmbr1 expression and the embryonic onset of the Hx mutant phenotype suggests that the mouse Hx mutation may be a regulatory allele of Lmbr1. The human ortholog of Lmbr1 maps within the recently described interval for human PPD, strengthening the possibility that both mouse and human limb abnormalities are due to defects in the same highly conserved gene.

A multiscale Bayesian data integration approach for mapping air dose rates around the Fukushima Daiichi Nuclear Power Plant.

PubMed

Wainwright, Haruko M; Seki, Akiyuki; Chen, Jinsong; Saito, Kimiaki

2017-02-01

This paper presents a multiscale data integration method to estimate the spatial distribution of air dose rates in the regional scale around the Fukushima Daiichi Nuclear Power Plant. We integrate various types of datasets, such as ground-based walk and car surveys, and airborne surveys, all of which have different scales, resolutions, spatial coverage, and accuracy. This method is based on geostatistics to represent spatial heterogeneous structures, and also on Bayesian hierarchical models to integrate multiscale, multi-type datasets in a consistent manner. The Bayesian method allows us to quantify the uncertainty in the estimates, and to provide the confidence intervals that are critical for robust decision-making. Although this approach is primarily data-driven, it has great flexibility to include mechanistic models for representing radiation transport or other complex correlations. We demonstrate our approach using three types of datasets collected at the same time over Fukushima City in Japan: (1) coarse-resolution airborne surveys covering the entire area, (2) car surveys along major roads, and (3) walk surveys in multiple neighborhoods. Results show that the method can successfully integrate three types of datasets and create an integrated map (including the confidence intervals) of air dose rates over the domain in high resolution. Moreover, this study provides us with various insights into the characteristics of each dataset, as well as radiocaesium distribution. In particular, the urban areas show high heterogeneity in the contaminant distribution due to human activities as well as large discrepancy among different surveys due to such heterogeneity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.

PubMed

Raghavan, Chitra; Mauleon, Ramil; Lacorte, Vanica; Jubay, Monalisa; Zaw, Hein; Bonifacio, Justine; Singh, Rakesh Kumar; Huang, B Emma; Leung, Hei

2017-06-07

Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations. Copyright © 2017 Raghavan et al.

Analysis and machine mapping of the distribution of band recoveries

USGS Publications Warehouse

Cowardin, L.M.

1977-01-01

A method of calculating distance and bearing from banding site to recovery location based on the solution of a spherical triangle is presented. X and Y distances on an ordinate grid were applied to computer plotting of recoveries on a map. The advantages and disadvantages of tables of recoveries by State or degree block, axial lines, and distance of recovery from banding site for presentation and comparison of the spatial distribution of band recoveries are discussed. A special web-shaped partition formed by concentric circles about the point of banding and great circles at 30-degree intervals through the point of banding has certain advantages over other methods. Comparison of distributions by means of a X? contingency test is illustrated. The statistic V = X?/N can be used as a measure of difference between two distributions of band recoveries and its possible use is illustrated as a measure of the degree of migrational homing.

Construction of a high-density linkage map and mapping quantitative trait loci for somatic embryogenesis using leaf petioles as explants in upland cotton (Gossypium hirsutum L.).

PubMed

Xu, Zhenzhen; Zhang, Chaojun; Ge, Xiaoyang; Wang, Ni; Zhou, Kehai; Yang, Xiaojie; Wu, Zhixia; Zhang, Xueyan; Liu, Chuanliang; Yang, Zuoren; Li, Changfeng; Liu, Kun; Yang, Zhaoen; Qian, Yuyuan; Li, Fuguang

2015-07-01

The first high-density linkage map was constructed to identify quantitative trait loci (QTLs) for somatic embryogenesis (SE) in cotton ( Gossypium hirsutum L.) using leaf petioles as explants. Cotton transformation is highly limited by only a few regenerable genotypes and the lack of understanding of the genetic and molecular basis of somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.). To construct a more saturated linkage map and further identify quantitative trait loci (QTLs) for SE using leaf petioles as explants, a high embryogenesis frequency line (W10) from the commercial Chinese cotton cultivar CRI24 was crossed with TM-1, a genetic standard upland cotton with no embryogenesis frequency. The genetic map spanned 2300.41 cM in genetic distance and contained 411 polymorphic simple sequence repeat (SSR) loci. Of the 411 mapped loci, 25 were developed from unigenes identified for SE in our previous study. Six QTLs for SE were detected by composite interval mapping method, each explaining 6.88-37.07% of the phenotypic variance. Single marker analysis was also performed to verify the reliability of QTLs detection, and the SSR markers NAU3325 and DPL0209 were detected by the two methods. Further studies on the relatively stable and anchoring QTLs/markers for SE in an advanced population of W10 × TM-1 and other cross combinations with different SE abilities may shed light on the genetic and molecular mechanism of SE in cotton.

Decoding fMRI events in sensorimotor motor network using sparse paradigm free mapping and activation likelihood estimates.

PubMed

Tan, Francisca M; Caballero-Gaudes, César; Mullinger, Karen J; Cho, Siu-Yeung; Zhang, Yaping; Dryden, Ian L; Francis, Susan T; Gowland, Penny A

2017-11-01

Most functional MRI (fMRI) studies map task-driven brain activity using a block or event-related paradigm. Sparse paradigm free mapping (SPFM) can detect the onset and spatial distribution of BOLD events in the brain without prior timing information, but relating the detected events to brain function remains a challenge. In this study, we developed a decoding method for SPFM using a coordinate-based meta-analysis method of activation likelihood estimation (ALE). We defined meta-maps of statistically significant ALE values that correspond to types of events and calculated a summation overlap between the normalized meta-maps and SPFM maps. As a proof of concept, this framework was applied to relate SPFM-detected events in the sensorimotor network (SMN) to six motor functions (left/right fingers, left/right toes, swallowing, and eye blinks). We validated the framework using simultaneous electromyography (EMG)-fMRI experiments and motor tasks with short and long duration, and random interstimulus interval. The decoding scores were considerably lower for eye movements relative to other movement types tested. The average successful rate for short and long motor events were 77 ± 13% and 74 ± 16%, respectively, excluding eye movements. We found good agreement between the decoding results and EMG for most events and subjects, with a range in sensitivity between 55% and 100%, excluding eye movements. The proposed method was then used to classify the movement types of spontaneous single-trial events in the SMN during resting state, which produced an average successful rate of 22 ± 12%. Finally, this article discusses methodological implications and improvements to increase the decoding performance. Hum Brain Mapp 38:5778-5794, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Decoding fMRI events in Sensorimotor Motor Network using Sparse Paradigm Free Mapping and Activation Likelihood Estimates

PubMed Central

Tan, Francisca M.; Caballero-Gaudes, César; Mullinger, Karen J.; Cho, Siu-Yeung; Zhang, Yaping; Dryden, Ian L.; Francis, Susan T.; Gowland, Penny A.

2017-01-01

Most fMRI studies map task-driven brain activity using a block or event-related paradigm. Sparse Paradigm Free Mapping (SPFM) can detect the onset and spatial distribution of BOLD events in the brain without prior timing information; but relating the detected events to brain function remains a challenge. In this study, we developed a decoding method for SPFM using a coordinate-based meta-analysis method of Activation Likelihood Estimation (ALE). We defined meta-maps of statistically significant ALE values that correspond to types of events and calculated a summation overlap between the normalized meta-maps and SPFM maps. As a proof of concept, this framework was applied to relate SPFM-detected events in the Sensorimotor Network (SMN) to six motor function (left/right fingers, left/right toes, swallowing and eye blinks). We validated the framework using simultaneous Electromyography-fMRI experiments and motor tasks with short and long duration, and random inter-stimulus interval. The decoding scores were considerably lower for eye movements relative to other movement types tested. The average successful rate for short and long motor events was 77 ± 13% and 74 ± 16% respectively, excluding eye movements. We found good agreement between the decoding results and EMG for most events and subjects, with a range in sensitivity between 55 and 100%, excluding eye movements. The proposed method was then used to classify the movement types of spontaneous single-trial events in the SMN during resting state, which produced an average successful rate of 22 ± 12%. Finally, this paper discusses methodological implications and improvements to increase the decoding performance. PMID:28815863

Optical mapping and its potential for large-scale sequencing projects.

PubMed

Aston, C; Mishra, B; Schwartz, D C

1999-07-01

Physical mapping has been rediscovered as an important component of large-scale sequencing projects. Restriction maps provide landmark sequences at defined intervals, and high-resolution restriction maps can be assembled from ensembles of single molecules by optical means. Such optical maps can be constructed from both large-insert clones and genomic DNA, and are used as a scaffold for accurately aligning sequence contigs generated by shotgun sequencing.

Adaptive wavelet collocation methods for initial value boundary problems of nonlinear PDE's

NASA Technical Reports Server (NTRS)

Cai, Wei; Wang, Jian-Zhong

1993-01-01

We have designed a cubic spline wavelet decomposition for the Sobolev space H(sup 2)(sub 0)(I) where I is a bounded interval. Based on a special 'point-wise orthogonality' of the wavelet basis functions, a fast Discrete Wavelet Transform (DWT) is constructed. This DWT transform will map discrete samples of a function to its wavelet expansion coefficients in O(N log N) operations. Using this transform, we propose a collocation method for the initial value boundary problem of nonlinear PDE's. Then, we test the efficiency of the DWT transform and apply the collocation method to solve linear and nonlinear PDE's.

Spatial point analysis based on dengue surveys at household level in central Brazil

PubMed Central

Siqueira-Junior, João B; Maciel, Ivan J; Barcellos, Christovam; Souza, Wayner V; Carvalho, Marilia S; Nascimento, Nazareth E; Oliveira, Renato M; Morais-Neto, Otaliba; Martelli, Celina MT

2008-01-01

Background Dengue virus (DENV) affects nonimunne human populations in tropical and subtropical regions. In the Americas, dengue has drastically increased in the last two decades and Brazil is considered one of the most affected countries. The high frequency of asymptomatic infection makes difficult to estimate prevalence of infection using registered cases and to locate high risk intra-urban area at population level. The goal of this spatial point analysis was to identify potential high-risk intra-urban areas of dengue, using data collected at household level from surveys. Methods Two household surveys took place in the city of Goiania (~1.1 million population), Central Brazil in the year 2001 and 2002. First survey screened 1,586 asymptomatic individuals older than 5 years of age. Second survey 2,906 asymptomatic volunteers, same age-groups, were selected by multistage sampling (census tracts; blocks; households) using available digital maps. Sera from participants were tested by dengue virus-specific IgM/IgG by EIA. A Generalized Additive Model (GAM) was used to detect the spatial varying risk over the region. Initially without any fixed covariates, to depict the overall risk map, followed by a model including the main covariates and the year, where the resulting maps show the risk associated with living place, controlled for the individual risk factors. This method has the advantage to generate smoothed risk factors maps, adjusted by socio-demographic covariates. Results The prevalence of antibody against dengue infection was 37.3% (95%CI [35.5–39.1]) in the year 2002; 7.8% increase in one-year interval. The spatial variation in risk of dengue infection significantly changed when comparing 2001 with 2002, (ORadjusted = 1.35; p < 0.001), while controlling for potential confounders using GAM model. Also increasing age and low education levels were associated with dengue infection. Conclusion This study showed spatial heterogeneity in the risk areas of dengue when using a spatial multivariate approach in a short time interval. Data from household surveys pointed out that low prevalence areas in 2001 surveys shifted to high-risk area in consecutive year. This mapping of dengue risks should give insights for control interventions in urban areas. PMID:18937868

Water-Level and land-subsidence studies in the Mojave River and Morongo groundwater basins

USGS Publications Warehouse

Stamos, Christina L.; Glockhoff, Carolyn S.; McPherson, Kelly R.; Julich, Raymond J.

2007-01-01

What's New! Water-level data, contours, and meta data for spring 2008 are included in Version 2.0 of SIR 2007-5097 (http://ca.water.usgs.gov/mojave/wl_studies/wl2008.html). All the original data are still available on the web site. Introduction Since 1992, the U.S. Geological Survey (USGS), in cooperation with the Mojave Water Agency (MWA), has constructed a series of regional water-table maps for intermittent years in a continuing effort to monitor groundwater conditions in the Mojave River and Morongo groundwater basins. The previously published data, which were used to construct these maps, can be accessed on the interactive map. The associated reports describing the groundwater conditions for the Mojave River groundwater basin for 1992 (Stamos and Predmore, 1995), the Morongo groundwater basin for 1994 (Trayler and Koczot, 1995), and for both groundwater basins for 1996 (Mendez and Christensen, 1997); for 1998 (Smith and Pimentel, 2000), for 2000 (Smith, 2002), for 2002 (Smith and others, 2004), for 2004 (Stamos and others, 2004), and for 2006 (Stamos and others, 2007) can be accessed using this web site. Spatially detailed maps of interferometric synthetic aperture radar (InSAR) methods were used to characterize land subsidence associated with groundwater-level declines during various intervals of time between 1992 and 1999 in the Mojave River and Morongo groundwater basins (Sneed and others, 2003). Concerns related to the potential for new or renewed land subsidence in the basins resulted in a cooperative study between the MWA and the USGS in 2006. InSAR data were developed to determine the location, extent, and magnitude of vertical land-surface changes in the Mojave River and Morongo groundwater basins for time intervals ranging from about 35 days to 14 months between 1999 and 2000 and between 2003 and 2004. (interactive Google map) The results from many future land-subsidence studies, which are scheduled about every 10 years, will be available on this website. Mapping of water-level contours, water-level change and numerous InSAR images were combined in an interactive map. This interactive map may be customized to your needs and viewed at a scale that is appropriate for the data.

Comparing the performance of various digital soil mapping approaches to map physical soil properties

NASA Astrophysics Data System (ADS)

Laborczi, Annamária; Takács, Katalin; Pásztor, László

2015-04-01

Spatial information on physical soil properties is intensely expected, in order to support environmental related and land use management decisions. One of the most widely used properties to characterize soils physically is particle size distribution (PSD), which determines soil water management and cultivability. According to their size, different particles can be categorized as clay, silt, or sand. The size intervals are defined by national or international textural classification systems. The relative percentage of sand, silt, and clay in the soil constitutes textural classes, which are also specified miscellaneously in various national and/or specialty systems. The most commonly used is the classification system of the United States Department of Agriculture (USDA). Soil texture information is essential input data in meteorological, hydrological and agricultural prediction modelling. Although Hungary has a great deal of legacy soil maps and other relevant soil information, it often occurs, that maps do not exist on a certain characteristic with the required thematic and/or spatial representation. The recent developments in digital soil mapping (DSM), however, provide wide opportunities for the elaboration of object specific soil maps (OSSM) with predefined parameters (resolution, accuracy, reliability etc.). Due to the simultaneous richness of available Hungarian legacy soil data, spatial inference methods and auxiliary environmental information, there is a high versatility of possible approaches for the compilation of a given soil map. This suggests the opportunity of optimization. For the creation of an OSSM one might intend to identify the optimum set of soil data, method and auxiliary co-variables optimized for the resources (data costs, computation requirements etc.). We started comprehensive analysis of the effects of the various DSM components on the accuracy of the output maps on pilot areas. The aim of this study is to compare and evaluate different digital soil mapping methods and sets of ancillary variables for producing the most accurate spatial prediction of texture classes in a given area of interest. Both legacy and recently collected data on PSD were used as reference information. The predictor variable data set consisted of digital elevation model and its derivatives, lithology, land use maps as well as various bands and indices of satellite images. Two conceptionally different approaches can be applied in the mapping process. Textural classification can be realized after particle size data were spatially extended by proper geostatistical method. Alternatively, the textural classification is carried out first, followed by the spatial extension through suitable data mining method. According to the first approach, maps of sand, silt and clay percentage have been computed through regression kriging (RK). Since the three maps are compositional (their sum must be 100%), we applied Additive Log-Ratio (alr) transformation, instead of kriging them independently. Finally, the texture class map has been compiled according to the USDA categories from the three maps. Different combinations of reference and training soil data and auxiliary covariables resulted several different maps. On the basis of the other way, the PSD were classified firstly into the USDA categories, then the texture class maps were compiled directly by data mining methods (classification trees and random forests). The various results were compared to each other as well as to the RK maps. The performance of the different methods and data sets has been examined by testing the accuracy of the geostatistically computed and the directly classified results to assess the most predictive and accurate method. Acknowledgement: Our work was supported by the Hungarian National Scientific Research Foundation (OTKA, Grant No. K105167).

High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

PubMed

Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

2016-06-01

The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

Cognitive ergonomics: the use of mind mapping tool in maintaining productive sector of a Brazilian paper company.

PubMed

Mattos, Diego; Mateus, José Roberto; Merino, Eugenio

2012-01-01

The use of mind maps as a method of building knowledge, planning, organizing activities and ideas can be seen in the literature related to ergonomics. The results of such use are relevant and its use in academic area found. However, regarding to its use in industrial environments, studies can't not be found. With this scenario, and based on the perception of the ergonomist about the importance of using methods such as mind maps in support of human cognition, it seems pertinent to its use in industry sectors whose cognitive demand requires. Given these assumptions, this study aimed to apply the method of Mind Maps in Productive Maintenance sector of a Brazilian paper. The Productive Maintenance sector in the Paper Industry has an important contribution to operational performance. With practical Predictive Maintenance, Preventive Maintenance and Corrective Maintenance, the industry advocates to make the machines to produce paper is not to stop producing when they are programmed to do so. Among the practices cited, the Preventive Maintenance is one that leads to pre-determined intervals in order to reduce the possibility of placing the equipment in a condition below the required level of acceptance. Therefore, this article aims to propose using the tool "mental maps" in order to collaborate in planning and implementation of preventive maintenance activities in the sector of mechanical maintenance of a pulp and paper industry in southern Brazil. The study investigated the maintenance sector through its employees, who went through training about the tool and then use it and ergonomists company.

HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics.

PubMed

Zheng, Jie; Rodriguez, Santiago; Laurin, Charles; Baird, Denis; Trela-Larsen, Lea; Erzurumluoglu, Mesut A; Zheng, Yi; White, Jon; Giambartolomei, Claudia; Zabaneh, Delilah; Morris, Richard; Kumari, Meena; Casas, Juan P; Hingorani, Aroon D; Evans, David M; Gaunt, Tom R; Day, Ian N M

2017-01-01

Fine mapping is a widely used approach for identifying the causal variant(s) at disease-associated loci. Standard methods (e.g. multiple regression) require individual level genotypes. Recent fine mapping methods using summary-level data require the pairwise correlation coefficients ([Formula: see text]) of the variants. However, haplotypes rather than pairwise [Formula: see text], are the true biological representation of linkage disequilibrium (LD) among multiple loci. In this article, we present an empirical iterative method, HAPlotype Regional Association analysis Program (HAPRAP), that enables fine mapping using summary statistics and haplotype information from an individual-level reference panel. Simulations with individual-level genotypes show that the results of HAPRAP and multiple regression are highly consistent. In simulation with summary-level data, we demonstrate that HAPRAP is less sensitive to poor LD estimates. In a parametric simulation using Genetic Investigation of ANthropometric Traits height data, HAPRAP performs well with a small training sample size (N < 2000) while other methods become suboptimal. Moreover, HAPRAP's performance is not affected substantially by single nucleotide polymorphisms (SNPs) with low minor allele frequencies. We applied the method to existing quantitative trait and binary outcome meta-analyses (human height, QTc interval and gallbladder disease); all previous reported association signals were replicated and two additional variants were independently associated with human height. Due to the growing availability of summary level data, the value of HAPRAP is likely to increase markedly for future analyses (e.g. functional prediction and identification of instruments for Mendelian randomization). The HAPRAP package and documentation are available at http://apps.biocompute.org.uk/haprap/ CONTACT: : jie.zheng@bristol.ac.uk or tom.gaunt@bristol.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Uncertainty Analysis in Large Area Aboveground Biomass Mapping

NASA Astrophysics Data System (ADS)

Baccini, A.; Carvalho, L.; Dubayah, R.; Goetz, S. J.; Friedl, M. A.

2011-12-01

Satellite and aircraft-based remote sensing observations are being more frequently used to generate spatially explicit estimates of aboveground carbon stock of forest ecosystems. Because deforestation and forest degradation account for circa 10% of anthropogenic carbon emissions to the atmosphere, policy mechanisms are increasingly recognized as a low-cost mitigation option to reduce carbon emission. They are, however, contingent upon the capacity to accurately measures carbon stored in the forests. Here we examine the sources of uncertainty and error propagation in generating maps of aboveground biomass. We focus on characterizing uncertainties associated with maps at the pixel and spatially aggregated national scales. We pursue three strategies to describe the error and uncertainty properties of aboveground biomass maps, including: (1) model-based assessment using confidence intervals derived from linear regression methods; (2) data-mining algorithms such as regression trees and ensembles of these; (3) empirical assessments using independently collected data sets.. The latter effort explores error propagation using field data acquired within satellite-based lidar (GLAS) acquisitions versus alternative in situ methods that rely upon field measurements that have not been systematically collected for this purpose (e.g. from forest inventory data sets). A key goal of our effort is to provide multi-level characterizations that provide both pixel and biome-level estimates of uncertainties at different scales.

Short communication: Evaluation of sampling socks for detection of Mycobacterium avium ssp. paratuberculosis on dairy farms.

PubMed

Wolf, R; Orsel, K; De Buck, J; Kanevets, U; Barkema, H W

2016-04-01

Mycobacterium avium ssp. paratuberculosis (MAP) causes Johne's disease, a production-limiting disease in cattle. Detection of infected herds is often done using environmental samples (ES) of manure, which are collected in cattle pens and manure storage areas. Disadvantages of the method are that sample accuracy is affected by cattle housing and type of manure storage area. Furthermore, some sampling locations (e.g., manure lagoons) are frequently not readily accessible. However, sampling socks (SO), as used for Salmonella spp. testing in chicken flocks, might be an easy to use and accurate alternative to ES. The objective of the study was to assess accuracy of SO for detection of MAP in dairy herds. At each of 102 participating herds, 6 ES and 2 SO were collected. In total, 45 herds had only negative samples in both methods and 29 herds had ≥1 positive ES and ≥1 positive SO. Furthermore, 27 herds with ≥1 positive ES had no positive SO, and 1 herd with no positive ES had 1 positive SO. Bayesian simulation with informative priors on sensitivity of ES and MAP herd prevalence provided a posterior sensitivity for SO of 43.5% (95% probability interval=33-58), and 78.5% (95% probability interval=62-93) for ES. Although SO were easy to use, accuracy was lower than for ES. Therefore, with improvements in the sampling protocol (e.g., more SO per farm and more frequent herd visits), as well as improvements in the laboratory protocol, perhaps SO would be a useful alternative for ES. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

General Approach for Rock Classification Based on Digital Image Analysis of Electrical Borehole Wall Images

NASA Astrophysics Data System (ADS)

Linek, M.; Jungmann, M.; Berlage, T.; Clauser, C.

2005-12-01

Within the Ocean Drilling Program (ODP), image logging tools have been routinely deployed such as the Formation MicroScanner (FMS) or the Resistivity-At-Bit (RAB) tools. Both logging methods are based on resistivity measurements at the borehole wall and therefore are sensitive to conductivity contrasts, which are mapped in color scale images. These images are commonly used to study the structure of the sedimentary rocks and the oceanic crust (petrologic fabric, fractures, veins, etc.). So far, mapping of lithology from electrical images is purely based on visual inspection and subjective interpretation. We apply digital image analysis on electrical borehole wall images in order to develop a method, which augments objective rock identification. We focus on supervised textural pattern recognition which studies the spatial gray level distribution with respect to certain rock types. FMS image intervals of rock classes known from core data are taken in order to train textural characteristics for each class. A so-called gray level co-occurrence matrix is computed by counting the occurrence of a pair of gray levels that are a certain distant apart. Once the matrix for an image interval is computed, we calculate the image contrast, homogeneity, energy, and entropy. We assign characteristic textural features to different rock types by reducing the image information into a small set of descriptive features. Once a discriminating set of texture features for each rock type is found, we are able to discriminate the entire FMS images regarding the trained rock type classification. A rock classification based on texture features enables quantitative lithology mapping and is characterized by a high repeatability, in contrast to a purely visual subjective image interpretation. We show examples for the rock classification between breccias, pillows, massive units, and horizontally bedded tuffs based on ODP image data.

Fine Mapping of Resistance Genes from Five Brown Stem Rot Resistance Sources in Soybean.

PubMed

Rincker, Keith; Hartman, Glen L; Diers, Brian W

2016-03-01

Brown stem rot (BSR) of soybean [ (L.) Merr.] caused by (Allington & Chamb.) T.C. Harr. & McNew can be controlled effectively with genetic host resistance. Three BSR resistance genes , , and , have been identified and mapped to a large region on chromosome 16. Marker-assisted selection (MAS) will be more efficient and gene cloning will be facilitated with a narrowed genomic interval containing an gene. The objective of this study was to fine map the positions of genes from five sources. Mapping populations were developed by crossing the resistant sources 'Bell', PI 84946-2, PI 437833, PI 437970, L84-5873, and PI 86150 with either the susceptible cultivar Colfax or Century 84. Plants identified as having a recombination event near genes were selected and individually harvested to create recombinant lines. Progeny from recombinant lines were tested in a root-dip assay and evaluated for foliar and stem BSR symptom development. Overall, 4878 plants were screened for recombination, and progeny from 52 recombinant plants were evaluated with simple-sequence repeat (SSR) genetic markers and assessed for symptom development. Brown stem rot resistance was mapped to intervals ranging from 0.34 to 0.04 Mb in the different sources. In all sources, resistance was fine mapped to intervals inclusive of BARCSOYSSR_16_1114 and BARCSOYSSR_16_1115, which provides further evidence that one locus provides BSR resistance in soybean. Copyright © 2016 Crop Science Society of America.

Rapid estimation of aquifer salinity structure from oil and gas geophysical logs

NASA Astrophysics Data System (ADS)

Shimabukuro, D.; Stephens, M.; Ducart, A.; Skinner, S. M.

2016-12-01

We describe a workflow for creating aquifer salinity maps using Archie's equation for areas that have geophysical data from oil and gas wells. We apply this method in California, where geophysical logs are available in raster format from the Division of Oil, Gas, and Geothermal Resource (DOGGR) online archive. This method should be applicable to any region where geophysical logs are readily available. Much of the work is controlled by computer code, allowing salinity estimates for new areas to be rapidly generated. For a region of interest, the DOGGR online database is scraped for wells that were logged with multi-tool suites, such as the Platform Express or Triple Combination Logging Tools. Then, well construction metadata, such as measured depth, spud date, and well orientation, is attached. The resultant local database allows a weighted criteria selection of wells that are most likely to have the shallow resistivity, deep resistivity, and density porosity measurements necessary to calculate salinity over the longest depth interval. The algorithm can be adjusted for geophysical log availability for older well fields and density of sampling. Once priority wells are identified, a student researcher team uses Neuralog software to digitize the raster geophysical logs. Total dissolved solid (TDS) concentration is then calculated in clean, wet sand intervals using the resistivity-porosity method, a modified form of Archie's equation. These sand intervals are automatically selected using a combination of spontaneous potential and the difference in shallow resistivity and deep resistivity measurements. Gamma ray logs are not used because arkosic sands common in California make it difficult to distinguish sand and shale. Computer calculation allows easy adjustment of Archie's parameters. The result is a semi-continuous TDS profile for the wells of interest. These profiles are combined and contoured using standard 3-d visualization software to yield preliminary salinity maps for the region of interest. We present results for select well fields in the Southern San Joaquin Valley, California.

Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep

PubMed Central

2010-01-01

Background The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (Ovis aries) to construct a linkage map for bighorn sheep, Ovis canadensis. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species. Results Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals. Conclusions We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of Ovis species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related Ovis species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and recombination rates of domesticated species. PMID:20920197

Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve

NASA Astrophysics Data System (ADS)

Shi, Yaohua; Guo, Ximing; Gu, Zhifeng; Wang, Aimin; Wang, Yan

2010-05-01

Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio ( P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.

Systematic search for wide periodic windows and bounds for the set of regular parameters for the quadratic map.

PubMed

Galias, Zbigniew

2017-05-01

An efficient method to find positions of periodic windows for the quadratic map f(x)=ax(1-x) and a heuristic algorithm to locate the majority of wide periodic windows are proposed. Accurate rigorous bounds of positions of all periodic windows with periods below 37 and the majority of wide periodic windows with longer periods are found. Based on these results, we prove that the measure of the set of regular parameters in the interval [3,4] is above 0.613960137. The properties of periodic windows are studied numerically. The results of the analysis are used to estimate that the true value of the measure of the set of regular parameters is close to 0.6139603.

Estimation of Flood Discharges at Selected Recurrence Intervals for Streams in New Hampshire

USGS Publications Warehouse

Olson, Scott A.

2009-01-01

This report provides estimates of flood discharges at selected recurrence intervals for streamgages in and adjacent to New Hampshire and equations for estimating flood discharges at recurrence intervals of 2-, 5-, 10-, 25-, 50-, 100-, and 500-years for ungaged, unregulated, rural streams in New Hampshire. The equations were developed using generalized least-squares regression. Flood-frequency and drainage-basin characteristics from 117 streamgages were used in developing the equations. The drainage-basin characteristics used as explanatory variables in the regression equations include drainage area, mean April precipitation, percentage of wetland area, and main channel slope. The average standard error of prediction for estimating the 2-, 5-, 10-, 25-, 50-, 100-, and 500-year recurrence interval flood discharges with these equations are 30.0, 30.8, 32.0, 34.2, 36.0, 38.1, and 43.4 percent, respectively. Flood discharges at selected recurrence intervals for selected streamgages were computed following the guidelines in Bulletin 17B of the U.S. Interagency Advisory Committee on Water Data. To determine the flood-discharge exceedence probabilities at streamgages in New Hampshire, a new generalized skew coefficient map covering the State was developed. The standard error of the data on new map is 0.298. To improve estimates of flood discharges at selected recurrence intervals for 20 streamgages with short-term records (10 to 15 years), record extension using the two-station comparison technique was applied. The two-station comparison method uses data from a streamgage with long-term record to adjust the frequency characteristics at a streamgage with a short-term record. A technique for adjusting a flood-discharge frequency curve computed from a streamgage record with results from the regression equations is described in this report. Also, a technique is described for estimating flood discharge at a selected recurrence interval for an ungaged site upstream or downstream from a streamgage using a drainage-area adjustment. The final regression equations and the flood-discharge frequency data used in this study will be available in StreamStats. StreamStats is a World Wide Web application providing automated regression-equation solutions for user-selected sites on streams.

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

PubMed Central

Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement. PMID:25942004

DAM - detection and mapping

NASA Technical Reports Server (NTRS)

1977-01-01

Integrated set of manual procedures, computer programs, and graphic devices processes multispectral scanner data from orbiting Landsat into precisely registered and formatted maps of surface water and other resources at variety of scales, sheet formats, and tick intervals.

A population of deletion mutants and an integrated mapping and Exome-seq pipeline for gene discovery in maize

USDA-ARS?s Scientific Manuscript database

To better understand maize endosperm filling and maturation, we developed a novel functional genomics platform that combined Bulked Segregant RNA and Exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. Using gamma-irradiation of B73 maize to...

The effects of intravenous anesthetics on QT interval during anesthetic induction with sevoflurane.

PubMed

Terao, Yoshiaki; Higashijima, Ushio; Toyoda, Tomomi; Ichinomiya, Taiga; Fukusaki, Makoto; Hara, Tetsuya

2016-12-01

Sevoflurane is known to prolong the QT interval. This study aimed to determine the effect of the interaction between intravenous anesthetics and sevoflurane on the QT interval. The study included 48 patients who underwent lumbar spine surgery. Patients received 3 μg/kg fentanyl and were then randomly allocated to either Group T, in which they received 5 mg/kg thiamylal, or Group P, in which they received 1.5 mg/kg propofol, at 2 min after administration of fentanyl injection for anesthetic induction. Vecuronium (1.5 mg/kg) and sevoflurane (3 % inhaled concentration) were administered immediately after loss of consciousness and tracheal intubation was performed 3 min after vecuronium injection. Heart rate (HR), mean arterial pressure (MAP), bispectral index score (BIS), and the heart rate-corrected QT (QTc) interval on a 12-lead electrocardiogram were recorded immediately before fentanyl administration (T1), 2 min after fentanyl injection (T2), immediately before intubation (T3), and 2 min after intubation (T4). There were no significant differences between the two groups in baseline patient characteristics. BIS and MAP significantly decreased after anesthesia induction in both groups. At T3, MAP in Group T was higher than in Group P, while HR had reduced in both groups. The QTc interval was prolonged after anesthesia induction in Group T, but did not change at any time point in Group P. The QTc interval after anesthesia induction in Group T was longer than in Group P. We concluded that an injection of propofol could counteract QTc interval prolongation associated with sevoflurane anesthesia induction.

Shaded seafloor relief, backscatter strength, and surficial geology; German Bank, Scotian Shelf, offshore Nova Scotia

USGS Publications Warehouse

Todd, B.J.; Valentine, Page C.

2010-01-01

This map is part of a three-map series of German Bank, located on the Scotian Shelf off southern Nova Scotia.  This map is the product of a number of surveys (1997-2003) that used a multibeam sonar system to map 5321 km2 of the seafloor.  Other surveys collected geological data for scientific interpretation.  This map sheet shows the seafloor topography of German Bank in shaded-relief view and seafloor depth (coded by colour) at a scale of 1:1000,000.  Topographic contours generated from the multibeam data are shown (in white) on the colour-coded multibeam topography at a depth interval of 20 m.  Bathymetic contours (in blue) outside the multibeam survey area, presented at a depth interval of 10 m, are from the Natural Resource Map series (Canadian Hydrographic Service, 1967, 1971a, 1971b, 1972). Sheet 2 shows coloured backscatter strength in shaded-relief view.  Sheet 3 shows seafloor topography in shaded-relief view with colour-coded surficial geological units.

A candidate region for Nevoid Basal Cell Carcinoma Syndrome defined by genetic and physical mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wainwright, B.; Negus, K.; Berkman, J.

1994-09-01

Nevoid Basal Cell Carcinoma Syndrome (NBCCS, or Gorlin`s syndrome) is a cancer predisposition syndrome charcterized by multiple basal cell carcinomas (BCCs) and diverse developmental defects. The gene responsible for NBCCS, which is most likely to be a tumor suppressor gene, has previously been mapped to 9q22.3-q31 in a 12 cM interval between the microsatellite marker loci D9S12 and D9S109. Combined multipoint and haplotype analyses of Australian pedigrees has further refined the localization to a 2 cM interval between markers D9S196 and D9S180. Our loss of heterozygosity (LOH) studies from sporadic (n= 58) and familial (n=41) BCCs indicate that 50% havemore » deletions within the NBCCS candidate region. All LOH is consistent with the genetic mapping of the NBCCS locus. Additionally, one sporadic tumor indicates that the smallest region of overlap in the deletions is within the interval D9S287 (proximal) and D9S180 (distal). A series of YAC clones from within this region has been mapped by FISH to examine chimerism. These clones, which have been mapped with respect to one another, form a contig which encompasses the candidate region from D9S196 to D9S180.« less

Characterization of a Thermo-Inducible Chlorophyll-Deficient Mutant in Barley.

PubMed

Wang, Rong; Yang, Fei; Zhang, Xiao-Qi; Wu, Dianxin; Tan, Cong; Westcott, Sharon; Broughton, Sue; Li, Chengdao; Zhang, Wenying; Xu, Yanhao

2017-01-01

Leaf color is an important trait for not only controlling crop yield but also monitoring plant status under temperature stress. In this study, a thermo-inducible chlorophyll-deficient mutant, named V-V-Y, was identified from a gamma-radiated population of the barley variety Vlamingh. The leaves of the mutant were green under normal growing temperature but turned yellowish under high temperature in the glasshouse experiment. The ratio of chlorophyll a and chlorophyll b in the mutant declined much faster in the first 7-9 days under heat treatment. The leaves of V-V-Y turned yellowish but took longer to senesce under heat stress in the field experiment. Genetic analysis indicated that a single nuclear gene controlled the mutant trait. The mutant gene ( vvy ) was mapped to the long arm of chromosome 4H between SNP markers 1_0269 and 1_1531 with a genetic distance of 2.2 cM and a physical interval of 9.85 Mb. A QTL for grain yield was mapped to the same interval and explained 10.4% of the yield variation with a LOD score of 4. This QTL is coincident with the vvy gene interval that is responsible for the thermo-inducible chlorophyll-deficient trait. Fine mapping, based on the barley reference genome sequence, further narrowed the vvy gene to a physical interval of 0.428 Mb with 11 annotated genes. This is the first report of fine mapping a thermo-inducible chlorophyll-deficient gene in barley.

fMRI Mapping of Brain Activity Associated with the Vocal Production of Consonant and Dissonant Intervals.

PubMed

González-García, Nadia; Rendón, Pablo L

2017-05-23

The neural correlates of consonance and dissonance perception have been widely studied, but not the neural correlates of consonance and dissonance production. The most straightforward manner of musical production is singing, but, from an imaging perspective, it still presents more challenges than listening because it involves motor activity. The accurate singing of musical intervals requires integration between auditory feedback processing and vocal motor control in order to correctly produce each note. This protocol presents a method that permits the monitoring of neural activations associated with the vocal production of consonant and dissonant intervals. Four musical intervals, two consonant and two dissonant, are used as stimuli, both for an auditory discrimination test and a task that involves first listening to and then reproducing given intervals. Participants, all female vocal students at the conservatory level, were studied using functional Magnetic Resonance Imaging (fMRI) during the performance of the singing task, with the listening task serving as a control condition. In this manner, the activity of both the motor and auditory systems was observed, and a measure of vocal accuracy during the singing task was also obtained. Thus, the protocol can also be used to track activations associated with singing different types of intervals or with singing the required notes more accurately. The results indicate that singing dissonant intervals requires greater participation of the neural mechanisms responsible for the integration of external feedback from the auditory and sensorimotor systems than does singing consonant intervals.

Magmatic Mapping: A Suggested Methodology And Results From The Springerville Volcanic Field, East-Central Arizona, USA

NASA Astrophysics Data System (ADS)

Mnich, M.; Condit, C.

2016-12-01

The Springerville Volcanic Field (SVF), located in east-central Arizona, is one of the best-characterized basaltic monogenetic volcanic fields in the world, with it's expanse of over 3000 km2 now mapped in it's entirety as a result of recent efforts in 2010 and 2011. The methods used, called "magmatic mapping" (Condit, 2007), provide a standardized, volcanic unit focused approach to characterizing volcanic fields. This approach focuses on delineating contacts between flows, completely characterizing each flow, and placing them into a temporal framework. Results of magmatic mapping in the SVF now provide a comprehensive overview of the lifespan of the field, representing a unique resource, useful not only in studying the petrogenetic evolution of this field, but in serving as a template for comparing similar volcanic fields. On Earth, several fields pose a significant risk to population centers, though these hazards are often poorly understood due to long intervals between eruptions. On other planets, remote mapping can be greatly enhanced by comparing it with a well-studied terrestrial analog that has been analyzed in detail; an area with ever heightening necessity as high-resolution data is becoming increasingly available. In the SVF, olivine phyric lavas are most abundance (22% of volcanic outcrop), followed by diktytaxitic and olivine/plagioclase phyric flows. However, lithology will vary depending on when an eruption takes place in a volcanic fields lifecycle. On the whole, the SVF is younger to the east and younger lavas are dominantly more alkalic. These trends are also displayed within individual geographic divisions, many of which correspond to temporal-geographic clusters as defined by Condit and Connor (1996). The mapping methods and patterns in geochemistry, lithology and age progression within the SVF represent a unique template for which to base basaltic mapping.

Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

NASA Astrophysics Data System (ADS)

Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition, we can obtain temporal dynamics (mpeg- files) of the main oscillation characteristics: amplitude, power and phase as a spatial-temporal coordinates. For periodogram mapping of data cubes as a method for the pre-analysis, we developed preparation of the color maps where the pixel's colour corresponds to the frequency of the power spectrum maximum. The computer system based on applications ION-scripts, algorithmic languages IDL and PHP, and Apache WEB server. The IDL ION-scripts use for preparation and configuration of network requests at the central data server with subsequent connection to IDL run-unit software and graphic output on FTP-server and screen. Web page is constructed using PHP language.

Shallow Vs Structure Accross Hayward Fault Zone Inferred from Multichannel Analysis of Surface Waves (MASW)

NASA Astrophysics Data System (ADS)

Chan, J. H.; Richardson, I. S.; Strayer, L. M.; Catchings, R.; McEvilly, A.; Goldman, M.; Criley, C.; Sickler, R. R.

2017-12-01

The Hayward Fault Zone (HFZ) includes the Hayward fault (HF), as well as several named and unnamed subparallel, subsidiary faults to the east, among them the Quaternary-active Chabot Fault (CF), the Miller Creek Fault (MCF), and a heretofore unnamed fault, the Redwood Thrust Fault (RTF). With an ≥M6.0 recurrence interval of 130 y for the HF and the last major earthquake in 1868, the HFZ is a major seismic hazard in the San Francisco Bay Area, exacerbated by the many unknown and potentially active secondary faults of the HFZ. In 2016, researchers from California State University, East Bay, working in concert with the United States Geological Survey conducted the East Bay Seismic Investigation (EBSI). We deployed 296 RefTek RT125 (Texan) seismographs along a 15-km-long linear seismic profile across the HF, extending from the bay in San Leandro to the hills in Castro Valley. Two-channel seismographs were deployed at 100 m intervals to record P- and S-waves, and additional single-channel seismographs were deployed at 20 m intervals where the seismic line crossed mapped faults. The active-source survey consisted of 16 buried explosive shots located at approximately 1-km intervals along the seismic line. We used the Multichannel Analysis of Surfaces Waves (MASW) method to develop 2-D shear-wave velocity models across the CF, MCF, and RTF. Preliminary MASW analysis show areas of anomalously low S-wave velocities , indicating zones of reduced shear modulus, coincident with these three mapped faults; additional velocity anomalies coincide with unmapped faults within the HFZ. Such compliant zones likely correspond to heavily fractured rock surrounding the faults, where the shear modulus is expected to be low compared to the undeformed host rock.

Application Of Holographic Interferometry For Investigation Of Microroughness Of Engineering Surfaces

NASA Astrophysics Data System (ADS)

Lech, Marek; Mruk, Irena; Stupnicki, Jacek

1985-01-01

The paper describes an improved immersion method of holographic interferometry /IMHI/ adjusted for studies of roughness of engineering surfaces. Special optical arrangement, with two types of immersion cells and adequate technique of preparing transparent replicas reproducting with high fidelity details of differently machined surfaces was elaborated. It permits to obtain the contour maps of the surface asperities with intervals between the planes of succesive contour lines within a range of 1 μm. The results obtained for some engineering surfaces are given.

Isopach map of interval between top of the Pictured Cliffs Sandstone and the Huerfanito Bentonite bed of the Lewis Shale, La Plata County, Colorado, and Rio Arriba and San Juan counties, New Mexico

USGS Publications Warehouse

Sandberg, D.T.

1986-01-01

Data used for the isopach map are mostly from interpretation of geophysical logs of oil and gas wells, southeast of the outcrop in parts of the Cortez, Durango, Farmington, and Navajo Reservoir 1: 100,000-scale quadrangles, Colorado and New Mexico. Cross sections A-A’ and B-B' give examples of geophysical logs that show some of the variations in the isopach interval.

Visualizing the Logistic Map with a Microcontroller

ERIC Educational Resources Information Center

Serna, Juan D.; Joshi, Amitabh

2012-01-01

The logistic map is one of the simplest nonlinear dynamical systems that clearly exhibits the route to chaos. In this paper, we explore the evolution of the logistic map using an open-source microcontroller connected to an array of light-emitting diodes (LEDs). We divide the one-dimensional domain interval [0,1] into ten equal parts, an associate…

Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

USDA-ARS?s Scientific Manuscript database

Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed bef...

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

A reference linkage map for Eucalyptus

PubMed Central

2012-01-01

Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research. PMID:22702473

Evaluating the Impact of Various Parameters on the Gamma Index Values of 2D Diode Array in IMRT Verification

PubMed Central

Jabbari, Keyvan; Pashaei, Fakhereh; Ay, Mohammad R.; Amouheidari, Alireza; Tavakoli, Mohammad B.

2018-01-01

Background: MapCHECK2 is a two-dimensional diode arrays planar dosimetry verification system. Dosimetric results are evaluated with gamma index. This study aims to provide comprehensive information on the impact of various factors on the gamma index values of MapCHECK2, which is mostly used for IMRT dose verification. Methods: Seven fields were planned for 6 and 18 MV photons. The azimuthal angle is defined as any rotation of collimators or the MapCHECK2 around the central axis, which was varied from 5 to −5°. The gantry angle was changed from −8 to 8°. Isodose sampling resolution was studied in the range of 0.5 to 4 mm. The effects of additional buildup on gamma index in three cases were also assessed. Gamma test acceptance criteria were 3%/3 mm. Results: The change of azimuthal angle in 5° interval reduced gamma index value by about 9%. The results of putting buildups of various thicknesses on the MapCHECK2 surface showed that gamma index was generally improved in thicker buildup, especially for 18 MV. Changing the sampling resolution from 4 to 2 mm resulted in an increase in gamma index by about 3.7%. The deviation of the gantry in 8° intervals in either directions changed the gamma index only by about 1.6% for 6 MV and 2.1% for 18 MV. Conclusion: Among the studied parameters, the azimuthal angle is one of the most effective factors on gamma index value. The gantry angle deviation and sampling resolution are less effective on gamma index value reduction. PMID:29535922

An atypical deletion of the Williams–Beuren syndrome interval implicates genes associated with defective visuospatial processing and autism

PubMed Central

Edelmann, Lisa; Prosnitz, Aaron; Pardo, Sherly; Bhatt, Jahnavi; Cohen, Ninette; Lauriat, Tara; Ouchanov, Leonid; González, Patricia J; Manghi, Elina R; Bondy, Pamela; Esquivel, Marcela; Monge, Silvia; Delgado, Marietha F; Splendore, Alessandra; Francke, Uta; Burton, Barbara K; McInnes, L Alison

2007-01-01

Background During a genetic study of autism, a female child who met diagnostic criteria for autism spectrum disorder, but also exhibited the cognitive–behavioural profile (CBP) associated with Williams–Beuren syndrome (WBS) was examined. The WBS CBP includes impaired visuospatial ability, an overly friendly personality, excessive non‐social anxiety and language delay. Methods Using array‐based comparative genomic hybridisation (aCGH), a deletion corresponding to BAC RP11‐89A20 in the distal end of the WBS deletion interval was detected. Hemizygosity was confirmed using fluorescence in situ hybridisation and fine mapping was performed by measuring the copy number of genomic DNA using quantitative polymerase chain reaction. Results The proximal breakpoint was mapped to intron 1 of GTF2IRD1 and the distal breakpoint lies 2.4–3.1 Mb towards the telomere. The subject was completely hemizygous for GTF2I, commonly deleted in carriers of the classic ∼1.5 Mb WBS deletion, and GTF2IRD2, deleted in carriers of the rare ∼1.84 Mb WBS deletion. Conclusion Hemizygosity of the GTF2 family of transcription factors is sufficient to produce many aspects of the WBS CBP, and particularly implicate the GTF2 transcription factors in the visuospatial construction deficit. Symptoms of autism in this case may be due to deletion of additional genes outside the typical WBS interval or remote effects on gene expression at other loci. PMID:16971481

Acquisition process of typing skill using hierarchical materials in the Japanese language.

PubMed

Ashitaka, Yuki; Shimada, Hiroyuki

2014-08-01

In the present study, using a new keyboard layout with only eight keys, we conducted typing training for unskilled typists. In this task, Japanese college students received training in typing words consisting of a pair of hiragana characters with four keystrokes, using the alphabetic input method, while keeping the association between the keys and typists' finger movements; the task was constructed so that chunking was readily available. We manipulated the association between the hiragana characters and alphabet letters (hierarchical materials: overlapped and nonoverlapped mappings). Our alphabet letter materials corresponded to the regular order within each hiragana word (within the four letters, the first and third referred to consonants, and the second and fourth referred to vowels). Only the interkeystroke intervals involved in the initiation of typing vowel letters showed an overlapping effect, which revealed that the effect was markedly large only during the early period of skill development (the effect for the overlapped mapping being larger than that for the nonoverlapped mapping), but that it had diminished by the time of late training. Conversely, the response time and the third interkeystroke interval, which are both involved in the latency of typing a consonant letter, did not reveal an overlapped effect, suggesting that chunking might be useful with hiragana characters rather than hiragana words. These results are discussed in terms of the fan effect and skill acquisition. Furthermore, we discuss whether there is a need for further research on unskilled and skilled Japanese typists.

Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat.

PubMed

Wu, Jianhui; Huang, Shuo; Zeng, Qingdong; Liu, Shengjie; Wang, Qilin; Mu, Jingmei; Yu, Shizhou; Han, Dejun; Kang, Zhensheng

2018-06-16

A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103. Five stable QTL were detected across multiple environments. A fter comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F 2:4 contrasting pools from cross Zhengmai 9023 × P10103. A consensus QTL (LOD = 26-40, PVE = 42-55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.

Influence analysis in quantitative trait loci detection.

PubMed

Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

2014-07-01

This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Method of and apparatus for modeling interactions

DOEpatents

Budge, Kent G.

2004-01-13

A method and apparatus for modeling interactions can accurately model tribological and other properties and accommodate topological disruptions. Two portions of a problem space are represented, a first with a Lagrangian mesh and a second with an ALE mesh. The ALE and Lagrangian meshes are constructed so that each node on the surface of the Lagrangian mesh is in a known correspondence with adjacent nodes in the ALE mesh. The interaction can be predicted for a time interval. Material flow within the ALE mesh can accurately model complex interactions such as bifurcation. After prediction, nodes in the ALE mesh in correspondence with nodes on the surface of the Lagrangian mesh can be mapped so that they are once again adjacent to their corresponding Lagrangian mesh nodes. The ALE mesh can then be smoothed to reduce mesh distortion that might reduce the accuracy or efficiency of subsequent prediction steps. The process, from prediction through mapping and smoothing, can be repeated until a terminal condition is reached.

An augmented parametric response map with consideration of image registration error: towards guidance of locally adaptive radiotherapy

NASA Astrophysics Data System (ADS)

Lausch, Anthony; Chen, Jeff; Ward, Aaron D.; Gaede, Stewart; Lee, Ting-Yim; Wong, Eugene

2014-11-01

Parametric response map (PRM) analysis is a voxel-wise technique for predicting overall treatment outcome, which shows promise as a tool for guiding personalized locally adaptive radiotherapy (RT). However, image registration error (IRE) introduces uncertainty into this analysis which may limit its use for guiding RT. Here we extend the PRM method to include an IRE-related PRM analysis confidence interval and also incorporate multiple graded classification thresholds to facilitate visualization. A Gaussian IRE model was used to compute an expected value and confidence interval for PRM analysis. The augmented PRM (A-PRM) was evaluated using CT-perfusion functional image data from patients treated with RT for glioma and hepatocellular carcinoma. Known rigid IREs were simulated by applying one thousand different rigid transformations to each image set. PRM and A-PRM analyses of the transformed images were then compared to analyses of the original images (ground truth) in order to investigate the two methods in the presence of controlled IRE. The A-PRM was shown to help visualize and quantify IRE-related analysis uncertainty. The use of multiple graded classification thresholds also provided additional contextual information which could be useful for visually identifying adaptive RT targets (e.g. sub-volume boosts). The A-PRM should facilitate reliable PRM guided adaptive RT by allowing the user to identify if a patient’s unique IRE-related PRM analysis uncertainty has the potential to influence target delineation.

Evaluation of using digital gravity field models for zoning map creation

NASA Astrophysics Data System (ADS)

Loginov, Dmitry

2018-05-01

At the present time the digital cartographic models of geophysical fields are taking a special significance into geo-physical mapping. One of the important directions to their application is the creation of zoning maps, which allow taking into account the morphology of geophysical field in the implementation automated choice of contour intervals. The purpose of this work is the comparative evaluation of various digital models in the creation of integrated gravity field zoning map. For comparison were chosen the digital model of gravity field of Russia, created by the analog map with scale of 1 : 2 500 000, and the open global model of gravity field of the Earth - WGM2012. As a result of experimental works the four integrated gravity field zoning maps were obtained with using raw and processed data on each gravity field model. The study demonstrates the possibility of open data use to create integrated zoning maps with the condition to eliminate noise component of model by processing in specialized software systems. In this case, for solving problem of contour intervals automated choice the open digital models aren't inferior to regional models of gravity field, created for individual countries. This fact allows asserting about universality and independence of integrated zoning maps creation regardless of detail of a digital cartographic model of geo-physical fields.

The effect of activation rate on left atrial bipolar voltage in patients with paroxysmal atrial fibrillation

PubMed Central

Linton, Nick; O'Neill, Louisa; Harrison, James; Whitaker, John; Mukherjee, Rahul; Rinaldi, Christopher A.; Gill, Jaswinder; Niederer, Steven; Wright, Matthew; O'Neill, Mark

2017-01-01

Abstract Introduction Bipolar voltage is used during electroanatomic mapping to define abnormal myocardium, but the effect of activation rate on bipolar voltage is not known. We hypothesized that bipolar voltage may change in response to activation rate. By examining corresponding unipolar signals we sought to determine the mechanisms of such changes. Methods and results LA extrastimulus mapping was performed during CS pacing in 10 patients undergoing first time paroxysmal atrial fibrillation ablation. Bipolar and unipolar electrograms were recorded using a PentaRay catheter (4‐4‐4 spacing) and indifferent IVC electrode, respectively. An S1S2 pacing protocol was delivered with extrastimulus coupling interval reducing from 350 to 200 milliseconds. At each recording site (119 ± 37 per LA), bipolar peak‐to‐peak voltage, unipolar peak to peak voltage and activation delay between unipole pairs was measured. Four patterns of bipolar voltage/extrastimulus coupling interval curves were seen: voltage attenuation with plateau voltage >1 mV (48 ± 15%) or <1 mV (22 ± 15%), and voltage unaffected by coupling interval with plateau voltage >1 mV (17 ± 10%) or <1 mV (13 ± 8%). Electrograms showing bipolar voltage attenuation were associated with significantly greater unipolar voltage attenuation at low (25 ± 28 mV/s vs. 9 ± 11 mV/s) and high (23 ± 29 mV/s vs. 6 ± 12 mV/s) plateau voltage sites (P < 0.001). There was a small but significant increase in conduction delay between unipole pairs at sites showing bipolar voltage attenuation (P = 0.026). Conclusions Bipolar electrogram voltage is dependent on activation rate at a significant proportion of sites. Changes in unipolar voltage and timing underlie these effects. These observations have important implications for use of voltage mapping to delineate abnormal atrial substrate. PMID:28639747

Starspots and Activity of the Flare Star GJ 1243

NASA Astrophysics Data System (ADS)

Savanov, I. S.; Dmitrienko, E. S.

2018-04-01

The photometric variability of the uniqueMdwarf flare star GJ 1243 (KIC 9726699) is investigated using the most complete set of observationalmaterial obtained with the Kepler Space Telescope. The analysis is based on 49 487 individual brightness measurements obtained during an interval of 1460 days (nearly four years). The periodicity of the brightness variations with the period P phot = 0.59261 ± 0.00060d is confirmed. The temperature inhomogeneities on the stellar surface reconstructed from the light curve are used to drive maps of these surface-temperature inhomogeneities (of the filling factor f). The resulting maps are used to determine the positions of active regions. Analysis of the surface-temperature maps for GJ 1243 led to the conclusion that the positions of spots on the stellar surface displayed appreciable evolution during the analyzed time interval. The maximum value for the lower limit on the differentialrotation parameter ΔΩ is 0.0022 rad/day. This more accurate estimate of ΔΩ is lower than the values presented earlier by Davenport et al. [1] (0.0058 and 0.0036 rad/day), due to the more accurate account of variations in the positions of the most active longitude in the current study. However, the differentialrotation estimate obtained in [1] using a method based on fitting the evolution of spots using twodimensional Gaussian functions essentially coincides with the new estimate presented here. The fractional area of the total spotted surface S of the star during the observing interval considered varied from 7 to 2%. The amplitude of the brightness variability of the star slowly decreased, varying in the range 1.6-0.5%. Overall, the position of GJ 1243 in spottedness-age, spottedness-rotation period, and spottedness-Rossby number diagrams agrees very well with the general character of the dependences displayed in earlier studies of M dwarfs.

Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

PubMed

Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

2015-10-01

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

A 2.5-Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1.

PubMed

Wunderlich, K R; Abbey, C A; Clayton, D R; Song, Y; Schein, J E; Georges, M; Coppieters, W; Adelson, D L; Taylor, J F; Davis, S L; Gill, C A

2006-12-01

The polled locus has been mapped by genetic linkage analysis to the proximal region of bovine chromosome 1. As an intermediate step in our efforts to identify the polled locus and the underlying causative mutation for the polled phenotype, we have constructed a BAC-based physical map of the interval containing the polled locus. Clones containing genes and markers in the critical interval were isolated from the TAMBT (constructed from Angus and Longhorn genomic DNA) and CHORI-240 (constructed from horned Hereford genomic DNA) BAC libraries and ordered based on fingerprinting and the presence or absence of 80 STS markers. A single contig spanning 2.5 Mb was assembled. Comparison of the physical order of STSs to the corresponding region of human chromosome 21 revealed the same order of genes within the polled critical interval. This contig of overlapping BAC clones from horned and polled breeds is a useful resource for SNP discovery and characterization of positional candidate genes.

Dynamic detection-rate-based bit allocation with genuine interval concealment for binary biometric representation.

PubMed

Lim, Meng-Hui; Teoh, Andrew Beng Jin; Toh, Kar-Ann

2013-06-01

Biometric discretization is a key component in biometric cryptographic key generation. It converts an extracted biometric feature vector into a binary string via typical steps such as segmentation of each feature element into a number of labeled intervals, mapping of each interval-captured feature element onto a binary space, and concatenation of the resulted binary output of all feature elements into a binary string. Currently, the detection rate optimized bit allocation (DROBA) scheme is one of the most effective biometric discretization schemes in terms of its capability to assign binary bits dynamically to user-specific features with respect to their discriminability. However, we learn that DROBA suffers from potential discriminative feature misdetection and underdiscretization in its bit allocation process. This paper highlights such drawbacks and improves upon DROBA based on a novel two-stage algorithm: 1) a dynamic search method to efficiently recapture such misdetected features and to optimize the bit allocation of underdiscretized features and 2) a genuine interval concealment technique to alleviate crucial information leakage resulted from the dynamic search. Improvements in classification accuracy on two popular face data sets vindicate the feasibility of our approach compared with DROBA.

High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

PubMed Central

Huang, Xin; Gollin, Susanne M.; Raja, Siva; Godfrey, Tony E.

2002-01-01

Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42–550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors. PMID:12172009

Paleogeography and the Late Cretaceous of the Western Interior of middle North America; coal distribution and sediment accumulation

USGS Publications Warehouse

Roberts, Laura N. Robinson; Kirschbaum, Mark A.

1995-01-01

A synthesis of Late Cretaceous paleogeography of the Western Interior from Mexico to southwestern Canada emphasizes the areal distribution of peat-forming environments during six biostratigraphically constrained time intervals. Isopach maps of strata for each interval reveal the locations and magnitude of major depocenters. The paleogeographic framework provides insight into the relative importance of tectonism, eustasy, and climate on the accumulation of thick peats and their preservation as coals. A total of 123 basin summaries and their data provide the ground truth for construction of the isopach and paleogeographic maps.

Flood-hazard mapping in Honduras in response to Hurricane Mitch

USGS Publications Warehouse

Mastin, M.C.

2002-01-01

The devastation in Honduras due to flooding from Hurricane Mitch in 1998 prompted the U.S. Agency for International Development, through the U.S. Geological Survey, to develop a country-wide systematic approach of flood-hazard mapping and a demonstration of the method at selected sites as part of a reconstruction effort. The design discharge chosen for flood-hazard mapping was the flood with an average return interval of 50 years, and this selection was based on discussions with the U.S. Agency for International Development and the Honduran Public Works and Transportation Ministry. A regression equation for estimating the 50-year flood discharge using drainage area and annual precipitation as the explanatory variables was developed, based on data from 34 long-term gaging sites. This equation, which has a standard error of prediction of 71.3 percent, was used in a geographic information system to estimate the 50-year flood discharge at any location for any river in the country. The flood-hazard mapping method was demonstrated at 15 selected municipalities. High-resolution digital-elevation models of the floodplain were obtained using an airborne laser-terrain mapping system. Field verification of the digital elevation models showed that the digital-elevation models had mean absolute errors ranging from -0.57 to 0.14 meter in the vertical dimension. From these models, water-surface elevation cross sections were obtained and used in a numerical, one-dimensional, steady-flow stepbackwater model to estimate water-surface profiles corresponding to the 50-year flood discharge. From these water-surface profiles, maps of area and depth of inundation were created at the 13 of the 15 selected municipalities. At La Lima only, the area and depth of inundation of the channel capacity in the city was mapped. At Santa Rose de Aguan, no numerical model was created. The 50-year flood and the maps of area and depth of inundation are based on the estimated 50-year storm tide.

Biomass Thermogravimetric Analysis: Uncertainty Determination Methodology and Sampling Maps Generation

PubMed Central

Pazó, Jose A.; Granada, Enrique; Saavedra, Ángeles; Eguía, Pablo; Collazo, Joaquín

2010-01-01

The objective of this study was to develop a methodology for the determination of the maximum sampling error and confidence intervals of thermal properties obtained from thermogravimetric analysis (TG), including moisture, volatile matter, fixed carbon and ash content. The sampling procedure of the TG analysis was of particular interest and was conducted with care. The results of the present study were compared to those of a prompt analysis, and a correlation between the mean values and maximum sampling errors of the methods were not observed. In general, low and acceptable levels of uncertainty and error were obtained, demonstrating that the properties evaluated by TG analysis were representative of the overall fuel composition. The accurate determination of the thermal properties of biomass with precise confidence intervals is of particular interest in energetic biomass applications. PMID:20717532

Dual-mode nested search method for categorical uncertain multi-objective optimization

NASA Astrophysics Data System (ADS)

Tang, Long; Wang, Hu

2016-10-01

Categorical multi-objective optimization is an important issue involved in many matching design problems. Non-numerical variables and their uncertainty are the major challenges of such optimizations. Therefore, this article proposes a dual-mode nested search (DMNS) method. In the outer layer, kriging metamodels are established using standard regular simplex mapping (SRSM) from categorical candidates to numerical values. Assisted by the metamodels, a k-cluster-based intelligent sampling strategy is developed to search Pareto frontier points. The inner layer uses an interval number method to model the uncertainty of categorical candidates. To improve the efficiency, a multi-feature convergent optimization via most-promising-area stochastic search (MFCOMPASS) is proposed to determine the bounds of objectives. Finally, typical numerical examples are employed to demonstrate the effectiveness of the proposed DMNS method.

Mapping Quantitative Field Resistance Against Apple Scab in a 'Fiesta' x 'Discovery' Progeny.

PubMed

Liebhard, R; Koller, B; Patocchi, A; Kellerhals, M; Pfammatter, W; Jermini, M; Gessler, C

2003-04-01

ABSTRACT Breeding of resistant apple cultivars (Malus x domestica) as a disease management strategy relies on the knowledge and understanding of the underlying genetics. The availability of molecular markers and genetic linkage maps enables the detection and the analysis of major resistance genes as well as of quantitative trait loci (QTL) contributing to the resistance of a genotype. Such a genetic linkage map was constructed, based on a segregating population of the cross between apple cvs. Fiesta (syn. Red Pippin) and Discovery. The progeny was observed for 3 years at three different sites in Switzerland and field resistance against apple scab (Venturia inaequalis) was assessed. Only a weak correlation was detected between leaf scab and fruit scab. A QTL analysis was performed, based on the genetic linkage map consisting of 804 molecular markers and covering all 17 chromosomes of apple. With the maximum likelihood-based interval mapping method, eight genomic regions were identified, six conferring resistance against leaf scab and two conferring fruit scab resistance. Although cv. Discovery showed a much stronger resistance against scab in the field, most QTL identified were attributed to the more susceptible parent 'Fiesta'. This indicated a high degree of homozygosity at the scab resistance loci in 'Discovery', preventing their detection in the progeny due to the lack of segregation.

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

PubMed Central

Nunes, José de Ribamar da Silva; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; de Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjiang; Coutinho, Luiz Lehmann

2017-01-01

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs. PMID:28387238

Entrainment and high-density three-dimensional mapping in right atrial macroreentry provide critical complementary information: Entrainment may unmask "visual reentry" as passive.

PubMed

Pathik, Bhupesh; Lee, Geoffrey; Nalliah, Chrishan; Joseph, Stephen; Morton, Joseph B; Sparks, Paul B; Sanders, Prashanthan; Kistler, Peter M; Kalman, Jonathan M

2017-10-01

With the recent advent of high-density (HD) 3-dimensional (3D) mapping, the utility of entrainment is uncertain. However, the limitations of visual representation and interpretation of these high-resolution 3D maps are unclear. The purpose of this study was to determine the strengths and limitations of both HD 3D mapping and entrainment mapping during mapping of right atrial macroreentry. Fifteen patients were studied. The number and type of circuits accounting for ≥90% of the tachycardia cycle length using HD 3D mapping were verified using systematic entrainment mapping. Entrainment sites with an unexpectedly long postpacing interval despite proximity to the active circuit were evaluated. Based on HD 3D mapping, 27 circuits were observed: 12 peritricuspid, 2 upper loop reentry, 10 lower loop reentry, and 3 lateral wall circuits. With entrainment, 17 of the 27 circuits were active: all 12 peritricuspid and 2 upper loop reentry. However, lower loop reentry was confirmed in only 3 of 10, and none of the 3 lateral wall circuits were present. Mean percentage of tachycardia cycle length covered by active circuits was 98% ± 1% vs 97% ± 2% for passive circuits (P = .09). None of the 345 entrainment runs terminated tachycardia or changed tachycardia mechanism. In 8 of 15 patients, 13 examples of unexpectedly long postpacing interval were observed at entrainment sites located distal to localized zones of slow conduction seen on HD 3D mapping. Using HD 3D mapping, "visual reentry" may be due to passive circuitous propagation rather than a critical reentrant circuit. HD 3D mapping provides new insights into regional conduction and helps explain unusual entrainment phenomena. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Communicating spatial uncertainty to non-experts using R

NASA Astrophysics Data System (ADS)

Luzzi, Damiano; Sawicka, Kasia; Heuvelink, Gerard; de Bruin, Sytze

2016-04-01

Effective visualisation methods are important for the efficient use of uncertainty information for various groups of users. Uncertainty propagation analysis is often used with spatial environmental models to quantify the uncertainty within the information. A challenge arises when trying to effectively communicate the uncertainty information to non-experts (not statisticians) in a wide range of cases. Due to the growing popularity and applicability of the open source programming language R, we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. The package has implemented Monte Carlo algorithms for uncertainty propagation, the output of which is represented by an ensemble of model outputs (i.e. a sample from a probability distribution). Numerous visualisation methods exist that aim to present such spatial uncertainty information both statically, dynamically and interactively. To provide the most universal visualisation tools for non-experts, we conducted a survey on a group of 20 university students and assessed the effectiveness of selected static and interactive methods for visualising uncertainty in spatial variables such as DEM and land cover. The static methods included adjacent maps and glyphs for continuous variables. Both allow for displaying maps with information about the ensemble mean, variance/standard deviation and prediction intervals. Adjacent maps were also used for categorical data, displaying maps of the most probable class, as well as its associated probability. The interactive methods included a graphical user interface, which in addition to displaying the previously mentioned variables also allowed for comparison of joint uncertainties at multiple locations. The survey indicated that users could understand the basics of the uncertainty information displayed in the static maps, with the interactive interface allowing for more in-depth information. Subsequently, the R package included a collation of the plotting functions that were evaluated in the survey. The implementation of static visualisations was done via calls to the 'ggplot2' package. This allowed the user to provide control over the content, legend, colours, axes and titles. The interactive methods were implemented using the 'shiny' package allowing users to activate the visualisation of statistical descriptions of uncertainty through interaction with a plotted map of means. This research brings uncertainty visualisation to a broader audience through the development of tools for visualising uncertainty using open source software.

Endocrine events during the periestrous period and the subsequent estrous cycle in ewes after estrus synchronization.

PubMed

Menegatos, J; Chadio, S; Kalogiannis, T; Kouskoura, T; Kouimtzis, S

2003-04-01

The aim of the present study was to investigate the endocrinology of the periestrus period and that of the subsequent estrous cycle in ewes synchronized during the breeding season. Animals were treated for 14 days with either MAP intravaginal sponges or subcutaneous progesterone implants, followed by administration of 500 IU PMSG at the time of withdrawal. The time to estrus occurrence following progestagen withdrawal differed significantly between groups (45.3+/-2.7h for the MAP and 21.5+/-1.2h for the implant group, P<0.001). Estradiol levels around estrus did not differ between groups, but a significant difference was detected for the interval from peak estradiol to estrus, with a shorter interval for the implant group (26.7+/-0.7 and 2.7+/-0.9h, P<0.001). Progesterone implants shortened the interval from removal to LH surge, compared to the MAP group (31.2+/-4.4 and 56.5+/-3.6h, respectively, P<0.05). An earlier response was also observed for the interval from estradiol peak to LH peak in the implant group (12.1+/-3.3 and 37+/-2h, respectively, P<0.005), but no difference was observed for the interval from estrus to LH surge. Progesterone levels, particularly during the Days 6 to 10 of the subsequent estrous cycle were significantly higher (P<0.05) in the implant group. It is concluded that the kind of progesterone treatment may affect the time of estrus and the LH peak as well as the progesterone levels of the subsequent cycle.

SNP Marker Integration and QTL Analysis of 12 Agronomic and Morphological Traits in F8 RILs of Pepper (Capsicum annuum L.)

PubMed Central

Lu, Fu-Hao; Kwon, Soon-Wook; Yoon, Min-Young; Kim, Ki-Taek; Cho, Myeong-Cheoul; Yoon, Moo-Kyung; Park, Yong-Jin

2012-01-01

Red pepper, Capsicum annuum L., has been attracting geneticists’ and breeders’ attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family. PMID:22684870

The Topography Tub Learning Activity

NASA Astrophysics Data System (ADS)

Glesener, G. B.

2014-12-01

Understanding the basic elements of a topographic map (i.e. contour lines and intervals) is just a small part of learning how to use this abstract representational system as a resource in geologic mapping. Interpretation of a topographic map and matching its features with real-world structures requires that the system is utilized for visualizing the shapes of these structures and their spatial orientation. To enrich students' skills in visualizing topography from topographic maps a spatial training activity has been developed that uses 3D objects of various shapes and sizes, a sighting tool, a plastic basin, water, and transparencies. In the first part of the activity, the student is asked to draw a topographic map of one of the 3D objects. Next, the student places the object into a plastic tub in which water is added to specified intervals of height. The shoreline at each interval is used to reference the location of the contour line the student draws on a plastic inkjet transparency directly above the object. A key part of this activity is the use of a sighting tool by the student to assist in keeping the pencil mark directly above the shoreline. It (1) ensures the accurate positioning of the contour line and (2) gives the learner experience with using a sight before going out into the field. Finally, after the student finishes drawing the contour lines onto the transparency, the student can compare and contrast the two maps in order to discover where improvements in their visualization of the contours can be made. The teacher and/or peers can also make suggestions on ways to improve. A number of objects with various shapes and sizes are used in this exercise to produce contour lines representing the different types of topography the student may encounter while field mapping. The intended outcome from using this visualization training activity is improvement in performance of visualizing topography as the student moves between the topographic representation and corresponding topography in the field.

Progressive myoclonus epilepsy EPM1 locus maps to a 175-kb interval in distal 21q

DOE Office of Scientific and Technical Information (OSTI.GOV)

Virtaneva, K.; Miao, J.; Traeskelin, A.L.

1996-06-01

The EPM1 locus responsible for progressive myoclonus epilepsy of Unverricht-Lundborg type (MIM 254800) maps to a region in distal chromosome 21q where positional cloning has been hampered by the lack of physical and genetic mapping resolution. We here report the use of a recently constituted contig of cosmid, BAC, and P1 clones that allowed new polymorphic markers to be positioned. These were typed in 53 unrelated disease families from an isolated Finnish population in which a putative single ancestral EPM1 mutation has segregated for an estimated 100 generations. By thus exploiting historical recombinations in haplotype analysis, EPM1 could be assignedmore » to the {approximately}175-kb interval between the markers D21S2040 and D21S1259. 26 refs., 2 figs., 4 tabs.« less

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

PubMed Central

2012-01-01

Background High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categorize and compare these elements using inferred descriptive annotation given this sequence information irrespective of the fact that it may not be representative of the identifier as a whole. Results All annotations, no matter the granularity, can be aligned to genomic sequences and therefore annotated by genomic intervals. We have developed AbsIDconvert, a methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The utility is demonstrated in three case studies: 1) comparative genomic study mapping plasmodium gene sequences to corresponding human and mosquito transcriptional regions; 2) cross-species study of Incyte clone sequences; and 3) analysis of human Ensembl transcripts mapped by Affymetrix®; and Agilent microarray probes. AbsIDconvert currently supports ID conversion of 53 species for a given list of input identifiers, genomic sequence, or genome intervals. Conclusion AbsIDconvert provides an efficient and reliable mechanism for conversion between identifier domains of interest. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval. As the genomes and the sequences for genetic elements are further refined, this tool will become increasingly useful and accurate. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bioinformatics.louisville.edu/abid/. PMID:22967011

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

PubMed Central

Qiu, Gao-Feng; Xiong, Liang-Wei; Han, Zhi-Ke; Liu, Zhi-Qiang; Feng, Jian-Bin; Wu, Xu-Gan; Yan, Yin-Long; Shen, Hong; Huang, Long; Chen, Li

2017-01-01

The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs. PMID:28045132

Absolute color scale for improved diagnostics with wavefront error mapping.

PubMed

Smolek, Michael K; Klyce, Stephen D

2007-11-01

Wavefront data are expressed in micrometers and referenced to the pupil plane, but current methods to map wavefront error lack standardization. Many use normalized or floating scales that may confuse the user by generating ambiguous, noisy, or varying information. An absolute scale that combines consistent clinical information with statistical relevance is needed for wavefront error mapping. The color contours should correspond better to current corneal topography standards to improve clinical interpretation. Retrospective analysis of wavefront error data. Historic ophthalmic medical records. Topographic modeling system topographical examinations of 120 corneas across 12 categories were used. Corneal wavefront error data in micrometers from each topography map were extracted at 8 Zernike polynomial orders and for 3 pupil diameters expressed in millimeters (3, 5, and 7 mm). Both total aberrations (orders 2 through 8) and higher-order aberrations (orders 3 through 8) were expressed in the form of frequency histograms to determine the working range of the scale across all categories. The standard deviation of the mean error of normal corneas determined the map contour resolution. Map colors were based on corneal topography color standards and on the ability to distinguish adjacent color contours through contrast. Higher-order and total wavefront error contour maps for different corneal conditions. An absolute color scale was produced that encompassed a range of +/-6.5 microm and a contour interval of 0.5 microm. All aberrations in the categorical database were plotted with no loss of clinical information necessary for classification. In the few instances where mapped information was beyond the range of the scale, the type and severity of aberration remained legible. When wavefront data are expressed in micrometers, this absolute scale facilitates the determination of the severity of aberrations present compared with a floating scale, particularly for distinguishing normal from abnormal levels of wavefront error. The new color palette makes it easier to identify disorders. The corneal mapping method can be extended to mapping whole eye wavefront errors. When refraction data are expressed in diopters, the previously published corneal topography scale is suggested.

Hidden Markov models for fault detection in dynamic systems

NASA Technical Reports Server (NTRS)

Smyth, Padhraic J. (Inventor)

1995-01-01

The invention is a system failure monitoring method and apparatus which learns the symptom-fault mapping directly from training data. The invention first estimates the state of the system at discrete intervals in time. A feature vector x of dimension k is estimated from sets of successive windows of sensor data. A pattern recognition component then models the instantaneous estimate of the posterior class probability given the features, p(w(sub i) (vertical bar)/x), 1 less than or equal to i isless than or equal to m. Finally, a hidden Markov model is used to take advantage of temporal context and estimate class probabilities conditioned on recent past history. In this hierarchical pattern of information flow, the time series data is transformed and mapped into a categorical representation (the fault classes) and integrated over time to enable robust decision-making.

Hidden Markov models for fault detection in dynamic systems

NASA Technical Reports Server (NTRS)

Smyth, Padhraic J. (Inventor)

1993-01-01

The invention is a system failure monitoring method and apparatus which learns the symptom-fault mapping directly from training data. The invention first estimates the state of the system at discrete intervals in time. A feature vector x of dimension k is estimated from sets of successive windows of sensor data. A pattern recognition component then models the instantaneous estimate of the posterior class probability given the features, p(w(sub i) perpendicular to x), 1 less than or equal to i is less than or equal to m. Finally, a hidden Markov model is used to take advantage of temporal context and estimate class probabilities conditioned on recent past history. In this hierarchical pattern of information flow, the time series data is transformed and mapped into a categorical representation (the fault classes) and integrated over time to enable robust decision-making.

Enhanced nonlinearity interval mapping scheme for high-performance simulation-optimization of watershed-scale BMP placement

NASA Astrophysics Data System (ADS)

Zou, Rui; Riverson, John; Liu, Yong; Murphy, Ryan; Sim, Youn

2015-03-01

Integrated continuous simulation-optimization models can be effective predictors of a process-based responses for cost-benefit optimization of best management practices (BMPs) selection and placement. However, practical application of simulation-optimization model is computationally prohibitive for large-scale systems. This study proposes an enhanced Nonlinearity Interval Mapping Scheme (NIMS) to solve large-scale watershed simulation-optimization problems several orders of magnitude faster than other commonly used algorithms. An efficient interval response coefficient (IRC) derivation method was incorporated into the NIMS framework to overcome a computational bottleneck. The proposed algorithm was evaluated using a case study watershed in the Los Angeles County Flood Control District. Using a continuous simulation watershed/stream-transport model, Loading Simulation Program in C++ (LSPC), three nested in-stream compliance points (CP)—each with multiple Total Maximum Daily Loads (TMDL) targets—were selected to derive optimal treatment levels for each of the 28 subwatersheds, so that the TMDL targets at all the CP were met with the lowest possible BMP implementation cost. Genetic Algorithm (GA) and NIMS were both applied and compared. The results showed that the NIMS took 11 iterations (about 11 min) to complete with the resulting optimal solution having a total cost of 67.2 million, while each of the multiple GA executions took 21-38 days to reach near optimal solutions. The best solution obtained among all the GA executions compared had a minimized cost of 67.7 million—marginally higher, but approximately equal to that of the NIMS solution. The results highlight the utility for decision making in large-scale watershed simulation-optimization formulations.

Topographic map of the Coronae Montes region of Mars - MTM 500k -35/087E OMKTT

USGS Publications Warehouse

Rosiek, Mark R.; Redding, Bonnie L.; Galuszca, Donna M.

2005-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetrically using Viking Orbiter stereo image pairs. The contour interval is 250 m. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

Topographic Map of the Northeast Ascraeus Mons Region of Mars - MTM 500k 15/257E OMKT

USGS Publications Warehouse

,

2004-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetically using Viking Orbiter stereo image pairs. The contour interval is 250 meters. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

Topographic Map of the Northwest Ascraeus Mons Region of Mars - MTM 500k 15/252E OMKT

USGS Publications Warehouse

,

2004-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetically using Viking Orbiter stereo image pairs. The contour interval is 250 meters. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

Topographic Map of the Southeast Ascraeus Mons Region of Mars - MTM 500k 10/257E OMKT

USGS Publications Warehouse

,

2004-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetically using Viking Orbiter stereo image pairs. The contour interval is 250 meters. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

Topographic Map of the Southwest Ascraeus Mons Region of Mars - MTM 500k 10/252E OMKT

USGS Publications Warehouse

,

2004-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetically using Viking Orbiter stereo image pairs. The contour interval is 250 meters. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

A high-resolution genetic, physical, and comparative gene map of the doublefoot (Dbf) region of mouse chromosome 1 and the region of conserved synteny on human chromosome 2q35.

PubMed

Hayes, C; Rump, A; Cadman, M R; Harrison, M; Evans, E P; Lyon, M F; Morriss-Kay, G M; Rosenthal, A; Brown, S D

2001-12-01

The mouse doublefoot (Dbf) mutant exhibits preaxial polydactyly in association with craniofacial defects. This mutation has previously been mapped to mouse chromosome 1. We have used a positional cloning strategy, coupled with a comparative sequencing approach using available human draft sequence, to identify putative candidates for the Dbf gene in the mouse and in homologous human region. We have constructed a high-resolution genetic map of the region, localizing the mutation to a 0.4-cM (+/-0.0061) interval on mouse chromosome 1. Furthermore, we have constructed contiguous BAC/PAC clone maps across the mouse and human Dbf region. Using existing markers and additional sequence tagged sites, which we have generated, we have anchored the physical map to the genetic map. Through the comparative sequencing of these clones we have identified 35 genes within this interval, indicating that the region is gene-rich. From this we have identified several genes that are known to be differentially expressed in the developing mid-gestation mouse embryo, some in the developing embryonic limb buds. These genes include those encoding known developmental signaling molecules such as WNT proteins and IHH, and we provide evidence that these genes are candidates for the Dbf mutation.

Test-retest reliability of the prefrontal response to affective pictures based on functional near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Yuxia; Mao, Mengchai; Zhang, Zong; Zhou, Hui; Zhao, Yang; Duan, Lian; Kreplin, Ute; Xiao, Xiang; Zhu, Chaozhe

2017-01-01

Functional near-infrared spectroscopy (fNIRS) is being increasingly applied to affective and social neuroscience research; however, the reliability of this method is still unclear. This study aimed to evaluate the test-retest reliability of the fNIRS-based prefrontal response to emotional stimuli. Twenty-six participants viewed unpleasant and neutral pictures, and were simultaneously scanned by fNIRS in two sessions three weeks apart. The reproducibility of the prefrontal activation map was evaluated at three spatial scales (mapwise, clusterwise, and channelwise) at both the group and individual levels. The influence of the time interval was also explored and comparisons were made between longer (intersession) and shorter (intrasession) time intervals. The reliabilities of the activation map at the group level for the mapwise (up to 0.88, the highest value appeared in the intersession assessment) and clusterwise scales (up to 0.91, the highest appeared in the intrasession assessment) were acceptable, indicating that fNIRS may be a reliable tool for emotion studies, especially for a group analysis and under larger spatial scales. However, it should be noted that the individual-level and the channelwise fNIRS prefrontal responses were not sufficiently stable. Future studies should investigate which factors influence reliability, as well as the validity of fNIRS used in emotion studies.

Spatial uncertainty of a geoid undulation model in Guayaquil, Ecuador

NASA Astrophysics Data System (ADS)

Chicaiza, E. G.; Leiva, C. A.; Arranz, J. J.; Buenańo, X. E.

2017-06-01

Geostatistics is a discipline that deals with the statistical analysis of regionalized variables. In this case study, geostatistics is used to estimate geoid undulation in the rural area of Guayaquil town in Ecuador. The geostatistical approach was chosen because the estimation error of prediction map is getting. Open source statistical software R and mainly geoR, gstat and RGeostats libraries were used. Exploratory data analysis (EDA), trend and structural analysis were carried out. An automatic model fitting by Iterative Least Squares and other fitting procedures were employed to fit the variogram. Finally, Kriging using gravity anomaly of Bouguer as external drift and Universal Kriging were used to get a detailed map of geoid undulation. The estimation uncertainty was reached in the interval [-0.5; +0.5] m for errors and a maximum estimation standard deviation of 2 mm in relation with the method of interpolation applied. The error distribution of the geoid undulation map obtained in this study provides a better result than Earth gravitational models publicly available for the study area according the comparison with independent validation points. The main goal of this paper is to confirm the feasibility to use geoid undulations from Global Navigation Satellite Systems and leveling field measurements and geostatistical techniques methods in order to use them in high-accuracy engineering projects.

CT-1-CP-induced ventricular electrical remodeling in mice.

PubMed

Chen, Shu-fen; Wei, Tao-zhi; Rao, Li-ya; Xu, Ming-guang; Dong, Zhan-ling

2015-02-01

The chronic effects of carboxyl-terminal polypeptide of Cardiotrophin-1 (CT-1-CP) on ventricular electrical remodeling were investigated. CT-1-CP, which contains 16 amino acids in sequence of the C-terminal of Cardiotrophin-1, was selected and synthesized, and then administered to Kunming mice (aged 5 weeks) by intraperitoneal injection (500 ng·g⁻¹·day⁻¹) (4 groups, n=10 and female: male=1:1 in each group) for 1, 2, 3 and 4 weeks, respectively. The control group (n=10, female: male=1:1) was injected by physiological saline for 4 weeks. The epicardial monophasic action potential (MAP) was recorded by using a contact-type MAP electrode placed vertically on the left ventricular (LV) epicardium surface, and the electrocardiogram (ECG) signal in lead II was monitored synchronously. ECG intervals (RR, PR, QRS and QT) and the amplitude of MAP (Am), the maximum upstroke velocity (Vmax), as well as action potential durations (APDs) at different repolarization levels (APD30, APD50, APD70, and APD90) of MAP were determined and analyzed in detail. There were no significant differences in RR and P intervals between CT-1-CP-treated groups and control group, but the PR segment and the QRS complex were greater in the former than in the latter (F=2.681 and 5.462 respectively, P<0.05). Though QT interval and the corrected QT interval (QTc) were shorter in CT-1-CP-treated groups than in control group, the QT dispersion (QTd) of them was greater in the latter than in the former (F=3.090, P<0.05) and increased with the time. The ECG monitoring synchronously with the MAP showed that the compression of MAP electrode on the left ventricular epicardium induced performance similar to myocardium ischemia. As compared with those before chest-opening, the PR segment and QT intervals remained basically unchanged in control group, but prolonged significantly in all CT-1-CP-treated groups and the prolongation of QT intervals increased gradually along with the time of exposure to CT-1-CP. The QRS complex had no significant change in control group, one-week and three-week CT-1-CP-treated groups, but prolonged significantly in two-week and four-week CT-1-CP-treated groups. Interestingly, the QTd after chest-opening was significantly greater than that before chest-opening in control group (t=5.242, P<0.01), but decreased along with the time in CT-1-CP-treated groups. The mean MAP amplitude, Vmax and APD were greater in CT-1-CP-treated groups than those in control group, and became more obvious along with the time. The APD in four CT-1-CP-treat groups was prolonged mainly in middle to final repolarization phase. The difference among these groups became significant in middle phase (APD50) (F=6.076, P<0.01) and increased furthermore in late and final phases (APD70: F=10.054; APD90: F=18.691, P<0.01) along with the time of injection of CT-1-CP. The chronic action of CT-1-CP might induce the adapting alteration in cardiac conductivity and ventricular repolarization. The amplitude and the Vmax of the anterior LV epicardial MAP increased obviously, and the APD prolonged mainly in late and final phase of repolarization.

Use of radiotelemetry to assess perinatal cardiac function in the ovine fetus and newborn.

PubMed

Antolic, A; Wood, C E; Keller-Wood, M

2017-12-01

The late gestation fetal ECG (fECG) has traditionally been difficult to characterize due to the low fECG signal relative to high maternal noise. Although new technologies have improved the feasibility of its acquisition and separation, little is known about its development in late gestation, a period in which the fetal heart undergoes extensive maturational changes. Here, we describe a method for the chronic implantation of radiotelemetry devices into late gestation ovine fetuses to characterize parameters of the fECG following surgery, throughout late gestation, and in the perinatal period. We found no significant changes in mean aortic pressure (MAP), heart rate (HR), or ECG in the 5 days following implantation; however, HR decreased in the first 24 h following the end of surgery, with associated increases in RR, PR, and QRS intervals. Over the last 14 days of fetal life, fetal MAP significantly increased, and HR significantly decreased, as expected. MAP and HR increased as labor progressed. Although there were no significant changes over time in the ECG during late gestation, the duration of the PR interval initially decreased and then increased as birth approached. These results indicate that although critical maturational changes occur in the late gestation fetal myocardium, the mechanisms that control the cardiac conduction are relatively mature in late gestation. The study demonstrates that radiotelemetry can be successfully used to assess fetal cardiac function, in particular conduction, through the process of labor and delivery, and may therefore be a useful tool for study of peripartum cardiac events. Copyright © 2017 the American Physiological Society.

Dynamic Contrast-Enhanced MRI of Cervical Cancers: Temporal Percentile Screening of Contrast Enhancement Identifies Parameters for Prediction of Chemoradioresistance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Erlend K.F.; Hole, Knut Hakon; Lund, Kjersti V.

Purpose: To systematically screen the tumor contrast enhancement of locally advanced cervical cancers to assess the prognostic value of two descriptive parameters derived from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Methods and Materials: This study included a prospectively collected cohort of 81 patients who underwent DCE-MRI with gadopentetate dimeglumine before chemoradiotherapy. The following descriptive DCE-MRI parameters were extracted voxel by voxel and presented as histograms for each time point in the dynamic series: normalized relative signal increase (nRSI) and normalized area under the curve (nAUC). The first to 100th percentiles of the histograms were included in a log-rank survival test,more » resulting in p value and relative risk maps of all percentile-time intervals for each DCE-MRI parameter. The maps were used to evaluate the robustness of the individual percentile-time pairs and to construct prognostic parameters. Clinical endpoints were locoregional control and progression-free survival. The study was approved by the institutional ethics committee. Results: The p value maps of nRSI and nAUC showed a large continuous region of percentile-time pairs that were significantly associated with locoregional control (p < 0.05). These parameters had prognostic impact independent of tumor stage, volume, and lymph node status on multivariate analysis. Only a small percentile-time interval of nRSI was associated with progression-free survival. Conclusions: The percentile-time screening identified DCE-MRI parameters that predict long-term locoregional control after chemoradiotherapy of cervical cancer.« less

Translation of Bernstein Coefficients Under an Affine Mapping of the Unit Interval

NASA Technical Reports Server (NTRS)

Alford, John A., II

2012-01-01

We derive an expression connecting the coefficients of a polynomial expanded in the Bernstein basis to the coefficients of an equivalent expansion of the polynomial under an affine mapping of the domain. The expression may be useful in the calculation of bounds for multi-variate polynomials.

Geologic and hydrostratigraphic map of the Anhalt, Fischer, and Spring Branch 7.5-minute quadrangles, Blanco, Comal, and Kendall Counties, Texas

USGS Publications Warehouse

Clark, Allan K.; Robert R. Morris,

2015-01-01

The hydrostratigraphic units of the Edwards and Trinity aquifers have been mapped and described herein using a classification system developed by Choquette and Pray (1970), which is based on porosity types being fabric or not-fabric selective. The naming of hydrostratigraphic units is also based on preexisting names and topographic or historical features that occur in outcrop. The only hydrostratigraphic unit of the Edwards aquifer present in the study area is VIII hydrostratigraphic unit. The mapped hydrostratigraphic units of the upper Trinity aquifer are, from top to bottom: the cavernous, Camp Bullis, upper evaporite, fossiliferous, and lower evaporite and they are interval equivalent to the upper member of the Glen Rose Limestone. The middle Trinity aquifer (interval equivalent to the lower member of the Glen Rose Limestone) contains, from top to bottom: the Bulverde, Little Blanco, Twin Sisters, Doeppenschmidt, Rust, and Honey Creek hydrostratigraphic units. The lower part of the middle Trinity aquifer is formed by the Hensell, Cow Creek, and Hammett hydrostratigraphic units which are interval equivalent to the Hensell Sand Member, the Cow Creek Limestone, and the Hammett Shale Member, respectively, of the Pearsall Formation.

A novel autosomal recessive non-syndromic hearing impairment locus (DFNB47) maps to chromosome 2p25.1-p24.3.

PubMed

Hassan, Muhammad Jawad; Santos, Regie Lyn P; Rafiq, Muhammad Arshad; Chahrour, Maria H; Pham, Thanh L; Wajid, Muhammad; Hijab, Nadine; Wambangco, Michael; Lee, Kwanghyuk; Ansar, Muhammad; Yan, Kai; Ahmad, Wasim; Leal, Suzanne M

2006-01-01

Hereditary hearing impairment (HI) displays extensive genetic heterogeneity. Autosomal recessive (AR) forms of prelingual HI account for approximately 75% of cases with a genetic etiology. A novel AR non-syndromic HI locus (DFNB47) was mapped to chromosome 2p25.1-p24.3, in two distantly related Pakistani kindreds. Genome scan and fine mapping were carried out using microsatellite markers. Multipoint linkage analysis resulted in a maximum LOD score of 4.7 at markers D2S1400 and D2S262. The three-unit support interval was bounded by D2S330 and D2S131. The region of homozygosity was found within the three-unit support interval and flanked by markers D2S2952 and D2S131, which corresponds to 13.2 cM according to the Rutgers combined linkage-physical map. This region contains 5.3 Mb according to the sequence-based physical map. Three candidate genes, KCNF1, ID2 and ATP6V1C2 were sequenced, and were found to be negative for functional sequence variants.

A novel autosomal recessive non-syndromic hearing impairment locus (DFNB47) maps to chromosome 2p25.1-p24.3

PubMed Central

Hassan, Muhammad Jawad; Santos, Regie Lyn P.; Rafiq, Muhammad Arshad; Chahrour, Maria H.; Pham, Thanh L.; Wajid, Muhammad; Hijab, Nadine; Wambangco, Michael; Lee, Kwanghyuk; Ansar, Muhammad; Yan, Kai; Ahmad, Wasim; Leal, Suzanne M.

2010-01-01

Hereditary hearing impairment (HI) displays extensive genetic heterogeneity. Autosomal recessive (AR) forms of prelingual HI account for ~75% of cases with a genetic etiology. A novel AR non-syndromic HI locus (DFNB47) was mapped to chromosome 2p25.1-p24.3, in two distantly related Pakistani kindreds. Genome scan and fine mapping were carried out using microsatellite markers. Multipoint linkage analysis resulted in a maximum LOD score of 4.7 at markers D2S1400 and D2S262. The three-unit support interval was bounded by D2S330 and D2S131. The region of homozygosity was found within the three-unit support interval and flanked by markers D2S2952 and D2S131, which corresponds to 13.2 cM according to the Rutgers combined linkage-physical map. This region contains 5.3 Mb according to the sequence-based physical map. Three candidate genes, KCNF1, ID2 and ATP6V1C2 were sequenced, and were found to be negative for functional sequence variants. PMID:16261342

A high-resolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis.

PubMed

Finkers-Tomczak, Anna; Danan, Sarah; van Dijk, Thijs; Beyene, Amelework; Bouwman, Liesbeth; Overmars, Hein; van Eck, Herman; Goverse, Aska; Bakker, Jaap; Bakker, Erin

2009-06-01

The Grp1 locus confers broad-spectrum resistance to the potato cyst nematode species Globodera pallida and Globodera rostochiensis and is located in the GP21-GP179 interval on the short arm of chromosome V of potato. A high-resolution map has been developed using the diploid mapping population RHAM026, comprising 1,536 genotypes. The flanking markers GP21 and GP179 have been used to screen the 1,536 genotypes for recombination events. Interval mapping of the resistances to G. pallida Pa2 and G. rostochiensis Ro5 resulted in two nearly identical LOD graphs with the highest LOD score just north of marker TG432. Detailed analysis of the 44 recombinant genotypes showed that G. pallida and G. rostochiensis resistance could not be separated and map to the same location between marker SPUD838 and TG432. It is suggested that the quantitative resistance to both nematode species at the Grp1 locus is mediated by one or more tightly linked R genes that might belong to the NBS-LRR class.

Cucheb: A GPU implementation of the filtered Lanczos procedure

NASA Astrophysics Data System (ADS)

Aurentz, Jared L.; Kalantzis, Vassilis; Saad, Yousef

2017-11-01

This paper describes the software package Cucheb, a GPU implementation of the filtered Lanczos procedure for the solution of large sparse symmetric eigenvalue problems. The filtered Lanczos procedure uses a carefully chosen polynomial spectral transformation to accelerate convergence of the Lanczos method when computing eigenvalues within a desired interval. This method has proven particularly effective for eigenvalue problems that arise in electronic structure calculations and density functional theory. We compare our implementation against an equivalent CPU implementation and show that using the GPU can reduce the computation time by more than a factor of 10. Program Summary Program title: Cucheb Program Files doi:http://dx.doi.org/10.17632/rjr9tzchmh.1 Licensing provisions: MIT Programming language: CUDA C/C++ Nature of problem: Electronic structure calculations require the computation of all eigenvalue-eigenvector pairs of a symmetric matrix that lie inside a user-defined real interval. Solution method: To compute all the eigenvalues within a given interval a polynomial spectral transformation is constructed that maps the desired eigenvalues of the original matrix to the exterior of the spectrum of the transformed matrix. The Lanczos method is then used to compute the desired eigenvectors of the transformed matrix, which are then used to recover the desired eigenvalues of the original matrix. The bulk of the operations are executed in parallel using a graphics processing unit (GPU). Runtime: Variable, depending on the number of eigenvalues sought and the size and sparsity of the matrix. Additional comments: Cucheb is compatible with CUDA Toolkit v7.0 or greater.

Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.)

PubMed Central

Gudys, Kornelia; Guzy-Wrobelska, Justyna; Janiak, Agnieszka; Dziurka, Michał A.; Ostrowska, Agnieszka; Hura, Katarzyna; Jurczyk, Barbara; Żmuda, Katarzyna; Grzybkowska, Daria; Śróbka, Joanna; Urban, Wojciech; Biesaga-Koscielniak, Jolanta; Filek, Maria; Koscielniak, Janusz; Mikołajczak, Krzysztof; Ogrodowicz, Piotr; Krystkowiak, Karolina; Kuczyńska, Anetta; Krajewski, Paweł; Szarejko, Iwona

2018-01-01

Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits. PMID:29946328

Historical shoreline mapping (II): Application of the Digital Shoreline Mapping and Analysis Systems (DSMS/DSAS) to shoreline change mapping in Puerto Rico

USGS Publications Warehouse

Thieler, E. Robert; Danforth, William W.

1994-01-01

A new, state-of-the-art method for mapping historical shorelines from maps and aerial photographs, the Digital Shoreline Mapping System (DSMS), has been developed. The DSMS is a freely available, public domain software package that meets the cartographic and photogrammetric requirements of precise coastal mapping, and provides a means to quantify and analyze different sources of error in the mapping process. The DSMS is also capable of resolving imperfections in aerial photography that commonly are assumed to be nonexistent. The DSMS utilizes commonly available computer hardware and software, and permits the entire shoreline mapping process to be executed rapidly by a single person in a small lab. The DSMS generates output shoreline position data that are compatible with a variety of Geographic Information Systems (GIS). A second suite of programs, the Digital Shoreline Analysis System (DSAS) has been developed to calculate shoreline rates-of-change from a series of shoreline data residing in a GIS. Four rate-of-change statistics are calculated simultaneously (end-point rate, average of rates, linear regression and jackknife) at a user-specified interval along the shoreline using a measurement baseline approach. An example of DSMS and DSAS application using historical maps and air photos of Punta Uvero, Puerto Rico provides a basis for assessing the errors associated with the source materials as well as the accuracy of computed shoreline positions and erosion rates. The maps and photos used here represent a common situation in shoreline mapping: marginal-quality source materials. The maps and photos are near the usable upper limit of scale and accuracy, yet the shoreline positions are still accurate ±9.25 m when all sources of error are considered. This level of accuracy yields a resolution of ±0.51 m/yr for shoreline rates-of-change in this example, and is sufficient to identify the short-term trend (36 years) of shoreline change in the study area.

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

PubMed

Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

2018-01-18

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Detection of Mycobacterium avium subspecies paratuberculosis in tie-stall dairy herds using a standardized environmental sampling technique and targeted pooled samples.

PubMed

Arango-Sabogal, Juan C; Côté, Geneviève; Paré, Julie; Labrecque, Olivia; Roy, Jean-Philippe; Buczinski, Sébastien; Doré, Elizabeth; Fairbrother, Julie H; Bissonnette, Nathalie; Wellemans, Vincent; Fecteau, Gilles

2016-07-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiologic agent of Johne's disease, a chronic contagious enteritis of ruminants that causes major economic losses. Several studies, most involving large free-stall herds, have found environmental sampling to be a suitable method for detecting MAP-infected herds. In eastern Canada, where small tie-stall herds are predominant, certain conditions and management practices may influence the survival and transmission of MAP and recovery (isolation). Our objective was to estimate the performance of a standardized environmental and targeted pooled sampling technique for the detection of MAP-infected tie-stall dairy herds. Twenty-four farms (19 MAP-infected and 5 non-infected) were enrolled, but only 20 were visited twice in the same year, to collect 7 environmental samples and 2 pooled samples (sick cows and cows with poor body condition). Concurrent individual sampling of all adult cows in the herds was also carried out. Isolation of MAP was achieved using the MGIT Para TB culture media and the BACTEC 960 detection system. Overall, MAP was isolated in 7% of the environmental cultures. The sensitivity of the environmental culture was 44% [95% confidence interval (CI): 20% to 70%] when combining results from 2 different herd visits and 32% (95% CI: 13% to 57%) when results from only 1 random herd visit were used. The best sampling strategy was to combine samples from the manure pit, gutter, sick cows, and cows with poor body condition. The standardized environmental sampling technique and the targeted pooled samples presented in this study is an alternative sampling strategy to costly individual cultures for detecting MAP-infected tie-stall dairies. Repeated samplings may improve the detection of MAP-infected herds.

A YAC contig spanning the dominant retinitis pigmentosa locus (RP9) on chromosome 7p

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keen, T.J.; Inglehearn, C.F.; Patel, R.J.

1995-08-10

The dominant retinitis pigmentosa locus RP9 has previously been localized to 7p13-p15, in the interval D7S526-D7S484. We now report refinement of the locus to the interval D7S795-D7S484 and YAC contig of approximately 4.8 Mb spanning this region and extending both distally and proximally from it. The contig was constructed by STS content mapping and physically orders 29 STSs in 28 YAC clones. The order of polymorphic markers in the contig is consistent with a genetic map that has been assembled using haplotype data from the CEPH pedigrees. This contig will provide a primary resource for the construction of a transcriptionalmore » map of this region and for the identification of the defective gene causing this form of adRP. 27 refs., 3 figs., 1 tab.« less

Linkage Disequilibrium Mapping in Domestic Dog Breeds Narrows the Progressive Rod-Cone Degeneration (prcd) Interval and Identifies Ancestral Disease Transmitting Chromosome

PubMed Central

Goldstein, Orly; Zangerl, Barbara; Pearce-Kelling, Sue; Sidjanin, Duska J.; Kijas, James W.; Felix, Jeanette; Acland, Gregory M; Aguirre, Gustavo D.

2014-01-01

Canine progressive rod-cone degeneration (prcd) is a retinal disease previously mapped to a broad, gene-rich centromeric region of canine chromosome 9. As allelic disorders are present in multiple breeds, we used linkage disequilibrium (LD) to narrow the ∼6.4 Mb interval candidate region. Multiple dog breeds, each representing genetically isolated populations, were typed for SNPs and other polymorphisms identified from BACs. The candidate region was initially localized to a 1.5 Mb zero recombination interval between growth factor receptor-bound protein 2 (GRB2) and SEC14-like 1 (SEC14L). A fine-scale haplotype of the region was developed which reduced the LD interval to 106 Kb, and identified a conserved haplotype of 98 polymorphisms present in all prcd-affected chromosomes from 14 different dog breeds. The findings strongly suggest that a common ancestor transmitted the prcd disease allele to many of the modern dog breeds, and demonstrate the power of LD approach in the canine model. PMID:16859891

Mapping AIS coverage for trusted surveillance

NASA Astrophysics Data System (ADS)

Lapinski, Anna-Liesa S.; Isenor, Anthony W.

2010-10-01

Automatic Identification System (AIS) is an unattended vessel reporting system developed for collision avoidance. Shipboard AIS equipment automatically broadcasts vessel positional data at regular intervals. The real-time position and identity data from a vessel is received by other vessels in the area thereby assisting with local navigation. As well, AIS broadcasts are beneficial to those concerned with coastal and harbour security. Land-based AIS receiving stations can also collect the AIS broadcasts. However, reception at the land station is dependent upon the ship's position relative to the receiving station. For AIS to be used as a trusted surveillance system, the characteristics of the AIS coverage area in the vicinity of the station (or stations) should be understood. This paper presents some results of a method being investigated at DRDC Atlantic, Canada) to map the AIS coverage characteristics of a dynamic AIS reception network. The method is shown to clearly distinguish AIS reception edges from those edges caused by vessel traffic patterns. The method can also be used to identify temporal changes in the coverage area, an important characteristic for local maritime security surveillance activities. Future research using the coverage estimate technique is also proposed to support surveillance activities.

Variable selection based on clustering analysis for improvement of polyphenols prediction in green tea using synchronous fluorescence spectra

NASA Astrophysics Data System (ADS)

Shan, Jiajia; Wang, Xue; Zhou, Hao; Han, Shuqing; Riza, Dimas Firmanda Al; Kondo, Naoshi

2018-04-01

Synchronous fluorescence spectra, combined with multivariate analysis were used to predict flavonoids content in green tea rapidly and nondestructively. This paper presented a new and efficient spectral intervals selection method called clustering based partial least square (CL-PLS), which selected informative wavelengths by combining clustering concept and partial least square (PLS) methods to improve models’ performance by synchronous fluorescence spectra. The fluorescence spectra of tea samples were obtained and k-means and kohonen-self organizing map clustering algorithms were carried out to cluster full spectra into several clusters, and sub-PLS regression model was developed on each cluster. Finally, CL-PLS models consisting of gradually selected clusters were built. Correlation coefficient (R) was used to evaluate the effect on prediction performance of PLS models. In addition, variable influence on projection partial least square (VIP-PLS), selectivity ratio partial least square (SR-PLS), interval partial least square (iPLS) models and full spectra PLS model were investigated and the results were compared. The results showed that CL-PLS presented the best result for flavonoids prediction using synchronous fluorescence spectra.

Variable selection based on clustering analysis for improvement of polyphenols prediction in green tea using synchronous fluorescence spectra.

PubMed

Shan, Jiajia; Wang, Xue; Zhou, Hao; Han, Shuqing; Riza, Dimas Firmanda Al; Kondo, Naoshi

2018-03-13

Synchronous fluorescence spectra, combined with multivariate analysis were used to predict flavonoids content in green tea rapidly and nondestructively. This paper presented a new and efficient spectral intervals selection method called clustering based partial least square (CL-PLS), which selected informative wavelengths by combining clustering concept and partial least square (PLS) methods to improve models' performance by synchronous fluorescence spectra. The fluorescence spectra of tea samples were obtained and k-means and kohonen-self organizing map clustering algorithms were carried out to cluster full spectra into several clusters, and sub-PLS regression model was developed on each cluster. Finally, CL-PLS models consisting of gradually selected clusters were built. Correlation coefficient (R) was used to evaluate the effect on prediction performance of PLS models. In addition, variable influence on projection partial least square (VIP-PLS), selectivity ratio partial least square (SR-PLS), interval partial least square (iPLS) models and full spectra PLS model were investigated and the results were compared. The results showed that CL-PLS presented the best result for flavonoids prediction using synchronous fluorescence spectra.

Detection of anomalous crop condition and soil variability mapping using a 26 year Landsat record and the Palmer crop moisture index

NASA Astrophysics Data System (ADS)

Venteris, E. R.; Tagestad, J. D.; Downs, J. L.; Murray, C. J.

2015-07-01

Cost-effective and reliable vegetation monitoring methods are needed for applications ranging from traditional agronomic mapping, to verifying the safety of geologic injection activities. A particular challenge is defining baseline crop conditions and subsequent anomalies from long term imagery records (Landsat) in the face of large spatiotemporal variability. We develop a new method for defining baseline crop response (near peak growth) using the normalized difference vegetation index (NDVI) from 26 years (1986-2011) of Landsat data for 400 km2 surrounding a planned geologic carbon sequestration site near Jacksonville, Illinois. The normal score transform (yNDVI) was applied on a field by field basis to accentuate spatial patterns and level differences due to planting times. We tested crop type and soil moisture (Palmer crop moisture index (CMI)) as predictors of expected crop condition. Spatial patterns in yNDVI were similar between corn and soybeans - the two major crops. Linear regressions between yNDVI and the cumulative CMI (CCMI) exposed complex interactions between crop condition, field location (topography and soils), and annual moisture. Wet toposequence positions (depressions) were negatively correlated to CCMI and dry positions (crests) positively correlated. However, only 21% of the landscape showed a statistically significant (p < 0.05) linear relationship. To map anomalous crop conditions, we defined a tolerance interval based on yNDVI statistics. Tested on an independent image (2013), 63 of 1483 possible fields showed unusual crop condition. While the method is not directly suitable for crop health assessment, the spatial patterns in correlation between yNDVI and CCMI have potential applications for pest damage detection and edaphological soil mapping, especially in the developing world.

Identifying Significant Changes in Cerebrovascular Reactivity to Carbon Dioxide.

PubMed

Sobczyk, O; Crawley, A P; Poublanc, J; Sam, K; Mandell, D M; Mikulis, D J; Duffin, J; Fisher, J A

2016-05-01

Changes in cerebrovascular reactivity can be used to assess disease progression and response to therapy but require discrimination of pathology from normal test-to-test variability. Such variability is due to variations in methodology, technology, and physiology with time. With uniform test conditions, our aim was to determine the test-to-test variability of cerebrovascular reactivity in healthy subjects and in patients with known cerebrovascular disease. Cerebrovascular reactivity was the ratio of the blood oxygen level-dependent MR imaging response divided by the change in carbon dioxide stimulus. Two standardized cerebrovascular reactivity tests were conducted at 3T in 15 healthy men (36.7 ± 16.1 years of age) within a 4-month period and were coregistered into standard space to yield voxelwise mean cerebrovascular reactivity interval difference measures, composing a reference interval difference atlas. Cerebrovascular reactivity interval difference maps were prepared for 11 male patients. For each patient, the test-retest difference of each voxel was scored statistically as z-values of the corresponding voxel mean difference in the reference atlas and then color-coded and superimposed on the anatomic images to create cerebrovascular reactivity interval difference z-maps. There were no significant test-to-test differences in cerebrovascular reactivity in either gray or white matter (mean gray matter, P = .431; mean white matter, P = .857; paired t test) in the healthy cohort. The patient cerebrovascular reactivity interval difference z-maps indicated regions where cerebrovascular reactivity increased or decreased and the probability that the changes were significant. Accounting for normal test-to-test differences in cerebrovascular reactivity enables the assessment of significant changes in disease status (stability, progression, or regression) in patients with time. © 2016 by American Journal of Neuroradiology.

Flood-inundation maps for the West Branch Delaware River, Delhi, New York, 2012

USGS Publications Warehouse

Coon, William F.; Breaker, Brian K.

2012-01-01

Digital flood-inundation maps for a 5-mile reach of the West Branch Delaware River through the Village and part of the Town of Delhi, New York, were created by the U.S. Geological Survey (USGS) in cooperation with the Village of Delhi, the Delaware County Soil and Water Conservation District, and the Delaware County Planning Department. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ and the Federal Flood Inundation Mapper Web site at http://wim.usgs.gov/FIMI/FloodInundationMapper.html, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) referenced to the USGS streamgage at West Branch Delaware River upstream from Delhi, N.Y. (station number 01421900). In this study, flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model that had been used to produce the flood insurance rate maps for the most recent flood insurance study for the Town and Village of Delhi. This hydraulic model was used to compute 10 water-surface profiles for flood stages at 1-foot (ft) intervals referenced to the streamgage datum and ranging from 7 ft or near bankfull to 16 ft, which exceeds the stages that correspond to both the estimated 0.2-percent annual-exceedance-probability flood (500-year recurrence interval flood) and the maximum recorded peak flow. The simulated water-surface profiles were then combined with a geographic information system (GIS) digital elevation model, which was derived from Light Detection and Ranging (LiDAR) data with a 1.2-ft (0.61-ft root mean squared error) vertical accuracy and 3.3-ft (1-meter) horizontal resolution, to delineate the area flooded at each water level. A map that was produced using this method to delineate the inundated area for the flood that occurred on August 28, 2011, agreed well with highwater marks that had been located in the field using a global positioning system. The availability of the 10 flood-inundation maps on the USGS Flood Inundation Mapping Science Web site, along with Internet information regarding current stage from the USGS streamgage, will provide emergency management personnel and residents with information that is critical for flood-response activities, such as evacuations and road closures, as well as for post-flood recovery efforts.

The Montana experience

NASA Technical Reports Server (NTRS)

Dundas, T. R.

1981-01-01

The development and capabilities of the Montana geodata system are discussed. The system is entirely dependent on the state's central data processing facility which serves all agencies and is therefore restricted to batch mode processing. The computer graphics equipment is briefly described along with its application to state lands and township mapping and the production of water quality interval maps.

Flood characteristics of streams in Owyhee County, Idaho

USGS Publications Warehouse

Riggs, H.C.; Harenberg, W.A.

1976-01-01

Channel-width measurements were used to estimate annual peaks with a recurrence interval of 10 years at 79 sites in Owyhee County, Idaho, and adjacent areas. These discharges and those from 33 gaging stations are plotted on a map of the area. The map will allow the user to interpolate between sites. (Woodard-USGS)

49 CFR Appendix C to Part 195 - Guidance for Implementation of an Integrity Management Program

Code of Federal Regulations, 2014 CFR

2014-10-01

... get this information from topographical maps such as U.S. Geological Survey quadrangle maps. (2... risk.)—Risk Value=3 Close interval survey: (yes/no)—no—Risk Value =5 Internal Inspection tool used..., including a summary of performance improvements, both qualitative and quantitative, to an operator's...

49 CFR Appendix C to Part 195 - Guidance for Implementation of an Integrity Management Program

Code of Federal Regulations, 2011 CFR

2011-10-01

... get this information from topographical maps such as U.S. Geological Survey quadrangle maps. (2... risk.)—Risk Value=3 Close interval survey: (yes/no)—no—Risk Value =5 Internal Inspection tool used..., including a summary of performance improvements, both qualitative and quantitative, to an operator's...

49 CFR Appendix C to Part 195 - Guidance for Implementation of an Integrity Management Program

Code of Federal Regulations, 2012 CFR

2012-10-01

... get this information from topographical maps such as U.S. Geological Survey quadrangle maps. (2... risk.)—Risk Value=3 Close interval survey: (yes/no)—no—Risk Value =5 Internal Inspection tool used..., including a summary of performance improvements, both qualitative and quantitative, to an operator's...

49 CFR Appendix C to Part 195 - Guidance for Implementation of an Integrity Management Program

Code of Federal Regulations, 2013 CFR

2013-10-01

... get this information from topographical maps such as U.S. Geological Survey quadrangle maps. (2... risk.)—Risk Value=3 Close interval survey: (yes/no)—no—Risk Value =5 Internal Inspection tool used..., including a summary of performance improvements, both qualitative and quantitative, to an operator's...

An integrated genetic and physical map of the autosomal recessive polycystic kidney disease region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lens, X.M.; Onuchic, L.F.; Daoust, M.

1997-05-01

Autosomal recessive polycystic kidney disease is one of the most common hereditary renal cystic diseases in children. Genetic studies have recently assigned the only known locus for this disorder, PKHD1, to chromosome 6p21-p12. We have generated a YAC contig that spans {approximately}5 cM of this region, defined by the markers D6S1253-D6S295, and have mapped 43 sequence-tagged sites (STS) within this interval. This set includes 20 novel STSs, which define 12 unique positions in the region, and three ESTs. A minimal set of two YACs spans the segment D6S465-D6S466, which contains PKHD1, and estimates of their sizes based on information inmore » public databases suggest that the size of the critical region is <3.1 Mb. Twenty-eight STSs map to this interval, giving an average STS density of <1/150 kb. These resources will be useful for establishing a complete trancription map of the PKHD1 region. 10 refs., 1 fig., 1 tab.« less

Contour maps of lunar remanent magnetic fields

NASA Technical Reports Server (NTRS)

Hood, L. L.; Russell, C. T.; Coleman, P. J., Jr.

1981-01-01

The 2605 usable orbits of Apollo 15 and 16 subsatellite magnetometer data have been reexamined for intervals suitable for analysis of crustal magnetic anomalies. To minimize plasma-related disturbances, segments from 274 of these orbits were selected from times when the moon was either in a lobe of the geomagnetic tail or in the solar wind with the subsatellites in the lunar wake. External field contributions which remained in the selected intervals were minimized by (1) quadratic detrending of individual orbit segments with lengths much greater than anomaly wavelengths and (2) two-dimensional filtering with minimum passed wavelengths less than or equal to anomaly wavelengths. Improvements in coverage, accuracy, and resolution of previously published anomaly maps produced from these data are obtained. In addition to improved maps of the Reiner Gamma and Van de Graaff-Aitken anomalies studied previously, a third region of relatively high-amplitude anomalies centered near the crater Gerasimovich on the southeastern far side has been mapped. Both the Van de Graaff-Aitken region and the Gerasimovich region are marked by the general occurrence of extensive groups of Reiner Gamma-type swirls.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, genetic homogeneity, and mapping of the locus within a 2-cM interval

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ducros, A.; Alamowitch, S.; Nagy, T.

1996-01-01

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a recently identified autosomal dominant cerebral arteriopathy characterized by the recurrence of subcortical infarcts leading to dementia. A genetic linkage analysis conducted in two large families recently allowed us to map the affected gene on chromosome 19 in a 12-cM interval bracketed by D19S221 and D19S215. In the present study, these first 2 families and 13 additional ones, including a total of 199 potentially informative meiosis, have been genotyped with eight polymorphic markers located between D19S221 and D19S215. All families were linked to chromosome 19. The highest combined lodmore » score (Z{sub max} = 37.24 at {theta} = .01) was obtained with marker D19S841, a new CA{sub n} microsatellite marker that we isolated from chromosome 19 cosmids. The recombinant events observed within these families were used to refine the genetic mapping of CADASIL within a 2-cM interval that is now bracketed by D19S226 and D19S199 on 19p13.1. These data strongly suggest the genetic homogeneity of this recently identified condition and establish the value of its clinical and neuroimaging diagnostic criteria. Besides their importance for the ongoing positional cloning of the CADASIL gene, these data help to refine the genetic mapping of CADASIL relative to familial hemiplegic migraine and hereditary paroxysmal cerebellar ataxia, conditions that we both mapped within the same chromosome 19 region. 35 refs., 5 figs., 2 tabs.« less

Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton.

PubMed

Xu, Peng; Gao, Jin; Cao, Zhibin; Chee, Peng W; Guo, Qi; Xu, Zhenzhen; Paterson, Andrew H; Zhang, Xianggui; Shen, Xinlian

2017-06-01

A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC 4 F 2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC 4 F 3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F 2 population, supporting these genes as candidates for qFL-chr1.

Analysis of Fundus Shape in Highly Myopic Eyes by Using Curvature Maps Constructed from Optical Coherence Tomography

PubMed Central

Miyake, Masahiro; Yamashiro, Kenji; Akagi-Kurashige, Yumiko; Oishi, Akio; Tsujikawa, Akitaka; Hangai, Masanori; Yoshimura, Nagahisa

2014-01-01

Purpose To evaluate fundus shape in highly myopic eyes using color maps created through optical coherence tomography (OCT) image analysis. Methods We retrospectively evaluated 182 highly myopic eyes from 113 patients. After obtaining 12 lines of 9-mm radial OCT scans with the fovea at the center, the Bruch’s membrane line was plotted and its curvature was measured at 1-µm intervals in each image, which was reflected as a color topography map. For the quantitative analysis of the eye shape, mean absolute curvature and variance of curvature were calculated. Results The color maps allowed staphyloma visualization as a ring of green color at the edge and as that of orange-red color at the bottom. Analyses of mean and variance of curvature revealed that eyes with myopic choroidal neovascularization tended to have relatively flat posterior poles with smooth surfaces, while eyes with chorioretinal atrophy exhibited a steep, curved shape with an undulated surface (P<0.001). Furthermore, eyes with staphylomas and those without clearly differed in terms of mean curvature and the variance of curvature: 98.4% of eyes with staphylomas had mean curvature ≥7.8×10−5 [1/µm] and variance of curvature ≥0.26×10−8 [1/µm]. Conclusions We established a novel method to analyze posterior pole shape by using OCT images to construct curvature maps. Our quantitative analysis revealed that fundus shape is associated with myopic complications. These values were also effective in distinguishing eyes with staphylomas from those without. This tool for the quantitative evaluation of eye shape should facilitate future research of myopic complications. PMID:25259853

Quantification of mammographic masking risk with volumetric breast density maps: how to select women for supplemental screening

NASA Astrophysics Data System (ADS)

Holland, Katharina; van Gils, Carla H.; Wanders, Johanna OP; Mann, Ritse M.; Karssemeijer, Nico

2016-03-01

The sensitivity of mammograms is low for women with dense breasts, since cancers may be masked by dense tissue. In this study, we investigated methods to identify women with density patterns associated with a high masking risk. Risk measures are derived from volumetric breast density maps. We used the last negative screening mammograms of 93 women who subsequently presented with an interval cancer (IC), and, as controls, 930 randomly selected normal screening exams from women without cancer. Volumetric breast density maps were computed from the mammograms, which provide the dense tissue thickness at each location. These were used to compute absolute and percentage glandular tissue volume. We modeled the masking risk for each pixel location using the absolute and percentage dense tissue thickness and we investigated the effect of taking the cancer location probability distribution (CLPD) into account. For each method, we selected cases with the highest masking measure (by thresholding) and computed the fraction of ICs as a function of the fraction of controls selected. The latter can be interpreted as the negative supplemental screening rate (NSSR). Between the models, when incorporating CLPD, no significant differences were found. In general, the methods performed better when CLPD was included. At higher NSSRs some of the investigated masking measures had a significantly higher performance than volumetric breast density. These measures may therefore serve as an alternative to identify women with a high risk for a masked cancer.

Machado Joseph disease maps to the same region of chromosome 14 as the spinocerebellar ataxia type 3 locus.

PubMed Central

Twist, E C; Casaubon, L K; Ruttledge, M H; Rao, V S; Macleod, P M; Radvany, J; Zhao, Z; Rosenberg, R N; Farrer, L A; Rouleau, G A

1995-01-01

Machado Joseph disease (MJD) is an autosomal dominantly inherited neuro-degenerative disorder primarily affecting the motor system. It can be divided into three phenotypes based on the variable combination of a range of clinical symptoms including pyramidal and extra-pyramidal features, cerebellar deficits, and distal muscle atrophy. MJD is thought to be caused by mutation of a single gene which has recently been mapped, using genetic linkage analysis, to a 29 cM region on chromosome 14q24.3-q32 in five Japanese families. A second disorder, spinocerebellar ataxia type 3 (SCA3), which has clinical symptoms similar to MJD, has also been linked to the same region of chromosome 14q in two French families. In order to narrow down the region of chromosome 14 which contains the MJD locus and to determine if this region overlaps with the predisposing locus for SCA3, we have performed genetic linkage analysis in seven MJD families, six of Portuguese/Azorean origin and one of Brazilian origin, using nine microsatellite markers mapped to 14q24.3-q32. Our results localise the MJD locus in these families to an 11 cM interval flanked by the markers D14S68 and AFM343vf1. In addition we show that this 11 cM interval maps within the 15 cM interval containing the SCA3 locus, suggesting that these diseases are allelic. PMID:7897622

Dynamic population mapping using mobile phone data.

PubMed

Deville, Pierre; Linard, Catherine; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R; Gaughan, Andrea E; Blondel, Vincent D; Tatem, Andrew J

2014-11-11

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography.

A Genetic and Molecular Analysis of the 46c Chromosomal Region Surrounding the Fmrfamide Neuropeptide Gene in Drosophila Melanogaster

PubMed Central

O'Brien, M. A.; Roberts, M. S.; Taghert, P. H.

1994-01-01

We have analyzed the FMRFamide neuropeptide gene region of Drosophila melanogaster. This gene maps to the 46C region of chromosome 2R; this interval previously was not well characterized. For this genetic and molecular analysis, we have used X-ray mutagenesis, EMS mutagenesis, and the recently reported local P element transposition method. We identified four overlapping deletions, two of which have proximal breakpoints that define a 50-60-kb region surrounding the FMRFamide gene in 46C. To this small region, we mapped three lethal complementation groups; 10 additional lethal complementation groups were mapped to more distal regions of 46CD. One of these groups corresponds to even-skipped, the other 12 are previously unidentified. Using various lines of evidence we excluded the possibility that FMRFamide corresponds to any of the three lethal complementation groups mapping to its immediate 50-60-kb vicinity. The positions of two of the three lethal complementation groups were identified with P elements using a local transposition scheme. The third lethal complementation group was excluded as being FMRFamide mutants by sequence analysis and by immunocytochemistry with proFMRFamide precursor-specific antibodies. This analysis has (1) provided a genetic map of the 46CD chromosomal region and a detailed molecular map of a portion of the 46C region and (2) provided additional evidence of the utility of local transposition for targeting nearby genes. PMID:8056304

Dynamic population mapping using mobile phone data

PubMed Central

Deville, Pierre; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R.; Gaughan, Andrea E.; Blondel, Vincent D.; Tatem, Andrew J.

2014-01-01

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography. PMID:25349388

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

PubMed Central

Feng, Chungang; Gao, Yu; Dorshorst, Ben; Song, Chi; Gu, Xiaorong; Li, Qingyuan; Li, Jinxiu; Liu, Tongxin; Rubin, Carl-Johan; Zhao, Yiqiang; Wang, Yanqiang; Fei, Jing; Li, Huifang; Chen, Kuanwei; Qu, Hao; Shu, Dingming; Ashwell, Chris; Da, Yang; Andersson, Leif; Hu, Xiaoxiang; Li, Ning

2014-01-01

Silky-feather has been selected and fixed in some breeds due to its unique appearance. This phenotype is caused by a single recessive gene (hookless, h). Here we map the silky-feather locus to chromosome 3 by linkage analysis and subsequently fine-map it to an 18.9 kb interval using the identical by descent (IBD) method. Further analysis reveals that a C to G transversion located upstream of the prenyl (decaprenyl) diphosphate synthase, subunit 2 (PDSS2) gene is causing silky-feather. All silky-feather birds are homozygous for the G allele. The silky-feather mutation significantly decreases the expression of PDSS2 during feather development in vivo. Consistent with the regulatory effect, the C to G transversion is shown to remarkably reduce PDSS2 promoter activity in vitro. We report a new example of feather structure variation associated with a spontaneous mutation and provide new insight into the PDSS2 function. PMID:25166907

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

PubMed Central

Pan, Lei; Wang, Nian; Wu, Zhihua; Guo, Rui; Yu, Xiaolu; Zheng, Yu; Xia, Qiuju; Gui, Songtao; Chen, Chanyou

2017-01-01

Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs). The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping) method, eleven quantitative trait loci (QTL) of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11) in cowpea. These QTL explained 0.05–17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW), two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna. PMID:28936219

Cigarette smoke chemistry market maps under Massachusetts Department of Public Health smoking conditions.

PubMed

Morton, Michael J; Laffoon, Susan W

2008-06-01

This study extends the market mapping concept introduced by Counts et al. (Counts, M.E., Hsu, F.S., Tewes, F.J., 2006. Development of a commercial cigarette "market map" comparison methodology for evaluating new or non-conventional cigarettes. Regul. Toxicol. Pharmacol. 46, 225-242) to include both temporal cigarette and testing variation and also machine smoking with more intense puffing parameters, as defined by the Massachusetts Department of Public Health (MDPH). The study was conducted over a two year period and involved a total of 23 different commercial cigarette brands from the U.S. marketplace. Market mapping prediction intervals were developed for 40 mainstream cigarette smoke constituents and the potential utility of the market map as a comparison tool for new brands was demonstrated. The over-time character of the data allowed for the variance structure of the smoke constituents to be more completely characterized than is possible with one-time sample data. The variance was partitioned among brand-to-brand differences, temporal differences, and the remaining residual variation using a mixed random and fixed effects model. It was shown that a conventional weighted least squares model typically gave similar prediction intervals to those of the more complicated mixed model. For most constituents there was less difference in the prediction intervals calculated from over-time samples and those calculated from one-time samples than had been anticipated. One-time sample maps may be adequate for many purposes if the user is aware of their limitations. Cigarette tobacco fillers were analyzed for nitrate, nicotine, tobacco-specific nitrosamines, ammonia, chlorogenic acid, and reducing sugars. The filler information was used to improve predicting relationships for several of the smoke constituents, and it was concluded that the effects of filler chemistry on smoke chemistry were partial explanations of the observed brand-to-brand variation.

Application of GNSS-RTK derived topographical maps for rapid environmental monitoring: a case study of Jack Finnery Lake (Perth, Australia).

PubMed

Schloderer, Glen; Bingham, Matthew; Awange, Joseph L; Fleming, Kevin M

2011-09-01

In environmental monitoring, environmental impact assessments and environmental audits, topographical maps play an essential role in providing a means by which the locations of sampling sites may be selected, in assisting with the interpretation of physical features, and in indicating the impact or potential impact on an area due to changes in the system being monitored (e.g., spatially changing features such as wetlands). Global Navigation Satellite Systems (GNSS) are hereby presented as a rapid method for monitoring spatial changes to support environmental monitoring decisions and policies. To validate the GNSS-based method, a comparison is made of results from a small-scale topographic survey using radio-based real-time kinematic GNSS (GNSS-RTK) and total station survey methods at Jack Finnery Lake, Perth, Australia. The accuracies achieved by the total station in this study were 2 cm horizontally and 6 cm vertically, while the GNSS-RTK also achieved an accuracy of 2 cm horizontally, but only 28 cm vertically. While the GNSS-RTK measurements were less accurate in the height component compared to those from the total station method, it is still capable of achieving accuracies sufficient for a topographic map at a scale of 1:1,750 that could support environmental monitoring tasks such as identifying spatial changes in small water bodies or wetlands. The time taken to perform the survey using GNSS-RTK, however, was much shorter compared to the total station method, thereby making it quite suitable for monitoring spatial changes within an environmental context, e.g., dynamic mining activities that require rapid surveys and the updating of the monitored data at regular intervals.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks.

PubMed

Illman, Walter A

2014-01-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss ) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this article, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling, and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability. © 2013, National Ground Water Association.

Hydraulic tomography offers improved imaging of heterogeneity in fractured rocks

NASA Astrophysics Data System (ADS)

Illman, W. A.

2013-12-01

Fractured rocks have presented formidable challenges for accurately predicting groundwater flow and contaminant transport. This is mainly due to our difficulty in mapping the fracture-rock matrix system, their hydraulic properties and connectivity at resolutions that are meaningful for groundwater flow and especially transport modeling. Over the last several decades, considerable effort has gone into creating maps of subsurface heterogeneity in hydraulic conductivity (K) and specific storage (Ss) of fractured rocks. Developed methods include kriging, stochastic simulation, stochastic inverse modeling, and hydraulic tomography. In this presentation, I review the evolution of various heterogeneity mapping approaches and contend that hydraulic tomography, a recently developed aquifer characterization technique for unconsolidated deposits, is also a promising approach in yielding robust maps (or tomograms) of K and Ss heterogeneity for fractured rocks. While hydraulic tomography has recently been shown to be a robust technique, the resolution of the K and Ss tomograms mainly depends on the density of pumping and monitoring locations and the quality of data. The resolution will be improved through the development of new devices for higher density monitoring of pressure responses at discrete intervals in boreholes and potentially through the integration of other data from single-hole tests, borehole flowmeter profiling and tracer tests. Other data from temperature and geophysical surveys as well as geological investigations may improve the accuracy of the maps, but more research is needed. Technological advances will undoubtedly lead to more accurate maps. However, more effort should go into evaluating these maps so that one can gain more confidence in their reliability.

Development of method for evaluating estimated inundation area by using river flood analysis based on multiple flood scenarios

NASA Astrophysics Data System (ADS)

Ono, T.; Takahashi, T.

2017-12-01

Non-structural mitigation measures such as flood hazard map based on estimated inundation area have been more important because heavy rains exceeding the design rainfall frequently occur in recent years. However, conventional method may lead to an underestimation of the area because assumed locations of dike breach in river flood analysis are limited to the cases exceeding the high-water level. The objective of this study is to consider the uncertainty of estimated inundation area with difference of the location of dike breach in river flood analysis. This study proposed multiple flood scenarios which can set automatically multiple locations of dike breach in river flood analysis. The major premise of adopting this method is not to be able to predict the location of dike breach correctly. The proposed method utilized interval of dike breach which is distance of dike breaches placed next to each other. That is, multiple locations of dike breach were set every interval of dike breach. The 2D shallow water equations was adopted as the governing equation of river flood analysis, and the leap-frog scheme with staggered grid was used. The river flood analysis was verified by applying for the 2015 Kinugawa river flooding, and the proposed multiple flood scenarios was applied for the Akutagawa river in Takatsuki city. As the result of computation in the Akutagawa river, a comparison with each computed maximum inundation depth of dike breaches placed next to each other proved that the proposed method enabled to prevent underestimation of estimated inundation area. Further, the analyses on spatial distribution of inundation class and maximum inundation depth in each of the measurement points also proved that the optimum interval of dike breach which can evaluate the maximum inundation area using the minimum assumed locations of dike breach. In brief, this study found the optimum interval of dike breach in the Akutagawa river, which enabled estimated maximum inundation area to predict efficiently and accurately. The river flood analysis by using this proposed method will contribute to mitigate flood disaster by improving the accuracy of estimated inundation area.

Fine genetic mapping of spot blotch resistance gene Sb3 in wheat (Triticum aestivum).

PubMed

Lu, Ping; Liang, Yong; Li, Delin; Wang, Zhengzhong; Li, Wenbin; Wang, Guoxin; Wang, Yong; Zhou, Shenghui; Wu, Qiuhong; Xie, Jingzhong; Zhang, Deyun; Chen, Yongxing; Li, Miaomiao; Zhang, Yan; Sun, Qixin; Han, Chenggui; Liu, Zhiyong

2016-03-01

Spot blotch disease resistance gene Sb3 was mapped to a 0.15 centimorgan (cM) genetic interval spanning a 602 kb physical genomic region on chromosome 3BS. Wheat spot blotch disease, caused by B. sorokiniana, is a devastating disease that can cause severe yield losses. Although inoculum levels can be reduced by planting disease-free seed, treatment of plants with fungicides and crop rotation, genetic resistance is likely to be a robust, economical and environmentally friendly tool in the control of spot blotch. The winter wheat line 621-7-1 confers immune resistance against B. sorokiniana. Genetic analysis indicates that the spot blotch resistance of 621-7-1 is controlled by a single dominant gene, provisionally designated Sb3. Bulked segregant analysis (BSA) and simple sequence repeat (SSR) mapping showed that Sb3 is located on chromosome arm 3BS linked with markers Xbarc133 and Xbarc147. Seven and twelve new polymorphic markers were developed from the Chinese Spring 3BS shotgun survey sequence contigs and 3BS reference sequences, respectively. Finally, Sb3 was mapped in a 0.15 cM genetic interval spanning a 602 kb physical genomic region of Chinese Spring chromosome 3BS. The genetic and physical maps of Sb3 provide a framework for map-based cloning and marker-assisted selection (MAS) of the spot blotch resistance.

Conflation and integration of archived geologic maps and associated uncertainties

USGS Publications Warehouse

Shoberg, Thomas G.

2016-01-01

Old, archived geologic maps are often available with little or no associated metadata. This creates special problems in terms of extracting their data to use with a modern database. This research focuses on some problems and uncertainties associated with conflating older geologic maps in regions where modern geologic maps are, as yet, non-existent as well as vertically integrating the conflated maps with layers of modern GIS data (in this case, The National Map of the U.S. Geological Survey). Ste. Genevieve County, Missouri was chosen as the test area. It is covered by six archived geologic maps constructed in the years between 1928 and 1994. Conflating these maps results in a map that is internally consistent with these six maps, is digitally integrated with hydrography, elevation and orthoimagery data, and has a 95% confidence interval useful for further data set integration.

Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height.

PubMed

Gupta, Shefali; Kumar, Tapan; Verma, Subodh; Bharadwaj, Chellapilla; Bhatia, Sabhyata

2015-11-01

Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

NASA Technical Reports Server (NTRS)

Royce, Thomas E.; Rozowsky, Joel S.; Bertone, Paul; Samanta, Manoj; Stolc, Viktor; Weissman, Sherman; Snyder, Michael; Gerstein, Mark

2005-01-01

Traditional microarrays use probes complementary to known genes to quantitate the differential gene expression between two or more conditions. Genomic tiling microarray experiments differ in that probes that span a genomic region at regular intervals are used to detect the presence or absence of transcription. This difference means the same sets of biases and the methods for addressing them are unlikely to be relevant to both types of experiment. We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology.

Mixing rates and limit theorems for random intermittent maps

NASA Astrophysics Data System (ADS)

Bahsoun, Wael; Bose, Christopher

2016-04-01

We study random transformations built from intermittent maps on the unit interval that share a common neutral fixed point. We focus mainly on random selections of Pomeu-Manneville-type maps {{T}α} using the full parameter range 0<α <∞ , in general. We derive a number of results around a common theme that illustrates in detail how the constituent map that is fastest mixing (i.e. smallest α) combined with details of the randomizing process, determines the asymptotic properties of the random transformation. Our key result (theorem 1.1) establishes sharp estimates on the position of return time intervals for the quenched dynamics. The main applications of this estimate are to limit laws (in particular, CLT and stable laws, depending on the parameters chosen in the range 0<α <1 ) for the associated skew product; these are detailed in theorem 3.2. Since our estimates in theorem 1.1 also hold for 1≤slant α <∞ we study a second class of random transformations derived from piecewise affine Gaspard-Wang maps, prove existence of an infinite (σ-finite) invariant measure and study the corresponding correlation asymptotics. To the best of our knowledge, this latter kind of result is completely new in the setting of random transformations.

An approach for mapping the number and distribution of Salmonella contamination on the poultry carcass.

PubMed

Oscar, T P

2008-09-01

Mapping the number and distribution of Salmonella on poultry carcasses will help guide better design of processing procedures to reduce or eliminate this human pathogen from poultry. A selective plating media with multiple antibiotics (xylose-lysine agar medium [XL] containing N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) and the antibiotics chloramphenicol, ampicillin, tetracycline, and streptomycin [XLH-CATS]) and a multiple-antibiotic-resistant strain (ATCC 700408) of Salmonella Typhimurium definitive phage type 104 (DT104) were used to develop an enumeration method for mapping the number and distribution of Salmonella Typhimurium DT104 on the carcasses of young chickens in the Cornish game hen class. The enumeration method was based on the concept that the time to detection by drop plating on XLH-CATS during incubation of whole chicken parts in buffered peptone water would be inversely related to the initial log number (N0) of Salmonella Typhimurium DT104 on the chicken part. The sampling plan for mapping involved dividing the chicken into 12 parts, which ranged in average size from 36 to 80 g. To develop the enumeration method, whole parts were spot inoculated with 0 to 6 log Salmonella Typhimurium DT104, incubated in 300 ml of buffered peptone water, and detected on XLH-CATS by drop plating. An inverse relationship between detection time on XLH-CATS and N0 was found (r = -0.984). The standard curve was similar for the individual chicken parts and therefore, a single standard curve for all 12 chicken parts was developed. The final standard curve, which contained a 95% prediction interval for providing stochastic results for N0, had high goodness of fit (r2 = 0.968) and was N0 (log) = 7.78 +/- 0.61 - (0.995 x detention time). Ninety-five percent of N0 were within +/- 0.61 log of the standard curve. The enumeration method and sampling plan will be used in future studies to map changes in the number and distribution of Salmonella on carcasses of young chickens fed the DT104 strain used in standard curve development and subjected to different processing procedures.

A novel locus for Usher syndrome type I, USH1G, maps to chromosome 17q24-25.

PubMed

Mustapha, Mirna; Chouery, Eliane; Torchard-Pagnez, Delphine; Nouaille, Sylvie; Khrais, Awni; Sayegh, Fouad N; Mégarbané, André; Loiselet, Jacques; Lathrop, Mark; Petit, Christine; Weil, Dominique

2002-04-01

Usher syndrome (USH) is an autosomal recessive disorder associated with sensorineural hearing impairment and progressive visual loss attributable to retinitis pigmentosa. This syndrome is both clinically and genetically heterogeneous. Three clinical types have been described of which type I (USH1) is the most severe. Six USH1 loci have been identified. We report a Palestinian consanguineous family from Jordan with three affected children. In view of the combination of profound hearing loss, vestibular dysfunction, and retinitis pigmentosa in the patients, we classified the disease as USH1. Linkage analysis excluded the involvement of any of the known USH1 loci. A genome-wide screening allowed us to map this novel locus, USH1G, in a 23-cM interval on chromosome 17q24-25. The USH1G interval overlaps the intervals for two dominant forms of isolated hearing loss, namely DFNA20 and DFNA26. Since several examples have been reported of syndromic and isolated forms of deafness being allelic, USH1G, DFNA20, and DFNA26 might result from alterations of the same gene. Finally, a mouse mutant, jackson shaker ( js), with deafness and circling behavior has been mapped to the murine homologous region on chromosome 11.

Laharz_py: GIS tools for automated mapping of lahar inundation hazard zones

USGS Publications Warehouse

Schilling, Steve P.

2014-01-01

Laharz_py is written in the Python programming language as a suite of tools for use in ArcMap Geographic Information System (GIS). Primarily, Laharz_py is a computational model that uses statistical descriptions of areas inundated by past mass-flow events to forecast areas likely to be inundated by hypothetical future events. The forecasts use physically motivated and statistically calibrated power-law equations that each has a form A = cV2/3, relating mass-flow volume (V) to planimetric or cross-sectional areas (A) inundated by an average flow as it descends a given drainage. Calibration of the equations utilizes logarithmic transformation and linear regression to determine the best-fit values of c. The software uses values of V, an algorithm for idenitifying mass-flow source locations, and digital elevation models of topography to portray forecast hazard zones for lahars, debris flows, or rock avalanches on maps. Laharz_py offers two methods to construct areas of potential inundation for lahars: (1) Selection of a range of plausible V values results in a set of nested hazard zones showing areas likely to be inundated by a range of hypothetical flows; and (2) The user selects a single volume and a confidence interval for the prediction. In either case, Laharz_py calculates the mean expected A and B value from each user-selected value of V. However, for the second case, a single value of V yields two additional results representing the upper and lower values of the confidence interval of prediction. Calculation of these two bounding predictions require the statistically calibrated prediction equations, a user-specified level of confidence, and t-distribution statistics to calculate the standard error of regression, standard error of the mean, and standard error of prediction. The portrayal of results from these two methods on maps compares the range of inundation areas due to prediction uncertainties with uncertainties in selection of V values. The Open-File Report document contains an explanation of how to install and use the software. The Laharz_py software includes an example data set for Mount Rainier, Washington. The second part of the documentation describes how to use all of the Laharz_py tools in an example dataset at Mount Rainier, Washington.

Premature Ventricular Contraction Coupling Interval Variability Destabilizes Cardiac Neuronal and Electrophysiological Control: Insights from Simultaneous Cardio-Neural Mapping

PubMed Central

Hamon, David; Rajendran, Pradeep S.; Chui, Ray W.; Ajijola, Olujimi A.; Irie, Tadanobu; Talebi, Ramin; Salavatian, Siamak; Vaseghi, Marmar; Bradfield, Jason S.; Armour, J. Andrew; Ardell, Jeffrey L.; Shivkumar, Kalyanam

2017-01-01

Background Variability in premature ventricular contraction (PVC) coupling interval (CI) increases the risk of cardiomyopathy and sudden death. The autonomic nervous system regulates cardiac electrical and mechanical indices, and its dysregulation plays an important role in cardiac disease pathogenesis. The impact of PVCs on the intrinsic cardiac nervous system (ICNS), a neural network on the heart, remains unknown. The objective was to determine the effect of PVCs and CI on ICNS function in generating cardiac neuronal and electrical instability using a novel cardio-neural mapping approach. Methods and Results In a porcine model (n=8) neuronal activity was recorded from a ventricular ganglion using a microelectrode array, and cardiac electrophysiological mapping was performed. Neurons were functionally classified based on their response to afferent and efferent cardiovascular stimuli, with neurons that responded to both defined as convergent (local reflex processors). Dynamic changes in neuronal activity were then evaluated in response to right ventricular outflow tract PVCs with fixed short, fixed long, and variable CI. PVC delivery elicited a greater neuronal response than all other stimuli (P<0.001). Compared to fixed short and long CI, PVCs with variable CI had a greater impact on neuronal response (P<0.05 versus short CI), particularly on convergent neurons (P<0.05), as well as neurons receiving sympathetic (P<0.05) and parasympathetic input (P<0.05). The greatest cardiac electrical instability was also observed following variable (short) CI PVCs. Conclusions Variable CI PVCs affect critical populations of ICNS neurons and alter cardiac repolarization. These changes may be critical for arrhythmogenesis and remodeling leading to cardiomyopathy. PMID:28408652

High-resolution linkage analyses to identify genes that influence Varroa sensitive hygiene behavior in honey bees.

PubMed

Tsuruda, Jennifer M; Harris, Jeffrey W; Bourgeois, Lanie; Danka, Robert G; Hunt, Greg J

2012-01-01

Varroa mites (V. destructor) are a major threat to honey bees (Apis melilfera) and beekeeping worldwide and likely lead to colony decline if colonies are not treated. Most treatments involve chemical control of the mites; however, Varroa has evolved resistance to many of these miticides, leaving beekeepers with a limited number of alternatives. A non-chemical control method is highly desirable for numerous reasons including lack of chemical residues and decreased likelihood of resistance. Varroa sensitive hygiene behavior is one of two behaviors identified that are most important for controlling the growth of Varroa populations in bee hives. To identify genes influencing this trait, a study was conducted to map quantitative trait loci (QTL). Individual workers of a backcross family were observed and evaluated for their VSH behavior in a mite-infested observation hive. Bees that uncapped or removed pupae were identified. The genotypes for 1,340 informative single nucleotide polymorphisms were used to construct a high-resolution genetic map and interval mapping was used to analyze the association of the genotypes with the performance of Varroa sensitive hygiene. We identified one major QTL on chromosome 9 (LOD score = 3.21) and a suggestive QTL on chromosome 1 (LOD = 1.95). The QTL confidence interval on chromosome 9 contains the gene 'no receptor potential A' and a dopamine receptor. 'No receptor potential A' is involved in vision and olfaction in Drosophila, and dopamine signaling has been previously shown to be required for aversive olfactory learning in honey bees, which is probably necessary for identifying mites within brood cells. Further studies on these candidate genes may allow for breeding bees with this trait using marker-assisted selection.

High-Resolution Linkage Analyses to Identify Genes That Influence Varroa Sensitive Hygiene Behavior in Honey Bees

PubMed Central

Tsuruda, Jennifer M.; Harris, Jeffrey W.; Bourgeois, Lanie; Danka, Robert G.; Hunt, Greg J.

2012-01-01

Varroa mites (V. destructor) are a major threat to honey bees (Apis melilfera) and beekeeping worldwide and likely lead to colony decline if colonies are not treated. Most treatments involve chemical control of the mites; however, Varroa has evolved resistance to many of these miticides, leaving beekeepers with a limited number of alternatives. A non-chemical control method is highly desirable for numerous reasons including lack of chemical residues and decreased likelihood of resistance. Varroa sensitive hygiene behavior is one of two behaviors identified that are most important for controlling the growth of Varroa populations in bee hives. To identify genes influencing this trait, a study was conducted to map quantitative trait loci (QTL). Individual workers of a backcross family were observed and evaluated for their VSH behavior in a mite-infested observation hive. Bees that uncapped or removed pupae were identified. The genotypes for 1,340 informative single nucleotide polymorphisms were used to construct a high-resolution genetic map and interval mapping was used to analyze the association of the genotypes with the performance of Varroa sensitive hygiene. We identified one major QTL on chromosome 9 (LOD score = 3.21) and a suggestive QTL on chromosome 1 (LOD = 1.95). The QTL confidence interval on chromosome 9 contains the gene ‘no receptor potential A’ and a dopamine receptor. ‘No receptor potential A’ is involved in vision and olfaction in Drosophila, and dopamine signaling has been previously shown to be required for aversive olfactory learning in honey bees, which is probably necessary for identifying mites within brood cells. Further studies on these candidate genes may allow for breeding bees with this trait using marker-assisted selection. PMID:23133626

Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels.

PubMed

Ries, David; Holtgräwe, Daniela; Viehöver, Prisca; Weisshaar, Bernd

2016-03-15

The combination of bulk segregant analysis (BSA) and next generation sequencing (NGS), also known as mapping by sequencing (MBS), has been shown to significantly accelerate the identification of causal mutations for species with a reference genome sequence. The usual approach is to cross homozygous parents that differ for the monogenic trait to address, to perform deep sequencing of DNA from F2 plants pooled according to their phenotype, and subsequently to analyze the allele frequency distribution based on a marker table for the parents studied. The method has been successfully applied for EMS induced mutations as well as natural variation. Here, we show that pooling genetically diverse breeding lines according to a contrasting phenotype also allows high resolution mapping of the causal gene in a crop species. The test case was the monogenic locus causing red vs. green hypocotyl color in Beta vulgaris (R locus). We determined the allele frequencies of polymorphic sequences using sequence data from two diverging phenotypic pools of 180 B. vulgaris accessions each. A single interval of about 31 kbp among the nine chromosomes was identified which indeed contained the causative mutation. By applying a variation of the mapping by sequencing approach, we demonstrated that phenotype-based pooling of diverse accessions from breeding panels and subsequent direct determination of the allele frequency distribution can be successfully applied for gene identification in a crop species. Our approach made it possible to identify a small interval around the causative gene. Sequencing of parents or individual lines was not necessary. Whenever the appropriate plant material is available, the approach described saves time compared to the generation of an F2 population. In addition, we provide clues for planning similar experiments with regard to pool size and the sequencing depth required.

Substantial prevalence of microdeletions of the Y-chromosome in infertile men with idiopathic azoospermia and oligozoospermia detected using a sequence-tagged site-based mapping strategy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Najmabadi, H.; Huang, V.; Bhasin, D.

1996-04-01

Genes on the long arm of Y (Yq), particularly within interval 6, are believed to play a critical role in human spermatogenesis. Cytogenetically detectable deletions of this region are associated with azoospermia in men, but are relatively uncommon. The objective of this study was to validate a sequence-tagged site (STS)-mapping strategy for the detection of Yq microdeletions and to use this method to determine the proportion of men with idiopathic azoospermia or severe oligozoospermia who carry microdeletions in Yq. STS mapping of a sufficiently large sample of infertile men should also help further localize the putative gene(s) involved in themore » pathogenesis of male infertility. Genomic DNA was extracted from peripheral leukocytes of 16 normal fertile men, 7 normal fertile women, 60 infertile men, and 15 patients with the X-linked disorder, ichthyosis. PCR primers were synthesized for 26 STSs that span Yq interval 6. None of the 16 normal men of known fertility had microdeletions. Seven normal fertile women failed to amplify any of the 26 STSs, providing evidence of their Y specificity. No microdeletions were detected in any of the 15 patients with ichthyosis. Of the 60 infertile men typed with 26 STSs, 11 (18%; 10 azoospermic and 1 oligozoospermic) failed to amplify 1 or more STS. Interestingly, 4 of the 11 patients had microdeletions in a region that is outside the Yq region from which the DAZ (deleted in azoospermia gene region) gene was cloned. In an additional 3 patients, microdeletions were present both inside and outside the DAZ region. The physical locations of these microdeletions provide further support for the concept that a gene(s) on Yq deletion interval 6 plays an important role in spermatogenesis. The presence of deletions that do not overlap with the DAZ region suggests that genes other than the DAZ gene may also be implicated in the pathogenesis of some subsets of male infertility. 48 refs., 2 figs., 2 tabs.« less

Inconsistencies in Numerical Simulations of Dynamical Systems Using Interval Arithmetic

NASA Astrophysics Data System (ADS)

Nepomuceno, Erivelton G.; Peixoto, Márcia L. C.; Martins, Samir A. M.; Rodrigues, Heitor M.; Perc, Matjaž

Over the past few decades, interval arithmetic has been attracting widespread interest from the scientific community. With the expansion of computing power, scientific computing is encountering a noteworthy shift from floating-point arithmetic toward increased use of interval arithmetic. Notwithstanding the significant reliability of interval arithmetic, this paper presents a theoretical inconsistency in a simulation of dynamical systems using a well-known implementation of arithmetic interval. We have observed that two natural interval extensions present an empty intersection during a finite time range, which is contrary to the fundamental theorem of interval analysis. We have proposed a procedure to at least partially overcome this problem, based on the union of the two generated pseudo-orbits. This paper also shows a successful case of interval arithmetic application in the reduction of interval width size on the simulation of discrete map. The implications of our findings on the reliability of scientific computing using interval arithmetic have been properly addressed using two numerical examples.

Topographic map of part of the Kasei Valles and Sacra Fossae regions of Mars - MTM 500k 20/287E OMKT

USGS Publications Warehouse

Rosiek, Mark R.; Redding, Bonnie L.; Galuszca, Donna M.

2005-01-01

This map is part of a series of topographic maps of areas of special scientific interest on Mars. The topography was compiled photogrammetrically using Viking Orbiter stereo image pairs and photoclinometry from a Viking Orbiter image. The contour interval is 250 m. Horizontal and vertical control was established using the USGS Mars Digital Image Model 2.0 (MDIM 2.0) and data from the Mars Orbiter Laser Altimeter (MOLA).

Topographic map of Golden Gate Estates, Collier County, Florida

USGS Publications Warehouse

Jurado, Antonio

1981-01-01

Construction of canals related to land development in the Golden Gate Estates area of Collier County, Fla., has altered the natural drainage pattern of the watershed. The area of approximately 300 square miles was topographically mapped with a contour interval of 0.5 foot to assist in determining the effects of canal construction on the surface-water and ground-water resources in the watershed. The topographic map was prepared at a scale of 1:48,000 using aerial photography and ground-control points. (USGS)

Bounded relative motion under zonal harmonics perturbations

NASA Astrophysics Data System (ADS)

Baresi, Nicola; Scheeres, Daniel J.

2017-04-01

The problem of finding natural bounded relative trajectories between the different units of a distributed space system is of great interest to the astrodynamics community. This is because most popular initialization methods still fail to establish long-term bounded relative motion when gravitational perturbations are involved. Recent numerical searches based on dynamical systems theory and ergodic maps have demonstrated that bounded relative trajectories not only exist but may extend up to hundreds of kilometers, i.e., well beyond the reach of currently available techniques. To remedy this, we introduce a novel approach that relies on neither linearized equations nor mean-to-osculating orbit element mappings. The proposed algorithm applies to rotationally symmetric bodies and is based on a numerical method for computing quasi-periodic invariant tori via stroboscopic maps, including extra constraints to fix the average of the nodal period and RAAN drift between two consecutive equatorial plane crossings of the quasi-periodic solutions. In this way, bounded relative trajectories of arbitrary size can be found with great accuracy as long as these are allowed by the natural dynamics and the physical constraints of the system (e.g., the surface of the gravitational attractor). This holds under any number of zonal harmonics perturbations and for arbitrary time intervals as demonstrated by numerical simulations about an Earth-like planet and the highly oblate primary of the binary asteroid (66391) 1999 KW4.

Potential of two submontane broadleaved species (Acer opalus, Quercus pubescens) to reveal spatiotemporal patterns of rockfall activity

NASA Astrophysics Data System (ADS)

Favillier, Adrien; Lopez-Saez, Jérôme; Corona, Christophe; Trappmann, Daniel; Toe, David; Stoffel, Markus; Rovéra, Georges; Berger, Frédéric

2015-10-01

Long-term records of rockfalls have proven to be scarce and typically incomplete, especially in increasingly urbanized areas where inventories are largely absent and the risk associated with rockfall events rises proportionally with urbanization. On forested slopes, tree-ring analyses may help to fill this gap, as they have been demonstrated to provide annually-resolved data on past rockfall activity over long periods. Yet, the reconstruction of rockfall chronologies has been hampered in the past by the paucity of studies that include broadleaved tree species, which are, in fact, quite common in various rockfall-prone environments. In this study, we test the sensitivity of two common, yet unstudied, broadleaved species - Quercus pubescens Willd. (Qp) and Acer opalus Mill. (Ao) - to record rockfall impacts. The approach is based on a systematic mapping of trees and the counting of visible scars on the stem surface of both species. Data are presented from a site in the Vercors massif (French Alps) where rocks are frequently detached from Valanginian limestone and marl cliffs. We compare recurrence interval maps obtained from both species and from two different sets of tree structures (i.e., single trees vs. coppice stands) based on Cohen's k coefficient and the mean absolute error. A total of 1230 scars were observed on the stem surface of 847 A. opalus and Q. pubescens trees. Both methods yield comparable results on the spatial distribution of relative rockfall activity with similar downslope decreasing recurrence intervals. Yet recurrence intervals vary significantly according to tree species and tree structure. The recurrence interval observed on the stem surface of Q. pubescens exceeds that of A. opalus by > 20 years in the lower part of the studied plot. Similarly, the recurrence interval map derived from A. opalus coppice stands, dominant at the stand scale, does not exhibit a clear spatial pattern. Differences between species may be explained by the bark thickness of Q. pubescens, which has been demonstrated to grow at twice the rate of A. opalus, thus constituting a mechanical barrier that is able to buffer low energy rockfalls and thus can avoid damage to the underlying tissues. The reasons for differences between tree structures are related to the clustered coppice-specific spatial stem distribution in clumps that could result on one hand in bigger gaps between clumps, which in turn decreases the probability of tree impacts for traveling blocks. On the other hand, data also indicate that several scars on the bark of coppice stands may stem from the same impact and thus may lead to an overestimation of rockfall activity.

Cerebral blood flow velocity declines before arterial pressure in patients with orthostatic vasovagal presyncope

NASA Technical Reports Server (NTRS)

Dan, Dan; Hoag, Jeffrey B.; Ellenbogen, Kenneth A.; Wood, Mark A.; Eckberg, Dwain L.; Gilligan, David M.

2002-01-01

OBJECTIVES: We studied hemodynamic changes leading to orthostatic vasovagal presyncope to determine whether changes of cerebral artery blood flow velocity precede or follow reductions of arterial pressure. BACKGROUND: Some evidence suggests that disordered cerebral autoregulation contributes to the occurrence of orthostatic vasovagal syncope. We studied cerebral hemodynamics with transcranial Doppler recordings, and we closely examined the temporal sequence of changes of cerebral artery blood flow velocity and systemic arterial pressure in 15 patients who did or did not faint during passive 70 degrees head-up tilt. METHODS: We recorded photoplethysmographic arterial pressure, RR intervals (electrocardiogram) and middle cerebral artery blood flow velocities (mean, total, mean/RR interval; Gosling's pulsatility index; and cerebrovascular resistance [mean cerebral velocity/mean arterial pressure, MAP]). RESULTS: Eight men developed presyncope, and six men and one woman did not. Presyncopal patients reported light-headedness, diaphoresis, or a sensation of fatigue 155 s (range: 25 to 414 s) before any cerebral or systemic hemodynamic change. Average cerebral blood flow velocity (CBFV) changes (defined by an iterative linear regression algorithm) began 67 s (range: 9 to 198 s) before reductions of MAP. Cerebral and systemic hemodynamic measurements remained constant in nonsyncopal patients. CONCLUSIONS: Presyncopal symptoms and CBFV changes precede arterial pressure reductions in patients with orthostatic vasovagal syncope. Therefore, changes of cerebrovascular regulation may contribute to the occurrence of vasovagal reactions.

Data series embedding and scale invariant statistics.

PubMed

Michieli, I; Medved, B; Ristov, S

2010-06-01

Data sequences acquired from bio-systems such as human gait data, heart rate interbeat data, or DNA sequences exhibit complex dynamics that is frequently described by a long-memory or power-law decay of autocorrelation function. One way of characterizing that dynamics is through scale invariant statistics or "fractal-like" behavior. For quantifying scale invariant parameters of physiological signals several methods have been proposed. Among them the most common are detrended fluctuation analysis, sample mean variance analyses, power spectral density analysis, R/S analysis, and recently in the realm of the multifractal approach, wavelet analysis. In this paper it is demonstrated that embedding the time series data in the high-dimensional pseudo-phase space reveals scale invariant statistics in the simple fashion. The procedure is applied on different stride interval data sets from human gait measurements time series (Physio-Bank data library). Results show that introduced mapping adequately separates long-memory from random behavior. Smaller gait data sets were analyzed and scale-free trends for limited scale intervals were successfully detected. The method was verified on artificially produced time series with known scaling behavior and with the varying content of noise. The possibility for the method to falsely detect long-range dependence in the artificially generated short range dependence series was investigated. (c) 2009 Elsevier B.V. All rights reserved.

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population.

PubMed

Ding, Junqiang; Zhang, Luyan; Chen, Jiafa; Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population

PubMed Central

Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize. PMID:26509792

Genetic mapping and predictive testing for multiple endocrine neoplasia type 1 (MEN1)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandit, S.D.; Read, C.; Liu, L.

1994-09-01

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder with an estimated prevalance of 20-200 per million persons. It is characterized by the combined occurence of tumors involving two or more endocrine glands, namely the parathyroid glands, the endocrine pancreas and the anterior pituitary. This disorder affects virtually all age groups with an average range of 20-60 years. Linkage analysis mapped the MEN1 locus to 11q13 near the human muscle glycogen phosphorylase (PYGM) locus. Additional genetic mapping and deletion analysis studies have refined the region containing the MEN1 locus to a 3 cM interval flanked by markers PYGMmore » and D11S146/D11S97, a physical distance of approximately 1.5 Mb. We have identified 8 large families segregating MEN1 (71 affected from a population of 389 individuals). A high resolution reference map for the 11q13 region has been constructed using four new microsatellite markers, the CEPH reference (40 family) pedigree resource, and the CRI-MAP program package. Subsequent analyses using the LINKAGE program package and 8 MEN 1 families placed the MEN1 locus within the context of the microsatellite map. This map was used to develop a linkage-based predictive test. These markers have also been used to further refine the interval containing the MEN1 locus from the study of chromosome deletions (loss of heterozygosity, LOH studies) in paired sets of tumor and germline DNA from 87 MEN 1 affected individuals.« less

EnviroAtlas - Austin, TX - Proximity to Parks

EPA Pesticide Factsheets

This EnviroAtlas dataset shows the approximate walking distance from a park entrance at any given location within the EnviroAtlas community boundary. The zones are estimated in 1/4 km intervals up to 1km then in 1km intervals up to 5km. Park entrances were included in this analysis if they were within 5km of the community boundary. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Hailey-Hailey disease maps to a 5 cM interval on chromosome 3q21-q24.

PubMed

Richard, G; Korge, B P; Wright, A R; Mazzanti, C; Harth, W; Annicchiarico-Petruzzelli, M; Compton, J G; Bale, S J

1995-09-01

Hailey-Hailey disease (HHD) is a rare autosomal dominant genodermatosis characterized by disturbed keratinocyte adhesion. The disease has recently been mapped to a 14 cM region on chromosome 3q. We have further refined the location of the HHD gene by linkage analysis in six HHD families from Germany and Italy using 11 polymorphic microsatellite markers and found no evidence for genetic heterogeneity. We observed complete cosegregation between HHD and marker D3S1587, with a maximal lod score of 4.54. Detailed haplotype analyses allowed us to narrow the interval containing the HHD locus to 5 cM, flanked by D3S1589 and D3S1290.

Novel Loci Associated with PR Interval in a Genome-Wide Association Study of Ten African American Cohorts

PubMed Central

Butler, Anne M.; Yin, Xiaoyan; Evans, Daniel S.; Nalls, Michael A.; Smith, Erin N.; Tanaka, Toshiko; Li, Guo; Buxbaum, Sarah G.; Whitsel, Eric A.; Alonso, Alvaro; Arking, Dan E.; Benjamin, Emelia J.; Berenson, Gerald S.; Bis, Josh C.; Chen, Wei; Deo, Rajat; Ellinor, Patrick T.; Heckbert, Susan R.; Heiss, Gerardo; Hsueh, Wen-Chi; Keating, Brendan J.; Kerr, Kathleen F.; Li, Yun; Limacher, Marian C.; Liu, Yongmei; Lubitz, Steven A.; Marciante, Kristin D.; Mehra, Reena; Meng, Yan A.; Newman, Anne B.; Newton-Cheh, Christopher; North, Kari E.; Palmer, Cameron D.; Psaty, Bruce M.; Quibrera, P. Miguel; Redline, Susan; Reiner, Alex P.; Rotter, Jerome I.; Schnabel, Renate B.; Schork, Nicholas J.; Singleton, Andrew B.; Smith, J. Gustav; Soliman, Elsayed Z.; Srinivasan, Sathanur R.; Zhang, Zhu-ming; Zonderman, Alan B.; Ferrucci, Luigi; Murray, Sarah S.; Evans, Michele K.; Sotoodehnia, Nona; Magnani, Jared W.; Avery, Christy L.

2013-01-01

Background The PR interval (PR) as measured by the resting, standard 12-lead electrocardiogram (ECG) reflects the duration of atrial/atrioventricular nodal depolarization. Substantial evidence exists for a genetic contribution to PR, including genome-wide association studies that have identified common genetic variants at nine loci influencing PR in populations of European and Asian descent. However, few studies have examined loci associated with PR in African Americans. Methods and Results We present results from the largest genome-wide association study to date of PR in 13,415 adults of African descent from ten cohorts. We tested for association between PR (ms) and approximately 2.8 million genotyped and imputed single nucleotide polymorphisms. Imputation was performed using HapMap 2 YRI and CEU panels. Study-specific results, adjusted for global ancestry and clinical correlates of PR, were meta-analyzed using the inverse variance method. Variation in genome-wide test statistic distributions was noted within studies (lambda range: 0.9–1.1), although not after genomic control correction was applied to the overall meta-analysis (lambda: 1.008). In addition to generalizing previously reported associations with MEIS1, SCN5A, ARHGAP24, CAV1, and TBX5 to African American populations at the genome-wide significance level (P<5.0×10−8), we also identified a novel locus: ITGA9, located in a region previously implicated in SCN5A expression. The 3p21 region harboring SCN5A also contained two additional independent secondary signals influencing PR (P<5.0×10−8). Conclusions This study demonstrates the ability to map novel loci in African Americans as well as the generalizability of loci associated with PR across populations of African, European and Asian descent. PMID:23139255

Multi-species Management Using Modeling and Decision Theory Applications to Integrated Natural Resources Management Planning

DTIC Science & Technology

2008-06-01

or just habitat area . They used linear interpolation to derive maps for each time step in the population model and population dynamics were...Metapopulation Map ............................................................................................................... 20  Figure 12. Habitat...Stephen’s kangaroo rat (SKR). In some areas of coastal sage scrub habitat short fire return intervals make the habitat suitable for the SKR while

Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine

NASA Astrophysics Data System (ADS)

Xing, Pengwei; Su, Ran; Guo, Fei; Wei, Leyi

2017-04-01

N6-methyladenosine (m6A) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear translocation and translation process. Numerous experiments have been done to successfully characterize m6A sites within sequences since high-resolution mapping of m6A sites was established. However, as the explosive growth of genomic sequences, using experimental methods to identify m6A sites are time-consuming and expensive. Thus, it is highly desirable to develop fast and accurate computational identification methods. In this study, we propose a sequence-based predictor called RAM-NPPS for identifying m6A sites within RNA sequences, in which we present a novel feature representation algorithm based on multi-interval nucleotide pair position specificity, and use support vector machine classifier to construct the prediction model. Comparison results show that our proposed method outperforms the state-of-the-art predictors on three benchmark datasets across the three species, indicating the effectiveness and robustness of our method. Moreover, an online webserver implementing the proposed predictor has been established at http://server.malab.cn/RAM-NPPS/. It is anticipated to be a useful prediction tool to assist biologists to reveal the mechanisms of m6A site functions.

Analysis of 133 meioses places the genes for nevoid basal cell carcinoma (gorlin) syndrome and fanconi anemia group C in a 2.6-cM interval and contributes to the fine map of 9q22.3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farndon, P.A.; Hardy, C.; Kilpatrick, M.W.

1994-09-15

Four disease genes (NBCCS, ESS1, XPAC, FACC) map to 9q22.3-q31. A fine map of this region was produced by linkage and haplotype analysis using 12 DNA markers. The gene for nevoid basal cell carcinoma syndrome (NBCCS, Gorlin) has an important role in congenital malformations and carcinogenesis. Phase-known recombinants in a study of 133 meioses place NBCCS between (D9S12/D9S151) and D9S176. Haplotype analysis in a two-generation family suggests that NBCCS lies in a smaller interval of 2.6 cM centromeric to D9S287. These flanking markers will be useful clinically for gene tracking. Recombinants also map FACC (Fanconi anemia, group C) to themore » same region, between (D9S12/D9S151) and D9S287. The recombination rate between (D9S12/D9S151) and D9S53 in males is 8.3% and 13.2% in females, giving a sex-specific male:female ratio of 1:1.6 and a sex-averaged map distance of 10.4 cM. No double recombinants were detected, in agreement with the apparently complete level of interference predicted from the male chiasmata map. 19 refs., 2 figs., 1 tab.« less

Tactile mapping system: a novel imaging technology for surface topography and elasticity of tissues or organs.

PubMed

Oie, Tomonori; Suzuki, Hisato; Fukuda, Toru; Murayama, Yoshinobu; Omata, Sadao; Kanda, Keiichi; Nakayama, Yasuhide

2009-11-01

: We demonstrated that the tactile mapping system (TMS) has a high degree of spatial precision in the distribution mapping of surface elasticity of tissues or organs. : Samples used were a circumferential section of a small-caliber porcine artery (diameter: ∼3 mm) and an elasticity test pattern with a line and space configuration for the distribution mapping of elasticity, prepared by regional micropatterning of a 14-μm thick gelatin hydrogel coating on a polyurethane sheet. Surface topography and elasticity in normal saline were simultaneously investigated by TMS using a probe with a diameter of 5 or 12 μm, a spatial interval of 1 to 5 μm, and an indentation depth of 4 μm. : In the test pattern, a spatial resolution in TMS of <5 μm was acquired under water with a minimal probe diameter and spatial interval of the probe movement. TMS was used for the distribution mapping of surface elasticity in a flat, circumferential section (thickness: ∼0.5 mm) of a porcine artery, and the concentric layers of the vascular wall, including the collagen-rich and elastin-rich layers, could be clearly differentiated in terms of surface elasticity at the spatial resolution of <2 μm. : TMS is a simple and inexpensive technique for the distribution mapping of the surface elasticity in vascular tissues at the spatial resolution <2 μm. TMS has the ability to analyze a complex structure of the tissue samples under normal saline.

Arrhythmic hazard map for a 3D whole-ventricles model under multiple ion channel block.

PubMed

Okada, Jun-Ichi; Yoshinaga, Takashi; Kurokawa, Junko; Washio, Takumi; Furukawa, Tetsushi; Sawada, Kohei; Sugiura, Seiryo; Hisada, Toshiaki

2018-05-10

To date, proposed in silico models for preclinical cardiac safety testing are limited in their predictability and usability. We previously reported a multi-scale heart simulation that accurately predicts arrhythmogenic risk for benchmark drugs. We extend this approach and report the first comprehensive hazard map of drug-induced arrhythmia based on the exhaustive in silico electrocardiogram (ECG) database of drug effects, developed using a petaflop computer. A total of 9075 electrocardiograms constitute the five-dimensional hazard map, with coordinates representing the extent of the block of each of the five ionic currents (rapid delayed rectifier potassium current (IKr), fast (INa) and late (INa,L) components of the sodium current, L-type calcium current (ICa,L) and slow delayed rectifier current (IKs)), involved in arrhythmogenesis. Results of the evaluation of arrhythmogenic risk based on this hazard map agreed well with the risk assessments reported in three references. ECG database also suggested that the interval between the J-point and the T-wave peak is a superior index of arrhythmogenicity compared to other ECG biomarkers including the QT interval. Because concentration-dependent effects on electrocardiograms of any drug can be traced on this map based on in vitro current assay data, its arrhythmogenic risk can be evaluated without performing costly and potentially risky human electrophysiological assays. Hence, the map serves as a novel tool for use in pharmaceutical research and development. This article is protected by copyright. All rights reserved.

Electric charge requirements of pediatric cochlear implant recipients enrolled in the Childhood Development After Cochlear Implantation study.

PubMed

Zwolan, Teresa A; O'Sullivan, Mary Beth; Fink, Nancy E; Niparko, John K

2008-02-01

To evaluate mapping characteristics of children with cochlear implants who are enrolled in the Childhood Development After Cochlear Implantation (CDACI) multicenter study. Longitudinal evaluation during 24 months of speech processor maps of children with cochlear implants prospectively enrolled in the study. Six tertiary referral centers. One hundred eighty-eight children enrolled in the CDACI study who were 5 years old or younger at the time of enrollment. Of these children, 184 received unilateral implants, and 4 received simultaneous bilateral implants. Children attended regular mapping sessions at their implant clinic as part of the study protocol. Maps were examined for each subject at 4 different time intervals: at device activation and 6, 12, and 24 months postactivation. Mean C/M levels (in charge per phase) were compared for 4 different time intervals, for 3 different devices, for 6 different implant centers, and for children with normal and abnormal cochleae. All 3 types of implant devices demonstrate significant increases in C/M levels between device activation and the 24-month appointment. Significant differences in mean C/M levels were noted between devices. Children with cochlear anomalies demonstrate significantly greater C/M levels than children with normal cochleae. The CDACI study has enabled us to evaluate the mapping characteristics of pediatric patients who use 3 different devices and were implanted at a variety of implant centers. Analysis of such data enables us to better understand the mapping characteristics of children with cochlear implants.

Estimating soil water content from ground penetrating radar coarse root reflections

NASA Astrophysics Data System (ADS)

Liu, X.; Cui, X.; Chen, J.; Li, W.; Cao, X.

2016-12-01

Soil water content (SWC) is an indispensable variable for understanding the organization of natural ecosystems and biodiversity. Especially in semiarid and arid regions, soil moisture is the plants primary source of water and largely determine their strategies for growth and survival, such as root depth, distribution and competition between them. Ground penetrating radar (GPR), a kind of noninvasive geophysical technique, has been regarded as an accurate tool for measuring soil water content at intermediate scale in past decades. For soil water content estimation with surface GPR, fixed antenna offset reflection method has been considered to have potential to obtain average soil water content between land surface and reflectors, and provide high resolution and few measurement time. In this study, 900MHz surface GPR antenna was used to estimate SWC with fixed offset reflection method; plant coarse roots (with diameters greater than 5 mm) were regarded as reflectors; a kind of advanced GPR data interpretation method, HADA (hyperbola automatic detection algorithm), was introduced to automatically obtain average velocity by recognizing coarse root hyperbolic reflection signals on GPR radargrams during estimating SWC. In addition, a formula was deduced to determine interval average SWC between two roots at different depths as well. We examined the performance of proposed method on a dataset simulated under different scenarios. Results showed that HADA could provide a reasonable average velocity to estimate SWC without knowledge of root depth and interval average SWC also be determined. When the proposed method was applied to estimation of SWC on a real-field measurement dataset, a very small soil water content vertical variation gradient about 0.006 with depth was captured as well. Therefore, the proposed method could be used to estimate average soil water content from ground penetrating radar coarse root reflections and obtain interval average SWC between two roots at different depths. It is very promising for measuring root-zone-soil-moisture and mapping soil moisture distribution around a shrub or even in field plot scale.

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis.

PubMed

Bakker, Erin; Achenbach, Ute; Bakker, Jeroen; van Vliet, Joke; Peleman, Johan; Segers, Bart; van der Heijden, Stefan; van der Linde, Piet; Graveland, Robert; Hutten, Ronald; van Eck, Herman; Coppoolse, Eric; van der Vossen, Edwin; Bakker, Jaap; Goverse, Aska

2004-06-01

The resistance gene H1 confers resistance to the potato cyst nematode Globodera rostochiensis and is located at the distal end of the long arm of chromosome V of potato. For marker enrichment of the H1 locus, a bulked segregant analysis (BSA) was carried out using 704 AFLP primer combinations. A second source of markers tightly linked to H1 is the ultra-high-density (UHD) genetic map of the potato cross SH x RH. This map has been produced with 387 AFLP primer combinations and consists of 10,365 AFLP markers in 1,118 bins (http://www.dpw.wageningen-ur.nl/uhd/). Comparing these two methods revealed that BSA resulted in one marker/cM and the UHD map in four markers/cM in the H1 interval. Subsequently, a high-resolution genetic map of the H1 locus has been developed using a segregating F(1) SH x RH population consisting of 1,209 genotypes. Two PCR-based markers were designed at either side of the H1 gene to screen the 1,209 genotypes for recombination events. In the high-resolution genetic map, two of the four co-segregating AFLP markers could be separated from the H1 gene. Marker EM1 is located at a distance of 0.2 cM, and marker EM14 is located at a distance of 0.8 cM. The other two co-segregating markers CM1 (in coupling) and EM15 (in repulsion) could not be separated from the H1 gene.

High Resolution Mapping of Genetic Factors Affecting Abdominal Bristle Number in Drosophila Melanogaster

PubMed Central

Long, A. D.; Mullaney, S. L.; Reid, L. A.; Fry, J. D.; Langley, C. H.; Mackay, TFC.

1995-01-01

Factors responsible for selection response for abdominal bristle number and correlated responses in sternopleural bristle number were mapped to the X and third chromosome of Drosophila melanogaster. Lines divergent for high and low abdominal bristle number were created by 25 generations of artificial selection from a large base population, with an intensity of 25 individuals of each sex selected from 100 individuals of each sex scored per generation. Isogenic chromosome substitution lines in which the high (H) X or third chromosome were placed in an isogenic low (L) background were derived from the selection lines and from the 93 recombinant isogenic (RI) HL X and 67 RI chromosome 3 lines constructed from them. Highly polymorphic neutral r00 transposable elements were hybridized in situ to the polytene chromosomes of the RI lines to create a set of cytogenetic markers. These techniques yielded a dense map with an average spacing of 4 cM between informative markers. Factors affecting bristle number, and relative viability of the chromosome 3 RI lines, were mapped using a multiple regression interval mapping approach, conditioning on all markers >/=10 cM from the tested interval. Two factors with large effects on abdominal bristle number were mapped on the X chromosome and five factors on the third chromosome. One factor with a large effect on sternopleural bristle number was mapped to the X and two were mapped to the third chromosome; all factors with sternopleural effects corresponded to those with effects on abdominal bristle number. Two of the chromosome 3 factors with large effects on abdominal bristle number were also associated with reduced viability. Significant sex-specific effects and epistatic interactions between mapped factors of the same order of magnitude as the additive effects were observed. All factors mapped to the approximate positions of likely candidate loci (ASC, bb, emc, h, mab, Dl and E(spl)), previously characterized by mutations with large effects on bristle number. PMID:7768438

Complete Bouguer gravity anomaly map of the state of Colorado

USGS Publications Warehouse

Abrams, Gerda A.

1993-01-01

The Bouguer gravity anomaly map is part of a folio of maps of Colorado cosponsored by the National Mineral Resources Assessment Program (NAMRAP) and the National Geologic Mapping Program (COGEOMAP) and was produced to assist in studies of the mineral resource potential and tectonic setting of the State. Previous compilations of about 12,000 gravity stations by Behrendt and Bajwa (1974a,b) are updated by this map. The data was reduced at a 2.67 g/cm3 and the grid contoured at 3 mGal intervals. This map will aid in the mineral resource assessment by indicating buried intrusive complexes, volcanic fields, major faults and shear zones, and sedimentary basins; helping to identify concealed geologic units; and identifying localities that might be hydrothermically altered or mineralized.

Resolved Stellar Streams around NGC 4631 from a Subaru/Hyper Suprime-Cam Survey

NASA Astrophysics Data System (ADS)

Tanaka, Mikito; Chiba, Masashi; Komiyama, Yutaka

2017-06-01

We present the first results of the Subaru/Hyper Suprime-Cam survey of the interacting galaxy system, NGC 4631 and NGC 4656. From the maps of resolved stellar populations, we identify 11 dwarf galaxies (including already-known dwarfs) in the outer region of NGC 4631 and the two tidal stellar streams around NGC 4631, named Stream SE and Stream NW, respectively. This paper describes the fundamental properties of these tidal streams. Based on the tip of the red giant branch method and the Bayesian statistics, we find that Stream SE (7.10 Mpc in expected a posteriori, EAP, with 90% credible intervals of [6.22, 7.29] Mpc) and Stream NW (7.91 Mpc in EAP with 90% credible intervals of [6.44, 7.97] Mpc) are located in front of and behind NGC 4631, respectively. We also calculate the metallicity distribution of stellar streams by comparing the member stars with theoretical isochrones on the color-magnitude diagram. We find that both streams have the same stellar population based on the Bayesian model selection method, suggesting that they originated from a tidal interaction between NGC 4631 and a single dwarf satellite. The expected progenitor has a positively skewed metallicity distribution function with {[M/H]}{EAP}=-0.92, with 90% credible intervals of [-1.46, -0.51]. The stellar mass of the progenitor is estimated as 3.7× {10}8 {M}⊙ , with 90% credible intervals of [5.8× {10}6,8.6× {10}9] {M}⊙ based on the mass-metallicity relation for Local group dwarf galaxies. This is in good agreement with the initial stellar mass of the progenitor that was presumed in the previous N-body simulation.

Map of Pseudo-F-statistics of seismic noise parameters as an indicator of current seismic danger in Japan

NASA Astrophysics Data System (ADS)

Lyubushin, Alexey

2016-04-01

The problem of estimate of current seismic danger based on monitoring of seismic noise properties from broadband seismic network F-net in Japan (84 stations) is considered. Variations of the following seismic noise parameters are analyzed: multifractal singularity spectrum support width, generalized Hurst exponent, minimum Hölder-Lipschitz exponent and minimum normalized entropy of squared orthogonal wavelet coefficients. These parameters are estimated within adjacent time windows of the length 1 day for seismic noise waveforms from each station. Calculating daily median values of these parameters by all stations provides 4-dimensional time series which describes integral properties of the seismic noise in the region covered by the network. Cluster analysis is applied to the sequence of clouds of 4-dimensional vectors within moving time window of the length 365 days with mutual shift 3 days starting from the beginning of 1997 up to the current time. The purpose of the cluster analysis is to find the best number of clusters (BNC) from probe numbers which are varying from 1 up to the maximum value 40. The BNC is found from the maximum of pseudo-F-statistics (PFS). A 2D map could be created which presents dependence of PFS on the tested probe number of clusters and the right-hand end of moving time window which is rather similar to usual spectral time-frequency diagrams. In the paper [1] it was shown that the BNC before Tohoku mega-earthquake on March 11, 2011, has strongly chaotic regime with jumps from minimum up to maximum values in the time interval 1 year before the event and this time intervals was characterized by high PFS values. The PFS-map is proposed as the method for extracting time intervals with high current seismic danger. The next danger time interval after Tohoku mega-EQ began at the end of 2012 and was finished at the middle of 2013. Starting from middle of 2015 the high PFS values and chaotic regime of BNC variations were returned. This could be interpreted as the increasing of the danger of the next mega-EQ in Japan in the region of Nankai Trough [1] at the first half of 2016. References 1. Lyubushin, A., 2013. How soon would the next mega-earthquake occur in Japan? // Natural Science, 5 (8A1), 1-7. http://dx.doi.org/10.4236/ns.2013.58A1001

Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Liu, Xiao-Ping; Gao, Bao-Zhen; Han, Feng-Qing; Fang, Zhi-Yuan; Yang, Li-Mei; Zhuang, Mu; Lv, Hong-Hao; Liu, Yu-Mei; Li, Zhan-Sheng; Cai, Cheng-Cheng; Yu, Hai-Long; Li, Zhi-Yuan; Zhang, Yang-Yong

2017-03-14

Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F 2 population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves). Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome '02-12', the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome '02-12' at this interval. Primers were designed based on 'TO1000', another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome 'TO1000'). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of '02-12', confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome '02-12'. This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene.

Procedure for locating 10 km UTM grid on Alabama County general highway maps

NASA Technical Reports Server (NTRS)

Paludan, C. T. N.

1975-01-01

Each county highway map has a geographic grid of degrees and tens of minutes in both longitude and latitude in the margins and within the map as intersection crosses. These will be used to locate the universal transverse mercator (UTM) grid at 10 km intervals. Since the maps used may have stretched or shrunk in height and/or width, interpolation should be done between the 10 min intersections when possible. A table of UTM coordinates of 10 min intersections is required and included. In Alabama, all eastings are referred to a false easting of 500,000 m at 87 deg W longitude (central meridian, CM).

A study on the measurement of the core body temperature change after radiofrequency ablation (RFA) through MR temperature mapping

NASA Astrophysics Data System (ADS)

Kim, Chang-Bok; Dong, Kyung-Rae; Yu, Young; Chung, Woon-Kwan; Cho, Jae-Hwan; Joo, Kyu-Ji

2013-09-01

This study examined the change in the heat generated during radiofrequency ablation (RFA) using a self-manufactured phantom and used magnetic resonance imaging (MRI) to analyze the change in the temperature of the core body and the tissues surrounding the phantom. In this experiment, the image and the phase image were obtained simultaneously from a gradient echo-based sequence using 1.5-Tesla MRI equipment and a 12-channel head coil. The temperature mapping technique was used to calculate the change in temperature. The regions of interest (ROIs) (ROI 1 - ROI 6) were set with a focus on the area where the RFA was performed, according to the temperature distribution, before monitoring the temperature change for one hour in time intervals of five minutes. The results showed that the temperature change in the ROI with time was largest in the ROI 1 and smallest in the ROI 5. In addition, after the RFA procedure, the temperature decreased from the initial value to 0 °C in one hour. The temperature changes in the core body and the surrounding tissues were confirmed by MRI temperature mapping, which is a noninvasive method.

Detecting chlorophyll, Secchi disk depth and surface temperature in a sub-alpine lake using Landsat imagery.

PubMed

Giardino, C; Pepe, M; Brivio, P A; Ghezzi, P; Zilioli, E

2001-03-14

Some bio-physical parameters, such as chlorophyll a concentration, Secchi disk depth and water surface temperature were mapped in the sub-alpine Lake Iseo (Italy) using Landsat Thematic Mapper (TM) data acquired on the 7 March 1997. In order to adequately investigate the water-leaving radiance, TM data were atmospherically corrected using a partially image-based method, and the atmospheric transmittance was measured in synchrony with the satellite passage. An empirical approach of relating atmospherically corrected TM spectral reflectance values to in situ measurements, collected during the satellite data acquisition, was used. The models developed were used to map the chlorophyll concentration and Secchi disk depth throughout the lake. Both models gave high determination coefficients (R2 = 0.99 for chlorophyll and R2 = 0.85 for the Secchi disk) and the spatial distribution of chlorophyll concentration and Secchi disk depth was mapped with contour intervals of 1 mg/m3 and 1 m, respectively. A scene-independent procedure was used to derive the surface temperature of the lake from the TM data with a root mean square error of 0.3 degrees C.

Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice.

PubMed

Kitomi, Yuka; Nakao, Emari; Kawai, Sawako; Kanno, Noriko; Ando, Tsuyu; Fukuoka, Shuichi; Irie, Kenji; Uga, Yusaku

2018-02-02

The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs) for maximal root length, QUICK ROOTING 1 ( QRO1 ) on chromosome 2 and QRO2 on chromosome 6, in cultivated rice ( Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC 4 F 2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC 4 F 3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice. Copyright © 2018 Kitomi et al.

A genome-wide interaction analysis of tri/tetracyclic antidepressants and RR and QT intervals: a pharmacogenomics study from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium

PubMed Central

Noordam, Raymond; Sitlani, Colleen M; Avery, Christy L; Stewart, James D; Gogarten, Stephanie M; Wiggins, Kerri L; Trompet, Stella; Warren, Helen R; Sun, Fangui; Evans, Daniel S; Li, Xiaohui; Li, Jin; Smith, Albert V; Bis, Joshua C; Brody, Jennifer A; Busch, Evan L; Caulfield, Mark J; Chen, Yii-Der I; Cummings, Steven R; Cupples, L Adrienne; Duan, Qing; Franco, Oscar H; Méndez-Giráldez, Rául; Harris, Tamara B; Heckbert, Susan R; van Heemst, Diana; Hofman, Albert; Floyd, James S; Kors, Jan A; Launer, Lenore J; Li, Yun; Li-Gao, Ruifang; Lange, Leslie A; Lin, Henry J; de Mutsert, Renée; Napier, Melanie D; Newton-Cheh, Christopher; Poulter, Neil; Reiner, Alexander P; Rice, Kenneth M; Roach, Jeffrey; Rodriguez, Carlos J; Rosendaal, Frits R; Sattar, Naveed; Sever, Peter; Seyerle, Amanda A; Slagboom, P Eline; Soliman, Elsayed Z; Sotoodehnia, Nona; Stott, David J; Stürmer, Til; Taylor, Kent D; Thornton, Timothy A; Uitterlinden, André G; Wilhelmsen, Kirk C; Wilson, James G; Gudnason, Vilmundur; Jukema, J Wouter; Laurie, Cathy C; Liu, Yongmei; Mook-Kanamori, Dennis O; Munroe, Patricia B; Rotter, Jerome I; Vasan, Ramachandran S; Psaty, Bruce M; Stricker, Bruno H; Whitsel, Eric A

2017-01-01

Background Increased heart rate and a prolonged QT interval are important risk factors for cardiovascular morbidity and mortality, and can be influenced by the use of various medications, including tri/tetracyclic antidepressants (TCAs). We aim to identify genetic loci that modify the association between TCA use and RR and QT intervals. Methods and Results We conducted race/ethnic-specific genome-wide interaction analyses (with HapMap Phase II imputed reference panel imputation) of TCAs and resting RR and QT intervals in cohorts of European (n=45,706; n=1,417 TCA users), African (n=10,235; n=296 TCA users) and Hispanic/Latino (n=13,808; n=147 TCA users) ancestry, adjusted for clinical covariates. Among the populations of European ancestry, two genome-wide significant loci were identified for RR interval: rs6737205 in BRE (β = 56.3, Pinteraction = 3.9e−9) and rs9830388 in UBE2E2 (β = 25.2, Pinteraction = 1.7e−8). In Hispanic/Latino cohorts, rs2291477 in TGFBR3 significantly modified the association between TCAs and QT intervals (β = 9.3, Pinteraction = 2.55e−8). In the meta-analyses of the other ethnicities, these loci either were excluded from the meta-analyses (as part of quality control), or their effects did not reach the level of nominal statistical significance (Pinteraction > 0.05). No new variants were identified in these ethnicities. No additional loci were identified after inverse-variance-weighted meta-analysis of the three ancestries. Conclusion Among Europeans, TCA interactions with variants in BRE and UBE2E2, were identified in relation to RR intervals. Among Hispanic/Latinos, variants in TGFBR3 modified the relation between TCAs and QT intervals. Future studies are required to confirm our results. PMID:28039329

Seismic hazard and seismic risk assessment based on the unified scaling law for earthquakes: Himalayas and adjacent regions

NASA Astrophysics Data System (ADS)

Nekrasova, A. K.; Kossobokov, V. G.; Parvez, I. A.

2015-03-01

For the Himalayas and neighboring regions, the maps of seismic hazard and seismic risk are constructed with the use of the estimates for the parameters of the unified scaling law for earthquakes (USLE), in which the Gutenberg-Richter law for magnitude distribution of seismic events within a given area is applied in the modified version with allowance for linear dimensions of the area, namely, log N( M, L) = A + B (5 - M) + C log L, where N( M, L) is the expected annual number of the earthquakes with magnitude M in the area with linear dimension L. The spatial variations in the parameters A, B, and C for the Himalayas and adjacent regions are studied on two time intervals from 1965 to 2011 and from 1980 to 2011. The difference in A, B, and C between these two time intervals indicates that seismic activity experiences significant variations on a scale of a few decades. With a global consideration of the seismic belts of the Earth overall, the estimates of coefficient A, which determines the logarithm of the annual average frequency of the earthquakes with a magnitude of 5.0 and higher in the zone with a linear dimension of 1 degree of the Earth's meridian, differ by a factor of 30 and more and mainly fall in the interval from -1.1 to 0.5. The values of coefficient B, which describes the balance between the number of earthquakes with different magnitudes, gravitate to 0.9 and range from less than 0.6 to 1.1 and higher. The values of coefficient C, which estimates the fractal dimension of the local distribution of epicenters, vary from 0.5 to 1.4 and higher. In the Himalayas and neighboring regions, the USLE coefficients mainly fall in the intervals of -1.1 to 0.3 for A, 0.8 to 1.3 for B, and 1.0 to 1.4 for C. The calculations of the local value of the expected peak ground acceleration (PGA) from the maximal expected magnitude provided the necessary basis for mapping the seismic hazards in the studied region. When doing this, we used the local estimates of the magnitudes which, according to USLE, corresponded to the probability of exceedance 1% and 10% during 50 years or, if the reliable estimate is absent, the maximal magnitudes reported during the instrumental period. As a result, the seismic hazard maps for the Himalayas and the adjacent regions in terms of standard seismic zoning were constructed. Based on these calculations, in order to exemplify the method, we present a series of seismic risk maps taking into account the population density prone to seismic hazard and the dependence of the risk on the vulnerability as a function of population density.

Atlas of depth-duration frequency of precipitation annual maxima for Texas

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.

2004-01-01

Ninety-six maps depicting the spatial variation of the depth-duration frequency of precipitation annual maxima for Texas are presented. The recurrence intervals represented are 2, 5, 10, 25, 50, 100, 250, and 500 years. The storm durations represented are 15 and 30 minutes; 1, 2, 3, 6, and 12 hours; and 1, 2, 3, 5, and 7 days. The maps were derived using geographically referenced parameter maps of probability distributions used in previously published research by the U.S. Geological Survey to model the magnitude and frequency of precipitation annual maxima for Texas. The maps in this report apply that research and update depth-duration frequency of precipitation maps available in earlier studies done by the National Weather Service.

Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.

PubMed

Norgard, Elizabeth A; Jarvis, Joseph P; Roseman, Charles C; Maxwell, Taylor J; Kenney-Hunt, Jane P; Samocha, Kaitlin E; Pletscher, L Susan; Wang, Bing; Fawcett, Gloria L; Leatherwood, Christopher J; Wolf, Jason B; Cheverud, James M

2009-04-01

Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F(2) intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F(9) and F(10) generations (n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F(2)-F(3) population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F(2)-F(3) QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length.

An easy-to-use technique to characterize cardiodynamics from first-return maps on ΔRR-intervals

NASA Astrophysics Data System (ADS)

Fresnel, Emeline; Yacoub, Emad; Freitas, Ubiratan; Kerfourn, Adrien; Messager, Valérie; Mallet, Eric; Muir, Jean-François; Letellier, Christophe

2015-08-01

Heart rate variability analysis using 24-h Holter monitoring is frequently performed to assess the cardiovascular status of a patient. The present retrospective study is based on the beat-to-beat interval variations or ΔRR, which offer a better view of the underlying structures governing the cardiodynamics than the common RR-intervals. By investigating data for three groups of adults (with normal sinus rhythm, congestive heart failure, and atrial fibrillation, respectively), we showed that the first-return maps built on ΔRR can be classified according to three structures: (i) a moderate central disk, (ii) a reduced central disk with well-defined segments, and (iii) a large triangular shape. These three very different structures can be distinguished by computing a Shannon entropy based on a symbolic dynamics and an asymmetry coefficient, here introduced to quantify the balance between accelerations and decelerations in the cardiac rhythm. The probability P111111 of successive heart beats without large beat-to-beat fluctuations allows to assess the regularity of the cardiodynamics. A characteristic time scale, corresponding to the partition inducing the largest Shannon entropy, was also introduced to quantify the ability of the heart to modulate its rhythm: it was significantly different for the three structures of first-return maps. A blind validation was performed to validate the technique.

A YAC contig encompassing the chromosome 7p locus for autosomal dominant retinitis pigmentosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inglehearn, C.F.; Keen, T.J.; Ratel, R.

1994-09-01

Retinitis pigmentosa is an inherited retinal degeneration characterized by night blindness and loss of peripheral vision, often leading to complete blindness. The autosomal dominant form (adRP) maps to at least six different loci, including the rhodopsin and peripherin/Rds genes and four loci identified only by linkage analysis on chromosomes 7p, 7q, 8cen and 19q. The 7p locus was reported by this laboratory in a large English family, with a lod score of 16.5. Several new genetic markers have been tested in the family and this locus has now been refined to an interval of approximately 1 cM between markers D7S795more » and D7S484 in the 7p13-15 region. In order to clone the gene for adRP, we have used microsatellites and STSs from the region to identify over 80 YACs, from four different libraries, which map to this interval. End clones from key YACs were isolated for the generation of additional STSs. Eleven microsatellite markers between D7S435 (distal) and D7S484 (proximal) have been ordered by a combination of both physical and genetic mapping. In this way we have now obtained a YAC contig spanning approximately 3 megabases of chromosome 7p within which the adRP gene must lie. One gene (aquaporin) and one chromosome 7 brain EST have been placed on the contig but both map distal to the region of interest. Sixteen other ESTs and three further known 7p genes mapping in the region have been excluded. We are now attempting to build a cosmid contig in the defined interval and identify further expressed sequences from both YACs and cosmids to test as candidates for the adRP gene.« less

Floods of 1971 and 1972 on Glover Creek and Little River in southeastern Oklahoma

USGS Publications Warehouse

Thomas, Wilbert O.; Corley, Robert K.

1973-01-01

Heavy rains of December 9-10, 1971, and Oct. 30-31, 1972, caused outstanding floods on Glover Creek and Little River in McCurtain County in southeastern Oklahoma. This report presents hydrologic data that document the extent of flooding, flood profiles, and frequency of flooding on reaches of both streams. The data presented provide a technical basis for formulating effective flood-plain zoning that will minimize existing and future flood problems. The report also can be useful for locating waste-disposal and water-treatment facilities, and for the development of recreational areas. The area studied includes the reach of Little River on the Garvin and Idabel 7 1/2-minute quadrangles (sheet 1) and the reach of Glover Creek on the southwest quarter of the Golden 15-minute quadrangle (sheet 2). The flood boundaries delineated on the maps are the limits of flooding during the December 1971 and October 1972 floods. Any attempt to delineate the flood boundaries on streams in the study area other than Glover Creek and Little River was considered to be beyond the scope of this report. The general procedure used in defining the flood boundaries was to construct the flood profiles from high-water marks obtained by field surveys and by records at three stream-gaging stations (two on Little River and one on Glover Creek.). The extent of flooding was delineated on the topographic maps by using the flood profiles to define the flood elevations at various points along the channel and locating the elevations on the map by interpolating between contours (lines of equal ground elevation). In addition, flood boundaries were defined in places by field survey, aerial photographs, and information from local residents. The accuracy of the flood boundaries is consistent with the scale and contour interval of the maps (1 inch = 2,000 feet; contour interval 10 and 20 feet), which means the flood boundaries are drawn as accurately as possible on maps having 10- and 20-foot contour intervals.

The gene for pancreatic polypeptide (PPY) and the anonymous marker D17S78 are within 45 kb of each other on chromosome 17q21

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandrasekharappa, S.C.; King, S.E.; Lee, Y.H.

1994-05-15

A gene for early-onset breast and ovarian cancer (BRCA1) has been localized to a small region of chromosome 17q21. A combination of genetic linkage studies, radiation-reduced hybrid analysis, and physical mapping by FISH has identified several genes/markers that lie in this interval. Among these are the gene encoding pancreatic polypeptide (PPY) and a polymorphic marker at locus D17S78. Efforts to construct a physical map of this region by isolating a large number of yeast artificial chromosome (YAC) and cosmid clones demonstrate that PPY and D17S78 are present within the same cosmid clone, and therefore no farther than 45 kb apart.more » This observation takes on particular significance since it excludes a recently described BRCA1 candidate gene from the interval defined by meiotic mapping. Although PPY and D17S78 were found to be no farther than 45 kb apart, identification of a smaller fragment that hybridizes to both probes would indicate that these two are much closer. The probe p131 and the gene PPY were previously mapped to 17q21-q23 and to the proximal long arm of chromosome 17, respectively. The demonstration of the close proximity of these markers should allow them to be treated as a single locus in terms of long-range genomic mapping of this region, and the genomic clones isolated should serve as useful resources for the identification of the BRCA1 gene. Analysis of a large number of a familial and spordic breast and ovarian cancers has identified frequent loss of heterozygosity near the BRCA1 locus. A recent report has suggested the responsible interval lies just telomeric to PPY, and a suggested candidate gene (MCD) for BRCA1 was found to be somatically rearranged in two of several hundred sporadic breast tumors.« less

Preliminary Geologic Map of the Big Pine Mountain Quadrangle, California

USGS Publications Warehouse

Vedder, J.G.; McLean, Hugh; Stanley, R.G.

1995-01-01

Reconnaissance geologic mapping of the San Rafael Primitive Area (now the San Rafael Wilderness) by Gower and others (1966) and Vedder an others (1967) showed s number of stratigraphic and structural ambiguities. To help resolve some of those problems, additional field work was done on parts of the Big Pine Moutain quadrangle during short intervals in 1981 and 1984, and 1990-1994.

Technical support for creating an artificial intelligence system for feature extraction and experimental design

NASA Technical Reports Server (NTRS)

Glick, B. J.

1985-01-01

Techniques for classifying objects into groups or clases go under many different names including, most commonly, cluster analysis. Mathematically, the general problem is to find a best mapping of objects into an index set consisting of class identifiers. When an a priori grouping of objects exists, the process of deriving the classification rules from samples of classified objects is known as discrimination. When such rules are applied to objects of unknown class, the process is denoted classification. The specific problem addressed involves the group classification of a set of objects that are each associated with a series of measurements (ratio, interval, ordinal, or nominal levels of measurement). Each measurement produces one variable in a multidimensional variable space. Cluster analysis techniques are reviewed and methods for incuding geographic location, distance measures, and spatial pattern (distribution) as parameters in clustering are examined. For the case of patterning, measures of spatial autocorrelation are discussed in terms of the kind of data (nominal, ordinal, or interval scaled) to which they may be applied.

A locus for isolated cataract on human Xp

PubMed Central

Francis, P; Berry, V; Hardcastle, A; Maher, E; Moore, A; Bhattacharya, S

2002-01-01

Purpose: To genetically map the gene causing isolated X linked cataract in a large European pedigree. Methods: Using the patient registers at Birmingham Women's Hospital, UK, we identified and examined 23 members of a four generation family with nuclear cataract. Four of six affected males also had complex congenital heart disease. Pedigree data were collated and leucocyte DNA extracted from venous blood. Linkage analysis by PCR based microsatellite marker genotyping was used to identify the disease locus and mutations within candidate genes screened by direct sequencing. Results: The disease locus was genetically refined to chromosome Xp22, within a 3 cM linkage interval flanked by markers DXS9902 and DXS999 (Zmax=3.64 at θ=0 for marker DXS8036). Conclusions: This is the first report of a locus for isolated inherited cataract on the X chromosome. The disease interval lies within the Nance-Horan locus suggesting allelic heterogeneity. The apparent association with congenital cardiac anomalies suggests a possible new oculocardiac syndrome. PMID:11836358

The steady part of the secular variation of the Earth's magnetic field

NASA Technical Reports Server (NTRS)

Bloxham, Jeremy

1992-01-01

The secular variation of the Earth's magnetic field results from the effects of magnetic induction in the fluid outer core and from the effects of magnetic diffusion in the core and the mantle. Adequate observations to map the magnetic field at the core-mantle boundary extend back over three centuries, providing a model of the secular variation at the core-mantle boundary. Here we consider how best to analyze this time-dependent part of the field. To calculate steady core flow over long time periods, we introduce an adaptation of our earlier method of calculating the flow in order to achieve greater numerical stability. We perform this procedure for the periods 1840-1990 and 1690-1840 and find that well over 90 percent of the variance of the time-dependent field can be explained by simple steady core flow. The core flows obtained for the two intervals are broadly similar to each other and to flows determined over much shorter recent intervals.

The application of remote sensing technology to the solution of problems in the management of resources in Indiana

NASA Technical Reports Server (NTRS)

Weismiller, R. A.; Mroczynski, R. P. (Principal Investigator)

1978-01-01

The author has identified the following significant results. Of the sampling techniques considered, a combination soil mapping and area sampling offered the most practical method for gathering soils data. Using the dot grid count, a relative percentage composition of soils can be calculated for each spectral class. From these percentages, a legend describing the dominant soils and inclusions can be developed. Interval drainage class seemed to be correlated with magnitude. For every parent material area, the more poorly drained soils had a lower magnitude of reflectance. Soil spectral classes seemed to be predominantly one internal drainage class.

A Narrow Quantitative Trait Locus in C. elegans Coordinately Affects Longevity, Thermotolerance, and Resistance to Paraquat

PubMed Central

Vertino, Anthony; Ayyadevara, Srinivas; Thaden, John J.; Reis, Robert J. Shmookler

2011-01-01

By linkage mapping of quantitative trait loci, we previously identified at least 11 natural genetic variants that significantly modulate Caenorhabditis elegans life-span (LS), many of which would have eluded discovery by knock-down or mutation screens. A region on chromosome IV between markers stP13 and stP35 had striking effects on longevity in three inter-strain crosses (each P < 10−9). In order to define the limits of that interval, we have now constructed two independent lines by marker-based selection during 20 backcross generations, isolating the stP13–stP35 interval from strain Bergerac-BO in a CL2a background. These congenic lines differed significantly from CL2a in LS, assayed in two environments (each P < 0.001). We then screened for exchange of flanking markers to isolate recombinants that partition this region, because fine-mapping the boundaries for overlapping heteroallelic spans can greatly narrow the implicated interval. Recombinants carrying the CL2a allele at stP35 were consistently long-lived compared to those retaining the Bergerac-BO allele (P < 0.001), and more resistant to temperature elevation and paraquat (each ∼1.7-fold, P < 0.0001), but gained little protection from ultraviolet or peroxide stresses. Two rounds of recombinant screening, followed by fine-mapping of break-points and survival testing, narrowed the interval to 0.18 Mb (13.35–13.53 Mb) containing 26 putative genes and six small-nuclear RNAs – a manageable number of targets for functional assessment. PMID:22303358

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash.

PubMed

Holdsworth, William L; LaPlant, Kyle E; Bell, Duane C; Jahn, Molly M; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

PubMed Central

Holdsworth, William L.; LaPlant, Kyle E.; Bell, Duane C.; Jahn, Molly M.; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection. PMID:27936008

Linkage map of the honey bee, Apis mellifera, based on RAPD markers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunt, G.J.; Page, R.E. Jr.

A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkagemore » groups. We estimate the total genome size to be {approximately}3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. 71 refs., 6 figs., 1 tab.« less

Fine genetic mapping of the gene for nevoid basal cell carcinoma syndrome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wicking, C.; Berkman, J.; Wainwright, B.

1994-08-01

Nevoid basal cell carcinoma syndrome (NBCCS, or Gorlin syndrome) is a cancer predisposition syndrome characterized by multiple basal cell carcinomas and diverse developmental defects. The gene responsible for NBCCS, which is most likely to be a tumor suppressor gene, has previously been mapped to 9q22.3-q31 in a 12-cM interval between the microsatellite marker loci D9S12.1 and D9S109. Combined multipoint and haplotype analyses of additional polymorphisms in this region in our collection of Australasian pedigrees have further refined the localization of the gene to between the markers D9S196 and D9S180, an interval reported to be approximately 2 cM. 27 refs., 4more » figs., 1 tab.« less

Digital soil mapping using remote sensing indices, terrain attributes, and vegetation features in the rangelands of northeastern Iran.

PubMed

Mahmoudabadi, Ebrahim; Karimi, Alireza; Haghnia, Gholam Hosain; Sepehr, Adel

2017-09-11

Digital soil mapping has been introduced as a viable alternative to the traditional mapping methods due to being fast and cost-effective. The objective of the present study was to investigate the capability of the vegetation features and spectral indices as auxiliary variables in digital soil mapping models to predict soil properties. A region with an area of 1225 ha located in Bajgiran rangelands, Khorasan Razavi province, northeastern Iran, was chosen. A total of 137 sampling sites, each containing 3-5 plots with 10-m interval distance along a transect established based on randomized-systematic method, were investigated. In each plot, plant species names and numbers as well as vegetation cover percentage (VCP) were recorded, and finally one composite soil sample was taken from each transect at each site (137 soil samples in total). Terrain attributes were derived from a digital elevation model, different bands and spectral indices were obtained from the Landsat7 ETM+ images, and vegetation features were calculated in the plots, all of which were used as auxiliary variables to predict soil properties using artificial neural network, gene expression programming, and multivariate linear regression models. According to R 2 RMSE and MBE values, artificial neutral network was obtained as the most accurate soil properties prediction function used in scorpan model. Vegetation features and indices were more effective than remotely sensed data and terrain attributes in predicting soil properties including calcium carbonate equivalent, clay, bulk density, total nitrogen, carbon, sand, silt, and saturated moisture capacity. It was also shown that vegetation indices including NDVI, SAVI, MSAVI, SARVI, RDVI, and DVI were more effective in estimating the majority of soil properties compared to separate bands and even some soil spectral indices.

Disseminating Landslide Hazard Information for California Local Government

NASA Astrophysics Data System (ADS)

Wills, C. J.

2010-12-01

Since 1969, the California Geological Survey has produced numerous maps showing landslide features and delineating potential slope-stability problem areas. These maps have been provided to local governments to encourage consideration of landslide hazards in planning and development decisions. Maps produced from 1986 through 1995 under the Landslide Hazard Mapping Act were advisory only, and their use by local government was never consistent. By contrast, maps of Zones of Required Investigation for seismically induced landslides produced under the Seismic Hazard Zoning Act since 1997 come with detailed guidelines and legal requirements. A legislative act that required landslide hazards be mapped and hazard maps disseminated to local government proved ineffective in landslide hazard mitigation. A later act with requirements that the hazard zone maps be used by local government proved more effective. Planning scenarios have proven to be an effective way of transmitting scientific information about natural hazards to emergency response professionals. Numerous earthquake planning scenarios have been prepared and used as the basis for emergency response exercises. An advantage of scenarios that include loss estimates is that the effects can be put in units of measure that everyone understands, principally deaths and dollars. HAZUS software available from FEMA allows calculation of losses for earthquake scenarios, but similar methods for landslides have not been developed. As part of the USGS Multi-Hazard Demonstration Project, we have estimated the landslide losses for a major west-coast winter storm scenario by developing a system based loosely on HAZUS. Data on landslide damage in past storms has been sparse and inconsistent, but a few data sets are available. The most detailed and complete available data on landslide damage was gathered by the City of Los Angeles following the 1978 storms. We extrapolate from that data to the entire state by first generalizing a landslide susceptibility map to give a single value of susceptibility for each census tract. We then calculated the loss ratio, the cost of landslide damage from the 1978 storms divided by the value of light wood frame structures in the census tract. The comparison suggests three general categories of damage: tracts with low landslide susceptibility have no landslide damage: tracts with moderate susceptibility have loss ratios of about 0.016%: and tracts with high susceptibility have loss ratios of 0.096%. Using these values, the susceptibility map becomes a landslide loss ratio map for the average storm intensity and landslide vulnerability of Los Angeles in 1978. Generalization to other storm intensities uses differences in storm intensity and landslide damage data from the 1982 storm in the Bay Area. In Santa Cruz County, that storm had a recurrence interval of over 100 years, and over 3 times the damage as our projection from the 1978 data. In Sonoma County, that storm had a recurrence interval of only 10 years and damage that was only 2% of our projection. If a relationship between storm intensity and the projections from the 1978 Los Angeles data can be developed, we may be able to estimate landslide losses for any projected storm intensity.

Seismic attribute analysis for reservoir and fluid prediction, Malay Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mansor, M.N.; Rudolph, K.W.; Richards, F.B.

1994-07-01

The Malay Basin is characterized by excellent seismic data quality, but complex clastic reservoir architecture. With these characteristics, seismic attribute analysis is a very important tool in exploration and development geoscience and is routinely used for mapping fluids and reservoir, recognizing and risking traps, assessment, depth conversion, well placement, and field development planning. Attribute analysis can be successfully applied to both 2-D and 3-D data as demonstrated by comparisons of 2-D and 3-D amplitude maps of the same area. There are many different methods of extracting amplitude information from seismic data, including amplitude mapping, horizon slice, summed horizon slice, isochronmore » slice, and horizon slice from AVO (amplitude versus offset) cube. Within the Malay Basin, horizon/isochron slice techniques have several advantages over simply extracting amplitudes from a picked horizon: they are much faster, permit examination of the amplitude structure of the entire cube, yield better results for weak/variable signatures, and aid summation of amplitudes. Summation in itself often yields improved results because it incorporates the signature from the entire reservoir interval, reducing any effects due to noise, mispicking, or waveform variations. Dip and azimuth attributes have been widely applied by industry for fault identification. In addition, these attributes can also be used to map signature variations associated with hydrocarbon contacts or stratigraphic changes, and this must be considered when using these attributes for structural interpretation.« less

Voxel-Based Lesion Symptom Mapping of Coarse Coding and Suppression Deficits in Patients With Right Hemisphere Damage

PubMed Central

Tompkins, Connie A.; Meigh, Kimberly M.; Prat, Chantel S.

2015-01-01

Purpose This study examined right hemisphere (RH) neuroanatomical correlates of lexical–semantic deficits that predict narrative comprehension in adults with RH brain damage. Coarse semantic coding and suppression deficits were related to lesions by voxel-based lesion symptom mapping. Method Participants were 20 adults with RH cerebrovascular accidents. Measures of coarse coding and suppression deficits were computed from lexical decision reaction times at short (175 ms) and long (1000 ms) prime-target intervals. Lesions were drawn on magnetic resonance imaging images and through normalization were registered on an age-matched brain template. Voxel-based lesion symptom mapping analysis was applied to build a general linear model at each voxel. Z score maps were generated for each deficit, and results were interpreted using automated anatomical labeling procedures. Results A deficit in coarse semantic activation was associated with lesions to the RH posterior middle temporal gyrus, dorsolateral prefrontal cortex, and lenticular nuclei. A maintenance deficit for coarsely coded representations involved the RH temporal pole and dorsolateral prefrontal cortex more medially. Ineffective suppression implicated lesions to the RH inferior frontal gyrus and subcortical regions, as hypothesized, along with the rostral temporal pole. Conclusion Beyond their scientific implications, these lesion–deficit correspondences may help inform the clinical diagnosis and enhance decisions about candidacy for deficit-focused treatment to improve narrative comprehension in individuals with RH damage. PMID:26425785

Successful gas hydrate prospecting using 3D seismic - A case study for the Mt. Elbert prospect, Milne Point, North Slope Alaska

USGS Publications Warehouse

Inks, T.L.; Agena, W.F.

2008-01-01

In February 2007, the Mt. Elbert Prospect stratigraphic test well, Milne Point, North Slope Alaska encountered thick methane gas hydrate intervals, as predicted by 3D seismic interpretation and modeling. Methane gas hydrate-saturated sediment was found in two intervals, totaling more than 100 ft., identified and mapped based on seismic character and wavelet modeling.

High-sensitivity aeromagnetic survey of the US Atlantic continental margin.

USGS Publications Warehouse

Behrendt, John C.; Klitgord, Kim D.

1980-01-01

The US Geological Survey contracted a high-sensitivity, digital aeromagnetic survey that was flown over the US Atlantic continental margin over a period of 15 months between 1974 and 1976. The 185 000 km of profile data have a relative accuracy approaching a few tenths of a nanotesla, which allowed compilation into maps at a scale of 1:250 000, with a contour interval of 2 nT. Automatic data processing using the Werner method allowed calculations of apparent depth to sources of the magnetic anomalies on all of the profiles, assuming a dike or interface as a source. Comparison of the computed depths to magnetic basement with multichannel seismic profiles across the survey area helped to reduce ambiguities in magnetic depth estimates and enabled interpolation of basement structures between seismic profiles. The resulting map showing depth to basement of the Atlantic continental margin is compatible with available multichannel seismic data, and we consider it a reasonable representation of the base of the sedimentary column. -Authors

Application LANDSAT imagery to geologic mapping in the ice-free valleys of Antarctica

NASA Technical Reports Server (NTRS)

Houston, R. S. (Principal Investigator); Marrs, R. W.; Smithson, S. B.

1976-01-01

The author has identified the following significant results. Studies in the Ice-Free Valleys are resulted in the compilation of a sizeable library of maps and publications. Rock reflectance measurements were taken during the Antarctic summer of 1973. Spectral reflectance of rocks (mostly mafic lava flows) in the McMurdo and Ice-Free Valleys areas were measured using a filter wheel photometer equipped to measure reflectances in the four Landsat bands. A series of samples were collected at regular intervals across a large differentiated, mafic sill near Lake Vida. Chemical analyses of the sample suggest that the tonal variations in this sill are controlled by changes in the iron content of the rock. False color images were prepared for a number of areas by the diazo method and with an optical multispectral biviewer. These images were useful in defining boundaries of sea ice, snow cover, and in the study of ablating glaciers, but were not very useful for rock discrimination.

Mapping the literature of nursing informatics

PubMed Central

Guenther, Johanna T.

2006-01-01

Objective: This study was part of the Medical Library Association's Nursing and Allied Health Resources Section's project to map the nursing literature. It identified core journals in nursing informatics and the journals referenced in them and analyzed coverage of those journals in selected indexes. Method: Five core journals were chosen and analyzed for 1996, 1997, and 1998. The references in the core journal articles were examined for type and number of formats cited during the selected time period. Bradford's Law of Scattering divided the journals into frequency zones. Results: The time interval, 1990 to 1998, produced 71% of the references. Internet references could not be tracked by date before 1990. Twelve journals were the most productive, 119 journals were somewhat productive, and 897 journals were the least productive. Journal of the American Medical Informatics Association was the most prolific core journal. The 1998 journal references were compared in CINAHL, PubMed/MEDLINE, Science Citation Index, and OCLC Article First. PubMed/MEDLINE had the highest indexing score. PMID:16710469

Spatiotemporal distribution of Holocene populations in North America

PubMed Central

Chaput, Michelle A.; Kriesche, Björn; Betts, Matthew; Martindale, Andrew; Kulik, Rafal; Schmidt, Volker; Gajewski, Konrad

2015-01-01

As the Cordilleran and Laurentide Ice Sheets retreated, North America was colonized by human populations; however, the spatial patterns of subsequent population growth are unclear. Temporal frequency distributions of aggregated radiocarbon (14C) dates are used as a proxy of population size and can be used to track this expansion. The Canadian Archaeological Radiocarbon Database contains more than 35,000 14C dates and is used in this study to map the spatiotemporal demographic changes of Holocene populations in North America at a continental scale for the past 13,000 y. We use the kernel method, which converts the spatial distribution of 14C dates into estimates of population density at 500-y intervals. The resulting maps reveal temporally distinct, dynamic patterns associated with paleodemographic trends that correspond well to genetic, archaeological, and ethnohistoric evidence of human occupation. These results have implications for hypothesizing and testing migration routes into and across North America as well as the relative influence of North American populations on the evolution of the North American ecosystem. PMID:26351683

a Performance Comparison of Feature Detectors for Planetary Rover Mapping and Localization

NASA Astrophysics Data System (ADS)

Wan, W.; Peng, M.; Xing, Y.; Wang, Y.; Liu, Z.; Di, K.; Teng, B.; Mao, X.; Zhao, Q.; Xin, X.; Jia, M.

2017-07-01

Feature detection and matching are key techniques in computer vision and robotics, and have been successfully implemented in many fields. So far there is no performance comparison of feature detectors and matching methods for planetary mapping and rover localization using rover stereo images. In this research, we present a comprehensive evaluation and comparison of six feature detectors, including Moravec, Förstner, Harris, FAST, SIFT and SURF, aiming for optimal implementation of feature-based matching in planetary surface environment. To facilitate quantitative analysis, a series of evaluation criteria, including distribution evenness of matched points, coverage of detected points, and feature matching accuracy, are developed in the research. In order to perform exhaustive evaluation, stereo images, simulated under different baseline, pitch angle, and interval of adjacent rover locations, are taken as experimental data source. The comparison results show that SIFT offers the best overall performance, especially it is less sensitive to changes of image taken at adjacent locations.

Slow wave contraction frequency plateaus in the small intestine are composed of discrete waves of interval increase associated with dislocations.

PubMed

Parsons, Sean P; Huizinga, Jan D

2018-06-03

What is the central question of this study? What is the nature of slow wave driven contraction frequency gradients in the small intestine? What is the main finding and its importance? Frequency plateaus are composed of discrete waves of increased interval, each wave associated with a contraction dislocation. Smooth frequency gradients are generated by localised neural modulation of wave frequency, leading to functionally important wave turbulence. Both patterns are emergent properties of a network of coupled oscillators, the interstitial cells of Cajal. A gut-wide network of interstitial cells of Cajal (ICC) generate electrical oscillations (slow waves) that orchestrate waves of muscle contraction. In the small intestine there is a gradient in slow wave frequency from high at the duodenum to low at the terminal ileum. Time-averaged measurements of frequency have suggested either a smooth or stepped (plateaued) gradient. We measured individual contraction intervals from diameter maps of the mouse small intestine to create interval maps (IMaps). IMaps showed that each frequency plateau was composed of discrete waves of increased interval. Each interval wave originated at a terminating contraction wave, a "dislocation", at the plateau's proximal boundary. In a model chain of coupled phase oscillators, interval wave frequency increased as coupling decreased or as the natural frequency gradient or noise increased. Injuring the intestine at a proximal point to destroy coupling, suppressed distal steps which then reappeared with gap junction block by carbenoxolone. This lent further support to our previous hypothesis that lines of dislocations were fixed by points of low coupling strength. Dislocations induced by electrical field pulses in the intestine and by equivalent phase shift in the model, were associated with interval waves. When the enteric nervous system was active, IMaps showed a chaotic, turbulent pattern of interval change with no frequency steps or plateaus. This probably resulted from local, stochastic release of neurotransmitters. Plateaus, dislocations, interval waves and wave turbulence arise from a dynamic interplay between natural frequency and coupling in the ICC network. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Quantitative retrieving forest ecological parameters based on remote sensing in Liping County of China

NASA Astrophysics Data System (ADS)

Tian, Qingjiu; Chen, Jing M.; Zheng, Guang; Xia, Xueqi; Chen, Junying

2006-09-01

Forest ecosystem is an important component of terrestrial ecosystem and plays an important role in global changes. Aboveground biomass (AGB) of forest ecosystem is an important factor in global carbon cycle studies. The purpose of this study was to retrieve the yearly Net Primary Productivity (NPP) of forest from the 8-days-interval MODIS-LAI images of a year and produce a yearly NPP distribution map. The LAI, DBH (diameter at breast height), tree height, and tree age field were measured in different 80 plots for Chinese fir, Masson pine, bamboo, broadleaf, mix forest in Liping County. Based on the DEM image and Landsat TM images acquired on May 14th, 2000, the geometric correction and terrain correction were taken. In addition, the "6S"model was used to gain the surface reflectance image. Then the correlation between Leaf Area Index (LAI) and Reduced Simple Ratio (RSR) was built. Combined with the Landcover map, forest stand map, the LAI, aboveground biomass, tree age map were produced respectively. After that, the 8-days- interval LAI images of a year, meteorology data, soil data, forest stand image and Landcover image were inputted into the BEPS model to get the NPP spatial distribution. At last, the yearly NPP spatial distribution map with 30m spatial resolution was produced. The values in those forest ecological parameters distribution maps were quite consistent with those of field measurements. So it's possible, feasible and time-saving to estimate forest ecological parameters at a large scale by using remote sensing.

Flood profiles for lower Brooker Creek, west-central Florida

USGS Publications Warehouse

Murphy, W.R.

1978-01-01

Flood heights are computed for a range of recurrence intervals for a 12.6 mile reach of Brooker Creek, beginning at the mouth at Lake Tarpon. A Geological Survey step-backwater computer program, E431, was used in these analyses using: (1) Stream and valley cross-section geometry and roughness data; (2) Recurrence interval flood-peak discharges; (3) Recurrence interval starting elevations; (4) Gaging station stage-discharge relations. Flood heights may be plotted versus distance above stream mouth and connected to construct flood profiles. They may also be used to indicate areas of inundation on detailed topographic maps.

A Practical and Automated Approach to Large Area Forest Disturbance Mapping with Remote Sensing

PubMed Central

Ozdogan, Mutlu

2014-01-01

In this paper, I describe a set of procedures that automate forest disturbance mapping using a pair of Landsat images. The approach is built on the traditional pair-wise change detection method, but is designed to extract training data without user interaction and uses a robust classification algorithm capable of handling incorrectly labeled training data. The steps in this procedure include: i) creating masks for water, non-forested areas, clouds, and cloud shadows; ii) identifying training pixels whose value is above or below a threshold defined by the number of standard deviations from the mean value of the histograms generated from local windows in the short-wave infrared (SWIR) difference image; iii) filtering the original training data through a number of classification algorithms using an n-fold cross validation to eliminate mislabeled training samples; and finally, iv) mapping forest disturbance using a supervised classification algorithm. When applied to 17 Landsat footprints across the U.S. at five-year intervals between 1985 and 2010, the proposed approach produced forest disturbance maps with 80 to 95% overall accuracy, comparable to those obtained from traditional approaches to forest change detection. The primary sources of mis-classification errors included inaccurate identification of forests (errors of commission), issues related to the land/water mask, and clouds and cloud shadows missed during image screening. The approach requires images from the peak growing season, at least for the deciduous forest sites, and cannot readily distinguish forest harvest from natural disturbances or other types of land cover change. The accuracy of detecting forest disturbance diminishes with the number of years between the images that make up the image pair. Nevertheless, the relatively high accuracies, little or no user input needed for processing, speed of map production, and simplicity of the approach make the new method especially practical for forest cover change analysis over very large regions. PMID:24717283

A practical and automated approach to large area forest disturbance mapping with remote sensing.

PubMed

Ozdogan, Mutlu

2014-01-01

In this paper, I describe a set of procedures that automate forest disturbance mapping using a pair of Landsat images. The approach is built on the traditional pair-wise change detection method, but is designed to extract training data without user interaction and uses a robust classification algorithm capable of handling incorrectly labeled training data. The steps in this procedure include: i) creating masks for water, non-forested areas, clouds, and cloud shadows; ii) identifying training pixels whose value is above or below a threshold defined by the number of standard deviations from the mean value of the histograms generated from local windows in the short-wave infrared (SWIR) difference image; iii) filtering the original training data through a number of classification algorithms using an n-fold cross validation to eliminate mislabeled training samples; and finally, iv) mapping forest disturbance using a supervised classification algorithm. When applied to 17 Landsat footprints across the U.S. at five-year intervals between 1985 and 2010, the proposed approach produced forest disturbance maps with 80 to 95% overall accuracy, comparable to those obtained from traditional approaches to forest change detection. The primary sources of mis-classification errors included inaccurate identification of forests (errors of commission), issues related to the land/water mask, and clouds and cloud shadows missed during image screening. The approach requires images from the peak growing season, at least for the deciduous forest sites, and cannot readily distinguish forest harvest from natural disturbances or other types of land cover change. The accuracy of detecting forest disturbance diminishes with the number of years between the images that make up the image pair. Nevertheless, the relatively high accuracies, little or no user input needed for processing, speed of map production, and simplicity of the approach make the new method especially practical for forest cover change analysis over very large regions.

Surface magnetic field mapping on high albedo marking areas of the moon

NASA Astrophysics Data System (ADS)

Shibuya, H.; Aikawa, K.; Tsunakawa, H.; Takahashi, F.; Shimizu, H.; Matsushima, M.

2009-12-01

The correlation between high albedo markings (HAM) on the surface of the moon and strong magnetic anomalies has been claimed since the early time of the lunar magnetic field study (Hood and Schubert, 1980). Hood et al. (1989) mapped the smoothed magnetic field over the Reiner Gamma region using Lunar Prospector magnetometer (LP-MAG) data, and showed that the position of them matches well. We have developed a method to recover the 3-d magnetic field from satellite field observations (EPR method which stands for Equivalent Pole Reduction; Toyoshima et al. 2008). Applying EPR to the several areas of strong magnetic anomalies, we calculated the magnetic anomaly maps of near surface regions, to see how the anomaly and the HAM correlate each other. The data used is of the Lunar Prospector magnetometer (LP-MAG). They are selected from low altitude observations performed in 1998 to 1999. The areas studied are Reiner Gamma, Airy, Descartes, Abel, and Crisium Antipode regions. The EPR determines a set of magnetic monopoles at the moon surface which produce the magnetic field of the observation. In each studied area, we put poles in 0.1° intervals of both latitude and longitude, then the magnetic field at 5km in altitude is calculated. The field distribution is superimposed with the albedo map made from Clementine data. The total force (Bf) maps indicate that the HMA occurs at the strong anomaly regions, but their shape does not quite overlie. However, taking horizontal component (Bh), not only position but the shape and size of the anomalies coincide with HMA regions. It is particularly true for the Reiner Gamma, and Descartes regions. The shape of HMA fits in a Bh contour. The HMA is argued to be formed by the reduction of solar wind particles which are shielded by the magnetic field. Since the deflection of the charged particle becomes large at large horizontal component, the Bh distribution showed here support the argument.

The slick hair coat locus maps to chromosome 20 in Senepol-derived cattle.

PubMed

Mariasegaram, M; Chase, C C; Chaparro, J X; Olson, T A; Brenneman, R A; Niedz, R P

2007-02-01

The ability to maintain normal temperatures during heat stress is an important attribute for cattle in the subtropics and tropics. Previous studies have shown that Senepol cattle and their crosses with Holstein, Charolais and Angus animals are as heat tolerant as Brahman cattle. This has been attributed to the slick hair coat of Senepol cattle, which is thought to be controlled by a single dominant gene. In this study, a genome scan using a DNA-pooling strategy indicated that the slick locus is most likely on bovine chromosome 20 (BTA20). Interval mapping confirmed the BTA20 assignment and refined the location of the locus. In total, 14 microsatellite markers were individually genotyped in two pedigrees consisting of slick and normal-haired cattle (n = 36), representing both dairy and beef breeds. The maximum LOD score was 9.4 for a 4.4-cM support interval between markers DIK2416 and BM4107. By using additional microsatellite markers in this region, and genotyping in six more pedigrees (n = 86), the slick locus was further localized to the DIK4835 - DIK2930 interval.

Recombination rate variation in mice from an isolated island.

PubMed

Wang, Richard J; Gray, Melissa M; Parmenter, Michelle D; Broman, Karl W; Payseur, Bret A

2017-01-01

Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales. © 2016 John Wiley & Sons Ltd.

Recombination rate variation in mice from an isolated island

PubMed Central

Wang, Richard J.; Gray, Melissa M.; Parmenter, Michelle D.; Broman, Karl W.; Payseur, Bret A.

2016-01-01

Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1,212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including sub-chromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genome-wide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbor a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales. PMID:27864900

Predicting depression based on dynamic regional connectivity: a windowed Granger causality analysis of MEG recordings.

PubMed

Lu, Qing; Bi, Kun; Liu, Chu; Luo, Guoping; Tang, Hao; Yao, Zhijian

2013-10-16

Abnormal inter-regional causalities can be mapped for the objective diagnosis of various diseases. These inter-regional connectivities are usually calculated over an entire scan and used to characterize the stationary strength of the connections. However, the connectivity within networks may undergo substantial changes during a scan. In this study, we developed an objective depression recognition approach using the dynamic regional interactions that occur in response to sad facial stimuli. The whole time-period magnetoencephalography (MEG) signals from the visual cortex, amygdala, anterior cingulate cortex (ACC) and inferior frontal gyrus (IFG) were separated into sequential time intervals. The Granger causality mapping method was used to identify the pairwise interaction pattern within each time interval. Feature selection was then undertaken within a minimum redundancy-maximum relevance (mRMR) framework. Typical classifiers were utilized to predict those patients who had depression. The overall performances of these classifiers were similar, and the highest classification accuracy rate was 87.5%. The best discriminative performance was obtained when the number of features was within a robust range. The discriminative network pattern obtained through support vector machine (SVM) analyses displayed abnormal causal connectivities that involved the amygdala during the early and late stages. These early and late connections in the amygdala appear to reveal a negative bias to coarse expression information processing and abnormal negative modulation in patients with depression, which may critically affect depression discrimination. © 2013 Elsevier B.V. All rights reserved.

A method to generate surface UV radiation maps over Europe using GOME, Meteosat, and ancillary geophysical data

NASA Astrophysics Data System (ADS)

Verdebout, Jean

2000-02-01

This paper presents a method for generating surface ultraviolet (UV) radiation maps over Europe, with a spatial resolution of 0.05°, and potentially on a half-hour basis. The UV irradiance is obtained by interpolation in a look-up table (LUT), the entries of which are solar zenith angle, total column ozone amount, cloud liquid water thickness, near-surface horizontal visibility, surface elevation, and UV albedo. Both satellite (Meteosat, GOME) and nonsatellite (synoptic observations, meteorological model results, digital elevation model) data are exploited to assign values to the influencing factors. With the help of another LUT simulating the visible signal, Meteosat data are processed to retrieve the cloud liquid water thickness. The radiative transfer calculations are performed with the UVspec code. A preliminary step consists in generating an effective surface Meteosat albedo map from a series of 10 consecutive days. In this process the well-known difficulty of distinguishing clouds from snow-covered surfaces is encountered. An attempt is made to partially resolve the ambiguity by using the Meteosat infrared channel and modeled snow cover data. After additional empirical cloud filtering, the effective albedo map is used as a baseline to estimate the cloud liquid water thickness. The UV surface albedo is assigned uniform values for land and sea/ocean, except in the presence of snow. In this case it is given a value proportional to the Meteosat effective albedo. The total column ozone is extracted from the level 3 GOME products. The aerosol optical thickness is mapped by gridding the daily measurements performed by ˜1000 ground stations. The digital elevation model is the GTOPO30 data set from the U.S. Geological Survey. European wide UV dose rate maps are presented for one day in April 1997, and the influence of the various factors is illustrated. A daily integrated dose map was also generated using 27 Meteosat acquisitions at half-hour intervals on the same day. The dose map produced in this way takes into account the evolution of the cloud field and is thought to be more accurate than if it were estimated from one data take, in particular at the relatively high spatial resolution of the product. Finally, a preliminary comparison of modeled dose rate and daily dose with measurements performed with a ground instrument is discussed.

Mapping the spatio-temporal evolution of irrigation in the Coastal Plain of Georgia, USA

Treesearch

Marcus D. Williams; Christie M.S. Hawley; Marguerite Madden; J. Marshall Shepherd

2017-01-01

This study maps the spatial and temporal evolution of acres irrigated in the Coastal Plain of Georgia over a 38 year period. The goal of this analysis is to create a time-series of irrigated areas in the Coastal Plain of Georgia at a sub-county level. From 1976 through 2013, Landsat images were obtained and sampled at four year intervals to manually...

Identification of a key recombinant narrows the CADASIL gene region to 8 cM and argues against allelism of CADASIL and familial hemiplegic migraine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dichgans, M.; Mayer, M.; Straube, A.

1996-02-15

This article reports on new information regarding the genetic mapping of the human CADASIL gene region. Previously, the gene had been mapped to human chromosome 19q12. Using the identification of a chromosomal crossover, the region has been refined to an 8-cM interval. 11 refs., 2 figs., 1 tab.

Non-Markovianity of Gaussian Channels.

PubMed

Torre, G; Roga, W; Illuminati, F

2015-08-14

We introduce a necessary and sufficient criterion for the non-Markovianity of Gaussian quantum dynamical maps based on the violation of divisibility. The criterion is derived by defining a general vectorial representation of the covariance matrix which is then exploited to determine the condition for the complete positivity of partial maps associated with arbitrary time intervals. Such construction does not rely on the Choi-Jamiolkowski representation and does not require optimization over states.

Upscaling NZ-DNDC using a regression based meta-model to estimate direct N2O emissions from New Zealand grazed pastures.

PubMed

Giltrap, Donna L; Ausseil, Anne-Gaëlle E

2016-01-01

The availability of detailed input data frequently limits the application of process-based models at large scale. In this study, we produced simplified meta-models of the simulated nitrous oxide (N2O) emission factors (EF) using NZ-DNDC. Monte Carlo simulations were performed and the results investigated using multiple regression analysis to produce simplified meta-models of EF. These meta-models were then used to estimate direct N2O emissions from grazed pastures in New Zealand. New Zealand EF maps were generated using the meta-models with data from national scale soil maps. Direct emissions of N2O from grazed pasture were calculated by multiplying the EF map with a nitrogen (N) input map. Three meta-models were considered. Model 1 included only the soil organic carbon in the top 30cm (SOC30), Model 2 also included a clay content factor, and Model 3 added the interaction between SOC30 and clay. The median annual national direct N2O emissions from grazed pastures estimated using each model (assuming model errors were purely random) were: 9.6GgN (Model 1), 13.6GgN (Model 2), and 11.9GgN (Model 3). These values corresponded to an average EF of 0.53%, 0.75% and 0.63% respectively, while the corresponding average EF using New Zealand national inventory values was 0.67%. If the model error can be assumed to be independent for each pixel then the 95% confidence interval for the N2O emissions was of the order of ±0.4-0.7%, which is much lower than existing methods. However, spatial correlations in the model errors could invalidate this assumption. Under the extreme assumption that the model error for each pixel was identical the 95% confidence interval was approximately ±100-200%. Therefore further work is needed to assess the degree of spatial correlation in the model errors. Copyright © 2015 Elsevier B.V. All rights reserved.

Chosen interval methods for solving linear interval systems with special type of matrix

NASA Astrophysics Data System (ADS)

Szyszka, Barbara

2013-10-01

The paper is devoted to chosen direct interval methods for solving linear interval systems with special type of matrix. This kind of matrix: band matrix with a parameter, from finite difference problem is obtained. Such linear systems occur while solving one dimensional wave equation (Partial Differential Equations of hyperbolic type) by using the central difference interval method of the second order. Interval methods are constructed so as the errors of method are enclosed in obtained results, therefore presented linear interval systems contain elements that determining the errors of difference method. The chosen direct algorithms have been applied for solving linear systems because they have no errors of method. All calculations were performed in floating-point interval arithmetic.

Scanning Laser Polarimetry and Optical Coherence Tomography for Detection of Retinal Nerve Fiber Layer Defects

PubMed Central

Oh, Jong-Hyun

2009-01-01

Purpose To compare the ability of scanning laser polarimetry with variable corneal compensation (GDx-VCC) and Stratus optical coherence tomography (OCT) to detect photographic retinal nerve fiber layer (RNFL) defects. Methods This retrospective cross-sectional study included 45 eyes of 45 consecutive glaucoma patients with RNFL defects in red-free fundus photographs. The superior and inferior temporal quadrants in each eye were included for data analysis separately. The location and presence of RNFL defects seen in red-free fundus photographs were compared with those seen in GDx-VCC deviation maps and OCT RNFL analysis maps for each quadrant. Results Of the 90 quadrants (45 eyes), 31 (34%) had no apparent RNFL defects, 29 (32%) had focal RNFL defects, and 30 (33%) had diffuse RNFL defects in red-free fundus photographs. The highest agreement between GDx-VCC and red-free photography was 73% when we defined GDx-VCC RNFL defects as a cluster of three or more color-coded squares (p<5%) along the traveling line of the retinal nerve fiber in the GDx-VCC deviation map (kappa value, 0.388; 95% confidence interval (CI), 0.195 to 0.582). The highest agreement between OCT and red-free photography was 85% (kappa value, 0.666; 95% CI, 0.506 to 0.825) when a value of 5% outside the normal limit for the OCT analysis map was used as a cut-off value for OCT RNFL defects. Conclusions According to the kappa values, the agreement between GDx-VCC deviation maps and red-free photography was poor, whereas the agreement between OCT analysis maps and red-free photography was good. PMID:19794943

Mapping on Slope Seepage Problem using Electrical Resistivity Imaging (ERI)

NASA Astrophysics Data System (ADS)

Hazreek, Z. A. M.; Nizam, Z. M.; Aziman, M.; Dan, M. F. Md; Shaylinda, M. Z. N.; Faizal, T. B. M.; Aishah, M. A. N.; Ambak, K.; Rosli, S.; Rais, Y.; Ashraf, M. I. M.; Alel, M. N. A.

2018-04-01

The stability of slope may influenced by several factors such as its geomaterial properties, geometry and environmental factors. Problematic slope due to seepage phenomenon will influenced the slope strength thus promoting to its failure. In the past, slope seepage mapping suffer from several limitation due to cost, time and data coverage. Conventional engineering tools to detect or mapped the seepage on slope experienced those problems involving large and high elevation of slope design. As a result, this study introduced geophysical tools for slope seepage mapping based on electrical resistivity method. Two spread lines of electrical resistivity imaging were performed on the slope crest using ABEM SAS 4000 equipment. Data acquisition configuration was based on long and short arrangement, schlumberger array and 2.5 m of equal electrode spacing interval. Raw data obtained from data acquisition was analyzed using RES2DINV software. Both of the resistivity results show that the slope studied consists of three different anomalies representing top soil (200 – 1000 Ωm), perched water (10 – 100 Ωm) and hard/dry layer (> 200 Ωm). It was found that seepage problem on slope studied was derived from perched water zones with electrical resistivity value of 10 – 100 Ωm. Perched water zone has been detected at 6 m depth from the ground level with varying thickness at 5 m and over. Resistivity results have shown some good similarity output with reference to borehole data, geological map and site observation thus verified the resistivity results interpretation. Hence, this study has shown that the electrical resistivity imaging was applicable in slope seepage mapping which consider efficient in term of cost, time, data coverage and sustainability.

Sodium Velocity Maps on Mercury

NASA Technical Reports Server (NTRS)

Potter, A. E.; Killen, R. M.

2011-01-01

The objective of the current work was to measure two-dimensional maps of sodium velocities on the Mercury surface and examine the maps for evidence of sources or sinks of sodium on the surface. The McMath-Pierce Solar Telescope and the Stellar Spectrograph were used to measure Mercury spectra that were sampled at 7 milliAngstrom intervals. Observations were made each day during the period October 5-9, 2010. The dawn terminator was in view during that time. The velocity shift of the centroid of the Mercury emission line was measured relative to the solar sodium Fraunhofer line corrected for radial velocity of the Earth. The difference between the observed and calculated velocity shift was taken to be the velocity vector of the sodium relative to Earth. For each position of the spectrograph slit, a line of velocities across the planet was measured. Then, the spectrograph slit was stepped over the surface of Mercury at 1 arc second intervals. The position of Mercury was stabilized by an adaptive optics system. The collection of lines were assembled into an images of surface reflection, sodium emission intensities, and Earthward velocities over the surface of Mercury. The velocity map shows patches of higher velocity in the southern hemisphere, suggesting the existence of sodium sources there. The peak earthward velocity occurs in the equatorial region, and extends to the terminator. Since this was a dawn terminator, this might be an indication of dawn evaporation of sodium. Leblanc et al. (2008) have published a velocity map that is similar.

Identifying fracture‐zone geometry using simulated annealing and hydraulic‐connection data

USGS Publications Warehouse

Day-Lewis, Frederick D.; Hsieh, Paul A.; Gorelick, Steven M.

2000-01-01

A new approach is presented to condition geostatistical simulation of high‐permeability zones in fractured rock to hydraulic‐connection data. A simulated‐annealing algorithm generates three‐dimensional (3‐D) realizations conditioned to borehole data, inferred hydraulic connections between packer‐isolated borehole intervals, and an indicator (fracture zone or background‐K bedrock) variogram model of spatial variability. We apply the method to data from the U.S. Geological Survey Mirror Lake Site in New Hampshire, where connected high‐permeability fracture zones exert a strong control on fluid flow at the hundred‐meter scale. Single‐well hydraulic‐packer tests indicate where permeable fracture zones intersect boreholes, and multiple‐well pumping tests indicate the degree of hydraulic connection between boreholes. Borehole intervals connected by a fracture zone exhibit similar hydraulic responses, whereas intervals not connected by a fracture zone exhibit different responses. Our approach yields valuable insights into the 3‐D geometry of fracture zones at Mirror Lake. Statistical analysis of the realizations yields maps of the probabilities of intersecting specific fracture zones with additional wells. Inverse flow modeling based on the assumption of equivalent porous media is used to estimate hydraulic conductivity and specific storage and to identify those fracture‐zone geometries that are consistent with hydraulic test data.

Oil shale resources of the Uinta Basin, Utah and Colorado

USGS Publications Warehouse

,

2010-01-01

The U.S. Geological Survey (USGS) recently completed a comprehensive assessment of in-place oil in oil shales of the Eocene Green River Formation of the Uinta Basin of eastern Utah and western Colorado. The oil shale interval was subdivided into eighteen roughly time-stratigraphic intervals, and each interval was assessed for variations in gallons per ton, barrels per acre, and total barrels in each township. The Radial Basis Function extrapolation method was used to generate isopach and isoresource maps, and to calculate resources. The total inplace resource for the Uinta Basin is estimated at 1.32 trillion barrels. This is only slightly lower than the estimated 1.53 trillion barrels for the adjacent Piceance Basin, Colorado, to the east, which is thought to be the richest oil shale deposit in the world. However, the area underlain by oil shale in the Uinta Basin is much larger than that of the Piceance Basin, and the average gallons per ton and barrels per acre values for each of the assessed oil shale zones are significantly lower in the depocenter in the Uinta Basin when compared to the Piceance Basin. These relations indicate that the oil shale resources in the Uinta Basin are of lower grade and are more dispersed than the oil shale resources of the Piceance Basin.

Monitoring the dynamics of surface water fraction from MODIS time series in a Mediterranean environment

NASA Astrophysics Data System (ADS)

Li, Linlin; Vrieling, Anton; Skidmore, Andrew; Wang, Tiejun; Turak, Eren

2018-04-01

Detailed spatial information of changes in surface water extent is needed for water management and biodiversity conservation, particularly in drier parts of the globe where small, temporally-variant wetlands prevail. Although global surface water histories are now generated from 30 m Landsat data, for many locations they contain large temporal gaps particularly for longer periods (>10 years) due to revisit intervals and cloud cover. Daily Moderate Resolution Imaging Spectrometer (MODIS) imagery has potential to fill such gaps, but its relatively coarse spatial resolution may not detect small water bodies, which can be of great ecological importance. To address this problem, this study proposes and tests options for estimating the surface water fraction from MODIS 16-day 500 m Bidirectional Reflectance Distribution Function (BRDF) corrected surface reflectance image composites. The spatial extent of two Landsat tiles over Spain were selected as test areas. We obtained a 500 m reference dataset on surface water fraction by spatially aggregating 30 m binary water masks obtained from the Landsat-derived C-version of Function of Mask (CFmask), which themselves were evaluated against high-resolution Google Earth imagery. Twelve regression tree models were developed with two approaches, Random Forest and Cubist, using spectral metrics derived from MODIS data and topographic parameters generated from a 30 m spatial resolution digital elevation model. Results showed that accuracies were higher when we included annual summary statistics of the spectral metrics as predictor variables. Models trained on a single Landsat tile were ineffective in mapping surface water in the other tile, but global models trained with environmental conditions from both tiles can provide accurate results for both study areas. We achieved the highest accuracy with Cubist global model (R2 = 0.91, RMSE = 11.05%, MAE = 7.67%). Our method was not only effective for mapping permanent water fraction, but also in accurately capturing temporal fluctuations of surface water. Based on this good performance, we produced surface water fraction maps at 16-day interval for the 2000-2015 MODIS archive. Our approach is promising for monitoring surface water fraction at high frequency time intervals over much larger regions provided that training data are collected across the spatial domain for which the model will be applied.

Markov Chain Monte Carlo estimation of species distributions: a case study of the swift fox in western Kansas

USGS Publications Warehouse

Sargeant, Glen A.; Sovada, Marsha A.; Slivinski, Christiane C.; Johnson, Douglas H.

2005-01-01

Accurate maps of species distributions are essential tools for wildlife research and conservation. Unfortunately, biologists often are forced to rely on maps derived from observed occurrences recorded opportunistically during observation periods of variable length. Spurious inferences are likely to result because such maps are profoundly affected by the duration and intensity of observation and by methods used to delineate distributions, especially when detection is uncertain. We conducted a systematic survey of swift fox (Vulpes velox) distribution in western Kansas, USA, and used Markov chain Monte Carlo (MCMC) image restoration to rectify these problems. During 1997–1999, we searched 355 townships (ca. 93 km) 1–3 times each for an average cost of $7,315 per year and achieved a detection rate (probability of detecting swift foxes, if present, during a single search) of = 0.69 (95% Bayesian confidence interval [BCI] = [0.60, 0.77]). Our analysis produced an estimate of the underlying distribution, rather than a map of observed occurrences, that reflected the uncertainty associated with estimates of model parameters. To evaluate our results, we analyzed simulated data with similar properties. Results of our simulations suggest negligible bias and good precision when probabilities of detection on ≥1 survey occasions (cumulative probabilities of detection) exceed 0.65. Although the use of MCMC image restoration has been limited by theoretical and computational complexities, alternatives do not possess the same advantages. Image models accommodate uncertain detection, do not require spatially independent data or a census of map units, and can be used to estimate species distributions directly from observations without relying on habitat covariates or parameters that must be estimated subjectively. These features facilitate economical surveys of large regions, the detection of temporal trends in distribution, and assessments of landscape-level relations between species and habitats. Requirements for the use of MCMC image restoration include study areas that can be partitioned into regular grids of mapping units, spatially contagious species distributions, reliable methods for identifying target species, and cumulative probabilities of detection ≥0.65.

Markov chain Monte Carlo estimation of species distributions: A case study of the swift fox in western Kansas

USGS Publications Warehouse

Sargeant, G.A.; Sovada, M.A.; Slivinski, C.C.; Johnson, D.H.

2005-01-01

Accurate maps of species distributions are essential tools for wildlife research and conservation. Unfortunately, biologists often are forced to rely on maps derived from observed occurrences recorded opportunistically during observation periods of variable length. Spurious inferences are likely to result because such maps are profoundly affected by the duration and intensity of observation and by methods used to delineate distributions, especially when detection is uncertain. We conducted a systematic survey of swift fox (Vulpes velox) distribution in western Kansas, USA, and used Markov chain Monte Carlo (MCMC) image restoration to rectify these problems. During 1997-1999, we searched 355 townships (ca. 93 km2) 1-3 times each for an average cost of $7,315 per year and achieved a detection rate (probability of detecting swift foxes, if present, during a single search) of ?? = 0.69 (95% Bayesian confidence interval [BCI] = [0.60, 0.77]). Our analysis produced an estimate of the underlying distribution, rather than a map of observed occurrences, that reflected the uncertainty associated with estimates of model parameters. To evaluate our results, we analyzed simulated data with similar properties. Results of our simulations suggest negligible bias and good precision when probabilities of detection on ???1 survey occasions (cumulative probabilities of detection) exceed 0.65. Although the use of MCMC image restoration has been limited by theoretical and computational complexities, alternatives do not possess the same advantages. Image models accommodate uncertain detection, do not require spatially independent data or a census of map units, and can be used to estimate species distributions directly from observations without relying on habitat covariates or parameters that must be estimated subjectively. These features facilitate economical surveys of large regions, the detection of temporal trends in distribution, and assessments of landscape-level relations between species and habitats. Requirements for the use of MCMC image restoration include study areas that can be partitioned into regular grids of mapping units, spatially contagious species distributions, reliable methods for identifying target species, and cumulative probabilities of detection ???0.65.

A subharmonic dynamical bifurcation during in vitro epileptiform activity

NASA Astrophysics Data System (ADS)

Perez Velazquez, Jose L.; Khosravani, Houman

2004-06-01

Epileptic seizures are considered to result from a sudden change in the synchronization of firing neurons in brain neural networks. We have used an in vitro model of status epilepticus (SE) to characterize dynamical regimes underlying the observed seizure-like activity. Time intervals between spikes or bursts were used as the variable to construct first-return interpeak or interburst interval plots, for studying neuronal population activity during the transition to seizure, as well as within seizures. Return maps constructed for a brief epoch before seizures were used for approximating the local system dynamics during that time window. Analysis of the first-return maps suggests that intermittency is a dynamical regime underlying the observed epileptic activity. This type of analysis may be useful for understanding the collective dynamics of neuronal populations in the normal and pathological brain.

Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.).

PubMed

Qi, Lan; Ding, Yingbin; Zheng, Xiaoming; Xu, Rui; Zhang, Lizhen; Wang, Yanyan; Wang, Xiaoning; Zhang, Lifang; Cheng, Yunlian; Qiao, Weihua; Yang, Qingwen

2018-04-19

A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F 2 population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F 3 recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.

Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea).

PubMed

Xiao, Zhiliang; Hu, Yang; Zhang, Xiaoli; Xue, Yuqian; Fang, Zhiyuan; Yang, Limei; Zhang, Yangyong; Liu, Yumei; Li, Zhansheng; Liu, Xing; Liu, Zezhou; Lv, Honghao; Zhuang, Mu

2017-06-05

Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage ( Brassica oleracea ) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2 , respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1 , seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380 ) were found, whereas in the region of BoHL2 , two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810 ) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.

The probability of lava inundation at the proposed and existing Kulani prison sites

USGS Publications Warehouse

Kauahikaua, J.P.; Trusdell, F.A.; Heliker, C.C.

1998-01-01

The State of Hawai`i has proposed building a 2,300-bed medium-security prison about 10 km downslope from the existing Kulani medium-security correctional facility. The proposed and existing facilities lie on the northeast rift zone of Mauna Loa, which last erupted in 1984 in this same general area. We use the best available geologic mapping and dating with GIS software to estimate the average recurrence interval between lava flows that inundate these sites. Three different methods are used to adjust the number of flows exposed at the surface for those flows that are buried to allow a better representation of the recurrence interval. Probabilities are then computed, based on these recurrence intervals, assuming that the data match a Poisson distribution. The probability of lava inundation for the existing prison site is estimated to be 11- 12% in the next 50 years. The probability of lava inundation for the proposed sites B and C are 2- 3% and 1-2%, respectively, in the same period. The probabilities are based on estimated recurrence intervals for lava flows, which are approximately proportional to the area considered. The probability of having to evacuate the prison is certainly higher than the probability of lava entering the site. Maximum warning times between eruption and lava inundation of a site are estimated to be 24 hours for the existing prison site and 72 hours for proposed sites B and C. Evacuation plans should take these times into consideration.

Intracellular Calcium and the Mechanism of Anodal Supernormal Excitability in Langendorff Perfused Rabbit Ventricles

PubMed Central

Joung, Boyoung; Park, Hyung-Wook; Maruyama, Mitsunori; Tang, Liang; Song, Juan; Han, Seongwook; Piccirillo, Gianfranco; Weiss, James N.; Lin, Shien-Fong; Chen, Peng-Sheng

2012-01-01

Background Anodal stimulation hyperpolarizes cell membrane and increases intracellular Ca2+ (Cai) transient. This study tested the hypothesis that The maximum slope of Cai decline (–(dCai/dt)max) corresponds to the timing of anodal dip on the strength-interval curve and the initiation of repetitive responses and ventricular fibrillation (VF) after a premature stimulus (S2). Methods and Results We simultaneously mapped membrane potential (Vm) and Cai in 23 rabbit ventricles. A dip was observed on the anodal strength-interval curve. During the anodal dip, ventricles were captured by anodal break excitation directly under the S2 electrode. The Cai following anodal stimuli is larger than that following cathodal stimuli. The S1-S2 intervals of the anodal dip (203 ± 10 ms) coincided with the -(dCai/dt)max (199 ± 10 ms, p=NS). BAPTA-AM (n=3), INCX inhibition by low extracellular Na+ (n=3), and combined ryanodine and thapsigargin infusion (n=2) eliminated the anodal supernormality. Strong S2 during the relative refractory period (n=5) induced 29 repetitive responses and 10 VF episodes. The interval between S2 and the first non-driven beat was coincidental with the time of -(dCai/dt)max. Conclusions Larger Cai transient and INCX activation induced by anodal stimulation produces anodal supernormality. Time of maximum INCX activation is coincidental to the induction of non- driven beats from the Cai sinkhole after a strong premature stimulation. PMID:21301131

Solution to the SLAM problem in low dynamic environments using a pose graph and an RGB-D sensor.

PubMed

Lee, Donghwa; Myung, Hyun

2014-07-11

In this study, we propose a solution to the simultaneous localization and mapping (SLAM) problem in low dynamic environments by using a pose graph and an RGB-D (red-green-blue depth) sensor. The low dynamic environments refer to situations in which the positions of objects change over long intervals. Therefore, in the low dynamic environments, robots have difficulty recognizing the repositioning of objects unlike in highly dynamic environments in which relatively fast-moving objects can be detected using a variety of moving object detection algorithms. The changes in the environments then cause groups of false loop closing when the same moved objects are observed for a while, which means that conventional SLAM algorithms produce incorrect results. To address this problem, we propose a novel SLAM method that handles low dynamic environments. The proposed method uses a pose graph structure and an RGB-D sensor. First, to prune the falsely grouped constraints efficiently, nodes of the graph, that represent robot poses, are grouped according to the grouping rules with noise covariances. Next, false constraints of the pose graph are pruned according to an error metric based on the grouped nodes. The pose graph structure is reoptimized after eliminating the false information, and the corrected localization and mapping results are obtained. The performance of the method was validated in real experiments using a mobile robot system.

New method for analysis of facial growth in a pediatric reconstructed mandible.

PubMed

Kau, Chung How; Kamel, Sherif Galal; Wilson, Jim; Wong, Mark E

2011-04-01

The aim of this article was to present a new method of analysis for the assessment of facial growth and morphology after surgical resection of the mandible in a growing patient. This was a 2-year longitudinal study of facial growth in a child who had undergone segmental resection of the mandible with immediate reconstruction as a treatment for juvenile aggressive fibromatosis. Three-dimensional digital stereo-photogrammteric cameras were used for image acquisition at several follow-up intervals: immediate, 6 months, and 2 years postresection. After processing and superimposition, shell-to-shell deviation maps were used for the analysis of the facial growth pattern and its deviation from normal growth. The changes were seen as mean surface changes and color maps. An average constructed female face from a previous study was used as a reference for a normal growth pattern. The patient showed significant growth during this period. Positive changes took place around the nose, lateral brow area, and lower lip and chin, whereas negative changes were evident at the lower lips and cheeks area. An increase in the vertical dimension of the face at the chin region was also seen prominently. Three-dimensional digital stereo-photogrammetry can be used as an objective, noninvasive method for quantifying and monitoring facial growth and its abnormalities. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

A constraint optimization based virtual network mapping method

NASA Astrophysics Data System (ADS)

Li, Xiaoling; Guo, Changguo; Wang, Huaimin; Li, Zhendong; Yang, Zhiwen

2013-03-01

Virtual network mapping problem, maps different virtual networks onto the substrate network is an extremely challenging work. This paper proposes a constraint optimization based mapping method for solving virtual network mapping problem. This method divides the problem into two phases, node mapping phase and link mapping phase, which are all NP-hard problems. Node mapping algorithm and link mapping algorithm are proposed for solving node mapping phase and link mapping phase, respectively. Node mapping algorithm adopts the thinking of greedy algorithm, mainly considers two factors, available resources which are supplied by the nodes and distance between the nodes. Link mapping algorithm is based on the result of node mapping phase, adopts the thinking of distributed constraint optimization method, which can guarantee to obtain the optimal mapping with the minimum network cost. Finally, simulation experiments are used to validate the method, and results show that the method performs very well.

Harmonization of forest disturbance datasets of the conterminous USA from 1986 to 2011

USGS Publications Warehouse

Soulard, Christopher E.; Acevedo, William; Cohen, Warren B.; Yang, Zhiqiang; Stehman, Stephen V.; Taylor, Janis L.

2017-01-01

Several spatial forest disturbance datasets exist for the conterminous USA. The major problem with forest disturbance mapping is that variability between map products leads to uncertainty regarding the actual rate of disturbance. In this article, harmonized maps were produced from multiple data sources (i.e., Global Forest Change, LANDFIRE Vegetation Disturbance, National Land Cover Database, Vegetation Change Tracker, and Web-Enabled Landsat Data). The harmonization process involved fitting common class ontologies and determining spatial congruency to produce forest disturbance maps for four time intervals (1986–1992, 1992–2001, 2001–2006, and 2006–2011). Pixels mapped as disturbed for two or more datasets were labeled as disturbed in the harmonized maps. The primary advantage gained by harmonization was improvement in commission error rates relative to the individual disturbance products. Disturbance omission errors were high for both harmonized and individual forest disturbance maps due to underlying limitations in mapping subtle disturbances with Landsat classification algorithms. To enhance the value of the harmonized disturbance products, we used fire perimeter maps to add information on the cause of disturbance.

Harmonization of forest disturbance datasets of the conterminous USA from 1986 to 2011.

PubMed

Soulard, Christopher E; Acevedo, William; Cohen, Warren B; Yang, Zhiqiang; Stehman, Stephen V; Taylor, Janis L

2017-04-01

Several spatial forest disturbance datasets exist for the conterminous USA. The major problem with forest disturbance mapping is that variability between map products leads to uncertainty regarding the actual rate of disturbance. In this article, harmonized maps were produced from multiple data sources (i.e., Global Forest Change, LANDFIRE Vegetation Disturbance, National Land Cover Database, Vegetation Change Tracker, and Web-Enabled Landsat Data). The harmonization process involved fitting common class ontologies and determining spatial congruency to produce forest disturbance maps for four time intervals (1986-1992, 1992-2001, 2001-2006, and 2006-2011). Pixels mapped as disturbed for two or more datasets were labeled as disturbed in the harmonized maps. The primary advantage gained by harmonization was improvement in commission error rates relative to the individual disturbance products. Disturbance omission errors were high for both harmonized and individual forest disturbance maps due to underlying limitations in mapping subtle disturbances with Landsat classification algorithms. To enhance the value of the harmonized disturbance products, we used fire perimeter maps to add information on the cause of disturbance.

HCMM satellite to take earth's temperature

NASA Technical Reports Server (NTRS)

1978-01-01

The heat capacity mapping mission (HCMM), a low cost modular spacecraft built for the Applications Explorer Missions (AEM), was designed to allow scientists to determine the feasibility of using day/night thermal infrared remote sensor-derived data to: (1) discriminate various rock types and locate mineral resources; (2) measure and monitor surface soil moisture changes; (3) measure plant canopy temperatures at frequent intervals to determine transpiration of water and plant stress; and (4) measure urban heat islands. The design of the spacecraft (AEM-A), its payload, launch vehicle, orbit, and data collection and processing methods are described. Projects in which the HCMM data will be applied by 12 American and 12 foreign investigators are summarized.

Quantitative maps of geomagnetic perturbation vectors during substorm onset and recovery

PubMed Central

Pothier, N M; Weimer, D R; Moore, W B

2015-01-01

We have produced the first series of spherical harmonic, numerical maps of the time-dependent surface perturbations in the Earth's magnetic field following the onset of substorms. Data from 124 ground magnetometer stations in the Northern Hemisphere at geomagnetic latitudes above 33° were used. Ground station data averaged over 5 min intervals covering 8 years (1998–2005) were used to construct pseudo auroral upper, auroral lower, and auroral electrojet (AU*, AL*, and AE*) indices. These indices were used to generate a list of substorms that extended from 1998 to 2005, through a combination of automated processing and visual checks. Events were sorted by interplanetary magnetic field (IMF) orientation (at the Advanced Composition Explorer (ACE) satellite), dipole tilt angle, and substorm magnitude. Within each category, the events were aligned on substorm onset. A spherical cap harmonic analysis was used to obtain a least error fit of the substorm disturbance patterns at 5 min intervals up to 90 min after onset. The fits obtained at onset time were subtracted from all subsequent fits, for each group of substorm events. Maps of the three vector components of the averaged magnetic perturbations were constructed to show the effects of substorm currents. These maps are produced for several specific ranges of values for the peak |AL*| index, IMF orientation, and dipole tilt angle. We demonstrate an influence of the dipole tilt angle on the response to substorms. Our results indicate that there are downward currents poleward and upward currents just equatorward of the peak in the substorms' westward electrojet. Key Points Show quantitative maps of ground geomagnetic perturbations due to substorms Three vector components mapped as function of time during onset and recovery Compare/contrast results for different tilt angle and sign of IMF Y-component PMID:26167445

An eceriferum locus, cer-zv, is associated with a defect in cutin responsible for water retention in barley (Hordeum vulgare) leaves.

PubMed

Li, Chao; Wang, Aidong; Ma, Xiaoying; Pourkheirandish, Mohammad; Sakuma, Shun; Wang, Ning; Ning, Shunzong; Nevo, Eviatar; Nawrath, Christiane; Komatsuda, Takao; Chen, Guoxiong

2013-03-01

Drought limits plant growth and threatens crop productivity. A barley (Hordeum vulgare) ethylene imine-induced monogenic recessive mutant cer-zv, which is sensitive to drought, was characterized and genetically mapped in the present study. Detached leaves of cer-zv lost 34.2 % of their initial weight after 1 h of dehydration. The transpiration was much higher in cer-zv leaves than in wild-type leaves under both light and dark conditions. The stomata of cer-zv leaves functioned normally, but the cuticle of cer-zv leaves showed increased permeability to ethanol and toluidine blue dye. There was a 50-90 % reduction in four major cutin monomers, but no reduction in wax loads was found in the cer-zv mutant as compared with the wild type. Two F(2) mapping populations were established by the crosses of 23-19 × cer-zv and cer-zv × OUH602. More polymorphisms were found in EST sequences between cer-zv and OUH602 than between cer-zv and 23-19. cer-zv was located in a pericentromeric region on chromosome 4H in a 10.8 cM interval in the 23-19 × cer-zv map based on 186 gametes tested and a 1.7 cM interval in the cer-zv × OUH602 map based on 176 gametes tested. It co-segregated with EST marker AK251484 in both maps. The results indicated that the cer-zv mutant is defective in cutin, which might be responsible for the increased transpiration rate and drought sensitivity, and that the F(2) of cer-zv × OUH602 might better facilitate high resolution mapping of cer-zv.

Real-Time Two-Dimensional Mapping of Relative Local Surface Temperatures with a Thin-Film Sensor Array

PubMed Central

Li, Gang; Wang, Zhenhai; Mao, Xinyu; Zhang, Yinghuang; Huo, Xiaoye; Liu, Haixiao; Xu, Shengyong

2016-01-01

Dynamic mapping of an object’s local temperature distribution may offer valuable information for failure analysis, system control and improvement. In this letter we present a computerized measurement system which is equipped with a hybrid, low-noise mechanical-electrical multiplexer for real-time two-dimensional (2D) mapping of surface temperatures. We demonstrate the performance of the system on a device embedded with 32 pieces of built-in Cr-Pt thin-film thermocouples arranged in a 4 × 8 matrix. The system can display a continuous 2D mapping movie of relative temperatures with a time interval around 1 s. This technique may find applications in a variety of practical devices and systems. PMID:27347969

Korean coastal water depth/sediment and land cover mapping (1:25,000) by computer analysis of LANDSAT imagery

NASA Technical Reports Server (NTRS)

Park, K. Y.; Miller, L. D.

1978-01-01

Computer analysis was applied to single date LANDSAT MSS imagery of a sample coastal area near Seoul, Korea equivalent to a 1:50,000 topographic map. Supervised image processing yielded a test classification map from this sample image containing 12 classes: 5 water depth/sediment classes, 2 shoreline/tidal classes, and 5 coastal land cover classes at a scale of 1:25,000 and with a training set accuracy of 76%. Unsupervised image classification was applied to a subportion of the site analyzed and produced classification maps comparable in results in a spatial sense. The results of this test indicated that it is feasible to produce such quantitative maps for detailed study of dynamic coastal processes given a LANDSAT image data base at sufficiently frequent time intervals.

Use of microcomputer in mapping depth of stratigraphic horizons in National Petroleum Reserve in Alaska

USGS Publications Warehouse

Payne, Thomas G.

1982-01-01

REGIONAL MAPPER is a menu-driven system in the BASIC language for computing and plotting (1) time, depth, and average velocity to geologic horizons, (2) interval time, thickness, and interval velocity of stratigraphic intervals, and (3) subcropping and onlapping intervals at unconformities. The system consists of three programs: FILER, TRAVERSER, and PLOTTER. A control point is a shot point with velocity analysis or a shot point at or near a well with velocity check-shot survey. Reflection time to and code number of seismic horizons are filed by digitizing tablet from record sections. TRAVERSER starts at a point of geologic control and, in traversing to another, parallels seismic events, records loss of horizons by onlap and truncation, and stores reflection time for geologic horizons at traversed shot points. TRAVERSER is basically a phantoming procedure. Permafrost thickness and velocity variations, buried canyons with low-velocity fill, and error in seismically derived velocity cause velocity anomalies that complicate depth mapping. Two depths to the top of the pebble is based shale are computed for each control point. One depth, designated Zs on seismically derived velocity. The other (Zw) is based on interval velocity interpolated linearly between wells and multiplied by interval time (isochron) to give interval thickness. Z w is computed for all geologic horizons by downward summation of interval thickness. Unknown true depth (Z) to the pebble shale may be expressed as Z = Zs + es and Z = Zw + ew where the e terms represent error. Equating the two expressions gives the depth difference D = Zs + Zw = ew + es A plot of D for the top of the pebble shale is readily contourable but smoothing is required to produce a reasonably simple surface. Seismically derived velocity used in computing Zs includes the effect of velocity anomalies but is subject to some large randomly distributed errors resulting in depth errors (es). Well-derived velocity used in computing Zw does not include the effect of velocity anomalies, but the error (ew) should reflect these anomalies and should be contourable (non-random). The D surface as contoured with smoothing is assumed to represent ew, that is, the depth effect of variations in permafrost thickness and velocity and buried canyon depth. Estimated depth (Zest) to each geologic horizon is the sum of Z w for that horizon and a constant e w as contoured for the pebble shale, which is the first highly continuous seismic horizon below the zone of anomalous velocity. Results of this 'depthing' procedure are compared with those of Tetra Tech, Inc., the subcontractor responsible for geologic and geophysical interpretation and mapping.

Geometry and Width of the Ringwoodite - Bridgmanite+Ferropericlase Binary Loop in the System (Mg,Fe)2SiO4: Interpretation of the Sharpness of the 660-km Discontinuity

NASA Astrophysics Data System (ADS)

Katsura, T.; Ishii, T.; Huang, R.; Maeda, F.; Yuan, L.; Bhat, S.; Farla, R. J.; Kawazoe, T.; Tsujino, N.; Liu, Z.; Fei, H.; Wang, L.; Druzhbin, D.; Yamamoto, T.; Kulik, E.; Koemets, I.; Higo, Y.; Tange, Y.

2017-12-01

Short wave-length seismic reflections from the 660 km discontinuity (D660) indicated an extreme sharp, namely less than 2 km thick boundary. To explain this observation, Ito and Takahashi [1989] estimated that the pressure interval of the dissociation of ringwoodite (Rw) to bridgmanite (Brg) plus ferropericlase (fPc) is < 0.15 GPa, corresponding to < 4 km, based on their multi-anvil press (MAP) experiment using the quench method. However, precision and accuracy in pressure determination of conventional MAP are no better than 1 GPa. In addition, although they estimated the pressure interval by combining the width of Rw-Brg-fPc coexistence with the temperature gradient in the furnace, very sluggish phase transition kinetics does not allow such a precise estimation of pressure. Using now established in situ X-ray diffraction techniques and accurate equations of state of MgO, we are able to revisit previous work to estimate the Rw-Brg-fPc pressure interval at 1700 K with uncertainty in the pressure estimation as low as 0.05 GPa. The majority of our efforts have been made to determine difference in transition pressure between Fo100 and Fo70 compositions. For this purpose, we prepared fine-grained mixtures of olivine (Ol), enstatite (En) and fPc with these two compositions and loaded in a MAP cell together with an MgO pressure marker and a WRe thermocouple. The cell was compressed to ca. 6 MN, heated to 1100 K to convert Ol and En to Rw and akimotoite (Ak), respectively, and further compressed until the sample pressure reached 22 24 GPa. Then, the sample was heated to 1700 K, and the temperature was maintained for 1-2 hours. Simultaneously, after several trials, the press load was increased at the right rate at the temperature to maintain nearly constant pressure within 0.2 GPa. X-ray diffractions of the samples and pressure maker were taken to determine pressure and phases present. An important finding is that the transition pressure in Fo70 is 0.1 GPa higher than that in Fo100. Namely, the hypothetical transition pressure in Fe2SiO4 is 0.3 GPa higher than the transition pressure in Mg2SiO4. This geometry is contrary to the previous understanding. The obtained pressure difference and the partition coefficients of Fe and Mg among Brg, Rw and fPc suggest that the pressure interval is almost zero, which explains the sharpness of the D660.

Alternative Confidence Interval Methods Used in the Diagnostic Accuracy Studies

PubMed Central

Gülhan, Orekıcı Temel

2016-01-01

Background/Aim. It is necessary to decide whether the newly improved methods are better than the standard or reference test or not. To decide whether the new diagnostics test is better than the gold standard test/imperfect standard test, the differences of estimated sensitivity/specificity are calculated with the help of information obtained from samples. However, to generalize this value to the population, it should be given with the confidence intervals. The aim of this study is to evaluate the confidence interval methods developed for the differences between the two dependent sensitivity/specificity values on a clinical application. Materials and Methods. In this study, confidence interval methods like Asymptotic Intervals, Conditional Intervals, Unconditional Interval, Score Intervals, and Nonparametric Methods Based on Relative Effects Intervals are used. Besides, as clinical application, data used in diagnostics study by Dickel et al. (2010) has been taken as a sample. Results. The results belonging to the alternative confidence interval methods for Nickel Sulfate, Potassium Dichromate, and Lanolin Alcohol are given as a table. Conclusion. While preferring the confidence interval methods, the researchers have to consider whether the case to be compared is single ratio or dependent binary ratio differences, the correlation coefficient between the rates in two dependent ratios and the sample sizes. PMID:27478491

Alternative Confidence Interval Methods Used in the Diagnostic Accuracy Studies.

PubMed

Erdoğan, Semra; Gülhan, Orekıcı Temel

2016-01-01

Background/Aim. It is necessary to decide whether the newly improved methods are better than the standard or reference test or not. To decide whether the new diagnostics test is better than the gold standard test/imperfect standard test, the differences of estimated sensitivity/specificity are calculated with the help of information obtained from samples. However, to generalize this value to the population, it should be given with the confidence intervals. The aim of this study is to evaluate the confidence interval methods developed for the differences between the two dependent sensitivity/specificity values on a clinical application. Materials and Methods. In this study, confidence interval methods like Asymptotic Intervals, Conditional Intervals, Unconditional Interval, Score Intervals, and Nonparametric Methods Based on Relative Effects Intervals are used. Besides, as clinical application, data used in diagnostics study by Dickel et al. (2010) has been taken as a sample. Results. The results belonging to the alternative confidence interval methods for Nickel Sulfate, Potassium Dichromate, and Lanolin Alcohol are given as a table. Conclusion. While preferring the confidence interval methods, the researchers have to consider whether the case to be compared is single ratio or dependent binary ratio differences, the correlation coefficient between the rates in two dependent ratios and the sample sizes.

Geology of the offshore Southeast Georgia Embayment, U.S. Atlantic continental margin, based on multichannel seismic reflection profiles

USGS Publications Warehouse

Buffler, Richard T.; Watkins, Joel S.; Dillon, William P.

1979-01-01

The sedimentary section is divided into three major seismic intervals. The intervals are separated by unconformities and can be mapped regionally. The oldest interval ranges in age from Early Cretaceous through middle Late Cretaceous, although it may contain Jurassic rocks where it thickens beneath the Blake Plateau. It probably consists of continental to nearshore clastic rocks where it onlaps basement and grades seaward to a restricted carbonate platform facies (dolomite-evaporite). The middle interval (Upper Cretaceous) is characterized by prograding clinoforms interpreted as open marine slope deposits. This interval represents a Late Cretaceous shift of the carbonate shelf margin from the Blake Escarpment shoreward to about its present location, probably due to a combination of co tinued subsidence, an overall Late Cretaceous rise in sea level, and strong currents across the Blake Plateau. The youngest (Cenozoic) interval represents a continued seaward progradation of the continental shelf and slope. Cenozoic sedimentation on the Blake Plateau was much abbreviated owing mainly to strong currents.

Predicting health-related quality of life (EQ-5D-5 L) and capability wellbeing (ICECAP-A) in the context of opiate dependence using routine clinical outcome measures: CORE-OM, LDQ and TOP.

PubMed

Peak, Jasmine; Goranitis, Ilias; Day, Ed; Copello, Alex; Freemantle, Nick; Frew, Emma

2018-05-30

Economic evaluation normally requires information to be collected on outcome improvement using utility values. This is often not collected during the treatment of substance use disorders making cost-effectiveness evaluations of therapy difficult. One potential solution is the use of mapping to generate utility values from clinical measures. This study develops and evaluates mapping algorithms that could be used to predict the EuroQol-5D (EQ-5D-5 L) and the ICEpop CAPability measure for Adults (ICECAP-A) from the three commonly used clinical measures; the CORE-OM, the LDQ and the TOP measures. Models were estimated using pilot trial data of heroin users in opiate substitution treatment. In the trial the EQ-5D-5 L, ICECAP-A, CORE-OM, LDQ and TOP were administered at baseline, three and twelve month time intervals. Mapping was conducted using estimation and validation datasets. The normal estimation dataset, which comprised of baseline sample data, used ordinary least squares (OLS) and tobit regression methods. Data from the baseline and three month time periods were combined to create a pooled estimation dataset. Cluster and mixed regression methods were used to map from this dataset. Predictive accuracy of the models was assessed using the root mean square error (RMSE) and the mean absolute error (MAE). Algorithms were validated using sample data from the follow-up time periods. Mapping algorithms can be used to predict the ICECAP-A and the EQ-5D-5 L in the context of opiate dependence. Although both measures can be predicted, the ICECAP-A was better predicted by the clinical measures. There were no advantages of pooling the data. There were 6 chosen mapping algorithms, which had MAE scores ranging from 0.100 to 0.138 and RMSE scores ranging from 0.134 to 0.178. It is possible to predict the scores of the ICECAP-A and the EQ-5D-5 L with the use of mapping. In the context of opiate dependence, these algorithms provide the possibility of generating utility values from clinical measures and thus enabling economic evaluation of alternative therapy options. ISRCTN22608399 . Date of registration: 27/04/2012. Date of first randomisation: 14/08/2012.

QTLs for Seed Vigor-Related Traits Identified in Maize Seeds Germinated under Artificial Aging Conditions

PubMed Central

Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, ShuLei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

2014-01-01

High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R2>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R2>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes. PMID:24651614

QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

PubMed

Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, Shulei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

2014-01-01

High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R(2)>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2)>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

Multiple interval QTL mapping and searching for PSTOL1 homologs associated with root morphology, biomass accumulation and phosphorus content in maize seedlings under low-P.

PubMed

Azevedo, Gabriel C; Cheavegatti-Gianotto, Adriana; Negri, Bárbara F; Hufnagel, Bárbara; E Silva, Luciano da Costa; Magalhaes, Jurandir V; Garcia, Antonio Augusto F; Lana, Ubiraci G P; de Sousa, Sylvia M; Guimaraes, Claudia T

2015-07-07

Modifications in root morphology are important strategies to maximize soil exploitation under phosphorus starvation in plants. Here, we used two multiple interval models to map QTLs related to root traits, biomass accumulation and P content in a maize RIL population cultivated in nutrient solution. In addition, we searched for putative maize homologs to PSTOL1, a gene responsible to enhance early root growth, P uptake and grain yield in rice and sorghum. Based on path analysis, root surface area was the root morphology component that most strongly contributed to total dry weight and to P content in maize seedling under low-P availability. Multiple interval mapping models for single (MIM) and multiple traits (MT-MIM) were combined and revealed 13 genomic regions significantly associated with the target traits in a complementary way. The phenotypic variances explained by all QTLs and their epistatic interactions using MT-MIM (23.4 to 35.5 %) were higher than in previous studies, and presented superior statistical power. Some of these QTLs were coincident with QTLs for root morphology traits and grain yield previously mapped, whereas others harbored ZmPSTOL candidate genes, which shared more than 55 % of amino acid sequence identity and a conserved serine/threonine kinase domain with OsPSTOL1. Additionally, four ZmPSTOL candidate genes co-localized with QTLs for root morphology, biomass accumulation and/or P content were preferentially expressed in roots of the parental lines that contributed the alleles enhancing the respective phenotypes. QTL mapping strategies adopted in this study revealed complementary results for single and multiple traits with high accuracy. Some QTLs, mainly the ones that were also associated with yield performance in other studies, can be good targets for marker-assisted selection to improve P-use efficiency in maize. Based on the co-localization with QTLs, the protein domain conservation and the coincidence of gene expression, we selected novel maize genes as putative homologs to PSTOL1 that will require further validation studies.

Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus

PubMed Central

Higgins, Michael J.; Day, Colleen D.; Smilinich, Nancy J.; Ni, L.; Cooper, Paul R.; Nowak, Norma J.; Davies, Chris; de Jong, Pieter J.; Hejtmancik, Fielding; Evans, Glen A.; Smith, Richard J.H.; Shows, Thomas B.

1998-01-01

Usher syndrome 1C (USH1C) is a congenital condition manifesting profound hearing loss, the absence of vestibular function, and eventual retinal degeneration. The USH1C locus has been mapped genetically to a 2- to 3-cM interval in 11p14–15.1 between D11S899 and D11S861. In an effort to identify the USH1C disease gene we have isolated the region between these markers in yeast artificial chromosomes (YACs) using a combination of STS content mapping and Alu–PCR hybridization. The YAC contig is ∼3.5 Mb and has located several other loci within this interval, resulting in the order CEN-LDHA-SAA1-TPH-D11S1310-(D11S1888/KCNC1)-MYOD1-D11S902D11S921-D11S1890-TEL. Subsequent haplotyping and homozygosity analysis refined the location of the disease gene to a 400-kb interval between D11S902 and D11S1890 with all affected individuals being homozygous for the internal marker D11S921. To facilitate gene identification, the critical region has been converted into P1 artificial chromosome (PAC) clones using sequence-tagged sites (STSs) mapped to the YAC contig, Alu–PCR products generated from the YACs, and PAC end probes. A contig of >50 PAC clones has been assembled between D11S1310 and D11S1890, confirming the order of markers used in haplotyping. Three PAC clones representing nearly two-thirds of the USH1C critical region have been sequenced. PowerBLAST analysis identified six clusters of expressed sequence tags (ESTs), two known genes (BIR,SUR1) mapped previously to this region, and a previously characterized but unmapped gene NEFA (DNA binding/EF hand/acidic amino-acid-rich). GRAIL analysis identified 11 CpG islands and 73 exons of excellent quality. These data allowed the construction of a transcription map for the USH1C critical region, consisting of three known genes and six or more novel transcripts. Based on their map location, these loci represent candidate disease loci for USH1C. The NEFA gene was assessed as the USH1C locus by the sequencing of an amplified NEFA cDNA from an USH1C patient; however, no mutations were detected. [The sequence data described in this paper have been submitted to GenBank under accession numbers AC000406–AC000407.] PMID:9445488

A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize

PubMed Central

Jia, Shangang; Li, Aixia; Morton, Kyla; Avoles-Kianian, Penny; Kianian, Shahryar F.; Zhang, Chi; Holding, David

2016-01-01

To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools. PMID:27261000

Harmonization of Multiple Forest Disturbance Data to Create a 1986-2011 Database for the Conterminous United States

NASA Astrophysics Data System (ADS)

Soulard, C. E.; Acevedo, W.; Yang, Z.; Cohen, W. B.; Stehman, S. V.; Taylor, J. L.

2015-12-01

A wide range of spatial forest disturbance data exist for the conterminous United States, yet inconsistencies between map products arise because of differing programmatic objectives and methodologies. Researchers on the Land Change Research Project (LCRP) are working to assess spatial agreement, characterize uncertainties, and resolve discrepancies between these national level datasets, in regard to forest disturbance. Disturbance maps from the Global Forest Change (GFC), Landfire Vegetation Disturbance (LVD), National Land Cover Dataset (NLCD), Vegetation Change Tracker (VCT), Web-enabled Landsat Data (WELD), and Monitoring Trends in Burn Severity (MTBS) were harmonized using a pixel-based data fusion process. The harmonization process reconciled forest harvesting, forest fire, and remaining forest disturbance across four intervals (1986-1992, 1992-2001, 2001-2006, and 2006-2011) by relying on convergence of evidence across all datasets available for each interval. Pixels with high agreement across datasets were retained, while moderate-to-low agreement pixels were visually assessed and either manually edited using reference imagery or discarded from the final disturbance map(s). National results show that annual rates of forest harvest and overall fire have increased over the past 25 years. Overall, this study shows that leveraging the best elements of readily-available data improves forest loss monitoring relative to using a single dataset to monitor forest change, particularly by reducing commission errors.

Zoonotic cutaneous leishmaniasis in northeastern Iran: a GIS-based spatio-temporal multi-criteria decision-making approach.

PubMed

Mollalo, A; Khodabandehloo, E

2016-07-01

Zoonotic cutaneous leishmaniasis (ZCL) constitutes a serious public health problem in many parts of the world including Iran. This study was carried out to assess the risk of the disease in an endemic province by developing spatial environmentally based models in yearly intervals. To fill the gap of underestimated true burden of ZCL and short study period, analytical hierarchy process (AHP) and fuzzy AHP decision-making methods were used to determine the ZCL risk zones in a Geographic Information System platform. Generated risk maps showed that high-risk areas were predominantly located at the northern and northeastern parts in each of the three study years. Comparison of the generated risk maps with geocoded ZCL cases at the village level demonstrated that in both methods more than 90%, 70% and 80% of the cases occurred in high and very high risk areas for the years 2010, 2011, and 2012, respectively. Moreover, comparison of the risk categories with spatially averaged normalized difference vegetation index (NDVI) images and a digital elevation model of the study region indicated persistent strong negative relationships between these environmental variables and ZCL risk degrees. These findings identified more susceptible areas of ZCL and will help the monitoring of this zoonosis to be more targeted.

Geological evaluation and applications of ERTS-1 imagery over Georgia

NASA Technical Reports Server (NTRS)

Pickering, S. M.; Jones, R. C.

1974-01-01

ERTS-1 70mm and 9 x 9 film negatives are being used by conventional and color enhancement methods as a tool for geologic investigation. Geologic mapping and mineral exploration by conventional methods is very difficult in Georgia. Thick soil cover and heavy vegetation cause outcrops of bed rock to be small, rare and obscure. ERTS imagery, and remote sensing in general have helped delineate: (1) major tectonic boundaries; (2) lithologic contacts; (3) foliation trends; (4) topographic lineaments; and (5) faults. The ERTS-1 MSS imagery yields the greatest amount of geologic information on the Piedomont, Blue Ridge, and Valley and Ridge Provinces of Georgia where topography is strongly controlled by the bedrock geology. ERTS imagery, and general remote sensing techniques, have provided us with a powerful tool to assist geologic research; have significantly increased the mapping efficiency of our field geologists; have shown new lineaments associated with known shear and fault zones; have delineated new structural features; have provided a tool to re-evaluate our tectonic history; have helped to locate potential ground water sources and areas of aquifer recharge; have defined areas of geologic hazards; have shown areas of heavy siltation in major reservoirs; and by its close interval repetition, have aided in monitoring surface mine reclamation activities and the environmental protection of our intricate marshland system.

Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).

PubMed

Cloutier, Sylvie; Ragupathy, Raja; Miranda, Evelyn; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Ward, Kerry; Rowland, Gordon; Duguid, Scott; Banik, Mitali

2012-12-01

Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.

High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato

NASA Technical Reports Server (NTRS)

Behringer, F. J.; Lomax, T. L.

1999-01-01

Mutation of the Lazy-2 (Lz-2) gene in tomato (Lycopersicon esculentum mill.) produces a phytochrome-dependent reversal of shoot gravitropism, providing a unique genetic resource for investigating how signals from light modulate gravitropism. We mapped the Lz-2 gene using RFLPs and a PCR-based technique to assess the feasibility of positional cloning. Analysis of a 1338 plant backcross population between L. esculentum and L. pennellii placed Lz-2 within a 1.2 cM interval on chromosome 5, 0.4 cM from TG504-CT201A interval. The inabililty to resolve these markers indicates that Lz-2 resides in a centromeric region in which recombination is highly suppressed. Lazy-2 is tightly linked to but does not encode the gene for ACC4, an enzyme involved in ethylene biosynthesis. We also observed that Lz-2 is partially dominant under certain conditions and stages of development.

Bouguer gravity map of Indonesia

NASA Astrophysics Data System (ADS)

Green, R.; Adkins, J. S.; Harrington, H. J.; Untung, M.

1981-01-01

A Bouguer gravity map of Indonesia on Mercator projection at a scale of 1: 5,000,000 and with a contour interval 20 mGal has been prepared over the past few years as part of a joint research program of the Geological Survey of Indonesia and the University of New England, Armidale. A new base station network was set up throughout Indonesia and tied to the IGSN stations at Sydney and Singapore. A discussion of the gravity features and the tectonic implications are given. The map is obtainable, in folded form only, from the Publications Department, University of New England, Armidale, N.S.W., Australia 2351 for $ A 5.- plus postage.

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.

PubMed

Muchero, Wellington; Guo, Jianjun; DiFazio, Stephen P; Chen, Jin-Gui; Ranjan, Priya; Slavov, Gancho T; Gunter, Lee E; Jawdy, Sara; Bryan, Anthony C; Sykes, Robert; Ziebell, Angela; Klápště, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry A; Douglas, Carl J; Mansfield, Shawn D; Martin, Joel; Schackwitz, Wendy; Evans, Luke M; Czarnecki, Olaf; Tuskan, Gerald A

2015-01-23

QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification. Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes. This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.

Finding safety: a pilot study of managed alcohol program participants' perceptions of housing and quality of life.

PubMed

Pauly, Bernadette Bernie; Gray, Erin; Perkin, Kathleen; Chow, Clifton; Vallance, Kate; Krysowaty, Bonnie; Stockwell, Timothy

2016-05-09

There is a higher prevalence of alcohol use and severe alcohol dependence among homeless populations. The combination of alcohol use and lack of housing contributes to increased vulnerability to the harms of substance use including stigma, injury, illness, and death. Managed alcohol programs (MAPs) administer prescribed doses of alcohol at regular intervals to people with severe and chronic alcohol dependence and homelessness. As a pilot for a larger national study of MAPs, we conducted an in-depth evaluation of one program in Ontario, Canada. In this paper, we report on housing and quality of life outcomes and experiences of the MAP participants and staff. We conducted a pilot study using mixed methods. The sample consisted of 38 people enrolled in or eligible for entry into a MAP who completed a structured quantitative survey that included measures related to their housing and quality of life. All of the participants self-identified as Indigenous. In addition, we conducted 11 in-depth qualitative interviews with seven MAP residents and four program staff and analyzed the interviews using constant comparative analysis. The qualitative analysis was informed by Rhodes' risk environment framework. When compared to controls, MAP participants were more likely to retain their housing and experienced increased safety and improved quality of life compared to life on the streets, in jails, shelters, or hospitals. They described the MAP as a safe place characterized by caring, respect, trust and a nonjudgmental approach with a sense of family and home as well as opportunities to reconnect with family members. The MAP was, as described by participants, a safer environment and a home with feelings of family and a sense of community that countered stigma, loss, and dislocation with potential for healing and recovery. The MAP environment characterized by caring, respect, trust, a sense of home, "feeling like family", and the opportunities for family and cultural reconnections is consistent with First Nations principles for healing and recovery and principles of harm reduction.

Homozygosity and linkage-disequilibrium mapping of the syndrome of congenital hypoparathyroidism, growth and mental retardation, and dysmorphism to a 1-cM interval on chromosome 1q42-43.

PubMed

Parvari, R; Hershkovitz, E; Kanis, A; Gorodischer, R; Shalitin, S; Sheffield, V C; Carmi, R

1998-07-01

The syndrome of hypoparathyroidism associated with growth retardation, developmental delay, and dysmorphism (HRD) is a newly described, autosomal recessive, congenital disorder with severe, often fatal consequences. Since the syndrome is very rare, with all parents of affected individuals being consanguineous, it is presumed to be caused by homozygous inheritance of a single recessive mutation from a common ancestor. To localize the HRD gene, we performed a genomewide screen using DNA pooling and homozygosity mapping for apparently unlinked kindreds. Analysis of a panel of 359 highly polymorphic markers revealed linkage to D1S235. The maximum LOD score obtained was 4.11 at a recombination fraction of 0. Analysis of three additional markers-GGAA6F06, D1S2678, and D1S179-in a 2-cM interval around D1S235 resulted in LOD scores >3. Analysis of additional chromosome 1 markers revealed evidence of genetic linkage disequilibrium and place the HRD locus within an approximately 1-cM interval defined by D1S1540 and D1S2678 on chromosome 1q42-43.

Homozygosity and linkage-disequilibrium mapping of the syndrome of congenital hypoparathyroidism, growth and mental retardation, and dysmorphism to a 1-cM interval on chromosome 1q42-43.

PubMed Central

Parvari, R; Hershkovitz, E; Kanis, A; Gorodischer, R; Shalitin, S; Sheffield, V C; Carmi, R

1998-01-01

The syndrome of hypoparathyroidism associated with growth retardation, developmental delay, and dysmorphism (HRD) is a newly described, autosomal recessive, congenital disorder with severe, often fatal consequences. Since the syndrome is very rare, with all parents of affected individuals being consanguineous, it is presumed to be caused by homozygous inheritance of a single recessive mutation from a common ancestor. To localize the HRD gene, we performed a genomewide screen using DNA pooling and homozygosity mapping for apparently unlinked kindreds. Analysis of a panel of 359 highly polymorphic markers revealed linkage to D1S235. The maximum LOD score obtained was 4.11 at a recombination fraction of 0. Analysis of three additional markers-GGAA6F06, D1S2678, and D1S179-in a 2-cM interval around D1S235 resulted in LOD scores >3. Analysis of additional chromosome 1 markers revealed evidence of genetic linkage disequilibrium and place the HRD locus within an approximately 1-cM interval defined by D1S1540 and D1S2678 on chromosome 1q42-43. PMID:9634513

QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments

PubMed Central

Gahlaut, Vijay; Jaiswal, Vandana; Tyagi, Bhudeva S.; Singh, Gyanendra; Sareen, Sindhu; Balyan, Harindra S.

2017-01-01

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat. PMID:28793327

Construction of a yeast artificial chromosome contig encompassing the chromosome 14 Alzheimer`s disease locus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, V.; Bonnycastle, L.; Poorkai, P.

1994-09-01

We have constructed a yeast artificial chromosome (YAC) contig of chromosome 14q24.3 which encompasses the chromosome 14 Alzheimer`s disease locus (AD3). Determined by linkage analysis of early-onset Alzheimer`s disease kindreds, this interval is bounded by the genetic markers D14S61-D14S63 and spans approximately 15 centimorgans. The contig consists of 29 markers and 74 YACs of which 57 are defined by one or more sequence tagged sites (STSs). The STS markers comprise 5 genes, 16 short tandem repeat polymorphisms and 8 cDNA clones. An additional number of genes, expressed sequence tags and cDNA fragments have been identified and localized to the contigmore » by hybridization and sequence analysis of anonymous clones isolated by cDNA direct selection techniques. A minimal contig of about 15 YACs averaging 0.5-1.5 megabase in length will span this interval and is, at first approximation, in rough agreement with the genetic map. For two regions of the contig, our coverage has relied on L1/THE fingerprint and Alu-PCR hybridization data of YACs provided by CEPH/Genethon. We are currently developing sequence tagged sites from these to confirm the overlaps revealed by the fingerprint data. Among the genes which map to the contig are transforming growth factor beta 3, c-fos, and heat shock protein 2A (HSPA2). C-fos is not a candidate gene for AD3 based on the sequence analysis of affected and unaffected individuals. HSPA2 maps to the proximal edge of the contig and Calmodulin 1, a candidate gene from 4q24.3, maps outside of the region. The YAC contig is a framework physical map from which cosmid or P1 clone contigs can be constructed. As more genes and cDNAs are mapped, a highly resolved transcription map will emerge, a necessary step towards positionally cloning the AD3 gene.« less

Structural Variation Shapes the Landscape of Recombination in Mouse

PubMed Central

Morgan, Andrew P.; Gatti, Daniel M.; Najarian, Maya L.; Keane, Thomas M.; Galante, Raymond J.; Pack, Allan I.; Mott, Richard; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel

2017-01-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. PMID:28592499

Structural Variation Shapes the Landscape of Recombination in Mouse.

PubMed

Morgan, Andrew P; Gatti, Daniel M; Najarian, Maya L; Keane, Thomas M; Galante, Raymond J; Pack, Allan I; Mott, Richard; Churchill, Gary A; de Villena, Fernando Pardo-Manuel

2017-06-01

Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape. Copyright © 2017 by the Genetics Society of America.

DISSECTING THE GENETICS OF HUMAN HIGH MYOPIA: A MOLECULAR BIOLOGIC APPROACH

PubMed Central

Young, Terri L

2004-01-01

ABSTRACT Purpose Despite the plethora of experimental myopia animal studies that demonstrate biochemical factor changes in various eye tissues, and limited human studies utilizing pharmacologic agents to thwart axial elongation, we have little knowledge of the basic physiology that drives myopic development. Identifying the implicated genes for myopia susceptibility will provide a fundamental molecular understanding of how myopia occurs and may lead to directed physiologic (ie, pharmacologic, gene therapy) interventions. The purpose of this proposal is to describe the results of positional candidate gene screening of selected genes within the autosomal dominant high-grade myopia-2 locus (MYP2) on chromosome 18p11.31. Methods A physical map of a contracted MYP2 interval was compiled, and gene expression studies in ocular tissues using complementary DNA library screens, microarray matches, and reverse-transcription techniques aided in prioritizing gene selection for screening. The TGIF, EMLIN-2, MLCB, and CLUL1 genes were screened in DNA samples from unrelated controls and in high-myopia affected and unaffected family members from the original seven MYP2 pedigrees. All candidate genes were screened by direct base pair sequence analysis. Results Consistent segregation of a gene sequence alteration (polymorphism) with myopia was not demonstrated in any of the seven families. Novel single nucleotide polymorphisms were found. Conclusion The positional candidate genes TGIF, EMLIN-2, MLCB, and CLUL1 are not associated with MYP2-linked high-grade myopia. Base change polymorphisms discovered with base sequence screening of these genes were submitted to an Internet database. Other genes that also map within the interval are currently undergoing mutation screening. PMID:15747770

Flood-inundation map and water-surface profiles for floods of selected recurrence intervals, Consumnes River and Deer Creek, Sacramento County, California

USGS Publications Warehouse

Guay, Joel R.; Harmon, Jerry G.; McPherson, Kelly R.

1998-01-01

The damage caused by the January 1997 floods along the Cosumnes River and Deer Creek generated new interest in planning and managing land use in the study area. The 1997 floodflow peak, the highest on record and considered to be a 150-year flood, caused levee failures at 24 locations. In order to provide a technical basis for floodplain management practices, the U.S. Goelogical Survey, in cooperation with the Federal Emergency Management Agency, completed a flood-inundation map of the Cosumnes River and Deer Creek drainage from Dillard Road bridge to State Highway 99. Flood frequency was estimated from streamflow records for the Cosumnes River at Michigan Bar and Deer Creek near Sloughhouse. Cross sections along a study reach, where the two rivers generally flow parallel to one another, were used with a step-backwater model (WSPRO) to estimate the water-surface profile for floods of selected recurrence intervals. A flood-inundation map was developed to show flood boundaries for the 100-year flood. Water-surface profiles were developed for the 5-, 10-, 50-, 100-, and 500-year floods.

Best's vitelliform dystrophy (VMD2) maps between D11S903 and PYGM: No evidence for locus heterogeneity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, B.H.F.; Walker, D.; Mar, L.

1994-03-15

Vitelliform macular dystrophy, also known as Best's disease (BD), is an autosomal dominant disorder typically characterized by an accumulation of yellowish material in the macular area. The disease is slowly progressive and eventually results in atrophy of the retinal pigment epithelium and photoreceptor cells, thus severely impairing central vision. The biochemical defect underlying this condition is unknown. More recently, the BD locus (VMD2) was mapped to chromosome 11 by genetic analysis in three multigeneration Best's disease families using eight microsatellite markers spanning approximately 26 cM around the putative BD locus. The authors demonstrate linkage between Best's disease and the markersmore » used. Furthermore, haplotype analysis in unrelated Best's disease families identified three distinct haplotypes associated with the disease, strongly suggesting independent origins of the BD mutation. Finally, they characterized two recombinant BD chromosomes that significantly refine the location of the disease gene to a 3.7-cM interval between markers at D11S903 and PYGM. PCR-hybrid mapping sublocalized this interval to the pericentromeric region of chromosome 11. 47 refs., 4 figs., 1 tab.« less

High-Resolution Patterns of Meiotic Recombination across the Human Major Histocompatibility Complex

PubMed Central

Cullen, Michael; Perfetto, Stephen P.; Klitz, William; Nelson, George; Carrington, Mary

2002-01-01

Definitive characteristics of meiotic recombination events over large (i.e., >1 Mb) segments of the human genome remain obscure, yet they are essential for establishing the haplotypic structure of the genome and for efficient mapping of complex traits. We present a high-resolution map of recombination at the kilobase level across a 3.3-Mb interval encompassing the major histocompatibility complex (MHC). Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes within genomic intervals as small as 7 kb. Several principal characteristics of recombination in this region were observed: (1) rates of recombination can differ significantly between individuals; (2) intense hot spots of recombination occur at least every 0.8 Mb but are not necessarily evenly spaced; (3) distribution in the location of recombination events can differ significantly among individuals; (4) between hot spots, low levels of recombination occur fairly evenly across 100-kb segments, suggesting the presence of warm spots of recombination; and (5) specific sequence motifs associate significantly with recombination distribution. These data provide a plausible model for recombination patterns of the human genome overall. PMID:12297984

[New method of mixed gas infrared spectrum analysis based on SVM].

PubMed

Bai, Peng; Xie, Wen-Jun; Liu, Jun-Hua

2007-07-01

A new method of infrared spectrum analysis based on support vector machine (SVM) for mixture gas was proposed. The kernel function in SVM was used to map the seriously overlapping absorption spectrum into high-dimensional space, and after transformation, the high-dimensional data could be processed in the original space, so the regression calibration model was established, then the regression calibration model with was applied to analyze the concentration of component gas. Meanwhile it was proved that the regression calibration model with SVM also could be used for component recognition of mixture gas. The method was applied to the analysis of different data samples. Some factors such as scan interval, range of the wavelength, kernel function and penalty coefficient C that affect the model were discussed. Experimental results show that the component concentration maximal Mean AE is 0.132%, and the component recognition accuracy is higher than 94%. The problems of overlapping absorption spectrum, using the same method for qualitative and quantitative analysis, and limit number of training sample, were solved. The method could be used in other mixture gas infrared spectrum analyses, promising theoretic and application values.

Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson.

PubMed

Thomson, M J; Tai, T H; McClung, A M; Lai, X-H; Hinga, M E; Lobos, K B; Xu, Y; Martinez, C P; McCouch, S R

2003-08-01

An advanced backcross population between an accession of Oryza rufipogon (IRGC 105491) and the U.S. cultivar Jefferson (Oryza sativa ssp. japonica) was developed to identify quantitative trait loci (QTLs) for yield, yield components and morphological traits. The genetic linkage map generated for this population consisted of 153 SSR and RFLP markers with an average interval size of 10.3 cM. Thirteen traits were examined, nine of which were measured in multiple environments. Seventy-six QTLs above an experiment-wise significance threshold of P<0.01 (corresponding to an interval mapping LOD>3.6 or a composite interval mapping LOD>3.9) were identified. For the traits measured in multiple environments, 47% of the QTLs were detected in at least two environments. The O. rufipogon allele was favorable for 53% of the yield and yield component QTLs, including loci for yield, grains per panicle, panicle length, and grain weight. Morphological traits related to the domestication process and/or weedy characteristics, including plant height, shattering, tiller type and awns, were found clustered on chromosomes 1 and 4. Comparisons to previous studies involving wild x cultivated crosses revealed O. rufipogon alleles with stable effects in multiple genetic backgrounds and environments, several of which have not been detected in studies between Oryza sativa cultivars, indicating potentially novel alleles from O. rufipogon. Some O. rufipogon-derived QTLs, however, were in similar regions as previously reported QTLs from Oryza sativa cultivars, providing evidence for conservation of these QTLs across the Oryza genus. In addition, several QTLs for grain weight, plant height, and flowering time were localized to putative homeologous regions in maize where QTLs for these traits have been previously reported, supporting the hypothesis of functional conservation of QTLs across the grasses.

Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line.

PubMed

Lyu, S; Arends, D; Nassar, M K; Brockmann, G A

2017-06-01

In our previous research, QTL analysis in an F 2 cross between the inbred New Hampshire (NHI) and White Leghorn (WL77) lines revealed a growth QTL in the distal part of chromosome 4. To physically reduce the chromosomal interval and the number of potential candidate genes, we performed fine mapping using individuals of generations F 10 , F 11 and F 12 in an advanced intercross line that had been established from the initial F 2 mapping population. Using nine single nucleotide polymorphism (SNP) markers within the QTL region for an association analysis with several growth traits from hatch to 20 weeks and body composition traits at 20 weeks, we could reduce the confidence interval from 26.9 to 3.4 Mb. Within the fine mapped region, markers rs14490774, rs314961352 and rs318175270 were in full linkage disequilibrium (D' = 1.0) and showed the strongest effect on growth and muscle mass (LOD ≥ 4.00). This reduced region contains 30 genes, compared to 292 genes in the original region. Chicken 60 K and 600 K SNP chips combined with DNA sequencing of the parental lines were used to call mutations in the reduced region. In the narrowed-down region, 489 sequence variants were detected between NHI and WL77. The most deleterious variants are a missense variant in ADGRA3 (SIFT = 0.02) and a frameshift deletion in the functional unknown gene ENSGALG00000014401 in NHI chicken. In addition, five synonymous variants were discovered in genes PPARGC1A, ADGRA3, PACRGL, SLIT2 and FAM184B. In our study, the confidence interval and the number of potential genes could be reduced 8- and 10- fold respectively. Further research will focus on functional effects of mutant genes. © 2017 Stichting International Foundation for Animal Genetics.

Characterization of the quantitative trait locus OilA1 for oil content in Brassica napus.

PubMed

Chen, Yubo; Qi, Lu; Zhang, Xiaoyu; Huang, Jixiang; Wang, Jibian; Chen, Hongcheng; Ni, Xiyuan; Xu, Fei; Dong, Yanjun; Xu, Haiming; Zhao, Jianyi

2013-10-01

Increasing seed oil content has become one of the most important breeding criteria in rapeseed (Brassica napus). However, oil content is a complex quantitative trait. QTL mapping in a double haploid population (SG population) emerging from a cross between a German (Sollux) and Chinese (Gaoyou) cultivars revealed one QTL for oil content on linkage group A1 (OilA1), which was mapped to a 17 cM genetic interval. To further validate and characterize the OilA1, we constructed a high-resolution map using B. rapa sequence resources and developed a set of near-isogenic lines (NILs) by employing a DH line SG-DH267 as donor and Chinese parent Gaoyou as recurrent background. The results showed highly conserved synteny order between B. rapa and B. napus within the linkage group A1 and revealed a possible centromere region between two markers ZAASA1-38 and NTP3 (2.5 cM). OilA1 was firstly validated by 250 BC5F2 plants and was confirmed in a 10.6 cM interval between the markers ZAASA1-47 and ZAASA1-77. Further substitution mapping was conducted by using two generations of QTL-NILs, 283 lines from eight BC5F3:4 families and 428 plants from six BC5F4 sub-NILs and thus narrowed the OilA1 interval to 6.9 cM and 4.3 cM (1.4 Mb), respectively. Field investigations with two replications using homozygous BC5F3:4 sister sub-NILs indicated that NILs, which carry a Sollux chromosome segment across the target region showed significant higher oil content (1.26 %, p < 0.001) than their sister NILs containing Gaoyou chromosome. The OilA1 locus is of particular interest for breeding purpose in China because 80 % of Chinese cultivars do not carry this desirable allele.

Geographic information systems supporting the solution of emergencies and their connection to self-actuated notification systems

NASA Astrophysics Data System (ADS)

Reil, Adam; Bureš, Luděk; Roub, Radek; Hejduk, Tomáš; Novák, Pavel

2015-04-01

Geographic information systems represent an important tool in supporting the operation and crisis management of Integrated Rescue System (IRS) branches. The technology of geographic information systems makes it possible to localize specific information directly in the concerned area. A basic pre-requisite for efficient IRS functioning is the identification of so-called critical points in the given territory. The next step is the identification of endangered persons and properties. In these issues, emphasis is put particularly on the time scale, which represents a key aspect of the crisis management. In case of flood danger, the Early Flood Warning Service would inform flood authorities responsible for warning the population, declaring flood activity degrees, IRS activation and organization. For their decision-making, the flood authorities need data on level heights, current discharge rates and inundation areas. The information about discharge rates and height levels can be obtained from the network of recording stream gauge stations operated by the Czech Hydrometeorological Institute. Inundation areas are plotted in the flood control plans of municipalities, which however contain default information about areas flooded at the N-year flood discharges Q5, Q20 and Q100. Because of large intervals, these three scenarios are insufficient for the crisis management of larger communities and towns. Therefore, a data store was suggested that would include maps showing flow rate fields and inundation areas for a finer scale of flood discharges at regular intervals. The scale should be based on the N-year flood discharges with a possibility of extension if required by flood authorities. The discharge interval size should be selected with regard to the dynamics of level height change in the given watercourse. The inundation areas will be then established by way of calculation using the MIKE 21C 2D hydrodynamic model. The novel approach was applied recently in the cadastral area of Lety on the Berounka River. Two sets of certified maps were created: (1) The map of endangered properties 1 - grid of depths, and (2) The map of endangered properties 2 - grid of flow rates. The maps were created from the discharge of 500 m3/s to 1460 m3/s at intervals of 60 m3/s. Two additional discharge values were 1500 m3/s and a calibration discharge of 990 m3/s. In total, thirty-eight maps were created the foundation of which was an orthophotograph map where endangered properties were plotted together with inundation areas. The next step will now be a specific proposal for data store version. The data store will be placed on the web interface where scenarios will be possible to display according to the selected discharge. At the same time, information will be available about the current discharge in the given watercourse. The web interface will be publicly accessible and will be connected to IRS. This study was supported from the Project VG20132015127 as a part of the Security Research conducted by the Ministry of the Interior of the Czech Republic. Keywords: IRS, MIKE 21C, flood

Spatial mapping of lead, arsenic, iron, and polycyclic aromatic hydrocarbon soil contamination in Sydney, Nova Scotia: community impact from the coke ovens and steel plant.

PubMed

Lambert, Timothy W; Boehmer, Jennifer; Feltham, Jason; Guyn, Lindsay; Shahid, Rizwan

2011-01-01

This paper presents spatial maps of the arsenic, lead, and polycyclic aromatic hydrocarbon (PAH) soil contamination in Sydney, Nova Scotia, Canada. The spatial maps were designed to create exposure cohorts to help understand the observed increase in health effects. To assess whether contamination can be a proxy for exposures, the following hypothesis was tested: residential soils were impacted by the coke oven and steel plant industrial complex. The spatial map showed contaminants are centered on the industrial facility, significantly correlated, and exceed Canadian health risk-based soil quality guidelines. Core samples taken at 5-cm intervals suggest a consistent deposition over time. The concentrations in Sydney significantly exceed background Sydney soil concentrations, and are significantly elevated compared with North Sydney, an adjacent industrial community. The contaminant spatial maps will also be useful for developing cohorts of exposure and guiding risk management decisions.

Spectral signature selection for mapping unvegetated soils

NASA Technical Reports Server (NTRS)

May, G. A.; Petersen, G. W.

1975-01-01

Airborne multispectral scanner data covering the wavelength interval from 0.40-2.60 microns were collected at an altitude of 1000 m above the terrain in southeastern Pennsylvania. Uniform training areas were selected within three sites from this flightline. Soil samples were collected from each site and a procedure developed to allow assignment of scan line and element number from the multispectral scanner data to each sampling location. These soil samples were analyzed on a spectrophotometer and laboratory spectral signatures were derived. After correcting for solar radiation and atmospheric attenuation, the laboratory signatures were compared to the spectral signatures derived from these same soils using multispectral scanner data. Both signatures were used in supervised and unsupervised classification routines. Computer-generated maps using the laboratory and multispectral scanner derived signatures resulted in maps that were similar to maps resulting from field surveys. Approximately 90% agreement was obtained between classification maps produced using multispectral scanner derived signatures and laboratory derived signatures.

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus).

PubMed

Feng, Xiu; Yu, Xiaomu; Fu, Beide; Wang, Xinhua; Liu, Haiyang; Pang, Meixia; Tong, Jingou

2018-04-02

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Physical and genetic mapping of the CMT4A locus and exclusion of PMP-2 as the defect in CMT4A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Othmane, K.B.; Loeb, D.; Roses, A.D.

1995-07-20

We have previously localized one form of the autosomal recessive Charcot-Marie-Tooth disease type 4 (CMT4A) to a 5-cM region of chromosome 8q13-q21. We now report the formation of a 7-Bp YAC contig spanning the region. This contig was used to map nine additional microsatellites and six STSs to this region, and subsequent haplotype analysis has narrowed the CMT4A flanking interval to less than 1 cM. In addition, using SSCP and our physical map, we have demonstrated that the myelin protein PMP-2, mapped by FISH to this region, is not the defect in CMT4A. 27 refs., 3 figs., 1 tab.

Empirical likelihood-based confidence intervals for mean medical cost with censored data.

PubMed

Jeyarajah, Jenny; Qin, Gengsheng

2017-11-10

In this paper, we propose empirical likelihood methods based on influence function and jackknife techniques for constructing confidence intervals for mean medical cost with censored data. We conduct a simulation study to compare the coverage probabilities and interval lengths of our proposed confidence intervals with that of the existing normal approximation-based confidence intervals and bootstrap confidence intervals. The proposed methods have better finite-sample performances than existing methods. Finally, we illustrate our proposed methods with a relevant example. Copyright © 2017 John Wiley & Sons, Ltd.

Use of fuzzy sets in modeling of GIS objects

NASA Astrophysics Data System (ADS)

Mironova, Yu N.

2018-05-01

The paper discusses modeling and methods of data visualization in geographic information systems. Information processing in Geoinformatics is based on the use of models. Therefore, geoinformation modeling is a key in the chain of GEODATA processing. When solving problems, using geographic information systems often requires submission of the approximate or insufficient reliable information about the map features in the GIS database. Heterogeneous data of different origin and accuracy have some degree of uncertainty. In addition, not all information is accurate: already during the initial measurements, poorly defined terms and attributes (e.g., "soil, well-drained") are used. Therefore, there are necessary methods for working with uncertain requirements, classes, boundaries. The author proposes using spatial information fuzzy sets. In terms of a characteristic function, a fuzzy set is a natural generalization of ordinary sets, when one rejects the binary nature of this feature and assumes that it can take any value in the interval.

Cosinor-based rhythmometry

PubMed Central

2014-01-01

A brief overview is provided of cosinor-based techniques for the analysis of time series in chronobiology. Conceived as a regression problem, the method is applicable to non-equidistant data, a major advantage. Another dividend is the feasibility of deriving confidence intervals for parameters of rhythmic components of known periods, readily drawn from the least squares procedure, stressing the importance of prior (external) information. Originally developed for the analysis of short and sparse data series, the extended cosinor has been further developed for the analysis of long time series, focusing both on rhythm detection and parameter estimation. Attention is given to the assumptions underlying the use of the cosinor and ways to determine whether they are satisfied. In particular, ways of dealing with non-stationary data are presented. Examples illustrate the use of the different cosinor-based methods, extending their application from the study of circadian rhythms to the mapping of broad time structures (chronomes). PMID:24725531

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

PubMed Central

2014-01-01

Background Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Results Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes. Conclusions Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species. PMID:24987520

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions

PubMed Central

Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

2017-01-01

Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen’s kappa statistic) and no significant difference to the reference tests (McNemar’s Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption. PMID:29312970

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions.

PubMed

Acharya, Kamal R; Dhand, Navneet K; Whittington, Richard J; Plain, Karren M

2017-01-01

Johne's disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen's kappa statistic) and no significant difference to the reference tests (McNemar's Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.

Simultaneous Anterior and Posterior Serosal Mapping of Gastric Slow Wave Dysrhythmias Induced by Vasopressin

PubMed Central

Du, Peng; O'Grady, Greg; Paskaranandavadivel, Niranchan; Tang, Shou-jiang; Abell, Thomas; Cheng, Leo K

2016-01-01

Background High-resolution (HR) mapping enables mechanistic insights into gastric slow wave dysrhythmias and is now achieving clinical translation. However, previous studies have focused mainly on dysrhythmias occurring on the anterior gastric wall. The present study simultaneously mapped the anterior and posterior gastric serosa during episodes of dysrhythmias induced by vasopressin to aid understanding of dysrhythmia initiation, maintenance and termination.. Methods HR mapping (8×16 electrodes on each serosa; 20-74 cm2) was performed in anesthetized subjects. Baseline recordings (21±8 min) were followed by intravenous vasopressin infusion (0.1-0.5 IU/mL at 60-190 mL/hour) and further recordings (22±13 min). Slow wave activation maps, amplitudes, velocity, interval, and frequency were calculated, and differences compared between baseline and post-infusion. Results All subjects demonstrated and increased prevalence of dysrhythmic events following infusion of vasopressin (17% vs 51%).Both amplitude and velocity demonstrated significant differences (baseline vs. post-infusion: 3.6 vs. 2.2 mV; 7.7 vs. 6.5 mm s−1; P < 0.05 for both). Dysrhythmias occurred simultaneously or independently on anterior and posterior serosa, and then interacted according to frequency dynamics. A number of persistent dysrhythmias were compared, including: ectopic activation (n=2 subjects), conduction block (n=1), rotor (n=2), retrograde (n=3), collision/merge of wavefronts (n=2). Conclusions Infusion of vasopressin induces gastric dysrhythmias, which occurred across a heterogeneous range of frequencies and patterns. The results demonstrated that different classes of gastric dysrhythmias may arise simultaneously or independently in one or both surfaces of the serosa, then interact according to their relative frequencies. These results will help inform clinical dysrhythmia interpretations. PMID:27265885

Computer-Aided Classification of Visual Ventilation Patterns in Patients with Chronic Obstructive Pulmonary Disease at Two-Phase Xenon-Enhanced CT

PubMed Central

Yoon, Soon Ho; Jung, Julip; Hong, Helen; Park, Eun Ah; Lee, Chang Hyun; Lee, Youkyung; Jin, Kwang Nam; Choo, Ji Yung; Lee, Nyoung Keun

2014-01-01

Objective To evaluate the technical feasibility, performance, and interobserver agreement of a computer-aided classification (CAC) system for regional ventilation at two-phase xenon-enhanced CT in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods Thirty-eight patients with COPD underwent two-phase xenon ventilation CT with resulting wash-in (WI) and wash-out (WO) xenon images. The regional ventilation in structural abnormalities was visually categorized into four patterns by consensus of two experienced radiologists who compared the xenon attenuation of structural abnormalities with that of adjacent normal parenchyma in the WI and WO images, and it served as the reference. Two series of image datasets of structural abnormalities were randomly extracted for optimization and validation. The proportion of agreement on a per-lesion basis and receiver operating characteristics on a per-pixel basis between CAC and reference were analyzed for optimization. Thereafter, six readers independently categorized the regional ventilation in structural abnormalities in the validation set without and with a CAC map. Interobserver agreement was also compared between assessments without and with CAC maps using multirater κ statistics. Results Computer-aided classification maps were successfully generated in 31 patients (81.5%). The proportion of agreement and the average area under the curve of optimized CAC maps were 94% (75/80) and 0.994, respectively. Multirater κ value was improved from moderate (κ = 0.59; 95% confidence interval [CI], 0.56-0.62) at the initial assessment to excellent (κ = 0.82; 95% CI, 0.79-0.85) with the CAC map. Conclusion Our proposed CAC system demonstrated the potential for regional ventilation pattern analysis and enhanced interobserver agreement on visual classification of regional ventilation. PMID:24843245

Causal Relationships Among Time Series of the Lange Bramke Catchment (Harz Mountains, Germany)

NASA Astrophysics Data System (ADS)

Aufgebauer, Britta; Hauhs, Michael; Bogner, Christina; Meesenburg, Henning; Lange, Holger

2016-04-01

Convergent Cross Mapping (CCM) has recently been introduced by Sugihara et al. for the identification and quantification of causal relationships among ecosystem variables. In particular, the method allows to decide on the direction of causality; in some cases, the causality might be bidirectional, indicating a network structure. We extend this approach by introducing a method of surrogate data to obtain confidence intervals for CCM results. We then apply this method to time series from stream water chemistry. Specifically, we analyze a set of eight dissolved major ions from three different catchments belonging to the hydrological monitoring system at the Bramke valley in the Harz Mountains, Germany. Our results demonstrate the potentials and limits of CCM as a monitoring instrument in forestry and hydrology or as a tool to identify processes in ecosystem research. While some networks of causally linked ions can be associated with simple physical and chemical processes, other results illustrate peculiarities of the three studied catchments, which are explained in the context of their special history.

A case study of carbon fluxes from land change in the southwest Brazilian Amazon

USGS Publications Warehouse

Barrett, K.; Rogan, J.; Eastman, J.R.

2009-01-01

Worldwide, land change is responsible for one-fifth of anthropogenic carbon emissions. In Brazil, three-quarters of carbon emissions originate from land change. This study represents a municipal-scale study of carbon fluxes from vegetation in Rio Branco, Brazil. Land-cover maps of pasture, forest, and secondary growth from 1993, 1996, 1999, and 2003 were produced using an unsupervised classification method (overall accuracy = 89%). Carbon fluxes from land change over the decade of imagery were estimated from transitions between land-cover categories for each time interval. This article presents new methods for estimating emissions reductions from carbon stored in the vegetation that replaces forests (e.g., pasture) and sequestration by new (>10-15 years) forests, which reduced gross emissions by 16, 15, and 22% for the period of 1993-1996, 1996-1999, and 1999-2003, respectively. The methods used in the analysis are broadly applicable and provide a comprehensive characterization of regional-scale carbon fluxes from land change.

Investigation of environmental change pattern in Japan

NASA Technical Reports Server (NTRS)

Maruyasu, T. (Principal Investigator)

1977-01-01

The author has identified the following significant results. In the Plains of Tokachi, where the scale of agricultural field was comparatively large in Japan, LANDSAT data with its accuracy have proved to be useful enough to observe the actual condition of agricultural land use and changes more accurately than present methods. Species and ages of grasses in pasture were identified and soils were classified into several types. The actual land cover and ecological environment were remarkably changeable at the rapidly industrialized area by the urbanization in the flat plane and also by the forest works and road construction in the mountainous area. The practical use of the recognition results was proved as the base map of the field survey or the retouching work of the vegetation and land use. There was a 10% cut in cost, labor, and time. Vegetation cover in Tokyo districts was estimated by both the multiregression model and the parametric model. Multicorrelation coefficient between observed value and estimated value was 0.87 and standard deviation was + or - 15%. Vegetation cover in Tokyo was mapped into five levels with equal intervals of 20%.

Multispectral image restoration of historical documents based on LAAMs and mathematical morphology

NASA Astrophysics Data System (ADS)

Lechuga-S., Edwin; Valdiviezo-N., Juan C.; Urcid, Gonzalo

2014-09-01

This research introduces an automatic technique designed for the digital restoration of the damaged parts in historical documents. For this purpose an imaging spectrometer is used to acquire a set of images in the wavelength interval from 400 to 1000 nm. Assuming the presence of linearly mixed spectral pixels registered from the multispectral image, our technique uses two lattice autoassociative memories to extract the set of pure pigments conforming a given document. Through an spectral unmixing analysis, our method produces fractional abundance maps indicating the distributions of each pigment in the scene. These maps are then used to locate cracks and holes in the document under study. The restoration process is performed by the application of a region filling algorithm, based on morphological dilation, followed by a color interpolation to restore the original appearance of the filled areas. This procedure has been successfully applied to the analysis and restoration of three multispectral data sets: two corresponding to artificially superimposed scripts and a real data acquired from a Mexican pre-Hispanic codex, whose restoration results are presented.

Land cover change monitoring within the east central Louisiana study site: A case for large area surveys with LANDSAT multispectral scanner data

NASA Technical Reports Server (NTRS)

Burns, G. S.

1983-01-01

Results established for four digital procedures developed for characterizing the radiometric changes between multidate LANDSAT spectral data sets into meaningful measures of land cover/use dynamics are documented. Each technique's performance was contrasted against digitized land use change maps, which were produced from contemporaneous, retrospective aerophoto coverage, in a cell by cell comparison over a one half by one degree area in east central Louisiana as a standard for comparison. The four techniques identify from 10.5 to 13.0% loss in area of forestland in a five year period; however, they differ more by how accurately this amount of change is distributed, the need for ancillary ground truth, and amount of usable information that is extractable. All require some method of digitally co-registering the two data sets. All are capable of providing tabular statistics as well as map products. Two are capable of detecting changes and identifying their locations. The other two, in addition to this, provide information to qualify land cover conditions at each end of the study interval.

A Numerical Study of New Logistic Map

NASA Astrophysics Data System (ADS)

Khmou, Youssef

In this paper, we propose a new logistic map based on the relation of the information entropy, we study the bifurcation diagram comparatively to the standard logistic map. In the first part, we compare the obtained diagram, by numerical simulations, with that of the standard logistic map. It is found that the structures of both diagrams are similar where the range of the growth parameter is restricted to the interval [0,e]. In the second part, we present an application of the proposed map in traffic flow using macroscopic model. It is found that the bifurcation diagram is an exact model of the Greenberg’s model of traffic flow where the growth parameter corresponds to the optimal velocity and the random sequence corresponds to the density. In the last part, we present a second possible application of the proposed map which consists of random number generation. The results of the analysis show that the excluded initial values of the sequences are (0,1).

Geological map and digital database of the San Rafael Mtn. 7.5-minute quadrangle, Santa Barbara County, California

USGS Publications Warehouse

Vedder, John G.; Stanley, Richard G.; Graham, S.E.; Valin, Z.C.

2001-01-01

Geologic mapping of the San Rafael Primitive Area (now the San Rafael Wilderness) by Gower and others (1966) and Vedder and others (1967) did not include all of the San Rafael Mtn. quadrangle, and the part that was mapped was done in reconnaissance fashion. To help resolve some of the structural and stratigraphic ambiguities of the earlier mapping and to complete the mapping of the quadrangle, additional field work was done during short intervals in 1980 and 1981 and from 1996 to 1998. Contacts within the belt of Franciscan rocks at the southwestern corner of the quadrangle were generalized from the detailed map by Wahl (1998). Because extensive areas were inaccessible owing to impenetrable chaparral, observations from several helicopter overflights (1965, 1980, 1981) and interpretations from aerial photographs were used as compilation aids. Consequently, some of the depicted contacts and faults are highly inferential, particularly within the Upper Cretaceous rocks throughout the middle part of the quadrangle.

Snake River Plain Geothermal Play Fairway Analysis - Phase 1 Raster Files

DOE Data Explorer

John Shervais

2015-10-09

Snake River Plain Play Fairway Analysis - Phase 1 CRS Raster Files. This dataset contains raster files created in ArcGIS. These raster images depict Common Risk Segment (CRS) maps for HEAT, PERMEABILITY, AND SEAL, as well as selected maps of Evidence Layers. These evidence layers consist of either Bayesian krige functions or kernel density functions, and include: (1) HEAT: Heat flow (Bayesian krige map), Heat flow standard error on the krige function (data confidence), volcanic vent distribution as function of age and size, groundwater temperature (equivalue interval and natural breaks bins), and groundwater T standard error. (2) PERMEABILTY: Fault and lineament maps, both as mapped and as kernel density functions, processed for both dilational tendency (TD) and slip tendency (ST), along with data confidence maps for each data type. Data types include mapped surface faults from USGS and Idaho Geological Survey data bases, as well as unpublished mapping; lineations derived from maximum gradients in magnetic, deep gravity, and intermediate depth gravity anomalies. (3) SEAL: Seal maps based on presence and thickness of lacustrine sediments and base of SRP aquifer. Raster size is 2 km. All files generated in ArcGIS.

High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato.

PubMed

Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

2011-04-01

Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene-derived markers. For the first time we report on the development and mapping of 83 Petunia microsatellites. The two maps retain the same marker order, but display significant differences of recombination frequencies at orthologous mapping intervals. A complex pattern of genomic rearrangements was detected with the related genome of tomato (Solanum lycopersicum), indicating that synteny between Petunia and other Solanaceae crops has been considerably disrupted. The newly developed markers will facilitate the genetic characterization of mutants and ecological studies on genetic diversity and speciation within the genus Petunia. The maps will provide a powerful tool to link genetic and genomic information and will be useful to support sequence assembly of the Petunia genome.

A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

PubMed Central

Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

2016-01-01

Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

PubMed Central

Everts-van der Wind, Annelie; Kata, Srinivas R.; Band, Mark R.; Rebeiz, Mark; Larkin, Denis M.; Everts, Robin E.; Green, Cheryl A.; Liu, Lei; Natarajan, Shreedhar; Goldammer, Tom; Lee, Jun Heon; McKay, Stephanie; Womack, James E.; Lewin, Harris A.

2004-01-01

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle–human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH5000 panel to 1913. Of these, 1463 have significant BLASTN hits (E < e–5) against the human genome sequence. A cattle–human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle–human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes. PMID:15231756

Using complexity metrics with R-R intervals and BPM heart rate measures.

PubMed

Wallot, Sebastian; Fusaroli, Riccardo; Tylén, Kristian; Jegindø, Else-Marie

2013-01-01

Lately, growing attention in the health sciences has been paid to the dynamics of heart rate as indicator of impending failures and for prognoses. Likewise, in social and cognitive sciences, heart rate is increasingly employed as a measure of arousal, emotional engagement and as a marker of interpersonal coordination. However, there is no consensus about which measurements and analytical tools are most appropriate in mapping the temporal dynamics of heart rate and quite different metrics are reported in the literature. As complexity metrics of heart rate variability depend critically on variability of the data, different choices regarding the kind of measures can have a substantial impact on the results. In this article we compare linear and non-linear statistics on two prominent types of heart beat data, beat-to-beat intervals (R-R interval) and beats-per-min (BPM). As a proof-of-concept, we employ a simple rest-exercise-rest task and show that non-linear statistics-fractal (DFA) and recurrence (RQA) analyses-reveal information about heart beat activity above and beyond the simple level of heart rate. Non-linear statistics unveil sustained post-exercise effects on heart rate dynamics, but their power to do so critically depends on the type data that is employed: While R-R intervals are very susceptible to non-linear analyses, the success of non-linear methods for BPM data critically depends on their construction. Generally, "oversampled" BPM time-series can be recommended as they retain most of the information about non-linear aspects of heart beat dynamics.

Using complexity metrics with R-R intervals and BPM heart rate measures

PubMed Central

Wallot, Sebastian; Fusaroli, Riccardo; Tylén, Kristian; Jegindø, Else-Marie

2013-01-01

Lately, growing attention in the health sciences has been paid to the dynamics of heart rate as indicator of impending failures and for prognoses. Likewise, in social and cognitive sciences, heart rate is increasingly employed as a measure of arousal, emotional engagement and as a marker of interpersonal coordination. However, there is no consensus about which measurements and analytical tools are most appropriate in mapping the temporal dynamics of heart rate and quite different metrics are reported in the literature. As complexity metrics of heart rate variability depend critically on variability of the data, different choices regarding the kind of measures can have a substantial impact on the results. In this article we compare linear and non-linear statistics on two prominent types of heart beat data, beat-to-beat intervals (R-R interval) and beats-per-min (BPM). As a proof-of-concept, we employ a simple rest-exercise-rest task and show that non-linear statistics—fractal (DFA) and recurrence (RQA) analyses—reveal information about heart beat activity above and beyond the simple level of heart rate. Non-linear statistics unveil sustained post-exercise effects on heart rate dynamics, but their power to do so critically depends on the type data that is employed: While R-R intervals are very susceptible to non-linear analyses, the success of non-linear methods for BPM data critically depends on their construction. Generally, “oversampled” BPM time-series can be recommended as they retain most of the information about non-linear aspects of heart beat dynamics. PMID:23964244

Modified dwell time optimization model and its applications in subaperture polishing.

PubMed

Dong, Zhichao; Cheng, Haobo; Tam, Hon-Yuen

2014-05-20

The optimization of dwell time is an important procedure in deterministic subaperture polishing. We present a modified optimization model of dwell time by iterative and numerical method, assisted by extended surface forms and tool paths for suppressing the edge effect. Compared with discrete convolution and linear equation models, the proposed model has essential compatibility with arbitrary tool paths, multiple tool influence functions (TIFs) in one optimization, and asymmetric TIFs. The emulational fabrication of a Φ200  mm workpiece by the proposed model yields a smooth, continuous, and non-negative dwell time map with a root-mean-square (RMS) convergence rate of 99.6%, and the optimization costs much less time. By the proposed model, influences of TIF size and path interval to convergence rate and polishing time are optimized, respectively, for typical low and middle spatial-frequency errors. Results show that (1) the TIF size is nonlinear inversely proportional to convergence rate and polishing time. A TIF size of ~1/7 workpiece size is preferred; (2) the polishing time is less sensitive to path interval, but increasing the interval markedly reduces the convergence rate. A path interval of ~1/8-1/10 of the TIF size is deemed to be appropriate. The proposed model is deployed on a JR-1800 and MRF-180 machine. Figuring results of Φ920  mm Zerodur paraboloid and Φ100  mm Zerodur plane by them yield RMS of 0.016λ and 0.013λ (λ=632.8  nm), respectively, and thereby validate the feasibility of proposed dwell time model used for subaperture polishing.

A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

PubMed Central

Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

2016-01-01

Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15–28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89–2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea. PMID:27695461

Reducing the width of confidence intervals for the difference between two population means by inverting adaptive tests.

PubMed

O'Gorman, Thomas W

2018-05-01

In the last decade, it has been shown that an adaptive testing method could be used, along with the Robbins-Monro search procedure, to obtain confidence intervals that are often narrower than traditional confidence intervals. However, these confidence interval limits require a great deal of computation and some familiarity with stochastic search methods. We propose a method for estimating the limits of confidence intervals that uses only a few tests of significance. We compare these limits to those obtained by a lengthy Robbins-Monro stochastic search and find that the proposed method is nearly as accurate as the Robbins-Monro search. Adaptive confidence intervals that are produced by the proposed method are often narrower than traditional confidence intervals when the distributions are long-tailed, skewed, or bimodal. Moreover, the proposed method of estimating confidence interval limits is easy to understand, because it is based solely on the p-values from a few tests of significance.

Altered skin flowmotion in hypertensive humans

PubMed Central

Bruning, R.S.; Kenney, W.L.; Alexander, L.M.

2017-01-01

Essential hypertensive humans exhibit attenuated cutaneous nitric oxide (NO)-dependent vasodilation. Using spectral analysis (fast Fourier transformation) we aimed to characterize the skin flowmotion contained in the laser-Doppler flowmetry recordings during local heating-induced vasodilation before and after concurrent pharmacological inhibition of nitric oxide synthase (NOS) in hypertensive and age-matched normotensive men and women. We hypothesized that hypertensive subjects would have lower total power spectral densities (PSD), specifically in the frequency intervals associated with intrinsic endothelial and neurogenic control of the microvasculature. Furthermore, we hypothesized that NOS inhibition would attenuate the endothelial frequency interval. Laser-Doppler flowmetry recordings during local heating experiments from 18 hypertensive (MAP: 108±2mmHg) and 18 normotensive (MAP: 88±2mmHg) men and women were analyzed. Within site NO-dependent vasodilation was assessed by perfusion of a non-specific NOS inhibitor (NG-nitro-L-arginine methyl ester; L-NAME) through intradermal microdialysis during the heating-induced plateau in skin blood flow. Local heating-induced vasodilation increased total PSD for all frequency intervals (all p<0.001). Hypertensives had a lower total PSD (p=0.03) and absolute neurogenic frequency intervals (p<0.01) compared to the normotensives. When normalized as a percentage of total PSD, hypertensives had reduced neurogenic (p<0.001) and augmented myogenic contributions (p=0.04) to the total spectrum. NOS inhibition decreased total PSD (p<0.001) for both groups, but hypertensives exhibited lower absolute endothelial (p<0.01), neurogenic (p<0.05), and total PSD (p<0.001) frequency intervals compared to normotensives. These data suggest that essential hypertension results in altered neurogenic and NOS-dependent control of skin flowmotion and support the use of spectral analysis as a non-invasive technique to study vasoreactivity. PMID:24418051

Rainfall erosivity in Central Chile

NASA Astrophysics Data System (ADS)

Bonilla, Carlos A.; Vidal, Karim L.

2011-11-01

SummaryOne of the most widely used indicators of potential water erosion risk is the rainfall-runoff erosivity factor ( R) of the Revised Universal Soil Loss Equation (RUSLE). R is traditionally determined by calculating a long-term average of the annual sum of the product of a storm's kinetic energy ( E) and its maximum 30-min intensity ( I30), known as the EI30. The original method used to calculate EI30 requires pluviograph records for at most 30-min time intervals. Such high resolution data is difficult to obtain in many parts of the world, and processing it is laborious and time-consuming. In Chile, even though there is a well-distributed rain gauge network, there is no systematic characterization of the territory in terms of rainfall erosivity. This study presents a rainfall erosivity map for most of the cultivated land in the country. R values were calculated by the prescribed method for 16 stations with continuous graphical record rain gauges in Central Chile. The stations were distributed along 800 km (north-south), and spanned a precipitation gradient of 140-2200 mm yr -1. More than 270 years of data were used, and 5400 storms were analyzed. Additionally, 241 spatially distributed R values were generated by using an empirical procedure based on annual rainfall. Point estimates generated by both methods were interpolated by using kriging to create a map of rainfall erosivity for Central Chile. The results show that the empirical procedure used in this study predicted the annual rainfall erosivity well (model efficiency = 0.88). Also, an increment in the rainfall erosivities was found as a result of the rainfall depths, a regional feature determined by elevation and increasing with latitude from north to south. R values in the study area range from 90 MJ mm ha -1 h -1 yr -1 in the north up to 7375 MJ mm ha -1 h -1 yr -1 in the southern area, at the foothills of the Andes Mountains. Although the map and the estimates could be improved in the future by generating additional data points, the erosivity map should prove to be a good tool for land-use planners in Chile and other areas with similar rainfall characteristics.

Neo-Deterministic and Probabilistic Seismic Hazard Assessments: a Comparative Analysis

NASA Astrophysics Data System (ADS)

Peresan, Antonella; Magrin, Andrea; Nekrasova, Anastasia; Kossobokov, Vladimir; Panza, Giuliano F.

2016-04-01

Objective testing is the key issue towards any reliable seismic hazard assessment (SHA). Different earthquake hazard maps must demonstrate their capability in anticipating ground shaking from future strong earthquakes before an appropriate use for different purposes - such as engineering design, insurance, and emergency management. Quantitative assessment of maps performances is an essential step also in scientific process of their revision and possible improvement. Cross-checking of probabilistic models with available observations and independent physics based models is recognized as major validation procedure. The existing maps from the classical probabilistic seismic hazard analysis (PSHA), as well as those from the neo-deterministic analysis (NDSHA), which have been already developed for several regions worldwide (including Italy, India and North Africa), are considered to exemplify the possibilities of the cross-comparative analysis in spotting out limits and advantages of different methods. Where the data permit, a comparative analysis versus the documented seismic activity observed in reality is carried out, showing how available observations about past earthquakes can contribute to assess performances of the different methods. Neo-deterministic refers to a scenario-based approach, which allows for consideration of a wide range of possible earthquake sources as the starting point for scenarios constructed via full waveforms modeling. The method does not make use of empirical attenuation models (i.e. Ground Motion Prediction Equations, GMPE) and naturally supplies realistic time series of ground shaking (i.e. complete synthetic seismograms), readily applicable to complete engineering analysis and other mitigation actions. The standard NDSHA maps provide reliable envelope estimates of maximum seismic ground motion from a wide set of possible scenario earthquakes, including the largest deterministically or historically defined credible earthquake. In addition, the flexibility of NDSHA allows for generation of ground shaking maps at specified long-term return times, which may permit a straightforward comparison between NDSHA and PSHA maps in terms of average rates of exceedance for specified time windows. The comparison of NDSHA and PSHA maps, particularly for very long recurrence times, may indicate to what extent probabilistic ground shaking estimates are consistent with those from physical models of seismic waves propagation. A systematic comparison over the territory of Italy is carried out exploiting the uniqueness of the Italian earthquake catalogue, a data set covering more than a millennium (a time interval about ten times longer than that available in most of the regions worldwide) with a satisfactory completeness level for M>5, which warrants the results of analysis. By analysing in some detail seismicity in the Vrancea region, we show that well constrained macroseismic field information for individual earthquakes may provide useful information about the reliability of ground shaking estimates. Finally, in order to generalise observations, the comparative analysis is extended to further regions where both standard NDSHA and PSHA maps are available (e.g. State of Gujarat, India). The final Global Seismic Hazard Assessment Program (GSHAP) results and the most recent version of Seismic Hazard Harmonization in Europe (SHARE) project maps, along with other national scale probabilistic maps, all obtained by PSHA, are considered for this comparative analysis.

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

PubMed Central

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cgQTL can be used to determine priority of candidate genes for QTN analysis based on differential expression in the target organ. PMID:17584498

A new approach to monitoring and alerting congestion in airspace sectors

DOT National Transportation Integrated Search

2014-09-28

The Federal Aviation Administration (FAA) Traffic Flow Management System (TFMS)currently declares an alert for any 15 minute interval in which the predicted demand exceeds the Monitor/Alert Parameter (MAP)for any airport, sector, or fix. For airports...

Spatiotemporal patterns of ERP based on combined ICA-LORETA analysis

NASA Astrophysics Data System (ADS)

Zhang, Jiacai; Guo, Taomei; Xu, Yaqin; Zhao, Xiaojie; Yao, Li

2007-03-01

In contrast to the FMRI methods widely used up to now, this method try to understand more profoundly how the brain systems work under sentence processing task map accurately the spatiotemporal patterns of activity of the large neuronal populations in the human brain from the analysis of ERP data recorded on the brain scalp. In this study, an event-related brain potential (ERP) paradigm to record the on-line responses to the processing of sentences is chosen as an example. In order to give attention to both utilizing the ERPs' temporal resolution of milliseconds and overcoming the insensibility of cerebral location ERP sources, we separate these sources in space and time based on a combined method of independent component analysis (ICA) and low-resolution tomography (LORETA) algorithms. ICA blindly separate the input ERP data into a sum of temporally independent and spatially fixed components arising from distinct or overlapping brain or extra-brain sources. And then the spatial maps associated with each ICA component are analyzed, with use of LORETA to uniquely locate its cerebral sources throughout the full brain according to the assumption that neighboring neurons are simultaneously and synchronously activated. Our results show that the cerebral computation mechanism underlies content words reading is mediated by the orchestrated activity of several spatially distributed brain sources located in the temporal, frontal, and parietal areas, and activate at distinct time intervals and are grouped into different statistically independent components. Thus ICA-LORETA analysis provides an encouraging and effective method to study brain dynamics from ERP.

Response Surface Methods For Spatially-Resolved Optical Measurement Techniques

NASA Technical Reports Server (NTRS)

Danehy, P. M.; Dorrington, A. A.; Cutler, A. D.; DeLoach, R.

2003-01-01

Response surface methods (or methodology), RSM, have been applied to improve data quality for two vastly different spatially-resolved optical measurement techniques. In the first application, modern design of experiments (MDOE) methods, including RSM, are employed to map the temperature field in a direct-connect supersonic combustion test facility at NASA Langley Research Center. The laser-based measurement technique known as coherent anti-Stokes Raman spectroscopy (CARS) is used to measure temperature at various locations in the combustor. RSM is then used to develop temperature maps of the flow. Even though the temperature fluctuations at a single point in the flowfield have a standard deviation on the order of 300 K, RSM provides analytic fits to the data having 95% confidence interval half width uncertainties in the fit as low as +/- 30 K. Methods of optimizing future CARS experiments are explored. The second application of RSM is to quantify the shape of a 5-meter diameter, ultra-lightweight, inflatable space antenna at NASA Langley Research Center. Photogrammetry is used to simultaneously measure the shape of the antenna at approximately 500 discrete spatial locations. RSM allows an analytic model to be developed that describes the shape of the majority of the antenna with an uncertainty of 0.4 mm, with 95% confidence. This model would allow a quantitative comparison between the actual shape of the antenna and the original design shape. Accurately determining this shape also allows confident interpolation between the measured points. Such a model could, for example, be used for ray tracing of radio-frequency waves up to 95 GHz. to predict the performance of the antenna.

Cropping Pattern Detection and Change Analysis in Central Luzon, Philippines Using Multi-Temporal MODIS Imagery and Artificial Neural Network Classifier

NASA Astrophysics Data System (ADS)

dela Torre, D. M.; Perez, G. J. P.

2016-12-01

Cropping practices in the Philippines has been intensifying with greater demand for food and agricultural supplies in view of an increasing population and advanced technologies for farming. This has not been monitored regularly using traditional methods but alternative methods using remote sensing has been promising yet underutilized. This study employed multi-temporal data from MODIS and neural network classifier to map annual land use in agricultural areas from 2001-2014 in Central Luzon, the primary rice growing area of the Philippines. Land use statistics derived from these maps were compared with historical El Nino events to examine how land area is affected by drought events. Fourteen maps of agricultural land use was produced, with the primary classes being single-cropping, double-cropping and perennial crops with secondary classes of forests, urban, bare, water and other classes. Primary classes were produced from the neural network classifier while secondary classes were derived from NDVI threshold masks. The overall accuracy for the 2014 map was 62.05% and a kappa statistic of 0.45. 155.56% increase in single-cropping systems from 2001 to 2014 was observed while double cropping systems decreased by 14.83%. Perennials increased by 76.21% while built-up areas decreased by 12.22% within the 14-year interval. There are several sources of error including mixed-pixels, scale-conversion problems and limited ground reference data. An analysis including El Niño events in 2004 and 2010 demonstrated that marginally irrigated areas that usually planted twice in a year resorted to single cropping, indicating that scarcity of water limited the intensification allowable in the area. Findings from this study can be used to predict future use of agricultural land in the country and also examine how farmlands have responded to climatic factors and stressors.

Mapping epibenthic assemblages and their relations to sedimentary features in shallow-water, high-energy environments

NASA Astrophysics Data System (ADS)

Sisson, John D.; Shimeta, Jeff; Zimmer, Cheryl Ann; Traykovski, Peter

2002-03-01

Knowledge of spatial relationships among benthic biota and sedimentary features in shallow-water (<30 m) high-energy environments has been severely limited by sampling technology. We describe and report tests of a SCUBA-diving mapping method specifically for this region. Underwater acoustic location is used to achieve meter-scale resolution over kilometer-scale regions of the sea floor. A triad of acoustic transponders is bottom-mounted at known positions, 300-500 m apart. Transported by underwater personal vehicles, SCUBA-divers map the bed using hand-held acoustic receivers that record ranges to the transponders. The mean error of acoustic fixes was 2.4±1.2 m in a 0.5 km×1.0 km test area. Dense assemblages of epibenthic animals were mapped relative to sediment texture and bedforms off the exposed south coast of Martha's Vineyard Island, Massachusetts, USA. Surveys one month apart within a 0.6 km×0.6 km area (8-12 m depth) revealed 100-m-scale patches of the tube worm Spiophanes bombyx (⩽30,000 m -2) in fine sand and of the sand dollar Echinarachnius parma (⩽55 m -2) in coarse sand. Raised mud patches that, together with fine sand, occurred in two shore-perpendicular belts are likely exposed, ancient marsh deposits. Depth gradients of sand-ripple geometry indicated that ripples in deeper areas were not in equilibrium with wave conditions monitored during surveys; i.e., they were relict ripples. Thus, sand dollars in some areas may have had >1 month to rework surficial sands since their transformation by physical processes. Linear regressions of ripple characteristics against sand dollar or tube worm densities were not significant, although such relationships would be highly dependent on temporal scale. The survey method described here can be used at more frequent intervals to explore such interactions between epibenthic animals and sediment-transport dynamics.

Building a flood hazard map due to magma effusion into the caldera lake of the Baekdusan Volcano

NASA Astrophysics Data System (ADS)

Lee, K.; Kim, S.; Yun, S.; Yu, S.; Kim, I.

2013-12-01

Many volcanic craters and calderas are filled with large amounts of water that can pose significant flood hazards to downstream communities due to their high elevation and the potential for catastrophic releases of water. Recent reports pointed out the Baekdusan volcano that is located between the border of China and North Korea as a potential active volcano. Since Millennium Eruption around 1000 AD, smaller eruptions have occurred at roughly 100-year intervals, with the last one in 1903. The volcano is showing signs of waking from a century-long slumber recently and the volcanic ash may spread up to the northeastern of Japan. The development of various forecasting techniques to prevent and minimize economic and social damage is in urgent need. Floods from lake-filled calderas may be particularly large and high. Volcanic flood may cause significant hydrologic hazards for this reason. This study focuses on constructing a flood hazard map triggered by the uplift of lake bottom due to magma effusion in the Baekdusan volcano. A physically-based uplift model was developed to compute the amount of water and time to peak flow. The ordinary differential equation was numerically solved using the finite difference method and Newton-Raphson iteration method was used to solve nonlinear equation. The magma effusion rate into the caldera lake is followed by the past record from other volcanic activities. As a result, the hydrograph serves as an upper boundary condition when hydrodynamic model (Flo-2D) runs to simulate channel routing downstream. The final goal of the study stresses the potential flood hazard represented by the huge volume of water in the caldera lake, the unique geography, and the limited control capability. he study will contribute to build a geohazard map for the decision-makers and practitioners. Keywords: Effusion rate, Volcanic flood, Caldera lake, Uplift, Flood hazard map Acknowledgement This research was supported by a grant [NEMA-BAEKDUSAN-2012-1-2] from the Volcanic Disaster Preparedness Research Center sponsored by National Emergency Management Agency of Korea. Inundation map triggered by magma effusion simulated by Flo-2D

Anisotropic models to account for large borehole washouts to estimate gas hydrate saturations in the Gulf of Mexico Gas Hydrate Joint Industry Project Leg II Alaminos 21 B well

USGS Publications Warehouse

Lee, M.W.; Collett, T.S.; Lewis, K.A.

2012-01-01

Through the use of 3-D seismic amplitude mapping, several gashydrate prospects were identified in the Alaminos Canyon (AC) area of the Gulf of Mexico. Two locations were drilled as part of the Gulf of MexicoGasHydrate Joint Industry Project Leg II (JIP Leg II) in May of 2009 and a comprehensive set of logging-while-drilling (LWD) logs were acquired at each well site. LWD logs indicated that resistivity in the range of ~2 ohm-m and P-wave velocity in the range of ~1.9 km/s were measured in the target sand interval between 515 and 645 feet below sea floor. These values were slightly elevated relative to those measured in the sediment above and below the target sand. However, the initial well log analysis was inconclusive regarding the presence of gashydrate in the logged sand interval, mainly because largewashouts caused by drilling in the target interval degraded confidence in the well log measurements. To assess gashydratesaturations in the sedimentary section drilled in the Alaminos Canyon 21B (AC21-B) well, a method of compensating for the effect of washouts on the resistivity and acoustic velocities was developed. The proposed method models the washed-out portion of the borehole as a vertical layer filled with sea water (drilling fluid) and the apparent anisotropic resistivity and velocities caused by a vertical layer are used to correct the measured log values. By incorporating the conventional marine seismic data into the well log analysis, the average gashydratesaturation in the target sand section in the AC21-Bwell can be constrained to the range of 8–28%, with 20% being our best estimate.

Predicting Ambulance Time of Arrival to the Emergency Department Using Global Positioning System and Google Maps

PubMed Central

Fleischman, Ross J.; Lundquist, Mark; Jui, Jonathan; Newgard, Craig D.; Warden, Craig

2014-01-01

Objective To derive and validate a model that accurately predicts ambulance arrival time that could be implemented as a Google Maps web application. Methods This was a retrospective study of all scene transports in Multnomah County, Oregon, from January 1 through December 31, 2008. Scene and destination hospital addresses were converted to coordinates. ArcGIS Network Analyst was used to estimate transport times based on street network speed limits. We then created a linear regression model to improve the accuracy of these street network estimates using weather, patient characteristics, use of lights and sirens, daylight, and rush-hour intervals. The model was derived from a 50% sample and validated on the remainder. Significance of the covariates was determined by p < 0.05 for a t-test of the model coefficients. Accuracy was quantified by the proportion of estimates that were within 5 minutes of the actual transport times recorded by computer-aided dispatch. We then built a Google Maps-based web application to demonstrate application in real-world EMS operations. Results There were 48,308 included transports. Street network estimates of transport time were accurate within 5 minutes of actual transport time less than 16% of the time. Actual transport times were longer during daylight and rush-hour intervals and shorter with use of lights and sirens. Age under 18 years, gender, wet weather, and trauma system entry were not significant predictors of transport time. Our model predicted arrival time within 5 minutes 73% of the time. For lights and sirens transports, accuracy was within 5 minutes 77% of the time. Accuracy was identical in the validation dataset. Lights and sirens saved an average of 3.1 minutes for transports under 8.8 minutes, and 5.3 minutes for longer transports. Conclusions An estimate of transport time based only on a street network significantly underestimated transport times. A simple model incorporating few variables can predict ambulance time of arrival to the emergency department with good accuracy. This model could be linked to global positioning system data and an automated Google Maps web application to optimize emergency department resource use. Use of lights and sirens had a significant effect on transport times. PMID:23865736

An automated mapping satellite system ( Mapsat).

USGS Publications Warehouse

Colvocoresses, A.P.

1982-01-01

The favorable environment of space permits a satellite to orbit the Earth with very high stability as long as no local perturbing forces are involved. Solid-state linear-array sensors have no moving parts and create no perturbing force on the satellite. Digital data from highly stabilized stereo linear arrays are amenable to simplified processing to produce both planimetric imagery and elevation data. A satellite imaging system, called Mapsat, including this concept has been proposed to produce data from which automated mapping in near real time can be accomplished. Image maps as large as 1:50 000 scale with contours as close as a 20-m interval may be produced from Mapsat data. -from Author

Design of preventive maintenance system using the reliability engineering and maintenance value stream mapping methods in PT. XYZ

NASA Astrophysics Data System (ADS)

Sembiring, N.; Panjaitan, N.; Angelita, S.

2018-02-01

PT. XYZ is a company owned by non-governmental organizations engaged in the field of production of rubber processing becoming crumb rubber. Part of the production is supported by some of machines and interacting equipment to achieve optimal productivity. Types of the machine that are used in the production process are Conveyor Breaker, Breaker, Rolling Pin, Hammer Mill, Mill Roll, Conveyor, Shredder Crumb, and Dryer. Maintenance system in PT. XYZ is corrective maintenance i.e. repairing or replacing the engine components after the crash on the machine. Replacement of engine components on corrective maintenance causes the machine to stop operating during the production process is in progress. The result is in the loss of production time due to the operator must replace the damaged engine components. The loss of production time can impact on the production targets which were not reached and lead to high loss costs. The cost for all components is Rp. 4.088.514.505. This cost is really high just for maintaining a Mill Roll Machine. Therefore PT. XYZ is needed to do preventive maintenance i.e. scheduling engine components and improving maintenance efficiency. The used methods are Reliability Engineering and Maintenance Value Stream Mapping (MVSM). The needed data in this research are the interval of time damage to engine components, opportunity cost, labor cost, component cost, corrective repair time, preventive repair time, Mean Time To Opportunity (MTTO), Mean Time To Repair (MTTR), and Mean Time To Yield (MTTY). In this research, the critical components of Mill Roll machine are Spier, Bushing, Bearing, Coupling and Roll. Determination of damage distribution, reliability, MTTF, cost of failure, cost of preventive, current state map, and future state map are done so that the replacement time for each critical component with the lowest maintenance cost and preparation of Standard Operation Procedure (SOP) are developed. For the critical component that has been determined, the Spier component replacement time interval is 228 days with a reliability value of 0,503171, Bushing component is 240 days with reliability value of 0.36861, Bearing component is 202 days with reliability value of 0,503058, Coupling component is 247 days with reliability value of 0,50108 and Roll component is 301 days with reliability value of 0,373525. The results show that the cost decreases from Rp 300,688,114 to Rp 244,384,371 obtained from corrective maintenance to preventive maintenance. While maintenance efficiency increases with the application of preventive maintenance i.e. for Spier component from 54,0540541% to 74,07407%, Bushing component from 52,3809524% to 68,75%, Bearing component from 40% to 52,63158%, Coupling component from 60.9756098% to 71.42857%, and Roll components from 64.516129% to 74.7663551%.

One-way ANOVA based on interval information

NASA Astrophysics Data System (ADS)

Hesamian, Gholamreza

2016-08-01

This paper deals with extending the one-way analysis of variance (ANOVA) to the case where the observed data are represented by closed intervals rather than real numbers. In this approach, first a notion of interval random variable is introduced. Especially, a normal distribution with interval parameters is introduced to investigate hypotheses about the equality of interval means or test the homogeneity of interval variances assumption. Moreover, the least significant difference (LSD method) for investigating multiple comparison of interval means is developed when the null hypothesis about the equality of means is rejected. Then, at a given interval significance level, an index is applied to compare the interval test statistic and the related interval critical value as a criterion to accept or reject the null interval hypothesis of interest. Finally, the method of decision-making leads to some degrees to accept or reject the interval hypotheses. An applied example will be used to show the performance of this method.

EGRET Diffuse Gamma Ray Maps Between 30 MeV and 10 GeV

NASA Technical Reports Server (NTRS)

Cillis, A, N.; Hartman, R. C.

2004-01-01

This paper presents all-sky maps of diffuse gamma radiation in various energy ranges between 30 MeV and 10 GeV, based on data collected by the EGRET instrument on the Compton Gamma Ray Observatory. Although the maps can be used for a variety of applications. the immediate goal is the generation of diffuse gamma-ray maps which can be used as a diffuse background/foreground for point source analysis of the data to be obtained from new high-energy gamma-ray missions like GLAST and AGILE. To generate the diffuse gamma maps from the raw EGRET maps, the point sources in the Third EGRET Catalog were subtracted out using the appropriate point spread function for each energy range. After that, smoothing was performed to minimize the effects of photon statistical noise. A smoothing length of 1 deg vas used for the Galactic plane maps. For the all-sky maps, a procedure was used which resulted in a smoothing length roughly equivalent to 4 deg. The result of this work is 16 maps of different energy intervals for absolute value of b < or equal to 20 deg, and 32 all-sky maps, 16 in equatorial coordinates (J2000) and 16 in Galactic coordinates.

EGRET Diffuse Gamma Ray Maps Between 30 MeV and 10 GeV

NASA Technical Reports Server (NTRS)

Cillis, A. N.; Hartman, R. C.

2004-01-01

This paper presents all-sky maps of diffuse gamma radiation in various energy ranges between 30 MeV and 10 GeV, based on data collected by the EGRET instrument on the Compton Gamma Ray Observatory. Although the maps can be used for a variety of applications, the immediate goal is the generation of diffuse gamma-ray maps which can be used as a diffuse background/foreground for point source analysis of the data to be obtained from new high-energy gamma-ray missions like GLAST and AGILE. To generate the diffuse gamma maps from the raw EGRET maps, the point sources in the Third EGRET Catalog were subtracted out using the appropriate point spread function for each energy range. After that, smoothing was performed to minimize the effects of photon statistical noise. A smoothing length of 1deg was used for the Galactic plane maps. For the all-sky maps, a procedure was used which resulted in a smoothing length roughly equivalent to 4deg. The result of this work is 16 maps of different energy intervals for [b]less than or equal to 20deg, and 32 all-sky maps, 16 in equatorial coordinates (J2000) and 16 in Galactic coordinates.

Method and system for processing optical elements using magnetorheological finishing

DOEpatents

Menapace, Joseph Arthur; Schaffers, Kathleen Irene; Bayramian, Andrew James; Molander, William A

2012-09-18

A method of finishing an optical element includes mounting the optical element in an optical mount having a plurality of fiducials overlapping with the optical element and obtaining a first metrology map for the optical element and the plurality of fiducials. The method also includes obtaining a second metrology map for the optical element without the plurality of fiducials, forming a difference map between the first metrology map and the second metrology map, and aligning the first metrology map and the second metrology map. The method further includes placing mathematical fiducials onto the second metrology map using the difference map to form a third metrology map and associating the third metrology map to the optical element. Moreover, the method includes mounting the optical element in the fixture in an MRF tool, positioning the optical element in the fixture; removing the plurality of fiducials, and finishing the optical element.

Time-slice maps showing age, distribution, and style of deformation in Alaska north of 60° N.

USGS Publications Warehouse

Moore, Thomas E.; Box, Stephen E.

2016-08-29

The structural architecture of Alaska is the product of a complex history of tectonism that occurred along the Cordilleran and Arctic margins of North America through interactions with ancient and modern ocean plates and with continental elements derived from Laurentia, Siberia, and Baltica. To unravel the tectonic history of Alaska, we constructed maps showing the age, distribution, structural style, and kinematics of contractional and penetrative extensional deformation in Alaska north of latitude 60° N. at a scale of 1:5,000,000. These maps use the Geologic Map of the Arctic (Harrison and others, 2011) as a base map and follow the guidelines in the Tectonic Map of the Arctic project (Petrov and others, 2013) for construction, including use of the International Commission on Stratigraphy time scale (Cohen and others, 2013) divided into 20 time intervals. We find evidence for deformation in 14 of the 20 time intervals and present maps showing the known or probable extent of deformation for each time interval. Maps and descriptions of deformational style, age constraints, kinematics, and information sources for each deformational episode are discussed in the text and are reported in tabular form. This report also contains maps showing the lithologies and structural geology of Alaska, a terrane map, and the distribution of tectonically important units including post-tectonic sedimentary basins, accretionary complexes, ophiolites, metamorphic rocks.These new maps show that most deformational belts in Alaska are relatively young features, having developed during the late Mesozoic and Cenozoic. The oldest episode of deformation recognized anywhere in Alaska is found in the basement of the Farewell terrane (~1.75 Ga). Paleozoic and early Mesozoic deformational events, including Devonian deformation in the Arctic Alaska terrane, Pennsylvanian deformation in the Alexander terrane, Permian deformation in the Yukon Composite (Klondike orogeny) and Farewell terranes (Browns Fork orogeny), Early and Late Jurassic deformation in the Peninsular-Wrangellia terranes, and Early Cretaceous deformation in northern Alaska (early Brookian orogeny) show that within-terrane amalgamation events occurred prior to assembly of Alaska. Widespread episodes of deformation in the Late Cretaceous and early Cenozoic, in contrast, affected multiple terranes, indicating they occurred during or following the time of assembly of most of Alaska.The primary deformational event in northern Alaska was the Late Jurassic and Early Cretaceous (early) Brookian orogeny, which affected most terranes north and west of the early Cenozoic Tintina, Victoria Creek, Kaltag, and Poorman dextral-slip faults in central Alaska. In southern Alaska, formation of the southern Alaska accretionary complex (Chugach, Prince William, Yakutat terranes) and associated magmatism in the Peninsular-Wrangellia terrane began near the Triassic-Jurassic boundary and continued episodically throughout the remainder of the Mesozoic and the Cenozoic. The collision of these terranes with the Farewell and Yukon Composite terranes in central Alaska is recorded by contractional deformation that emanated from the intervening basins in the Late Cretaceous. The boundary between northern and central Alaska is constrained to late Early Cretaceous but is enigmatic and not obviously marked by contractional deformation. Early Cenozoic shortening and transpressional deformation is the most widespread event recorded in Alaska and produced the widespread late Brookian orogenic event in northern Alaska. Middle and late Cenozoic shortening and transpression is significant in southern Alaska inboard of the underthrusting Yakutat terrane at the Pacific margin subduction zone as well as in northeastern Alaska.

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

PubMed

Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Functional mapping of quantitative trait loci associated with rice tillering.

PubMed

Liu, G F; Li, M; Wen, J; Du, Y; Zhang, Y-M

2010-10-01

Several biologically significant parameters that are related to rice tillering are closely associated with rice grain yield. Although identification of the genes that control rice tillering and therefore influence crop yield would be valuable for rice production management and genetic improvement, these genes remain largely unidentified. In this study, we carried out functional mapping of quantitative trait loci (QTLs) for rice tillering in 129 doubled haploid lines, which were derived from a cross between IR64 and Azucena. We measured the average number of tillers in each plot at seven developmental stages and fit the growth trajectory of rice tillering with the Wang-Lan-Ding mathematical model. Four biologically meaningful parameters in this model--the potential maximum for tiller number (K), the optimum tiller time (t(0)), and the increased rate (r), or the reduced rate (c) at the time of deviation from t(0)--were our defined variables for multi-marker joint analysis under the framework of penalized maximum likelihood, as well as composite interval mapping. We detected a total of 27 QTLs that accounted for 2.49-8.54% of the total phenotypic variance. Nine common QTLs across multi-marker joint analysis and composite interval mapping showed high stability, while one QTL was environment-specific and three were epistatic. We also identified several genomic segments that are associated with multiple traits. Our results describe the genetic basis of rice tiller development, enable further marker-assisted selection in rice cultivar development, and provide useful information for rice production management.

Mapping soil texture targeting predefined depth range or synthetizing from standard layers?

NASA Astrophysics Data System (ADS)

Laborczi, Annamária; Dezső Kaposi, András; Szatmári, Gábor; Takács, Katalin; Pásztor, László

2017-04-01

There are increasing demands nowadays on spatial soil information in order to support environmental related and land use management decisions. Physical soil properties, especially particle size distribution play important role in this context. A few of the requirements can be satisfied by the sand-, silt-, and clay content maps compiled according to global standards such as GlobalSoilMap (GSM) or Soil Grids. Soil texture classes (e. g. according to USDA classification) can be derived from these three fraction data, in this way texture map can be compiled based on the proper separate maps. Soil texture class as well as fraction information represent direct input of crop-, meteorological- and hydrological models. The model inputs frequently require maps representing soil features of 0-30 cm depth, which is covered by three consecutive depth intervals according to standard specifications: 0-5 cm, 5-15 cm, 15-30 cm. Becoming GSM and SoilGrids the most detailed freely available spatial soil data sources, the common model users (e. g. meteorologists, agronomists, or hydrologists) would produce input map from (the weighted mean of) these three layers. However, if the basic soil data and proper knowledge is obtainable, a soil texture map targeting directly the 0-30 cm layer could be independently compiled. In our work we compared Hungary's soil texture maps compiled using the same reference and auxiliary data and inference methods but for differing layer distribution. We produced the 0-30 cm clay, silt and sand map as well as the maps for the three standard layers (0-5 cm, 5-15 cm, 15-30 cm). Maps of sand, silt and clay percentage were computed through regression kriging (RK) applying Additive Log-Ratio (alr) transformation. In addition to the Hungarian Soil Information and Monitoring System as reference soil data, digital elevation model and its derived components, soil physical property maps, remotely sensed images, land use -, geological-, as well as meteorological data were applied as auxiliary variables. We compared the directly compiled and the synthetized clay-, sand content, and texture class maps by different tools. In addition to pairwise comparison of basic statistical features (histograms, scatter plots), we examined the spatial distribution of the differences. We quantified the taxonomical distances of the textural classes, in order to investigate the differences of the map-pairs. We concluded that the directly computed and the synthetized maps show various differences. In the case of clay-, and sand content maps, the map-pairs have to be considered statistically different. On the other hand, the differences of the texture class maps are not significant. However, in all cases, the differences rather concern the extreme ranges and categories. Using of synthetized maps can intensify extremities by error propagation in models and scenarios. Based on our results, we suggest the usage of the directly composed maps.

Effects of spectrometer band pass, sampling, and signal-to-noise ratio on spectral identification using the Tetracorder algorithm

USGS Publications Warehouse

Swayze, G.A.; Clark, R.N.; Goetz, A.F.H.; Chrien, T.H.; Gorelick, N.S.

2003-01-01

Estimates of spectrometer band pass, sampling interval, and signal-to-noise ratio required for identification of pure minerals and plants were derived using reflectance spectra convolved to AVIRIS, HYDICE, MIVIS, VIMS, and other imaging spectrometers. For each spectral simulation, various levels of random noise were added to the reflectance spectra after convolution, and then each was analyzed with the Tetracorder spectra identification algorithm [Clark et al., 2003]. The outcome of each identification attempt was tabulated to provide an estimate of the signal-to-noise ratio at which a given percentage of the noisy spectra were identified correctly. Results show that spectral identification is most sensitive to the signal-to-noise ratio at narrow sampling interval values but is more sensitive to the sampling interval itself at broad sampling interval values because of spectral aliasing, a condition when absorption features of different materials can resemble one another. The band pass is less critical to spectral identification than the sampling interval or signal-to-noise ratio because broadening the band pass does not induce spectral aliasing. These conclusions are empirically corroborated by analysis of mineral maps of AVIRIS data collected at Cuprite, Nevada, between 1990 and 1995, a period during which the sensor signal-to-noise ratio increased up to sixfold. There are values of spectrometer sampling and band pass beyond which spectral identification of materials will require an abrupt increase in sensor signal-to-noise ratio due to the effects of spectral aliasing. Factors that control this threshold are the uniqueness of a material's diagnostic absorptions in terms of shape and wavelength isolation, and the spectral diversity of the materials found in nature and in the spectral library used for comparison. Array spectrometers provide the best data for identification when they critically sample spectra. The sampling interval should not be broadened to increase the signal-to-noise ratio in a photon-noise-limited system when high levels of accuracy are desired. It is possible, using this simulation method, to select optimum combinations of band-pass, sampling interval, and signal-to-noise ratio values for a particular application that maximize identification accuracy and minimize the volume of imaging data.

Geologic map of Ophir and central Candor Chasmata (MTM -05072) of Mars

USGS Publications Warehouse

Lucchitta, Baerbel K.

1999-01-01

The geologic map of Ophir and central Candor Chasmata is one of a series of 1:500,000 scale maps prepared for areas on Mars that are of particular scientific interest and may serve as potential future landing sites. This map is also part of a set that includes east Candor Chasma, west Candor Chasma, and Melas Chasma. The geologic interpretations are based dominantly on medium- and high-resolution Viking images, many of them stereoscopic, and supplemented by lower resolution apoapsis and other color images. A strip of very high resolution stereoscopic images (~20 m/pixel) crosses the central part of the quadrangle from northwest to southeast and served to clarify detailed relations not obvious on other images. A topographic map with contour intervals of 200 m was also used, as were multidirectional oblique images derived from merged image mosaics and topography (see fig. 1) (Bertolini and McEwen, 1990). Geologic relations and interpretations are based on the entire central Valles Marineris map set. The map area is included in the Valles Marineris map of Witbeck and others (1991), but units were defined independently. Age assignments, however, were integrated with those by Witbeck and others and Scott and Tanaka (1986).

CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease

PubMed Central

Bhatnagar, Vibha; Garcia, Erin P.; O’Connor, Daniel T.; Brophy, Victoria H.; Alcaraz, John; Richard, Erin; Bakris, George L.; Middleton, John P.; Norris, Keith C.; Wright, Jackson; Hiremath, Leena; Contreras, Gabriel; Appel, Lawrence J.; Lipkowitz, Michael S.

2010-01-01

Purpose To explore the association between CYP3A4 and CYP3A5 gene polymorphisms and blood pressure response to amlodipine among participants from the African-American Study of Kidney Disease and Hypertension Trial randomized to amlodipine (n = 164). Methods Cox proportional hazards models were used to determine the risk of reaching a target mean arterial pressure (MAP) of ≤107 mm Hg by CYP3A4 (A–392G and T16090C) and CYP3A5 (A6986G) gene polymorphisms, stratified by MAP randomization group (low or usual) and controlling for other predictors for blood pressure response. Results Women randomized to a usual MAP goal with an A allele at CYP3A4 A–392G were more likely to reach a target MAP of 107 mm Hg. The adjusted hazard ratio (AA/AG compared to GG) with 95% confidence interval was 3.41 (1.20–9.64; p = 0.020). Among participants randomized to a lower MAP goal, those with the C allele at CYP3A4 T16090C were more likely to reach target MAP: The adjusted hazard ratio was 2.04 (1.17–3.56; p = 0.010). After adjustment for multiple testing using a threshold significance level of p = 0.016, only the CYP3A4 T16090C SNP remained significant. CYP3A5 A6986G was not associated with blood pressure response. Conclusions Our findings suggest that blood pressure response to amlodipine among high-risk African-Americans appears to be determined by CYP3A4 genotypes, and sex specificity may be an important consideration. Clinical applications of CYP3A4 genotype testing for individualized treatment regimens warrant further study. PMID:19907160

A contiguous clone map over 3 Mb on the long arm of chromosome 11 across a balanced translocation associated with schizophrenia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, K.L.; Shibasaki, Yoshiro; Devon, R.S.

1995-08-10

Forty-nine clones derived by microdissection of a schizophrenia-associated t(1;11)(q42.1;q14.3) breakpoint region have been assigned by somatic cell hybrid mapping to seven discrete intervals on the long arm of human chromosome 11. Eleven of the clones were shown to map to a small region immediately distal to the translocation breakpoint on 11q. A 3-Mb contiguous clone map of this region was established by isolation of corresponding YAC recombinants. The contig was oriented and shown to traverse the translocation breakpoint by FISH and microsatellite marker analysis. This contig will facilitate the isolation of candidate sequences whose expression may be affected by themore » translocation. 28 refs., 4 figs., 3 tabs.« less

Quantitative assessment of the T2 relaxation time of the gluteus muscles in children with Duchenne muscular dystrophy: a comparative study before and after steroid treatment.

PubMed

Kim, Hee Kyung; Laor, Tal; Horn, Paul S; Wong, Brenda

2010-01-01

To determine the feasibility of using T2 mapping as a quantitative method to longitudinally follow the disease activity in children with Duchenne muscular dystrophy (DMD) who are treated with steroids. ELEVEN BOYS WITH DMD (AGE RANGE: 5-14 years) underwent evaluation with the clinical functional score (CFS), and conventional pelvic MRI and T2 mapping before and during steroid therapy. The gluteus muscle inflammation and fatty infiltration were evaluated on conventional MRI. The histograms and mean T2 relaxation times were obtained from the T2 maps. The CFS, the conventional MRI findings and the T2 values were compared before and during steroid therapy. None of the patients showed interval change of their CFSs. On conventional MRI, none of the images showed muscle inflammation. During steroid treatment, two boys showed increased fatty infiltration on conventional MRI, and both had an increase of the mean T2 relaxation time (p < 0.05). The remaining nine boys had no increase in fatty infiltration. Of these, three showed an increased mean T2 relaxation time (p < 0.05), two showed no change and four showed a decreased mean T2 relaxation time (p < 0.05). T2 mapping is a feasible technique to evaluate the longitudinal muscle changes in those children who receive steroid therapy for DMD. The differences of the mean T2 relaxation time may reflect alterations in disease activity, and even when the conventional MRI and CFS remain stable.

Integration of InSAR and GIS in the Study of Surface Faults Caused by Subsidence-Creep-Fault Processes in Celaya, Guanajuato, Mexico

NASA Astrophysics Data System (ADS)

Avila-Olivera, Jorge A.; Farina, Paolo; Garduño-Monroy, Victor H.

2008-05-01

In Celaya city, Subsidence-Creep-Fault Processes (SCFP) began to become visible at the beginning of the 1980s with the sprouting of the crackings that gave rise to the surface faults "Oriente" and "Poniente". At the present time, the city is being affected by five surface faults that display a preferential NNW-SSE direction, parallel to the regional faulting system "Taxco-San Miguel de Allende". In order to study the SCFP in the city, the first step was to obtain a map of surface faults, by integrating in a GIS field survey and an urban city plan. The following step was to create a map of the current phreatic level decline in city with the information of deep wells and using the "kriging" method in order to obtain a continuous surface. Finally the interferograms maps resulted of an InSAR analysis of 9 SAR images covering the time interval between July 12 of 2003 and May 27 of 2006 were integrated to a GIS. All the maps generated, show how the surface faults divide the city from North to South, in two zones that behave in a different way. The difference of the phreatic level decline between these two zones is 60 m; and the InSAR study revealed that the Western zone practically remains stable, while sinkings between the surface faults "Oriente" and "Universidad Pedagógica" are present, as well as in portions NE and SE of the city, all of these sinkings between 7 and 10 cm/year.

Application of Modern Design of Experiments to CARS Thermometry in a Model Scramjet Engine

NASA Technical Reports Server (NTRS)

Danehy, P. M.; DeLoach, R.; Cutler, A. D.

2002-01-01

We have applied formal experiment design and analysis to optimize the measurement of temperature in a supersonic combustor at NASA Langley Research Center. We used the coherent anti-Stokes Raman spectroscopy (CARS) technique to map the temperature distribution in the flowfield downstream of an 1160 K, Mach 2 freestream into which supersonic hydrogen fuel is injected at an angle of 30 degrees. CARS thermometry is inherently a single-point measurement technique; it was used to map thc flow by translating the measurement volume through the flowfield. The method known as "Modern Design of Experiments" (MDOE) was used to estimate the data volume required, design the test matrix, perform the experiment and analyze the resulting data. MDOE allowed us to match the volume of data acquired to the precision requirements of the customer. Furthermore, one aspect of MDOE, known as response surface methodology, allowed us to develop precise maps of the flowfield temperature, allowing interpolation between measurement points. An analytic function in two spatial variables was fit to the data from a single measurement plane. Fitting with a Cosine Series Bivariate Function allowed the mean temperature to be mapped with 95% confidence interval half-widths of +/- 30 Kelvin, comfortably meeting the confidence of +/- 50 Kelvin specified prior to performing the experiments. We estimate that applying MDOE to the present experiment saved a factor of 5 in data volume acquired, compared to experiments executed in the traditional manner. Furthermore, the precision requirements could have been met with less than half the data acquired.

High-order computer-assisted estimates of topological entropy

NASA Astrophysics Data System (ADS)

Grote, Johannes

The concept of Taylor Models is introduced, which offers highly accurate C0-estimates for the enclosures of functional dependencies, combining high-order Taylor polynomial approximation of functions and rigorous estimates of the truncation error, performed using verified interval arithmetic. The focus of this work is on the application of Taylor Models in algorithms for strongly nonlinear dynamical systems. A method to obtain sharp rigorous enclosures of Poincare maps for certain types of flows and surfaces is developed and numerical examples are presented. Differential algebraic techniques allow the efficient and accurate computation of polynomial approximations for invariant curves of certain planar maps around hyperbolic fixed points. Subsequently we introduce a procedure to extend these polynomial curves to verified Taylor Model enclosures of local invariant manifolds with C0-errors of size 10-10--10 -14, and proceed to generate the global invariant manifold tangle up to comparable accuracy through iteration in Taylor Model arithmetic. Knowledge of the global manifold structure up to finite iterations of the local manifold pieces enables us to find all homoclinic and heteroclinic intersections in the generated manifold tangle. Combined with the mapping properties of the homoclinic points and their ordering we are able to construct a subshift of finite type as a topological factor of the original planar system to obtain rigorous lower bounds for its topological entropy. This construction is fully automatic and yields homoclinic tangles with several hundred homoclinic points. As an example rigorous lower bounds for the topological entropy of the Henon map are computed, which to the best knowledge of the authors yield the largest such estimates published so far.

QTL analysis of late blight resistance in a diploid potato family of Solanum phureja x S. stenotomum.

PubMed

Costanzo, S; Simko, I; Christ, B J; Haynes, K G

2005-08-01

Field resistance to Phytophthora infestans (Mont.) de Bary, the causal agent of late blight in potatoes, has been characterized in a potato segregating family of 230 full-sib progenies derived from a cross between two hybrid Solanum phureja x S. stenotomum clones. The distribution of area under the disease progress curve values, measured in different years and locations, was consistent with the inheritance of multigenic resistance. Relatively high levels of resistance and transgressive segregations were also observed within this family. A genetic linkage map of this population was constructed with the intent of mapping quantitative trait loci (QTLs) associated with this late blight field resistance. A total of 132 clones from this family were genotyped based on 162 restriction fragment length polymorphism (RFLP) markers. The genome coverage by the map (855.2 cM) is estimated to be at least 70% and includes 112 segregating RFLP markers and two phenotypic markers, with an average distance of 7.7 cM between two markers. Two methods were employed to determine trait-marker association, the non-parametric Kruskal-Wallis test and interval mapping analysis. Three major QTLs were detected on linkage group III, V, and XI, explaining 23, 17, and 10%, respectively, of the total phenotypic variation. The present study revealed the presence of potentially new genetic loci in this diploid potato family contributing to general resistance against late blight. The identification of these QTLs represents the first step toward their introgression into cultivated tetraploid potato cultivars through marker-assisted selection.

Integration of InSAR and GIS in the Study of Surface Faults Caused by Subsidence-Creep-Fault Processes in Celaya, Guanajuato, Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avila-Olivera, Jorge A.; Instituto de Investigaciones Metalurgicas, Universidad Michoacana de San Nicolas de Hidalgo, C.U., 58030 Morelia, Michoacan; Farina, Paolo

2008-05-07

In Celaya city, Subsidence-Creep-Fault Processes (SCFP) began to become visible at the beginning of the 1980s with the sprouting of the crackings that gave rise to the surface faults 'Oriente' and 'Poniente'. At the present time, the city is being affected by five surface faults that display a preferential NNW-SSE direction, parallel to the regional faulting system 'Taxco-San Miguel de Allende'. In order to study the SCFP in the city, the first step was to obtain a map of surface faults, by integrating in a GIS field survey and an urban city plan. The following step was to create amore » map of the current phreatic level decline in city with the information of deep wells and using the 'kriging' method in order to obtain a continuous surface. Finally the interferograms maps resulted of an InSAR analysis of 9 SAR images covering the time interval between July 12 of 2003 and May 27 of 2006 were integrated to a GIS. All the maps generated, show how the surface faults divide the city from North to South, in two zones that behave in a different way. The difference of the phreatic level decline between these two zones is 60 m; and the InSAR study revealed that the Western zone practically remains stable, while sinkings between the surface faults 'Oriente' and 'Universidad Pedagogica' are present, as well as in portions NE and SE of the city, all of these sinkings between 7 and 10 cm/year.« less

The Simple Map for a Single-null Divertor Tokamak: How to Find the Last Good Surface

NASA Astrophysics Data System (ADS)

Phan, Huong; Ali, Halima; Punjabi, Alkesh

2000-10-01

The Simple Map^1 is a representation of the magnetic field inside a single-null divertor tokamak. It is given by the equations: X_n+1=X_n kYn (1-Y_n), Y_n+1= Y_n+kX_n+1. These equations mimic the motion of the magnetic field lines in a single-null divertor tokamak. The fixed stable point is (0,0) and the unstable fixed oint is (0,1). k is fixed at 0.60. In our work, the starting values of Y in the map is kept in the interval of 0 to 1, and the starting value of X is 0. Using the successive bifurcation method, we first run these equations for 10^6 iterations to find the approximate value of Y when chaos occurs. We examine the neighborhood of this Y value to find the exact value of Y for the last good surface. We call this value Y_lgs. We find Y_lgs to be 0.997135768 for k=0.60 and X=0. This work is supported by US DOE OFES. Ms. Huong Phan is a HU CFRT Summer Fusion High School Workshop Scholar from Andrew P. Hill High School in California. She is supported by NASA SHARP Plus Program. 1. Punjabi A, Verma A and Boozer A, Phys Rev Lett 69 3322 (1992) and J Plasma Phys 52 91 (1994)

Investigating fluvial pattern and delta-planform geometry based on varying intervals of flood and interflood

NASA Astrophysics Data System (ADS)

Rambo, J. E.; Kim, W.; Miller, K.

2017-12-01

Physical modeling of a delta's evolution can represent how changing the intervals of flood and interflood can alter a delta's fluvial pattern and geometry. Here we present a set of six experimental runs in which sediment and water were discharged at constant rates over each experiment. During the "flood" period, both sediment and water were discharged at rates of 0.25 cm3/s and 15 ml/s respectively, and during the "interflood" period, only water was discharged at 7.5 ml/s. The flood periods were only run for 30 minutes to keep the total volume of sediment constant. Run 0 did not have an interflood period and therefore ran with constant sediment and water discharge for the duration of the experiment.The other five runs had either 5, 10, or 15-min intervals of flood with 5, 10, or 15-min intervals of interflood. The experimental results show that Run 0 had the smallest topset area. This is due to a lack of surface reworking that takes place during interflood periods. Run 1 had 15-minute intervals of flood and 15-minute intervals of interflood, and it had the largest topset area. Additionally, the experiments that had longer intervals of interflood than flood had more elongated delta geometries. Wetted fraction color maps were also created to plot channel locations during each run. The maps show that the runs with longer interflood durations had channels occurring predominantly down the middle with stronger incisions; these runs produced deltas with more elongated geometries. When the interflood duration was even longer, however, strong channels started to occur at multiple locations. This increased interflood period allowed for the entire area over the delta's surface to be reworked, thus reducing the downstream slope and allowing channels to be more mobile laterally. Physical modeling of a delta allows us to predict a delta's resulting geometry given a set of conditions. This insight is needed especially with delta's being the home to many populations of people and a habitat for various other species.

Channel Equalization for Single Carrier MIMO Underwater Acoustic Communications

DTIC Science & Technology

2010-01-01

II Tx 1 Tx 2 Symbol mapping s1 s2 x1 x2 sa Figure 2: Signalling at the transmitter in Makai05 experiment. fc = 32 kHz and the symbol interval was...frequency was fc = 37.5 kHz and the symbol interval was 0.05ms. The occupied channel bandwidth was fb = 25 kHz due to a pulse shaping filter with roll...water. QPSK modulation was used with a symbol rate of 4 ksps. The carrier frequency was fc = 17 kHz. The structure of the transmission packet is

A New Model Based on Adaptation of the External Loop to Compensate the Hysteresis of Tactile Sensors

PubMed Central

Sánchez-Durán, José A.; Vidal-Verdú, Fernando; Oballe-Peinado, Óscar; Castellanos-Ramos, Julián; Hidalgo-López, José A.

2015-01-01

This paper presents a novel method to compensate for hysteresis nonlinearities observed in the response of a tactile sensor. The External Loop Adaptation Method (ELAM) performs a piecewise linear mapping of the experimentally measured external curves of the hysteresis loop to obtain all possible internal cycles. The optimal division of the input interval where the curve is approximated is provided by the error minimization algorithm. This process is carried out off line and provides parameters to compute the split point in real time. A different linear transformation is then performed at the left and right of this point and a more precise fitting is achieved. The models obtained with the ELAM method are compared with those obtained from three other approaches. The results show that the ELAM method achieves a more accurate fitting. Moreover, the involved mathematical operations are simpler and therefore easier to implement in devices such as Field Programmable Gate Array (FPGAs) for real time applications. Furthermore, the method needs to identify fewer parameters and requires no previous selection process of operators or functions. Finally, the method can be applied to other sensors or actuators with complex hysteresis loop shapes. PMID:26501279

High-resolution meiotic and physical mapping of the Best vitelliform macular dystrophy (VMD2) locus to pericentromeric chromosome 11

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, B.H.F.; Vogt, G.; Stoehr, H.

1994-12-01

Best vitelliform macular dystrophy (VMD2) has previously been linked to several microsatellite markers from chromosome 11. Subsequently, additional genetic studies have refined the Best disease region to a 3.7-cM interval flanked by markers at D11S903 and PYGM. To further narrow the interval containing the Best disease gene and to obtain an estimate of the physical size of the minimal candidate region, we used a combination of high-resolution PCR hybrid mapping and analysis of recombinant Best disease chromosomes. We identified six markers from within the D11S903-PYGM interval that show no recombination with the defective gene in three multigeneration Best disease pedigrees.more » Our hybrid panel localizes these markers on either side of the centromere on chromosome 11. The closest markers flanking the disease gene are at D11S986 in band p12-11.22 on the short arm and at D11S480 in band q13.2-13.3 on the proximal long arm. This study demonstrates that the physical size of the Best disease region is exceedingly larger than previously estimated from the genetic data, because of the proximity of the defective gene to the centromere of chromosome 11.« less

Development of genic cleavage markers in association with seed glucosinolate content in canola.

PubMed

Fu, Ying; Lu, Kun; Qian, Lunwen; Mei, Jiaqin; Wei, Dayong; Peng, Xuhui; Xu, Xinfu; Li, Jiana; Frauen, Martin; Dreyer, Felix; Snowdon, Rod J; Qian, Wei

2015-06-01

The orthologues of Arabidopsis involved in seed glucosinolates metabolism within QTL confidence intervals were identified, and functional markers were developed to facilitate breeding for ultra-low glucosinolates in canola. Further reducing the content of seed glucosinolates will have a positive impact on the seed quality of canola (Brassica napus). In this study 43 quantitative trait loci (QTL) for seed glucosinolate (GSL) content in a low-GSL genetic background were mapped over seven environments in Germany and China in a doubled haploid population from a cross between two low-GSL oilseed rape parents with transgressive segregation. By anchoring these QTL to the reference genomes of B. rapa and B. oleracea, we identified 23 orthologues of Arabidopsis involved in GSL metabolism within the QTL confidence intervals. Sequence polymorphisms between the corresponding coding regions of the parental lines were used to develop cleaved amplified polymorphic site markers for two QTL-linked genes, ISOPROPYLMALATE DEHYDROGENASE1 and ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE 3. The genic cleavage markers were mapped in the DH population into the corresponding intervals of QTL explaining 3.36-6.88 and 4.55-8.67 % of the phenotypic variation for seed GSL, respectively. The markers will facilitate breeding for ultra-low seed GSL content in canola.

Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon.

PubMed

Xie, Xiaobo; Song, Mi-Hee; Jin, Fengxue; Ahn, Sang-Nag; Suh, Jung-Pil; Hwang, Hung-Goo; McCouch, S R

2006-09-01

A quantitative trait locus (QTL) for grain weight (GW) was detected near SSR marker RM210 on chromosome 8 in backcross populations derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491). The O. rufipogon allele increased GW in the Hwaseongbyeo background despite the fact that O. rufipogon was the small-seeded parent. Using sister BC(3)F(3) near-isogenic lines (NILs), gw8.1 was validated and mapped to a 6.1 cM region in the interval between RM42 and RM210 (P < or = 0.0001). Substitution mapping with eight BC(3)F(4) sub-NILs further narrowed the interval containing gw8.1 to about 306.4 kb between markers RM23201.CNR151 and RM30000.CNR99. A yield trial using homozygous BC(3)F(4) sister sub-NILs and the Hwaseongbyeo recurrent parent indicated that the NIL carrying an O. rufipogon chromosome segment across the entire gw8.1 target region out-yielded its sister NIL (containing Hwaseongbyeo chromosome in the RM42-RM210 interval) by 9% (P=0.029). The higher-yielding NIL produced 19.3% more grain than the Hwaseongbyeo recurrent parent (P=0.018). Analysis of a BC(3)F(4) NIL indicated that the variation for GW is associated with variation in grain shape, specifically grain length. The locus, gw8.1 is of particular interest because of its independence from undesirable height and grain quality traits. SSR markers tightly linked to the GW QTL will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in GW in an applied breeding program.

Pharmacokinetics and electrophysiological effects of sotalol hydrochloride in horses.

PubMed

Broux, B; De Clercq, D; Decloedt, A; Vera, L; Devreese, M; Gehring, R; Croubels, S; van Loon, G

2018-05-01

Arrhythmias in horses may require long-term anti-arrhythmic therapy. Unfortunately, oral anti-arrhythmic drugs for use in horses are currently scarce. In human patients and small animals, sotalol, a β-blocker with class III anti-arrhythmic properties, is often used for long-term treatment. To determine the pharmacokinetics of sotalol at multiple oral dosages in unfasted horses, as well as the effects on electro- and echocardiographic measurements, right atrial and ventricular monophasic action potential (MAP) and effective refractory period (ERP). Placebo controlled, double-blinded experiment. Six healthy, unfasted Warmblood horses were given either 0, 2, 3 or 4 mg/kg bodyweight (bwt) sotalol orally (PO) twice daily (bid) for 9 days in a randomised cross-over design. Echocardiography and surface electrocardiography were performed and plasma concentrations of sotalol and right atrial and right ventricular MAPs and ERPs were determined at steady-state conditions. Statistical analysis was performed using a repeated measures univariate analysis with post hoc Bonferroni corrections. Calculated mean steady-state plasma concentrations determined by nonlinear mixed-effect modelling were 287 (range 234-339), 409 (359-458) and 543 (439-646) ng/mL for 2, 3 and 4 mg/kg bwt sotalol PO bid respectively. Sotalol significantly increased the QT interval and ERPs, but, despite increasing plasma concentrations, higher dosages did not result in a progressive increase in QT interval or ERPs. Echocardiographic and other electrocardiographic measurements did not change significantly. MAP durations at 90% repolarisation were not significantly different during sotalol treatment. Besides transient local sweating, no side effects were noted. Study size and ad libitum feeding of hay. Sotalol at a dose of 2, 3 and 4 mg/kg bwt PO bid increases the QT interval and ERP and might be a useful drug for long-term anti-arrhythmic therapy in horses. © 2017 EVJ Ltd.

PHYSICAL CONDITIONS OF CORONAL PLASMA AT THE TRANSIT OF A SHOCK DRIVEN BY A CORONAL MASS EJECTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Susino, R.; Bemporad, A.; Mancuso, S., E-mail: susino@oato.inaf.it

2015-10-20

We report here on the determination of plasma physical parameters across a shock driven by a coronal mass ejection using white light (WL) coronagraphic images and radio dynamic spectra (RDS). The event analyzed here is the spectacular eruption that occurred on 2011 June 7, a fast CME followed by the ejection of columns of chromospheric plasma, part of them falling back to the solar surface, associated with a M2.5 flare and a type-II radio burst. Images acquired by the Solar and Heliospheric Observatory/LASCO coronagraphs (C2 and C3) were employed to track the CME-driven shock in the corona between 2–12 R{submore » ⊙} in an angular interval of about 110°. In this interval we derived two-dimensional (2D) maps of electron density, shock velocity, and shock compression ratio, and we measured the shock inclination angle with respect to the radial direction. Under plausible assumptions, these quantities were used to infer 2D maps of shock Mach number M{sub A} and strength of coronal magnetic fields at the shock's heights. We found that in the early phases (2–4 R{sub ⊙}) the whole shock surface is super-Alfvénic, while later on (i.e., higher up) it becomes super-Alfvénic only at the nose. This is in agreement with the location for the source of the observed type-II burst, as inferred from RDS combined with the shock kinematic and coronal densities derived from WL. For the first time, a coronal shock is used to derive a 2D map of the coronal magnetic field strength over intervals of 10 R{sub ⊙} altitude and ∼110° latitude.« less

Interval sampling methods and measurement error: a computer simulation.

PubMed

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

Constraint-based Attribute and Interval Planning

NASA Technical Reports Server (NTRS)

Jonsson, Ari; Frank, Jeremy

2013-01-01

In this paper we describe Constraint-based Attribute and Interval Planning (CAIP), a paradigm for representing and reasoning about plans. The paradigm enables the description of planning domains with time, resources, concurrent activities, mutual exclusions among sets of activities, disjunctive preconditions and conditional effects. We provide a theoretical foundation for the paradigm, based on temporal intervals and attributes. We then show how the plans are naturally expressed by networks of constraints, and show that the process of planning maps directly to dynamic constraint reasoning. In addition, we de ne compatibilities, a compact mechanism for describing planning domains. We describe how this framework can incorporate the use of constraint reasoning technology to improve planning. Finally, we describe EUROPA, an implementation of the CAIP framework.

Measuring Scale Errors in a Laser Tracker’s Horizontal Angle Encoder Through Simple Length Measurement and Two-Face System Tests

PubMed Central

Muralikrishnan, B.; Blackburn, C.; Sawyer, D.; Phillips, S.; Bridges, R.

2010-01-01

We describe a method to estimate the scale errors in the horizontal angle encoder of a laser tracker in this paper. The method does not require expensive instrumentation such as a rotary stage or even a calibrated artifact. An uncalibrated but stable length is realized between two targets mounted on stands that are at tracker height. The tracker measures the distance between these two targets from different azimuthal positions (say, in intervals of 20° over 360°). Each target is measured in both front face and back face. Low order harmonic scale errors can be estimated from this data and may then be used to correct the encoder’s error map to improve the tracker’s angle measurement accuracy. We have demonstrated this for the second order harmonic in this paper. It is important to compensate for even order harmonics as their influence cannot be removed by averaging front face and back face measurements whereas odd orders can be removed by averaging. We tested six trackers from three different manufacturers. Two of those trackers are newer models introduced at the time of writing of this paper. For older trackers from two manufacturers, the length errors in a 7.75 m horizontal length placed 7 m away from a tracker were of the order of ± 65 μm before correcting the error map. They reduced to less than ± 25 μm after correcting the error map for second order scale errors. Newer trackers from the same manufacturers did not show this error. An older tracker from a third manufacturer also did not show this error. PMID:27134789

Proximity to crops and residential to agricultural herbicides in Iowa

USGS Publications Warehouse

Ward, M.H.; Lubin, J.; Giglierano, J.; Colt, J.S.; Wolter, C.; Bekiroglu, N.; Camann, D.; Hartge, P.; Nuckols, J.R.

2006-01-01

Rural residents can be exposed to agricultural pesticides through the proximity of their homes to crop fields. Previously, we developed a method to create historical crop maps using a geographic information system. The aim of the present study was to determine whether crop maps are useful for predicting levels of crop herbicides in carpet dust samples from residences. From homes of participants in a case-control study of non-Hodgkin lymphoma in Iowa (1998-2000), we collected vacuum cleaner dust and measured 14 herbicides with high use on corn and soybeans in Iowa. Of 112 homes, 58% of residences had crops within 500 m of their home, an intermediate distance for primary drift from aerial and ground applications. Detection rates for herbicides ranged from 0% for metribuzin and cyanazine to 95% for 2,4-dichlorophenoxyacetic acid. Six herbicides used almost exclusively in agriculture were detected in 28% of homes. Detections and concentrations were highest in homes with an active farmer. Increasing acreage of corn and soybean fields within 750 m of homes was associated with significantly elevated odds of detecting agricultural herbicides compared with homes with no crops within 750 m (adjusted odds ratio per 10 acres = 1.06; 95% confidence interval, 1.02-1.11). Herbicide concentrations also increased significantly with increasing acreage within 750 m. We evaluated the distance of crop fields from the home at < 100, 101-250, 251-500, and 501-750 m. Including the crop buffer distance parameters in the model did not significantly improve the fit compared with a model with total acres within 750 m. Our results indicate that crop maps may be a useful method for estimating levels of herbicides in homes from nearby crop fields.

Estimating Unbiased Land Cover Change Areas In The Colombian Amazon Using Landsat Time Series And Statistical Inference Methods

NASA Astrophysics Data System (ADS)

Arevalo, P. A.; Olofsson, P.; Woodcock, C. E.

2017-12-01

Unbiased estimation of the areas of conversion between land categories ("activity data") and their uncertainty is crucial for providing more robust calculations of carbon emissions to the atmosphere, as well as their removals. This is particularly important for the REDD+ mechanism of UNFCCC where an economic compensation is tied to the magnitude and direction of such fluxes. Dense time series of Landsat data and statistical protocols are becoming an integral part of forest monitoring efforts, but there are relatively few studies in the tropics focused on using these methods to advance operational MRV systems (Monitoring, Reporting and Verification). We present the results of a prototype methodology for continuous monitoring and unbiased estimation of activity data that is compliant with the IPCC Approach 3 for representation of land. We used a break detection algorithm (Continuous Change Detection and Classification, CCDC) to fit pixel-level temporal segments to time series of Landsat data in the Colombian Amazon. The segments were classified using a Random Forest classifier to obtain annual maps of land categories between 2001 and 2016. Using these maps, a biannual stratified sampling approach was implemented and unbiased stratified estimators constructed to calculate area estimates with confidence intervals for each of the stable and change classes. Our results provide evidence of a decrease in primary forest as a result of conversion to pastures, as well as increase in secondary forest as pastures are abandoned and the forest allowed to regenerate. Estimating areas of other land transitions proved challenging because of their very small mapped areas compared to stable classes like forest, which corresponds to almost 90% of the study area. Implications on remote sensing data processing, sample allocation and uncertainty reduction are also discussed.

Comparing the Effect of Thinking Maps Training Package Developed by the Thinking Maps Method on the Reading Performance of Dyslexic Students.

PubMed

Faramarzi, Salar; Moradi, Mohammadreza; Abedi, Ahmad

2018-06-01

The present study aimed to develop the thinking maps training package and compare its training effect with the thinking maps method on the reading performance of second and fifth grade of elementary school male dyslexic students. For this mixed method exploratory study, from among the above mentioned grades' students in Isfahan, 90 students who met the inclusion criteria were selected by multistage sampling and randomly assigned into six experimental and control groups. The data were collected by reading and dyslexia test and Wechsler Intelligence Scale for Children-fourth edition. The results of covariance analysis indicated a significant difference between the reading performance of the experimental (thinking maps training package and thinking maps method groups) and control groups ([Formula: see text]). Moreover, there were significant differences between the thinking maps training package group and thinking maps method group in some of the subtests ([Formula: see text]). It can be concluded that thinking maps training package and the thinking maps method exert a positive influence on the reading performance of dyslexic students; therefore, thinking maps can be used as an effective training and treatment method.

Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.

PubMed

Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San

2016-07-01

Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes. Copyright © 2016 Elsevier Inc. All rights reserved.

Carotid-femoral pulse wave velocity in a healthy adult sample: The ELSA-Brasil study.

PubMed

Baldo, Marcelo Perim; Cunha, Roberto S; Molina, Maria Del Carmen B; Chór, Dora; Griep, Rosane H; Duncan, Bruce B; Schmidt, Maria Inês; Ribeiro, Antonio L P; Barreto, Sandhi M; Lotufo, Paulo A; Bensenor, Isabela M; Pereira, Alexandre C; Mill, José Geraldo

2018-01-15

Aging declines essential physiological functions, and the vascular system is strongly affected by artery stiffening. We intended to define the age- and sex-specific reference values for carotid-to-femoral pulse wave velocity (cf-PWV) in a sample free of major risk factors. The ELSA-Brasil study enrolled 15,105 participants aged 35-74years. The healthy sample was achieved by excluding diabetics, those over the optimal and normal blood pressure levels, body mass index ≤18.5 or ≥25kg/m 2 , current and former smokers, and those with self-report of previous cardiovascular disease. After exclusions, the sample consisted of 2158 healthy adults (1412 women). Although cf-PWV predictors were similar between sex (age, mean arterial pressure (MAP) and heart rate), cf-PWV was higher in men (8.74±1.15 vs. 8.31±1.13m/s; adjusted for age and MAP, P<0.001) for all age intervals. When divided by MAP categories, cf-PWV was significantly higher in those which MAP ≥85mmHg, regardless of sex, and for all age intervals. Risk factors for arterial stiffening in the entire ELSA-Brasil population (n=15,105) increased by twice the age-related slope of cf-PWV growth, regardless of sex (0.0919±0.182 vs. 0.0504±0.153m/s per year for men, 0.0960±0.173 vs. 0.0606±0.139m/s per year for women). cf-PWV is different between men and women and even in an optimal and normal range of MAP and free of other classical risk factors for arterial stiffness, reference values for cf-PWV should take into account MAP levels. Also, the presence of major risk factors in the general population doubles the age-related rise in cf-PWV. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

PubMed

Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

2014-10-01

Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

Intervals for posttest probabilities: a comparison of 5 methods.

PubMed

Mossman, D; Berger, J O

2001-01-01

Several medical articles discuss methods of constructing confidence intervals for single proportions and the likelihood ratio, but scant attention has been given to the systematic study of intervals for the posterior odds, or the positive predictive value, of a test. The authors describe 5 methods of constructing confidence intervals for posttest probabilities when estimates of sensitivity, specificity, and the pretest probability of a disorder are derived from empirical data. They then evaluate each method to determine how well the intervals' coverage properties correspond to their nominal value. When the estimates of pretest probabilities, sensitivity, and specificity are derived from more than 80 subjects and are not close to 0 or 1, all methods generate intervals with appropriate coverage properties. When these conditions are not met, however, the best-performing method is an objective Bayesian approach implemented by a simple simulation using a spreadsheet. Physicians and investigators can generate accurate confidence intervals for posttest probabilities in small-sample situations using the objective Bayesian approach.

Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis

PubMed Central

Khowaja, Farkhanda S; Norton, Gareth J; Courtois, Brigitte; Price, Adam H

2009-01-01

Background Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought related QTLs in the Bala × Azucena mapping population compiles data from 13 experiments and 25 independent screens providing 1,650 individual QTLs separated into 5 trait categories; drought avoidance, plant height, plant biomass, leaf morphology and root traits. A heat map of the overlapping 1 LOD confidence intervals provides an overview of the distribution of QTLs. The programme BioMercator is then used to conduct a formal meta-analysis at example QTL clusters to illustrate the value of meta-analysis of QTLs in this population. Results The heat map graphically illustrates the genetic complexity of drought related traits in rice. QTLs can be linked to their physical position on the rice genome using Additional file 1 provided. Formal meta-analysis on chromosome 1, where clusters of QTLs for all trait categories appear close, established that the sd1 semi-dwarfing gene coincided with a plant height meta-QTL, that the drought avoidance meta-QTL was not likely to be associated with this gene, and that this meta-QTL was not pleiotropic with close meta-QTLs for leaf morphology and root traits. On chromosome 5, evidence suggests that a drought avoidance meta-QTL was pleiotropic with leaf morphology and plant biomass meta-QTLs, but not with meta-QTLs for root traits and plant height 10 cM lower down. A region of dense root QTL activity graphically visible on chromosome 9 was dissected into three meta-QTLs within a space of 35 cM. The confidence intervals for meta-QTLs obtained ranged from 5.1 to 14.5 cM with an average of 9.4 cM, which is approximately 180 genes in rice. Conclusion The meta-analysis is valuable in providing improved ability to dissect the complex genetic structure of traits, and distinguish between pleiotropy and close linkage. It also provides relatively small target regions for the identification of positional candidate genes. PMID:19545420

Comparing the Performance of Japan's Earthquake Hazard Maps to Uniform and Randomized Maps

NASA Astrophysics Data System (ADS)

Brooks, E. M.; Stein, S. A.; Spencer, B. D.

2015-12-01

The devastating 2011 magnitude 9.1 Tohoku earthquake and the resulting shaking and tsunami were much larger than anticipated in earthquake hazard maps. Because this and all other earthquakes that caused ten or more fatalities in Japan since 1979 occurred in places assigned a relatively low hazard, Geller (2011) argued that "all of Japan is at risk from earthquakes, and the present state of seismological science does not allow us to reliably differentiate the risk level in particular geographic areas," so a map showing uniform hazard would be preferable to the existing map. Defenders of the maps countered by arguing that these earthquakes are low-probability events allowed by the maps, which predict the levels of shaking that should expected with a certain probability over a given time. Although such maps are used worldwide in making costly policy decisions for earthquake-resistant construction, how well these maps actually perform is unknown. We explore this hotly-contested issue by comparing how well a 510-year-long record of earthquake shaking in Japan is described by the Japanese national hazard (JNH) maps, uniform maps, and randomized maps. Surprisingly, as measured by the metric implicit in the JNH maps, i.e. that during the chosen time interval the predicted ground motion should be exceeded only at a specific fraction of the sites, both uniform and randomized maps do better than the actual maps. However, using as a metric the squared misfit between maximum observed shaking and that predicted, the JNH maps do better than uniform or randomized maps. These results indicate that the JNH maps are not performing as well as expected, that what factors control map performance is complicated, and that learning more about how maps perform and why would be valuable in making more effective policy.

X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3

PubMed Central

Bennett, Craig L.; Yoshioka, Ritsuko; Kiyosawa, Hidenori; Barker, David F.; Fain, Pamela R.; Shigeoka, Ann O.; Chance, Phillip F.

2000-01-01

Summary We describe genetic analysis of a large pedigree with an X-linked syndrome of polyendocrinopathy, immune dysfunction, and diarrhea (XPID), which frequently results in death during infancy or childhood. Linkage analysis mapped the XPID gene to a 17-cM interval defined by markers DXS8083 and DXS8107 on the X chromosome, at Xp11.23-Xq13.3. The maximum LOD score was 3.99 (recombination fraction0) at DXS1235. Because this interval also harbors the gene for Wiskott-Aldrich syndrome (WAS), we investigated mutations in the WASP gene, as the molecular basis of XPID. Northern blot analysis detected the same relative amount and the same-sized WASP message in patients with XPID and in a control. Analysis of the WASP coding sequence, an alternate promoter, and an untranslated upstream first exon was carried out, and no mutations were found in patients with XPID. A C→T transition within the alternate translation start site cosegregated with the XPID phenotype in this family; however, the same transition site was detected in a normal control male. We conclude that XPID maps to Xp11.23-Xq13.3 and that mutations of WASP are not associated with XPID. PMID:10677306

Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca).

PubMed

Mariette, Stéphanie; Wong Jun Tai, Fabienne; Roch, Guillaume; Barre, Aurélien; Chague, Aurélie; Decroocq, Stéphane; Groppi, Alexis; Laizet, Yec'han; Lambert, Patrick; Tricon, David; Nikolski, Macha; Audergon, Jean-Marc; Abbott, Albert G; Decroocq, Véronique

2016-01-01

In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm. © 2015 INRA, UMR 1332 BFP New Phytologist © 2015 New Phytologist Trust.

Comparison of the chromosome maps around a resistance hot spot on chromosome 5 of potato and tomato using BAC-FISH painting.

PubMed

Achenbach, Ute C; Tang, Xiaomin; Ballvora, Agim; de Jong, Hans; Gebhardt, Christiane

2010-02-01

Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans. The genes make up part of a "hot spot" for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21-GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21-GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato.

Development of Generation System of Simplified Digital Maps

NASA Astrophysics Data System (ADS)

Uchimura, Keiichi; Kawano, Masato; Tokitsu, Hiroki; Hu, Zhencheng

In recent years, digital maps have been used in a variety of scenarios, including car navigation systems and map information services over the Internet. These digital maps are formed by multiple layers of maps of different scales; the map data most suitable for the specific situation are used. Currently, the production of map data of different scales is done by hand due to constraints related to processing time and accuracy. We conducted research concerning technologies for automatic generation of simplified map data from detailed map data. In the present paper, the authors propose the following: (1) a method to transform data related to streets, rivers, etc. containing widths into line data, (2) a method to eliminate the component points of the data, and (3) a method to eliminate data that lie below a certain threshold. In addition, in order to evaluate the proposed method, a user survey was conducted; in this survey we compared maps generated using the proposed method with the commercially available maps. From the viewpoint of the amount of data reduction and processing time, and on the basis of the results of the survey, we confirmed the effectiveness of the automatic generation of simplified maps using the proposed methods.

Improving 3d Spatial Queries Search: Newfangled Technique of Space Filling Curves in 3d City Modeling

NASA Astrophysics Data System (ADS)

Uznir, U.; Anton, F.; Suhaibah, A.; Rahman, A. A.; Mioc, D.

2013-09-01

The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc.. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using web standards. However, these 3D city models consume much more storage compared to two dimensional (2D) spatial data. They involve extra geometrical and topological information together with semantic data. Without a proper spatial data clustering method and its corresponding spatial data access method, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban objects. In this research, we propose an opponent data constellation technique of space-filling curves (3D Hilbert curves) for 3D city model data representation. Unlike previous methods, that try to project 3D or n-dimensional data down to 2D or 3D using Principal Component Analysis (PCA) or Hilbert mappings, in this research, we extend the Hilbert space-filling curve to one higher dimension for 3D city model data implementations. The query performance was tested using a CityGML dataset of 1,000 building blocks and the results are presented in this paper. The advantages of implementing space-filling curves in 3D city modeling will improve data retrieval time by means of optimized 3D adjacency, nearest neighbor information and 3D indexing. The Hilbert mapping, which maps a subinterval of the [0, 1] interval to the corresponding portion of the d-dimensional Hilbert's curve, preserves the Lebesgue measure and is Lipschitz continuous. Depending on the applications, several alternatives are possible in order to cluster spatial data together in the third dimension compared to its clustering in 2D.

Drawing Road Networks with Mental Maps.

PubMed

Lin, Shih-Syun; Lin, Chao-Hung; Hu, Yan-Jhang; Lee, Tong-Yee

2014-09-01

Tourist and destination maps are thematic maps designed to represent specific themes in maps. The road network topologies in these maps are generally more important than the geometric accuracy of roads. A road network warping method is proposed to facilitate map generation and improve theme representation in maps. The basic idea is deforming a road network to meet a user-specified mental map while an optimization process is performed to propagate distortions originating from road network warping. To generate a map, the proposed method includes algorithms for estimating road significance and for deforming a road network according to various geometric and aesthetic constraints. The proposed method can produce an iconic mark of a theme from a road network and meet a user-specified mental map. Therefore, the resulting map can serve as a tourist or destination map that not only provides visual aids for route planning and navigation tasks, but also visually emphasizes the presentation of a theme in a map for the purpose of advertising. In the experiments, the demonstrations of map generations show that our method enables map generation systems to generate deformed tourist and destination maps efficiently.

Environmental Impact Research Program: Reservoir Bank Erosion and Cultural Resources: Experiments in Mapping and Predicting the Erosion of Archeological Sediments at Reservoirs Along the Middle Missouri River with Sequential Historical Aerial Photographs

DTIC Science & Technology

1989-08-01

points on both the photos and base map. Transects placed at 100-m intervals along the waterline, oriented perpendicular to the gradient or slope just...the identifica- tion of major factors influencing bank erosion, independent variables measured included gradient of the land at the intersection of...have a very steep gradient , approaching vertical in some cases, broken only by intermittent minor drainages which have dissected terrace margins. b

Water table in rocks of Cenozoic and Paleozoic age, 1980, Yucca Flat, Nevada Test Site, Nevada

USGS Publications Warehouse

Doty, G.C.; Thordarson, William

1983-01-01

The water table at Yucca Flat, Nevada Test Site, Nevada, occurs in rocks of Paleozoic age and in tuffs and alluvium of Cenozoic age and ranges in altitude from about 2,425 feet to about 3,500 feet. The configuration of the water table is depicted by contours with intervals of 25 to 500 feet. Control for the map consists of water-level information from 61 drill holes, whose locations and age of geologic units penetrated are shown by symbols on the map. (USGS)

USING DIRECT-PUSH TOOLS TO MAP HYDROSTRATIGRAPHY AND PREDICT MTBE PLUME DIVING

EPA Science Inventory

MTBE plumes have been documented to dive beneath screened intervals of conventional monitoring well networks at a number of LUST sites. This behavior makes these plumes difficult both to detect and remediate. Electrical conductivity logging and pneumatic slug testing performed in...

US LAND-COVER MONITORING AND DETECTION OF CHANGES IN SCALE AND CONTEXT OF FOREST

EPA Science Inventory

Disparate land-cover mapping programs, previously focused solely on mission-oriented goals, have organized themselves as the Multi-Resolution Land Characteristics (MRLC) Consortium with a unified goal of producing land-cover nationwide at routine intervals. Under MRLC, United Sta...

Flood-plain delineation for Occoquan River, Wolf Run, Sandy Run, Elk Horn Run, Giles Run, Kanes Creek, Racoon Creek, and Thompson Creek, Fairfax County, Virginia

USGS Publications Warehouse

Soule, Pat LeRoy

1978-01-01

Water-surface profiles of the 25-, 50-, and 100-year recurrence interval discharges have been computed for all streams and reaches of channels in Fairfax County, Virginia, having a drainage area greater than 1 square mile except for Dogue Creek, Little Hunting Creek, and that portion of Cameron Run above Lake Barcroft. Maps having a 2-foot contour interval and a horizontal scale of 1 inch equals 100 feet were used for base on which flood boundaries were delineated for 25-, 50-, and 100-year floods to be expected in each basin under ultimate development conditions. This report is one of a series and presents a discussion of techniques employed in computing discharges and profiles as well as the flood profiles and maps on which flood boundaries have been delineated for the Occoquan River and its tributaries within Fairfax County and those streams on Mason Neck within Fairfax County tributary to the Potomac River. (Woodard-USGS)

The Calcitonin Receptor Gene Is a Candidate for Regulation of Susceptibility to Herpes simplex Type 1 Neuronal Infection Leading to Encephalitis in Rat

PubMed Central

Abdelmagid, Nada; Bereczky-Veress, Biborka; Guerreiro-Cacais, André Ortlieb; Bergman, Petra; Luhr, Katarina M.; Bergström, Tomas; Sköldenberg, Birgit; Piehl, Fredrik

2012-01-01

Herpes simplex encephalitis (HSE) is a fatal infection of the central nervous system (CNS) predominantly caused by Herpes simplex virus type 1. Factors regulating the susceptibility to HSE are still largely unknown. To identify host gene(s) regulating HSE susceptibility we performed a genome-wide linkage scan in an intercross between the susceptible DA and the resistant PVG rat. We found one major quantitative trait locus (QTL), Hse1, on rat chromosome 4 (confidence interval 24.3–31 Mb; LOD score 29.5) governing disease susceptibility. Fine mapping of Hse1 using recombinants, haplotype mapping and sequencing, as well as expression analysis of all genes in the interval identified the calcitonin receptor gene (Calcr) as the main candidate, which also is supported by functional studies. Thus, using unbiased genetic approach variability in Calcr was identified as potentially critical for infection and viral spread to the CNS and subsequent HSE development. PMID:22761571

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

PubMed Central

Wang, Xinchen; Tucker, Nathan R; Rizki, Gizem; Mills, Robert; Krijger, Peter HL; de Wit, Elzo; Subramanian, Vidya; Bartell, Eric; Nguyen, Xinh-Xinh; Ye, Jiangchuan; Leyton-Mange, Jordan; Dolmatova, Elena V; van der Harst, Pim; de Laat, Wouter; Ellinor, Patrick T; Newton-Cheh, Christopher; Milan, David J; Kellis, Manolis; Boyer, Laurie A

2016-01-01

Genetic variants identified by genome-wide association studies explain only a modest proportion of heritability, suggesting that meaningful associations lie 'hidden' below current thresholds. Here, we integrate information from association studies with epigenomic maps to demonstrate that enhancers significantly overlap known loci associated with the cardiac QT interval and QRS duration. We apply functional criteria to identify loci associated with QT interval that do not meet genome-wide significance and are missed by existing studies. We demonstrate that these 'sub-threshold' signals represent novel loci, and that epigenomic maps are effective at discriminating true biological signals from noise. We experimentally validate the molecular, gene-regulatory, cellular and organismal phenotypes of these sub-threshold loci, demonstrating that most sub-threshold loci have regulatory consequences and that genetic perturbation of nearby genes causes cardiac phenotypes in mouse. Our work provides a general approach for improving the detection of novel loci associated with complex human traits. DOI: http://dx.doi.org/10.7554/eLife.10557.001 PMID:27162171

Soils of Walker Branch Watershed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lietzke, D.A.

1994-03-01

The soil survey of Walker Branch Watershed (WBW) utilized the most up-to-date knowledge of soils, geology, and geohydrology in building the soils data base needed to reinterpret past research and to begin new research in the watershed. The soils of WBW were also compared with soils mapped elsewhere along Chestnut Ridge on the Oak Ridge Reservation to (1) establish whether knowledge obtained elsewhere could be used within the watershed, (2) determine whether there were any soils restricted to the watershed, and (3) evaluate geologic formation lateral variability. Soils, surficial geology, and geomorphology were mapped at a scale of 1:1,200 usingmore » a paper base map having 2-ft contour intervals. Most of the contours seemed to reasonably represent actual landform configurations, except for dense wooded areas. For example, the very large dolines or sinkholes were shown on the contour base map, but numerous smaller ones were not. In addition, small drainageways and gullies were often not shown. These often small but important features were located approximately as soil mapping progressed.« less

Isopach map of the interval from surface elevation to the top of the Pennsylvanian and Permian Minnelusa Formation and equivalents, Powder River basin, Wyoming and Montana

USGS Publications Warehouse

Crysdale, B.L.

1990-01-01

This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 1,480 of these wells that penetrate the Minnelusa Formation and equivalents.

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

PubMed Central

Vipin, Cina Ann; Luckett, David J.; Harper, John D.I.; Ash, Gavin J.; Kilian, Andrzej; Ellwood, Simon R.; Phan, Huyen T.T.; Raman, Harsh

2013-01-01

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies. PMID:24273424

Central Limit Theorems for the Shrinking Target Problem

NASA Astrophysics Data System (ADS)

Haydn, Nicolai; Nicol, Matthew; Vaienti, Sandro; Zhang, Licheng

2013-12-01

Suppose B i := B( p, r i ) are nested balls of radius r i about a point p in a dynamical system ( T, X, μ). The question of whether T i x∈ B i infinitely often (i.o.) for μ a.e. x is often called the shrinking target problem. In many dynamical settings it has been shown that if diverges then there is a quantitative rate of entry and for μ a.e. x∈ X. This is a self-norming type of strong law of large numbers. We establish self-norming central limit theorems (CLT) of the form (in distribution) for a variety of hyperbolic and non-uniformly hyperbolic dynamical systems, the normalization constants are . Dynamical systems to which our results apply include smooth expanding maps of the interval, Rychlik type maps, Gibbs-Markov maps, rational maps and, in higher dimensions, piecewise expanding maps. For such central limit theorems the main difficulty is to prove that the non-stationary variance has a limit in probability.

A method to correct coordinate distortion in EBSD maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Y.B., E-mail: yubz@dtu.dk; Elbrønd, A.; Lin, F.X.

2014-10-15

Drift during electron backscatter diffraction mapping leads to coordinate distortions in resulting orientation maps, which affects, in some cases significantly, the accuracy of analysis. A method, thin plate spline, is introduced and tested to correct such coordinate distortions in the maps after the electron backscatter diffraction measurements. The accuracy of the correction as well as theoretical and practical aspects of using the thin plate spline method is discussed in detail. By comparing with other correction methods, it is shown that the thin plate spline method is most efficient to correct different local distortions in the electron backscatter diffraction maps. -more » Highlights: • A new method is suggested to correct nonlinear spatial distortion in EBSD maps. • The method corrects EBSD maps more precisely than presently available methods. • Errors less than 1–2 pixels are typically obtained. • Direct quantitative analysis of dynamic data are available after this correction.« less

Modified Confidence Intervals for the Mean of an Autoregressive Process.

DTIC Science & Technology

1985-08-01

Validity of the method 45 3.6 Theorem 47 4 Derivation of corrections 48 Introduction 48 The zero order pivot 50 4.1 Algorithm 50 CONTENTS The first...of standard confidence intervals. There are several standard methods of setting confidence intervals in simulations, including the regener- ative... method , batch means, and time series methods . We-will focus-s on improved confidence intervals for the mean of an autoregressive process, and as such our