Role of syn-eruptive plagioclase disequilibrium crystallization in basaltic magma ascent dynamics.

PubMed

La Spina, G; Burton, M; De' Michieli Vitturi, M; Arzilli, F

2016-12-12

Timescales of magma ascent in conduit models are typically assumed to be much longer than crystallization and gas exsolution for basaltic eruptions. However, it is now recognized that basaltic magmas may rise fast enough for disequilibrium processes to play a key role on the ascent dynamics. The quantification of the characteristic times for crystallization and exsolution processes are fundamental to our understanding of such disequilibria and ascent dynamics. Here we use observations from Mount Etna's 2001 eruption and a magma ascent model to constrain timescales for crystallization and exsolution processes. Our results show that plagioclase reaches equilibrium in 1-2 h, whereas ascent times were <1 h. Using these new constraints on disequilibrium plagioclase crystallization we also reproduce observed crystal abundances for different basaltic eruptions. The strong relation between magma ascent rate and disequilibrium crystallization and exsolution plays a key role in controlling eruption dynamics in basaltic volcanism.

Observations of 231Pa/ 235U disequilibrium in volcanic rocks

NASA Astrophysics Data System (ADS)

Pickett, David A.; Murrell, Michael T.

1997-04-01

We present here the first survey of ( 231Pa/ 235U) ratios in volcanic rocks; such measurements are made possible by new mass spectrometric techniques. The data place new constraints on the timing and extent of magma source and evolutionary processes, particularly due to the sensitivity of the 231Pa- 235U pair and its intermediate time scale ( 231Pat 1/2 = 33 ky). ( 231Pa/ 235U) is found to vary widely, from 0.2 in carbonatites to 1.1-2.9 in basalts and 0.9-2.2 in arcs. Substantial Pa enrichment is nearly ubiquitous, suggestive of the relative incompatibility of Pa, qualitatively consistent with available partitioning data. The level of 231Pa- 235U disequilibrium typically far exceeds that of 230Th- 238U and is comparable to 226Ra- 230Th. The high ( 231Pa/ 235U) ratios in MORB and other basalts reflect a large degree of discrimination between two incompatible elements, posing challenges for modelling of melt generation and migration. Fundamental differences in ( 231Pa/ 235U) among different basaltic environments are likely related to contrasts in melting zone conditions (e.g., melting rate). Strong ( 231Pa/ 235U) disequilibria in continental basalts, for which ( 230Th/ 238U) disequilibria are small or absent, demonstrate that Pa-U fractionation is possible in both garnet and spinel mantle stability fields. In arcs, correlation of ( 231Pa/ 235U) and ( 230Th/ 238U) is consistent with U enrichment via slab-derived fluids, a process which is additional to the still dominant Pa enrichment. An important new constraint is provided by the observation that the near-equilibrium ( 230Th/ 238U) common to arcs and continental basalts is not typically accompanied by near-equilibrium ( 231Pa/ 235U), arguing against the influence of long magma history, crustal material, or equilibrium mantle sources in affecting decay-series ratios. Small sample sets from two silicic centers illustrate: (1) recent, rapid U enrichment in the magma chamber (El Chichón); and (2) the failure of

Role of syn-eruptive plagioclase disequilibrium crystallization in basaltic magma ascent dynamics

PubMed Central

La Spina, G.; Burton, M.; de' Michieli Vitturi, M.; Arzilli, F.

2016-01-01

Timescales of magma ascent in conduit models are typically assumed to be much longer than crystallization and gas exsolution for basaltic eruptions. However, it is now recognized that basaltic magmas may rise fast enough for disequilibrium processes to play a key role on the ascent dynamics. The quantification of the characteristic times for crystallization and exsolution processes are fundamental to our understanding of such disequilibria and ascent dynamics. Here we use observations from Mount Etna's 2001 eruption and a magma ascent model to constrain timescales for crystallization and exsolution processes. Our results show that plagioclase reaches equilibrium in 1–2 h, whereas ascent times were <1 h. Using these new constraints on disequilibrium plagioclase crystallization we also reproduce observed crystal abundances for different basaltic eruptions. The strong relation between magma ascent rate and disequilibrium crystallization and exsolution plays a key role in controlling eruption dynamics in basaltic volcanism. PMID:27941750

Effect of Linkage Disequilibrium on the Identification of Functional Variants

PubMed Central

Thomas, Alun; Abel, Haley J; Di, Yanming; Faye, Laura L; Jin, Jing; Liu, Jin; Wu, Zheyan; Paterson, Andrew D

2011-01-01

We summarize the contributions of Group 9 of Genetic Analysis Workshop 17. This group addressed the problems of linkage disequilibrium and other longer range forms of allelic association when evaluating the effects of genotypes on phenotypes. Issues raised by long-range associations, whether a result of selection, stratification, possible technical errors, or chance, were less expected but proved to be important. Most contributors focused on regression methods of various types to illustrate problematic issues or to develop adaptations for dealing with high-density genotype assays. Study design was also considered, as was graphical modeling. Although no method emerged as uniformly successful, most succeeded in reducing false-positive results either by considering clusters of loci within genes or by applying smoothing metrics that required results from adjacent loci to be similar. Two unexpected results that questioned our assumptions of what is required to model linkage disequilibrium were observed. The first was that correlations between loci separated by large genetic distances can greatly inflate single-locus test statistics, and, whether the result of selection, stratification, possible technical errors, or chance, these correlations seem overabundant. The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium. PMID:22128051

Significant Admixture Linkage Disequilibrium across 30 cM around the FY Locus in African Americans

PubMed Central

Lautenberger, James A.; Stephens, J. Claiborne; O'Brien, Stephen J.; Smith, Michael W.

2000-01-01

Scientists, to understand the importance of allelic polymorphisms on phenotypes that are quantitative and environmentally interacting, are now turning to population-association screens, especially in instances in which pedigree analysis is difficult. Because association screens require linkage disequilibrium between markers and disease loci, maximizing the degree of linkage disequilibrium increases the chances of discovering functional gene-marker associations. One theoretically valid approach—mapping by admixture linkage disequilibrium (MALD), using recently admixed African Americans—is empirically evaluated here by measurement of marker associations with 15 short tandem repeats (STRs) and an insertion/deletion polymorphism of the AT3 locus in a 70-cM segment at 1q22-23, around the FY (Duffy) locus. The FY polymorphism (−46T→C) disrupts the GATA promoter motif, specifically blocking FY erythroid expression and has a nearly fixed allele-frequency difference between European Americans and native Africans that is likely a consequence of a selective advantage of FY−/− in malaria infections. Analysis of linkage disequilibrium around the FY gene has indicated that there is strong and consistent linkage disequilibrium between FY and three flanking loci (D1S303, SPTA1, and D1S484) spanning 8 cM. We observed significant linkage-disequilibrium signals over a 30-cM region from −4.4 to 16.3 cM (from D1S2777 to D1S196) for STRs and at 26.4 cM (AT3), which provided quantitative estimates of centimorgan limits, by MALD assessment in African American population-association analyses, of 5–10 cM. PMID:10712211

Estimating glacier response times and disequilibrium in a changing climate

NASA Astrophysics Data System (ADS)

Christian, J. E.; Koutnik, M.; Roe, G.

2017-12-01

Glaciers respond to climate variations according to a characteristic timescale that, for most mountain glaciers, is on the order of 10—100 years. An important consequence of this multi-decadal memory is that a glacier's transient response to a climate trend exhibits a persistent lag behind the equilibrium response. In the context of anthropogenic warming, this means that most glaciers are currently well out of equilibrium, and that a substantial amount of retreat is committed even without further warming. The degree of disequilibrium depends fundamentally on the glacier response timescale, making it an important parameter to constrain. A common and robust metric for the response timescale is τ=H/bt, where H and bt are characteristic values for ice thickness and the terminus mass-balance rate, respectively. However, sparse observations, climate variability, and glacier disequilibrium make it difficult to define these characteristic values. We compare several sources of uncertainty that will affect estimates of the response timescale and thus the degree of disequilibrium. Ice thickness is poorly constrained for many glaciers, which bears directly on estimates of the response timescale. However, errors may also arise from estimating thickness and mass-balance rates in a variable climate. We assess how noisy mass balance and observed terminus fluctuations introduce sampling errors into estimates of the glacier's response timescale and the expected equilibrium response to a climate change. Additionally, the instantaneous value of τ evolves during sustained warming as the glacier thins and retreats. Perhaps counterintuitively, τ can increase if retreat into higher elevations exceeds thinning. This has implications for estimating the timescale based on currently observed geometry and mass balance. We use shallow-ice and 3-stage linear models to explore these effects with synthetic glacier geometries and climate forcings. In this way, we can diagnose the geometric and

Linkage Disequilibrium in a Finite Population That Is Partially Selfing

PubMed Central

Golding, G. B.; Strobeck, C.

1980-01-01

The linkage disequilibrium expected in a finite, partially selfing population is analyzed, assuming the infinite allele model. Formulas for the expected sum of squares of the linkage disequilibria and the squared standard linkage disequilibrium are derived from the equilibrium values of sixteen inbreeding coefficients required to describe the behavior of the system. These formulas are identical to those obtained with random mating if the effective population size Ne = (1-½S)N and the effective recombination value re = (1-S)r/(1-½S), where S is the proportion of selfing, are substituted for the population size and the recombination value. Therefore, the effect of partial selfing at equilibrium is to reduce the population size by a factor 1-½S and the recombination value by a factor (1-S)/(1-½S). PMID:17249017

Patterns of linkage disequilibrium at PARK16 may explain variances in genetic association studies.

PubMed

Li, Huihua; Teo, Yik-Ying; Tan, Eng-King

2015-09-01

Reproducing genomewide association studies findings in different populations is challenging, because the reproducibility fundamentally relies on the similar patterns of linkage disequilibrium between the unknown causal variants and the genotyped single-nucleotide polymorphisms (SNPs). The PARK16 locus was reported to alter the risk of Parkinson's disease (PD) in genomewide association studies in Japanese and Caucasians. We evaluated the regional linkage disequilibrium pattern at PARK16 locus in Caucasians, Japanese, and Chinese from HapMap and Chinese, Malays, and Indians from the Singapore Genome Variation Project, using the traditional heatmaps and targeted analysis of PARK16 gene via Monte Carlo simulation through varLD scores of these ethnic groups. One hundred SNPs in Caucasians, 95 SNPs in Chinese, 78 SNPs in Japanese from HapMap, 86 SNPs in Chinese, 99 SNPs in Indians, and 97 SNPs in Malays from the Singapore Genome Variation Project were included. Our targeted analysis showed that the linkage disequilibrium pattern of SNPs close to rs947211 was similar in Caucasians and Asians, including Chinese, Japanese, and Malay (all P > 0.0001), whereas different linkage disequilibrium patterns around rs823128, rs823156, and rs708730 were found between Caucasians and these Asian groups (all P < 0.0001). Our study suggests a higher chance to detect the association between rs947211 and PD in Chinese, Malay, and other Caucasian groups because of the similar linkage disequilibrium pattern around rs947211. The associations between rs823128/rs823156/rs708730 and PD are more likely to be replicated in Chinese and Malay populations. © 2015 International Parkinson and Movement Disorder Society.

A study of disequilibrium between 220Rn and 216Po for 220Rn measurements using a flow-through Lucas scintillation cell.

PubMed

Sathyabama, N; Datta, D; Gaware, J J; Mayya, Y S; Tripathi, R M

2014-01-01

Lucas-type scintillation cells (LSCs) are commonly used for rapid measurements of (220)Rn concentrations in flow-through mode in field and for calibration experiments in laboratories. However, in those measurements, equilibrium between (220)Rn and (216)Po is generally assumed and two alpha particles are considered to be emitted per (220)Rn decay due to very short half-life of (216)Po. In this paper, a small, yet significant disequilibrium existing between (220)Rn and (216)Po has been examined and shown that less than two alpha particles are actually emitted per (220)Rn decay in the cell when flow is maintained. A theoretical formula has been derived for the first time for a correction factor (CF) to be applied to this measured concentration to account for the disequilibrium. The existence of this disequilibrium has been verified experimentally and is found to increase with the increase in the ratio of flow rate to cell volume. The reason for the disequilibrium is attributed to the flushing out of (216)Po formed in the cell before its decay due to the flow. Uncertainties in measured concentrations have been estimated and the estimated CF values have been found to be significant for the flow rates considered above 5 dm(3) min(-1) for a cell of volume 0.125 dm(3). The calculated values of the CF are about 1.055 to 1.178 in the flow rate range of 4 to 15 dm(3) min(-1) for the cell of volume 0.125 dm(3), while the corresponding experimental values are 1.023 to 1.264. This is a systematic error introduced in (220)Rn measurements using a flow-through LSC, which can be removed either by correct formulation or by proper design of a measurement set-up.

Linkage Disequilibrium Under Recurrent Bottlenecks

PubMed Central

Schaper, E.; Eriksson, A.; Rafajlovic, M.; Sagitov, S.; Mehlig, B.

2012-01-01

To model deviations from selectively neutral genetic variation caused by different forms of selection, it is necessary to first understand patterns of neutral variation. Best understood is neutral genetic variation at a single locus. But, as is well known, additional insights can be gained by investigating multiple loci. The resulting patterns reflect the degree of association (linkage) between loci and provide information about the underlying multilocus gene genealogies. The statistical properties of two-locus gene genealogies have been intensively studied for populations of constant size, as well as for simple demographic histories such as exponential population growth and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright–Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci in samples of two chromosomes. This covariance reflects the degree of association and thus linkage disequilibrium between these loci. We find, first, that an effective population-size approximation describes the numerically observed association between two loci provided that recombination occurs either much faster or much more slowly than the population-size fluctuations. Second, when recombination occurs frequently between but rarely within bottlenecks, we observe that the association of gene histories becomes independent of physical distance over a certain range of distances. Third, we show that in this case, a commonly used measure of linkage disequilibrium, σd2 (closely related to r^2), fails to capture the long-range association between two loci. The reason is that constituent terms, each reflecting the long-range association, cancel. Fourth, we analyze a limiting case in which the long-range association can be described in terms of

Effect of heterophoria measurement technique on the clinical accommodative convergence to accommodation ratio.

PubMed

Escalante, Jaime Bernal; Rosenfield, Mark

2006-05-01

Measurement of the stimulus accommodative convergence to accommodation (AC/A) ratio is a standard procedure in clinical optometric practice. Typically, heterophoria is assessed at several accommodative stimulus levels, and the gradient of the vergence to accommodation function computed. A number of procedures are available for the subjective measurement of heterophoria, but it is unclear whether the use of different vergence measurement techniques will alter the obtained AC/A value. Accordingly, the current study compared AC/A ratios measured using 3 clinical subjective heterophoria tests, namely the von Graefe (VG), Maddox Rod (MR), and Modified Thorington (MT) procedures. The AC/A ratio was measured in 60 visually normal subjects between 20 and 25 years of age using each of the 3 procedures listed above. The accommodative stimulus was varied by the introduction of +/-1.00 diopter (D) spherical lenses over the distance refractive correction while subjects viewed a target at a viewing distance of 40 cm. To examine the repeatability of each procedure, the AC/A ratio was measured on 2 separate occasions for each measurement technique, with the 2 sessions being separated by at least 24 hours. Mean values of stimulus AC/A ratio measured using the VG, MR, and MT procedures were 3.47, 2.99, and 2.46Delta/D, respectively. These differences were significant (p=0.0001). In addition, the coefficient of repeatability for the 3 techniques was 2.22, 1.99, and 1.20 Delta/D, respectively. Ratios obtained using the Modified Thorington technique with +/-1.00 D lenses showed the best repeatability, whereas the poorest repeatability was found with the von Graefe technique when only +1.00 D lenses were used to vary the accommodative stimulus. Accordingly, we recommend that that Modified Thorington procedure with +/-1.00 D lenses be used to quantify heterophoria during clinical measurement of the stimulus AC/A ratio.

Linkage disequilibrium and association mapping.

PubMed

Weir, B S

2008-01-01

Linkage disequilibrium refers to the association between alleles at different loci. The standard definition applies to two alleles in the same gamete, and it can be regarded as the covariance of indicator variables for the states of those two alleles. The corresponding correlation coefficient rho is the parameter that arises naturally in discussions of tests of association between markers and genetic diseases. A general treatment of association tests makes use of the additive and nonadditive components of variance for the disease gene. In almost all expressions that describe the behavior of association tests, additive variance components are modified by the squared correlation coefficient rho2 and the nonadditive variance components by rho4, suggesting that nonadditive components have less influence than additive components on association tests.

Local thermodynamic equilibrium for globally disequilibrium open systems under stress

NASA Astrophysics Data System (ADS)

Podladchikov, Yury

2016-04-01

Predictive modeling of far and near equilibrium processes is essential for understanding of patterns formation and for quantifying of natural processes that are never in global equilibrium. Methods of both equilibrium and non-equilibrium thermodynamics are needed and have to be combined. For example, predicting temperature evolution due to heat conduction requires simultaneous use of equilibrium relationship between internal energy and temperature via heat capacity (the caloric equation of state) and disequilibrium relationship between heat flux and temperature gradient. Similarly, modeling of rocks deforming under stress, reactions in system open for the porous fluid flow, or kinetic overstepping of the equilibrium reaction boundary necessarily needs both equilibrium and disequilibrium material properties measured under fundamentally different laboratory conditions. Classical irreversible thermodynamics (CIT) is the well-developed discipline providing the working recipes for the combined application of mutually exclusive experimental data such as density and chemical potential at rest under constant pressure and temperature and viscosity of the flow under stress. Several examples will be presented.

Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?

PubMed

Cierco-Ayrolles, Christine; Dejean, Sébastien; Legarra, Andrés; Gilbert, Hélène; Druet, Tom; Ytournel, Florence; Estivals, Delphine; Oumouhou, Naïma; Mangin, Brigitte

2010-10-22

Since 2001, the use of more and more dense maps has made researchers aware that combining linkage and linkage disequilibrium enhances the feasibility of fine-mapping genes of interest. So, various method types have been derived to include concepts of population genetics in the analyses. One major drawback of many of these methods is their computational cost, which is very significant when many markers are considered. Recent advances in technology, such as SNP genotyping, have made it possible to deal with huge amount of data. Thus the challenge that remains is to find accurate and efficient methods that are not too time consuming. The study reported here specifically focuses on the half-sib family animal design. Our objective was to determine whether modelling of linkage disequilibrium evolution improved the mapping accuracy of a quantitative trait locus of agricultural interest in these populations. We compared two methods of fine-mapping. The first one was an association analysis. In this method, we did not model linkage disequilibrium evolution. Therefore, the modelling of the evolution of linkage disequilibrium was a deterministic process; it was complete at time 0 and remained complete during the following generations. In the second method, the modelling of the evolution of population allele frequencies was derived from a Wright-Fisher model. We simulated a wide range of scenarios adapted to animal populations and compared these two methods for each scenario. Our results indicated that the improvement produced by probabilistic modelling of linkage disequilibrium evolution was not significant. Both methods led to similar results concerning the location accuracy of quantitative trait loci which appeared to be mainly improved by using four flanking markers instead of two. Therefore, in animal half-sib designs, modelling linkage disequilibrium evolution using a Wright-Fisher model does not significantly improve the accuracy of the QTL location when compared to a

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps

PubMed Central

Jacobs, Guy S.; Sluckin, Timothy J.; Kivisild, Toomas

2016-01-01

During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly’s ZnS and ωmax) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly’s ZnS offers high power, but is outperformed by a novel statistic that we test, which we call Zα. We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics—ωmax, Kelly’s ZnS, and Zα—are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While ωmax replicates most candidates when recombination map data are not available, the ZnS and Zα statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available. PMID:27516617

Linking environmental filtering and disequilibrium to biogeography with a community climate framework.

PubMed

Blonder, Benjamin; Nogués-Bravo, David; Borregaard, Michael K; Donoghue, John C; Jørgensen, Peter M; Kraft, Nathan J B; Lessard, Jean-Philippe; Morueta-Holme, Naia; Sandel, Brody; Svenning, Jens-Christian; Violle, Cyrille; Rahbek, Carsten; Enquist, Brian J

2015-04-01

We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial-interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

PubMed Central

Garris, Amanda J; McCouch, Susan R; Kresovich, Stephen

2003-01-01

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice. PMID:14573486

Signal-to-noise ratio analysis and evaluation of the Hadamard imaging technique

NASA Technical Reports Server (NTRS)

Jobson, D. J.; Katzberg, S. J.; Spiers, R. B., Jr.

1977-01-01

The signal-to-noise ratio performance of the Hadamard imaging technique is analyzed and an experimental evaluation of a laboratory Hadamard imager is presented. A comparison between the performances of Hadamard and conventional imaging techniques shows that the Hadamard technique is superior only when the imaging objective lens is required to have an effective F (focus) number of about 2 or slower.

Statistical manifestation of quantum correlations via disequilibrium

NASA Astrophysics Data System (ADS)

Pennini, F.; Plastino, A.

2017-12-01

The statistical notion of disequilibrium (D) was introduced by López-Ruiz, Mancini, and Calbet (LMC) (1995) [1] more than 20 years ago. D measures the amount of ;correlational structure; of a system. We wish to use D to analyze one of the simplest types of quantum correlations, those present in gaseous systems due to symmetry considerations. To this end we extend the LMC formalism to the grand canonical environment and show that D displays distinctive behaviors for simple gases, that allow for interesting insights into their structural properties.

Germany's Persistent Balance-of-Payments Disequilibrium Revisited. German Studies Notes.

ERIC Educational Resources Information Center

Kindleberger, Charles P.

This essay compares Germany's persistent financial disequilibrium with the balance of payments situation in the United States. Delivered at a Symposium on German Economic Growth and Stability, the author concentrates on Germany's balance of payments surplus and presents U.S. figures mainly as a point of comparison. The material on Germany has been…

Nucleon-Alpha Particle Disequilibrium and Short-Lived r-Process Radioactivities

NASA Technical Reports Server (NTRS)

Meyer, B. S.; Clayton, D. D.; Chellapilla, S.; The, L.-S.

2002-01-01

r-Process yields can be extremely sensitive to expansion parameters when a persistent disequilibrium between free nucleons and alpha particles is present. This may provide a natural scenario for understanding the variation of heavy and light r-process isotopes in different r-process events. Additional information is contained in the original extended abstract.

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.

PubMed

Jacobs, Guy S; Sluckin, Tim J; Kivisild, Toomas

2016-08-01

During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's [Formula: see text] and [Formula: see text]) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly's [Formula: see text] offers high power, but is outperformed by a novel statistic that we test, which we call [Formula: see text] We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics-[Formula: see text] Kelly's [Formula: see text] and [Formula: see text]-are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While [Formula: see text] replicates most candidates when recombination map data are not available, the [Formula: see text] and [Formula: see text] statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available. Copyright © 2016 by the Genetics Society of America.

Role for syn-eruptive plagioclase disequilibrium crystallisation in basaltic magma ascent dynamics

NASA Astrophysics Data System (ADS)

La Spina, Giuseppe; Burton, Mike; de'Michieli Vitturi, Mattia; Arzilli, Fabio

2017-04-01

Magma ascent dynamics in volcanic conduits play a key role in determining the eruptive style of a volcano. The lack of direct observations inside the conduit means that numerical conduit models, constrained with observational data, provide invaluable tools for quantitative insights into complex magma ascent dynamics. The highly nonlinear, interdependent processes involved in magma ascent dynamics require several simplifications when modelling their ascent. For example, timescales of magma ascent in conduit models are typically assumed to be much longer than crystallisation and gas exsolution for basaltic eruptions. However, it is now recognized that basaltic magmas may rise fast enough for disequilibrium processes to play a key role on the ascent dynamics. The quantification of the characteristic times for crystallisation and exsolution processes are fundamental to our understanding of such disequilibria and ascent dynamics. Using observations from Mount Etna's 2001 eruption and a magma ascent model we are able to constrain timescales for crystallisation and exsolution processes. Our results show that plagioclase reaches equilibrium in 1-2 h, whereas ascent times were 1 h. Furthermore, we have related the amount of plagioclase in erupted products with the ascent dynamics of basaltic eruptions. We find that relatively high plagioclase content requires crystallisation in a shallow reservoir, whilst a low plagioclase content reflects a disequilibrium crystallisation occurring during a fast ascent from depth to the surface. Using these new constraints on disequilibrium plagioclase crystallisation we also reproduce observed crystal abundances for different basaltic eruptions: Etna 2002/2003, Stromboli 2007 (effusive eruption) and 1930 (paroxysm) and different Pu'u' O'o eruptions at Kilauea (episodes 49-53). Therefore, our results show that disequilibrium processes play a key role on the ascent dynamics of basaltic magmas and cannot be neglected when describing basaltic

Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

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

Stephens, J.C.; Briscoe, D.; O`Brien, S.J.

1994-10-01

Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient`s relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racialmore » groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of {ge}.3 between admixed parent populations) to produce an efficient approach (>95% ascertainment) for locating genes not easily tracked in human pedigrees. 321 refs., 8 figs., 7 tabs.« less

[Analysis of HLA haplotype frequency and linkage disequilibrium in patients with acute lymphoblastic leukemia from Northern Chinese Han].

PubMed

Gao, Su-qing; Cheng, Liang-hong; Lu, Liang; Jing, Shi-zheng; Cheng, Xi; Zhang, Yin-ze; Zou, Hong-yan; Deng, Zhi-hui

2009-02-01

To analyze the difference between the frequencies of HLA-A-B, B-DRB1 and A-B-DRB1 haplotype, as well as their linkage disequilibrium pattern in patients with acute lymphoblastic leukemia(ALL) and healthy controls from Northern Chinese Han. The frequencies of HLA-A-B, B-DRB1, A-B-DR haplotypes and linkage disequilibrium were estimated by Expectation Maximization method based on the genotypes of 643 patients with ALL and 2 0359 unrelated healthy donors, and the statistical significance between the two groups were estimated by chi-square test. Linkage disequilibrium was analyzed with population genetic methods. The most common HLA-A-B, B-DRB1, and A-B-DR haplotypes were A30-B13, A2-B46, A33-B58, B13-DR7, B46-DR9, B52-DR15, B58-DR17, A30-B13-DR7, A33-B58-DR17 and A1-B37-DR10 in both groups. The frequencies of A30-B13, A2-B46, A33-B44, B13-DR7, A30-B13-DR7 and A2-B46-DR9 haplotypes and linkage disequilibrium value were significantly decreased (P<0.05) in the patient group than that in the control group. On the other hand, the frequencies of A2-B52, A31-B61, A24- B8, B60-DR9, B27-DR4, B52-DR14, B44-DR17, B27-DR12 and A11-B27-DR12 haplotypes and linkage disequilibrium value were significantly increased (P<0.05) in the patient group than that in the control group. There are some common and positive linkage disequilibrium haplotypes in both the ALL patients and the healthy donors in Northern Chinese Han. Interestingly, some haplotypes and their linkage disequilibrium patterns had significantly different distributions between the two groups. The study provided basic data for the relationship of ALL and HLA haplotype and for finding the HLA-A, B, DR matching donors.

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Sulfur isotopic disequilibrium and fluid-rock interaction during metamorphism of sulfidic black shales from the Waterville-Augusta area, Maine, USA

USGS Publications Warehouse

Oliver, N.H.S.; Hoering, T.C.; Johnson, T.W.; Rumble, D.; Shanks, Wayne C.

1992-01-01

Sulfur isotope ratios of pyrite (py) and pyrrhotite (po) from regionally metamorphosed graphitic sulfidic schists and related rocks from south-central Maine, USA, were analysed using SO2 and SF6 techniques. There is a broad range in ??34S values for both pyrite and pyrrhotite at most outcrops, up to 8%. and overall the values are isotopically light, averaging ~ -27??? for the entire data set, suggesting that the rocks have not been grossly isotopically disturbed by regional metamorphism from their inferred organic-rich sedimentary origins. At all temperatures from chlorite to sillimanite grades, sulfide analysed from veins and blebs within the schists show predominantly disequilibrium fractionations ranging from ??34Spy-po -3.0 to +3.5???, as do matrix sulfides from rocks that attained temperatures 500??C do matrix pyrite-pyrrhotite pairs with polygonal or aligned granoblastic microstructures approach isotopic equilibrium at millimeter to centimeter scales, suggesting that the process that favoured equilibration was recrystallization accompanying metamorphism and deformation. This disequilibrium may be a function of preferential interaction of one of the phases with an infiltrating fluid, but the lack of any systematic trends in the data, particularly with both negative and positive ??34Spy-po at some outcrops, does not permit ready identification of fluid sources, fluxes, or compositions. By combining published fluid fluxes for the area and a knowledge of the mass of sulfur contained in the rocks and the inferred infiltrating fluid, it appears that sulfur should have been homogenized over at least 10's to 1000's of meters, if equilibrium had been attained between rock sulfides and an infiltrating fluid of constant composition. That this did not occur was probably due to lack of equilibration between sulfides and the fluid but may also have arisen because of channelling of fluid flow along rather than across layers, or a lack of fluid infiltration through this unit

Significant linkage disequilibrium between the Huntington disease gene and the loci D4S10 and D4S95 in the Dutch population

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

Skraastad, M.I.; Van de Vosse, E.; Belfroid, R.

1992-10-01

Significant linkage disequilibrium has been found between the Huntington disease (HD) gene and DNA markers located around D4S95 and D4S98. The linkage-disequilibrium studies favor the proximal location of the HD gene, in contrast to the conflicting results of recombination analyses. The authors have analyzed 45 Dutch HD families with 19 DNA markers and have calculated the strength of linkage disequilibrium. Highly significant linkage disequilibrium has been detected with D4S95, consistent with the studies in other populations. In contrast with most other studies, however, the area of linkage disequilibrium extends from D4S10 proximally to D4S95, covering 1,100 kb. These results confirmmore » that the HD gene most likely maps near D4S95. 28 refs., 1 fig., 2 tabs.« less

Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

USDA-ARS?s Scientific Manuscript database

The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatell...

Enhancement of digital images through band ratio techniques for geological applications

NASA Technical Reports Server (NTRS)

Filho, R. A. (Principal Investigator); Vitorello, I.

1982-01-01

The fundamentals in the use of band ratio techniques to enhance spectral signatures of geologic interest are discussed. The path radiance, additive term of the measured radiance at any given wavelength, is almost completely eliminated from LANDSAT images by subtracting the smallest value of the radiance measured in each channel, at shadows caused by topographic relief and clouds, and deep clear water bodies. By ratioing successive spectral channels the effect of solar angle of elevation is minimized and the product expresses, to a first approximation, a relationship between reflectances, which are intrinsic characteristics of the targets. Ratios between noncorrelated channels, such as R 7/4, R 7/5, and R 6/4 are useful to show variations in the vegetation cover, probably related to geobotanical associations.

Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium

PubMed Central

Dapper, Amy L; Payseur, Bret A

2018-01-01

Abstract In some species, meiotic recombination is concentrated in small genomic regions. These “recombination hotspots” leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. PMID:29045724

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

PubMed

Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

2012-03-01

Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure.

Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.

PubMed

Dapper, Amy L; Payseur, Bret A

2018-02-01

In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A model that helps explain Sr-isotope disequilibrium between feldspar phenocrysts and melt in large-volume silicic magma systems

USGS Publications Warehouse

Duffield, W.A.; Ruiz, J.

1998-01-01

Feldspar phenocrysts of silicic volcanic rocks are commonly in Sr-isotopic disequilibrium with groundmass. In some cases the feldspar is more radiogenic, and in others it is less radiogenic. Several explanations have been published previously, but none of these is able to accommodate both senses of disequilibrium. We present a model by which either more- or less-radiogenic feldspar (or even both within a single eruptive unit) can originate. The model requires a magma body open to interaction with biotite- and feldspar-bearing wall rock. Magma is incrementally contaminated as wall rock melts incongruently. Biotite preferentially melts first, followed by feldspar. Such melting behavior, which is supported by both field and experimental studies, first contaminates magma with a relatively radiogenic addition, followed by a less-radiogenic addition. Feldspar phenocrysts lag behind melt (groundmass of volcanic rock) in incorporating the influx of contaminant, thus resulting in Sr-isotopic disequilibrium between the crystals and melt. The sense of disequilibrium recorded in a volcanic rock depends on when eruption quenches the contamination process. This model is testable by isotopic fingerprinting of individual feldspar crystals. For a given set of geologic boundary conditions, specific core-to-rim Sr-isotopic profiles are expectable. Moreover, phenocrysts that nucleate at different times during the contamination process should record different and predictable parts of the history. Initial results of Sr-isotopic fingerprinting of sanidine phenocrysts from the Taylor Creek Rhyolite are consistent with the model. More tests of the model are desirable.Feldspar phenocrysts of silicic volcanic rocks are commonly in Sr-isotopic disequilibrium with groundmass. In some cases the feldspar is more radiogenic, and in others it is less radiogenic. Several explanations have been published previously, but none of these is able to accommodate both senses of disequilibrium. We present a

Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees

PubMed Central

Burgess, Treena I.; Le Roux, Johannes J.; Richardson, David M.; Slippers, Bernard; Wingfield, Michael J.

2017-01-01

Abstract Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilize these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. PMID:28013250

Aripiprazole-Cyclodextrin Binary Systems for Dissolution Enhancement: Effect of Preparation Technique, Cyclodextrin Type and Molar Ratio

PubMed Central

M. Badr-Eldin, Shaimaa; A. Ahmed, Tarek; R Ismail, Hatem

2013-01-01

Objective(s): The aim of this work was to investigate the effect of the natural and the chemically modified form of cyclodextrins namely; β-cyclodextrin (β-CD) and hydroxypropyl-β-cyclodextrin (HP-β-CD) respectively on the solubility and dissolution rate of aripiprazole; an antipsychotic medication showing poor aqueous solubility. Materials and Methods: Phase solubility of aripiprazole with the studied CDs and the complexation efficiency values (CE) which reflect the solubilizing power of the CDs towards the drug was performed. Solid binary systems of aripiprazole with CDs were prepared by kneading, microwave irradiation and freeze-drying techniques at 1:1 and 1:2 (drug to CD) molar ratios. Drug-CD physical mixtures were also prepared in the same molar ratios for comparison. The dissolution of aripiprazole-binary systems was carried out to select the most appropriate CD type, molar ratio and preparation technique. Results: Phase solubility study indicated formation of higher order complexes and the complexation efficiency values was higher for HP-β-CD compared to β-CD. Drug dissolution study revealed that aripiprazole dissolution was increased upon increasing the CD molar ratio and, the freeze-drying technique was superior to the other studied methods especially when combined with the HP-β-CD. The cyclodextrin type, preparation technique and molar ratio exhibited statistically significant effect on the drug dissolution at P≤ 0.05. Conclusion: The freeze-dried system prepared at molar ratio 1:2 (drug: CD) can be considered as efficient tool for enhancing aripiprazole dissolution with the possibility of improving its bioavailability. PMID:24570827

Measuring U-series Disequilibrium in Weathering Rinds to Study the Influence of Environmental Factors to Weathering Rates in Tropical Basse-Terre Island (French Guadeloupe)

NASA Astrophysics Data System (ADS)

Guo, J.; Ma, L.; Sak, P. B.; Gaillardet, J.; Chabaux, F. J.; Brantley, S. L.

2015-12-01

Chemical weathering is a critical process to global CO2 consumption, river/ocean chemistry, and nutrient import to biosphere. Weathering rinds experience minimal physical erosion and provide a well-constrained system to study the chemical weathering process. Here, we applied U-series disequilibrium dating method to study weathering advance rates on the wet side of Basse-Terre Island, French Guadeloupe, aiming to understand the role of the precipitation in controlling weathering rates and elucidate the behavior and immobilization mechanisms of U-series isotopes during rind formation. Six weathering clasts from 5 watersheds with mean annual precipitation varying from 2000 to 3000 mm/yr were measured for U-series isotope ratios and major element compositions on linear core-to-rind transects. One sample experienced complete core-to-rind transformation, while the rest clasts contain both rinds and unweathered cores. Our results show that the unweathered cores are under U-series secular equilibrium, while all the rind materials show significant U-series disequilibrium. For most rinds, linear core-to-rind increases of (230Th/232Th) activity ratios suggest a simple continuous U addition history. However, (234U/238U) and (238U/232Th) trends in several clasts show evidences of remobilization of Uranium besides the U addition, complicating the use of U-series dating method. The similarity between U/Th ratios and major elements trends like Fe, Al, P in some transects and the ongoing leaching experiments suggest that redox and organic colloids could control the mobilization of U-series isotopes in the rinds. Rind formation ages and weathering advance rate (0.07-0.29mm/kyr) were calculated for those rinds with a simple U-addition history. Our preliminary results show that local precipitation gradient significantly influenced the weathering advance rate, revealing the potential of estimating weathering advance rates at a large spatial scale using the U-series dating method.

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

Treesearch

S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

2004-01-01

Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

Unconsciously Indigenous Leadership: The Role of Cognitive Disequilibrium in Preparing Democratic Educational Leaders

ERIC Educational Resources Information Center

Farmer, Tod Allen

2008-01-01

This paper focuses on the role of cognitive disequilibrium in preparing democratic educational leaders. Followers emerge into leaders with what are many times unconsciously socialized norms and values indigenous to their local culture. One of the roles of a democratic leadership preparation program is to challenge these unconsciously accepted…

Measurements of K shell absorption jump factors and jump ratios using EDXRF technique

NASA Astrophysics Data System (ADS)

Kacal, Mustafa Recep; Han, İbrahim; Akman, Ferdi

2015-04-01

In the present work, the K-shell absorption jump factors and jump ratios for 30 elements between Ti ( Z = 22) and Er ( Z = 68) were measured by energy dispersive X-ray fluorescence (EDXRF) technique. The jump factors and jump ratios for these elements were determined by measuring the K shell fluorescence parameters such as the Kα X-ray production cross-sections, K shell fluorescence yields, Kβ-to- Kα X-rays intensity ratios, total atomic absorption cross sections and mass attenuation coefficients. The measurements were performed using an Am-241 radioactive point source and a Si (Li) detector in direct excitation and transmission experimental geometry. The results for jump factors and jump ratios were compared with theoretically calculated and the ones available in the literature.

Extended Intermarker Linkage Disequilibrium in the Afrikaners

PubMed Central

Hall, Diana; Wijsman, Ellen M.; Roos, J. Louw; Gogos, Joseph A.; Karayiorgou, Maria

2002-01-01

In this study we conducted an investigation of the background level of linkage disequilibrium (LD) in the Afrikaner population to evaluate the appropriateness of this genetic isolate for mapping complex traits. We analyzed intermarker LD in 62 nuclear families using microsatellite markers covering extended chromosomal regions. The markers were selected to allow the first direct comparison of long-range LD in the Afrikaners to LD in other demographic groups. Using several statistical measures, we find significant evidence for LD in the Afrikaners extending remarkably over a 6-cM range. In contrast, LD decays significantly beyond 3-cM distances in the other founder and outbred populations examined. This study strongly supports the appropriateness of the Afrikaner population for genome-wide scans that exploit LD to map common, multigenic disorders. PMID:12045148

Extended intermarker linkage disequilibrium in the Afrikaners.

PubMed

Hall, Diana; Wijsman, Ellen M; Roos, J Louw; Gogos, Joseph A; Karayiorgou, Maria

2002-06-01

In this study we conducted an investigation of the background level of linkage disequilibrium (LD) in the Afrikaner population to evaluate the appropriateness of this genetic isolate for mapping complex traits. We analyzed intermarker LD in 62 nuclear families using microsatellite markers covering extended chromosomal regions. The markers were selected to allow the first direct comparison of long-range LD in the Afrikaners to LD in other demographic groups. Using several statistical measures, we find significant evidence for LD in the Afrikaners extending remarkably over a 6-cM range. In contrast, LD decays significantly beyond 3-cM distances in the other founder and outbred populations examined. This study strongly supports the appropriateness of the Afrikaner population for genome-wide scans that exploit LD to map common, multigenic disorders.

Insights into solar nebula formation of pyrrhotite from nanoscale disequilibrium phases produced by H2S sulfidation of Fe metal

DOE PAGES

Gainsforth, Z; Lauretta, DS; Tamura, N; ...

2017-09-01

© 2017 by Walter de Gruyter Berlin/Boston. Lauretta (2005) produced sulfide in the laboratory by exposing canonical nebular metal analogs to H 2 S gas under temperatures and pressures relevant to the formation of the Solar System. The resulting reactions produced a suite of sulfides and nanophase materials not visible at the microprobe scale, but which we have now analyzed by TEM for comparison with interplanetary dust samples and comet Wild 2 samples returned by the Stardust mission. We find the unexpected result that disequilibrium formation favors pyrrhotite over troilite and also produces minority schreibersite, daubréelite, barringerite, taenite, oldhamite, andmore » perryite at the metal-sulfide interface. TEM identification of nanophases and analysis of pyrrhotite superlattice reflections illuminate the formation pathway of disequilibrium sulfide. We discuss the conditions under which such disequilibrium can occur, and implications for formation of sulfide found in extraterrestrial materials.« less

Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

USDA-ARS?s Scientific Manuscript database

Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in ...

Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon

USDA-ARS?s Scientific Manuscript database

The wide phenotypic diversity, in melon fruits, is the result of consumer preferences combined with genotype fitness to the different agro-climatic zones. There is no sufficient information with respect to the extent of genetic divergence, population structure and linkage disequilibrium (LD) in mel...

Differences in the Stimulus Accommodative Convergence/Accommodation Ratio using Various Techniques and Accommodative Stimuli.

PubMed

Satou, Tsukasa; Ito, Misae; Shinomiya, Yuma; Takahashi, Yoshiaki; Hara, Naoto; Niida, Takahiro

2018-04-04

To investigate differences in the stimulus accommodative convergence/accommodation (AC/A) ratio using various techniques and accommodative stimuli, and to describe a method for determining the stimulus AC/A ratio. A total of 81 subjects with a mean age of 21 years (range, 20-23 years) were enrolled. The relationship between ocular deviation and accommodation was assessed using two methods. Ocular deviation was measured by varying the accommodative requirement using spherical plus/minus lenses to create an accommodative stimulus of 10.00 diopters (D) (in 1.00 D steps). Ocular deviation was assessed using the alternate prism cover test in method 1 at distance (5 m) and near (1/3 m), and the major amblyoscope in method 2. The stimulus AC/A ratios obtained using methods 1 and 2 were calculated and defined as the stimulus AC/A ratios with low and high accommodation, respectively, using the following analysis method. The former was calculated as the difference between the convergence response to an accommodative stimulus of 3 D and 0 D, divided by 3. The latter was calculated as the difference between the convergence response to a maximum (max) accommodative stimulus with distinct vision of the subject and an accommodative stimulus of max minus 3.00 D, divided by 3. The median stimulus AC/A ratio with low accommodation (1.0 Δ/D for method 1 at distance, 2.0 Δ/D for method 1 at near, and 2.7 Δ/D for method 2) differed significantly among the measurement methods (P < 0.01). Differences in the median stimulus AC/A ratio with high accommodation (4.0 Δ/D for method 1 at distance, 3.7 Δ/D for method 1 at near, and 4.7 Δ/D for method 2) between method 1 at distance and method 2 were statistically significant (P < 0.05), while method 1 at near was not significantly different compared with other methods. Differences in the stimulus AC/A ratio value were significant according to measurement technique and accommodative stimuli. However, differences caused by

Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

PubMed

Carmichael, Gordon A

2008-07-17

Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demographic transition theory postulates initially high birth and death rates, this equilibrium eventually being broken by falling mortality. In Thailand, however, there is likely to have been both significant mortality decline and appreciable fertility increase after 1850, as the virtual elimination of indigenous warfare, rapid growth of the export rice economy and the demise of slavery and corvée labour created a new domestic environment. Characterized by more dispersed, often frontier, settlement, this environment was unprecedentedly sedate and settled, afforded ordinary households a previously unknown level of control over their resources of labour, and generated optimism about prospects for the next generation.

Demographic Disequilibrium in Early Twentieth Century Thailand: Falling Mortality, Rising Fertility, or Both?

PubMed Central

Carmichael, Gordon A.

2011-01-01

Estimates of Thai crude birth and death rates date from 1920 when the former was around 20 per thousand higher than the latter, implying natural increase of 2 percent per annum. Such disequilibrium cannot have been the norm over the long term historical past, when population growth must have been comparatively slow. This paper explores the bases for likely past relative equilibrium between Siamese birth and death rates, then seeks to explain the disequilibrium apparent by 1920. Classic demographic transition theory postulates initially high birth and death rates, this equilibrium eventually being broken by falling mortality. In Thailand, however, there is likely to have been both significant mortality decline and appreciable fertility increase after 1850, as the virtual elimination of indigenous warfare, rapid growth of the export rice economy and the demise of slavery and corvée labour created a new domestic environment. Characterized by more dispersed, often frontier, settlement, this environment was unprecedentedly sedate and settled, afforded ordinary households a previously unknown level of control over their resources of labour, and generated optimism about prospects for the next generation. PMID:21966299

Equilibrium and disequilibrium chemistry of adiabatic, solar-composition planetary atmospheres

NASA Technical Reports Server (NTRS)

Lewis, J. S.

1976-01-01

The impact of atmospheric and cloud-structure models on the nonequilibrium chemical behavior of the atmospheres of the Jovian planets is discussed. Quantitative constraints on photochemical, lightning, and charged-particle production of organic matter and chromophores are emphasized whenever available. These considerations imply that inorganic chromophore production is far more important than that of organic chromophores, and that lightning is probably a negligibly significant process relative to photochemistry on Jupiter. Production of complex molecules by gas-phase disequilibrium processes on Saturn, Uranus, and Neptune is severely limited by condensation of even simple intermediates.

Neuroendocrine–immune disequilibrium and endometriosis: an interdisciplinary approach

PubMed Central

Tariverdian, Nadja; Theoharides, Theoharis C.; Siedentopf, Friederike; Gutiérrez, Gabriela; Jeschke, Udo; Rabinovich, Gabriel A.; Blois, Sandra M.

2007-01-01

Endometriosis, a chronic disease characterized by endometrial tissue located outside the uterine cavity, affects one fourth of young women and is associated with chronic pelvic pain and infertility. However, an in-depth understanding of the pathophysiology and effective treatment strategies of endometriosis is still largely elusive. Inadequate immune and neuroendocrine responses are significantly involved in the pathophysiology of endometriosis, and key findings are summarized in the present review. We discuss here the role of different immune mechanisms particularly adhesion molecules, protein–glycan interactions, and pro-angiogenic mediators in the development and progression of the disease. Finally, we introduce the concept of endometrial dissemination as result of a neuroendocrine-immune disequilibrium in response to high levels of perceived stress caused by cardinal clinical symptoms of endometriosis. PMID:17621704

U isotopes distribution in the Lower Rhone River and its implication on radionuclides disequilibrium within the decay series.

PubMed

Zebracki, Mathilde; Cagnat, Xavier; Gairoard, Stéphanie; Cariou, Nicolas; Eyrolle-Boyer, Frédérique; Boulet, Béatrice; Antonelli, Christelle

2017-11-01

The large rivers are main pathways for the delivery of suspended sediments into coastal environments, affecting the biogeochemical fluxes and the ecosystem functioning. The radionuclides from 238 U and 232 Th-series can be used to understand the dynamic processes affecting both catchment soil erosion and sediment delivery to oceans. Based on annual water discharge the Rhone River represents the largest river of the Mediterranean Sea. The Rhone valley also represents the largest concentration in nuclear power plants in Europe. A radioactive disequilibrium between particulate 226 Ra (p) and 238 U (p) was observed in the suspended sediment discharged by the Lower Rhone River (Eyrolle et al. 2012), and a fraction of particulate 234 Th was shown to derive from dissolved 238 U (d) (Zebracki et al. 2013). This extensive study has investigated the dissolved U isotopes distribution in the Lower Rhone River and its implication on particulate radionuclides disequilibrium within the decay series. The suspended sediment and filtered river waters were collected at low and high water discharges. During the 4-months of the study, two flood events generated by the Rhone southern tributaries were monitored. In river waters, the total U (d) concentration and U isotopes distribution were obtained through Q-ICP-MS measurements. The Lower Rhone River has displayed non-conservative U-behavior, and the variations in U (d) concentration between southern tributaries were related to the differences in bedrock lithology. The artificially occurring 236 U was detected in the Rhone River at low water discharges, and was attributed to the liquid releases from nuclear industries located along the river. The ( 235 U/ 238 U) (d) activity ratio (=AR) in river waters was representative of the 235 U natural abundance on Earth. The ( 226 Ra/ 238 U) (p) AR in suspended sediment has indicated a radioactive disequilibrium (average 1.3 ± 0.1). The excess of 234 Th in suspended sediment =( 234 Th xs

Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and po...

Cytonuclear disequilibrium and genetic drift in a natural population of ponderosa pine.

PubMed Central

Latta, R G; Linhart, Y B; Mitton, J B

2001-01-01

We measured the cytonuclear disequilibrium between 11 nuclear allozyme loci and both mitochondrial and chloroplast DNA haplotypes in a natural population of ponderosa pine (Pinus ponderosa, Laws). Three allozyme loci showed significant associations with mtDNA variation, while two other loci showed significant association with cpDNA. However, the absolute number of individuals involved in any of the associations was small, such that in none of the nuclear-organellar combinations was the difference between observed and expected numbers >11 individuals. Patterns of association were not consistent across loci or organellar genomes, suggesting that they are not the result of mating patterns, which would act uniformly on all loci. This pattern of disequilibria is consistent with the action of genetic drift and with existing knowledge of the structure of this population and thus does not imply the action of other evolutionary processes. The overall magnitude (normalized disequilibrium) of associations was greater for maternally inherited mtDNA than for paternally inherited cpDNA, though this difference was neither large nor significant. Such significant disequilibria involving the paternally inherited organelle indicate that not only are there a limited number of seed parents, but the effective number of pollen parents is also limited. PMID:11404345

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

USDA-ARS?s Scientific Manuscript database

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collectio...

Design of a Low Aspect Ratio Transonic Compressor Stage Using CFD Techniques

NASA Technical Reports Server (NTRS)

Sanger, Nelson L.

1994-01-01

A transonic compressor stage has been designed for the Naval Postgraduate School Turbopropulsion Laboratory. The design relied heavily on CFD techniques while minimizing conventional empirical design methods. The low aspect ratio (1.2) rotor has been designed for a specific head ratio of .25 and a tip relative inlet Mach number of 1.3. Overall stage pressure ratio is 1.56. The rotor was designed using an Euler code augmented by a distributed body force model to account for viscous effects. This provided a relatively quick-running design tool, and was used for both rotor and stator calculations. The initial stator sections were sized using a compressible, cascade panel code. In addition to being used as a case study for teaching purposes, the compressor stage will be used as a research stage. Detailed measurements, including non-intrusive LDV, will be compared with the design computations, and with the results of other CFD codes, as a means of assessing and improving the computational codes as design tools.

Th-230 - U-238 series disequilibrium of the Olkaria rhyolites Gregory Rift Valley, Kenya: Residence times

NASA Technical Reports Server (NTRS)

Black, S.; Macdonald, R.; Kelly, M.

1993-01-01

U-series disequilibrium analyses have been conducted on samples from Olkaria rhyolite centers with ages being available for all but one center using both internal and whole rock isochrons. 67 percent of the rhyolites analyzed show U-Th disequilibrium, ranging from 27 percent excess thorium to 36 percent excess uranium. Internal and whole rock isochrons give crystallization/formation ages between 65 ka and 9 ka, in every case these are substantially older than the eruptive dates. The residence times of the rhyolites (U-Th age minus the eruption date) have decreased almost linearly with time, from 45 ka to 7 Ka suggesting a possible increase of activity within the system related to increased basaltic input. The long residence times are mirrored by large Rn-222 fluxes from the centers which cannot be explained by larger U contents.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.).

PubMed

Tascioglu, Tulin; Metin, Ozge Karakas; Aydin, Yildiz; Sakiroglu, Muhammet; Akan, Kadir; Uncuoglu, Ahu Altinkut

2016-08-01

Bread wheat (Triticum aestivum L.) gene pool was analyzed with 117 microsatellite markers scattered throughout A, B, and D genomes. Ninety microsatellite markers were giving 1620 polymorphic alleles in 55 different bread wheat genotypes. These genotypes were found to be divided into three subgroups based on Bayesian model and Principal component analysis. The highest polymorphism information content value for the markers resides on A genome was estimated for wmc262 marker located on 4A chromosome with the polymorphism information content value of 0.960. The highest polymorphism information content value (0.954) among the markers known to be located on B genome was realized for wmc44 marker located on 1B chromosome. The highest polymorphism information content value for the markers specific to D genome was found in gwm174 marker located on 5D chromosome with the polymorphism information content value of 0.948. The presence of linkage disequilibrium between 81 pairwise SSR markers reside on the same chromosome was tested and very limited linkage disequilibrium was observed. The results confirmed that the most distant genotype pairs were as follows Ceyhan-99-Behoth 6, Gerek 79-Douma 40989, and Karahan-99-Douma 48114.

Equilibrium gas-oil ratio measurements using a microfluidic technique.

PubMed

Fisher, Robert; Shah, Mohammad Khalid; Eskin, Dmitry; Schmidt, Kurt; Singh, Anil; Molla, Shahnawaz; Mostowfi, Farshid

2013-07-07

A method for measuring the equilibrium GOR (gas-oil ratio) of reservoir fluids using microfluidic technology is developed. Live crude oils (crude oil with dissolved gas) are injected into a long serpentine microchannel at reservoir pressure. The fluid forms a segmented flow as it travels through the channel. Gas and liquid phases are produced from the exit port of the channel that is maintained at atmospheric conditions. The process is analogous to the production of crude oil from a formation. By using compositional analysis and thermodynamic principles of hydrocarbon fluids, we show excellent equilibrium between the produced gas and liquid phases is achieved. The GOR of a reservoir fluid is a key parameter in determining the equation of state of a crude oil. Equations of state that are commonly used in petroleum engineering and reservoir simulations describe the phase behaviour of a fluid at equilibrium state. Therefore, to accurately determine the coefficients of an equation of state, the produced gas and liquid phases have to be as close to the thermodynamic equilibrium as possible. In the examples presented here, the GORs measured with the microfluidic technique agreed with GOR values obtained from conventional methods. Furthermore, when compared to conventional methods, the microfluidic technique was simpler to perform, required less equipment, and yielded better repeatability.

Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

2008-02-01

The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs

PubMed Central

Chang, Hsueh-Wei; Chuang, Li-Yeh; Chang, Yan-Jhu; Cheng, Yu-Huei; Hung, Yu-Chen; Chen, Hsiang-Chi; Yang, Cheng-Hong

2009-01-01

Background Linkage disequilibrium (LD) mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping. Results We developed a freeware called LD2SNPing, which provides a complete package of mining tools for genotyping and LD analysis environments. The software provides SNP ID- and gene-centric online retrievals for SNP information and tag SNP selection from dbSNP/NCBI and HapMap, respectively. Restriction fragment length polymorphism (RFLP) enzyme information for SNP genotype is available to all SNP IDs and tag SNPs. Single and multiple SNP inputs are possible in order to perform LD analysis by online retrieval from HapMap and NCBI. An LD statistics section provides D, D', r2, δQ, ρ, and the P values of the Hardy-Weinberg Equilibrium for each SNP marker, and Chi-square and likelihood-ratio tests for the pair-wise association of two SNPs in LD calculation. Finally, 2D and 3D plots, as well as plain-text output of the results, can be selected. Conclusion LD2SNPing thus provides a novel visualization environment for multiple SNP input, which facilitates SNP association studies. The software, user manual, and tutorial are freely available at . PMID:19500380

Potential linkage disequilibrium between schizophrenia and locus D22S278 on the long arm of chromosome 22

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

Moises, H.W.; Yang, L.; Havsteen, B.

Locus D22S278 at 22q12 has been implicated in schizophrenia by sib-pair analysis. In order to replicate these results, we performed the transmission test for linkage disequilibrium (TDT) in 113 unrelated schizophrenic patients and their 226 parents. Evidence for potential linkage disequilibrium was obtained between schizophrenia and allele 243 of the marker AFM 182xd12 at the locus D22S278 (P = 0.02). The results of our study suggest a detectable oligogenic gene in a multigene system for schizophrenia closely linked to D22S278 on the long arm of chromosome 22. If confirmed by others, this finding could lead to the identification of amore » schizophrenia susceptibility gene. 12 refs., 1 tab.« less

[Transmission disequilibrium test for nonsyndromic cleft lip and palate and segment homeobox gene-1 gene].

PubMed

Wu, Ping-An; Li, Yun-Liang; Wu, Han-Jiang; Wang, Kai; Fan, Guo-Zheng

2007-09-01

To investigate the relationship between muscle segment homeobox gene-1 (MSX1) and the genetic susceptibility of nonsyndromic cleft lip and palate (NSCLP) in Hunan Hans. One microsatellite DNA marker CA repeat in MSX1 intron region was used as genetic marker. The genotypes of 387 members in 129 NSCLP nuclear family trios were analyzed by polymerase chain reaction (PCR) and denaturing polyacrylamide gel electrophoresis. Then transmission disequilibrium test (TDT) and Logistic regression analysis were used to conduct association analysis. TDT analysis confirmed that CA4 allele in CL/P and CPO groups preferentially transmitted to the affected offspring (P = 0.018, P = 0.041). Logistic regression analysis indicated that the recessive model of inheritance was supported, and CA4 itself or CA4 acting as a marker for a disease allele or haplotype was inherited in a recessive fashion (P = 0.009). MSX1 gene is associated with NSCLP, and MSX1 gene may be directly involved either in the etiology of NSCLP or in linkage disequilibrium with disease-predisposing sites.

Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes.

PubMed Central

van Endert, P M; Lopez, M T; Patel, S D; Monaco, J J; McDevitt, H O

1992-01-01

Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes. Images PMID:1360671

Linkage disequilibrium at the SCA2 locus

PubMed Central

Didierjean, O.; Cancel, G.; Stevanin, G.; Durr, A.; Burk, K.; Benomar, A.; Lezin, A.; Belal, S.; Abada-Bendid, M.; Klockgether, T.; Brice, A.

1999-01-01

Spinocerebellar ataxia type 2 (SCA2) is caused by the expansion of an unstable CAG repeat encoding a polyglutamine tract. Repeats with 32 to 200 CAGs are associated with the disease, whereas normal chromosomes contain 13 to 33 repeats. We tested 220 families of different geographical origins for the SCA2 mutation. Thirty three were positive (15%). Twenty three families with at least two affected subjects were tested for linkage disequilibium (LD) between the SCA2 mutation and three microsatellite markers, two of which (D12S1332-D12S1333) closely flanked the mutation; the other (D12S1672) was intragenic. Many different haplotypes were observed, indicating the occurrence of several ancestral mutations. However, the same haplotype, not observed in controls, was detected in the German, the Serbian, and some of the French families, suggesting a founder effect or recurrent mutations on an at risk haplotype.


Keywords: linkage disequilibrium; SCA2; trinucleotide repeat expansion; founder effect PMID:10353790

Uneven recombination and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD) and recombination (R) analyses are the basis for plant breeding. LD and R vary by breeding system, by generation of inbreeding or outcrossing and by region of the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome and n=...

The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets

PubMed Central

McCaskie, Pamela A; Carter, Kim W; McCaskie, Simon R; Palmer, Lyle J

2005-01-01

We used our newly developed linkage disequilibrium (LD) plotting software, JLIN, to plot linkage disequilibrium between pairs of single-nucleotide polymorphisms (SNPs) for three chromosomes of the Genetic Analysis Workshop 14 Aipotu simulated population to assess the effect of missing data on LD calculations. Our haplotype analysis program, SIMHAP, was used to assess the effect of missing data on haplotype-phenotype association. Genotype data was removed at random, at levels of 1%, 5%, and 10%, and the LD calculations and haplotype association results for these levels of missingness were compared to those for the complete dataset. It was concluded that ignoring individuals with missing data substantially affects the number of regions of LD detected which, in turn, could affect tagging SNPs chosen to generate haplotypes. PMID:16451612

Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel

PubMed Central

Houle, David; Márquez, Eladio J.

2015-01-01

We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines. PMID:26068573

Anonymous marker loci within 400 kb of HLA-A generate haplotypes in linkage disequilibrium with the hemochromatosis gene (HFE)

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

Yaouanq, J.; Perichon, M.; Treut, A.L.

1994-02-01

The hemochromatosis gene (HFE) maps to 6p21.3 and is less than 1 cM from the HLA class I gene; however, the precise physical location of the gene has remained elusive and controversial. The unambiguous identification of a crossover event within hemochromatosis families is very difficult; it is particularly hampered by the variability of the phenotypic expression as well as by the sex- and age-related penetrance of the disease. For these considerations, traditional linkage analysis could prove of limited value in further refining the extrapolated physical position of HFE. The authors therefore embarked upon a linkage-disequilibrium analysis of HFE and normalmore » chromosomes for the Brittany population. In this report, 66 hemochromatosis families yielding 151 hemochromatosis chromosomes and 182 normal chromosomes were RFLP-typed with a battery of probes, including two newly derived polymorphic markers from the 6.7 and HLA-F loci located 150 and 250 kb telomeric to HLA-A, respectively. The results suggest a strong peak of existing linkage disequilibrium focused within the i82-to-6.7 interval (approximately 250 kb). The zone of linkage disequilibrium is flanked by the i97 locus, positioned 30 kb proximal to i82, and the HLA-F gene, found 250 kb distal to HLA-A, markers of which display no significant association with HFE. These data support the possibility that HFE resides within the 400-kb expanse of DNA between i97 and HLA-F. Alternatively, the very tight association of HLA-A3 and allele 1 of the 6.7 locus, both of which are comprised by the major ancestral or founder HFE haplotype in Brittany, supports the possibility that the disease gene may reside immediately telomeric to the 6.7 locus within the linkage-disequilibrium zone. Additionally, hemochromatosis haplotypes possessing HLA-A11 and the low-frequency HLA-F polymorphism (allele 2) are supportive of a separate founder chromosome containing a second, independently arising mutant allele. 69 refs., 1 fig., 5

MICA diversity and linkage disequilibrium with HLA-B alleles in renal-transplant candidates in southern Brazil.

PubMed

Yamakawa, Roger Haruki; Saito, Patrícia Keiko; Gelmini, Geórgia Fernanda; da Silva, José Samuel; Bicalho, Maria da Graça; Borelli, Sueli Donizete

2017-01-01

The major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located centromerically to the human leukocyte antigen (HLA)-B. The short distance between these loci in the MHC indicates the presence of linkage disequilibrium (LD). Similarly to the HLA, the MICA is highly polymorphic, and this polymorphism has not been well documented in different populations. In this study, we estimated the allelic frequencies of MICA and the linkage disequilibrium with HLA-B alleles in 346 renal-transplant candidates in southern Brazil. MICA and HLA were typed using the polymerase chain reaction-sequence-specific primer method (PCR-SSO), combined with the Luminex technology. A total of 19 MICA allele groups were identified. The most frequent allele groups were MICA*008 (21.6%), MICA*002 (17.0%) and MICA*004 (14.8%). The most common haplotypes were MICA*009-B*51 (7.8%), MICA*004-B*44 (6.06%) and MICA*002-B*35 (5.63%). As expected from the proximity of the MICA and HLA-B loci, most haplotypes showed strong LD. Renal patients and healthy subjects in the same region of Brazil showed statistically significant differences in their MICA polymorphisms. The MICA*027 allele group was more frequent in renal patients (Pc = 0.018, OR: 3.421, 95% CI: 1.516-7.722), while the MICA*019 allele group was more frequent in healthy subjects (Pc = 0.001, OR: 0.027, 95% CI: 0.002-0.469). This study provided information on the distribution of MICA polymorphisms and linkage disequilibrium with HLA-B alleles in Brazilian renal-transplant candidates. This information should help to determine the mechanisms of susceptibility to different diseases in patients with chronic kidney disease, and to elucidate the mechanisms involved in allograft rejection associated with MICA polymorphisms in a Brazilian population.

Dynamics of a durable commodity market involving trade at disequilibrium

NASA Astrophysics Data System (ADS)

Panchuk, A.; Puu, T.

2018-05-01

The present work considers a simple model of a durable commodity market involving two agents who trade stocks of two different types. Stock commodities, in contrast to flow commodities, remain on the market from period to period and, consequently, there is neither unique demand function nor unique supply function exists. We also set up exact conditions for trade at disequilibrium, the issue being usually neglected, though a fact of reality. The induced iterative system has infinite number of fixed points and path dependent dynamics. We show that a typical orbit is either attracted to one of the fixed points or eventually sticks at a no-trade point. For the latter the stock distribution always remains the same while the price displays periodic or chaotic oscillations.

Disequilibrium δ18O values in microbial carbonates as a tracer of metabolic production of dissolved inorganic carbon

NASA Astrophysics Data System (ADS)

Thaler, Caroline; Millo, Christian; Ader, Magali; Chaduteau, Carine; Guyot, François; Ménez, Bénédicte

2017-02-01

Carbon and oxygen stable isotope compositions of carbonates are widely used to retrieve paleoenvironmental information. However, bias may exist in such reconstructions as carbonate precipitation is often associated with biological activity. Several skeleton-forming eukaryotes have been shown to precipitate carbonates with significant offsets from isotopic equilibrium with water. Although poorly understood, the origin of these biologically-induced isotopic shifts in biogenic carbonates, commonly referred to as "vital effects", could be related to metabolic effects that may not be restricted to mineralizing eukaryotes. The aim of our study was to determine whether microbially-mediated carbonate precipitation can also produce offsets from equilibrium for oxygen isotopes. We present here δ18O values of calcium carbonates formed by the activity of Sporosarcina pasteurii, a carbonatogenic bacterium whose ureolytic activity produces ammonia (thus increasing pH) and dissolved inorganic carbon (DIC) that precipitates as solid carbonates in the presence of Ca2+. We show that the 1000 lnαCaCO3-H2O values for these bacterially-precipitated carbonates are up to 24.7‰ smaller than those expected for precipitation at isotopic equilibrium. A similar experiment run in the presence of carbonic anhydrase (an enzyme able to accelerate oxygen isotope equilibration between DIC and water) resulted in δ18O values of microbial carbonates in line with values expected at isotopic equilibrium with water. These results demonstrate for the first time that bacteria can induce calcium carbonate precipitation in strong oxygen isotope disequilibrium with water, similarly to what is observed for eukaryotes. This disequilibrium effect can be unambiguously ascribed to oxygen isotope disequilibrium between DIC and water inherited from the oxygen isotope composition of the ureolytically produced CO2, probably combined with a kinetic isotope effect during CO2 hydration/hydroxylation. The fact that

Linkage Disequilibrium and Inversion-Typing of the Drosophila melanogaster Genome Reference Panel.

PubMed

Houle, David; Márquez, Eladio J

2015-06-10

We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r(2) ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines. Copyright © 2015 Houle and Márquez.

'Signs of disequilibrium chemistry in extrasolar hot-Jupiter type planets?'

NASA Astrophysics Data System (ADS)

Rocha, Graca; Swain, Mark; Line, Michael; West, Robert

2018-01-01

In the recent years Infrared spectroscopy of hot exoplanets has been revealing their atmospheric composition. For example the spectra of the planet HD189733b exhibits signatures of CH4, CO2, CO and H2O molecules (Swain et al 2008, 2009, etc.). The original 2008 detection of CH4 was a surprise because it is not thermochemically favored at the relatively high temperature (~1300 K) of the atmosphere of HD 189733b. More recent analysis of HD 189733b measurements (Swain, Line, Deroo 2014) implied a CH4 enhancement of ~1000x greater than has been assumed. Significantly more data has recently become available from WFC3 observations (Mccullah et al. 2014, Crozet at al. 2015) of this planet. In the meantime theoretical models by Moses et al. 2011 showed that large enhancement of quenched methane is possible due to transport if vertical eddy diffusion is significant.In this talk we will present results from a new study of CH4 enhancement in the atmosphere of HD189733b. We analysise the transit spectra of this planet obtained with the Hubble Space Telescope, combining the shorter wavelength 1.1-1.6 μm data from WFC3 measurements with the 1.5-2.4 μm data from NICMOS measurements. We also introduce a new methodology, implemented within a Bayesian framework, where hypothesis testing is conducted via evidence based model selection. Our analysis indicates, for the first time, that the observed excess of Methane in HD189733b’s atmosphere requires disequilibrium chemistry. However the Evidence has a modest discriminatory power amongst a subset of models. Furthermore our constraints confirm Swain et al. 2014 results with an excess of Methane with a mixing ratio of 10 2.26 ppm with EvidencelogZ=-58.602 +/- 0.109.

Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars.

PubMed

Campoy, José Antonio; Lerigoleur-Balsemin, Emilie; Christmann, Hélène; Beauvieux, Rémi; Girollet, Nabil; Quero-García, José; Dirlewanger, Elisabeth; Barreneche, Teresa

2016-02-24

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry. A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method. The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.

Significant evidence for linkage disequilibrium over a 5-cM region among Afrikaners.

PubMed

Gordon, D; Simonic, I; Ott, J

2000-05-15

We explore the extent of deviations from Hardy-Weinberg equilibrium (HWE) at a marker locus and linkage disequilibrium (LD) between pairs of marker loci in the Afrikaner population of South Africa. DNA samples were used for genotyping of 23 loci on six chromosomes. The samples were collected from 91 healthy unrelated Afrikaner adults. Exact tests were used to determine evidence for deviations from HWE at a single marker locus or LD between pairs of marker loci. At the 0.05 level of significance, evidence was found for deviation from HWE at only one of the 23 loci. At the same level of significance, LD was found among 8 of the 34 intrachromosomal pairs of loci. On chromosome 21, there was evidence for LD (P = 0.02) between a pair of loci with a genetic distance of 5.51 cM. On chromosome 2, there was evidence for LD between a pair of loci with a genetic distance of 5.28 cM (P = 0.002) and a pair of loci with a genetic distance of 3.68 cM (P = 0.0004). Detailed analysis of LD for one locus pair indicated that only a few of all alleles participated in the LD and that strong LD was most often positive. Our findings indicate that Afrikaans-speaking Afrikaners represent one of those special populations deemed particularly suitable for disequilibrium mapping. Copyright 2000 Academic Press.

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

PubMed Central

2014-01-01

Background Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. Methods By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. Results For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. Conclusions The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. PMID:24592996

The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

PubMed

Huang, J; Jiang, Y

2001-01-01

We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

Convective Dynamics and Disequilibrium Chemistry in the Atmospheres of Giant Planets and Brown Dwarfs

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2018-02-01

Disequilibrium chemical processes significantly affect the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step toward addressing this problem, we study the localized, small-scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically stratified, plane-parallel atmospheres in 2D and 3D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2D and 3D, chemical species quench deeper than would be predicted based on simple mixing-length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, that can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.

Transmission disequilibrium testing of arginine vasopressin receptor 1A (AVPR1A) polymorphisms in autism.

PubMed

Kim, S-J; Young, L J; Gonen, D; Veenstra-VanderWeele, J; Courchesne, R; Courchesne, E; Lord, C; Leventhal, B L; Cook, E H; Insel, T R

2002-01-01

Impairment in social reciprocity is a central component of autism. In preclinical studies, arginine vasopressin (AVP) has been shown to increase a range of social behaviors, including affiliation and attachment, via the V(1a) receptor (AVPR1A) in the brain. Both the behavioral effects of AVP and the neural distribution of the V1a receptor vary greatly across mammalian species. This difference in regional receptor expression as well as differences in social behavior may result from a highly variable repetitive sequence in the 5' flanking region of the V1a gene (AVPR1A). Given this comparative evidence for a role in inter-species variation in social behavior, we explored whether within our own species, variation in the human AVPR1A may contribute to individual variations in social behavior, with autism representing an extreme form of social impairment. We genotyped two microsatellite polymorphisms from the 5' flanking region of AVPR1A for 115 autism trios and found nominally significant transmission disequilibrium between autism and one of the microsatellite markers by Multiallelic Transmission/Disequilibrium test (MTDT) that was not significant after Bonferroni correction. We also screened approximately 2 kb of the 5' flanking region and the coding region and identified 10 single nucleotide polymorphisms.

SU-E-T-554: Comparison of Electron Disequilibrium Factor in External Photon Beams for Different Models of Linear Accelerators

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

LIU, B; Zhu, T

Purpose: The dose in the buildup region of a photon beam is usually determined by the transport of the primary secondary electrons and the contaminating electrons from accelerator head. This can be quantified by the electron disequilibrium factor, E, defined as the ratio between total dose and equilibrium dose (proportional to total kerma), E = 1 in regions beyond buildup region. Ecan be different among accelerators of different models and/or manufactures of the same machine. This study compares E in photon beams from different machine models/ Methods: Photon beam data such as fractional depth dose curve (FDD) and phantom scattermore » factors as a function of field size and phantom depth were measured for different Linac machines. E was extrapolated from these fractional depth dose data while taking into account inverse-square law. The ranges of secondary electron were chosen as 3 and 6 cm for 6 and 15 MV photon beams, respectively. The field sizes range from 2x2 to 40x40 cm{sup 2}. Results: The comparison indicates the standard deviations of electron contamination among different machines are about 2.4 - 3.3% at 5 mm depth for 6 MV and 1.2 - 3.9% at 1 cm depth for 15 MV for the same field size. The corresponding maximum deviations are 3.0 - 4.6% and 2 - 4% for 6 and 15 MV, respectively. Both standard and maximum deviations are independent of field sizes in the buildup region for 6 MV photons, and slightly decreasing with increasing field size at depths up to 1 cm for 15 MV photons. Conclusion: The deviations of electron disequilibrium factor for all studied Linacs are less than 3% beyond the depth of 0.5 cm for the photon beams for the full range of field sizes (2-40 cm) so long as they are from the same manufacturer.« less

Lamp mapping technique for independent determination of the water vapor mixing ratio calibration factor for a Raman lidar system

NASA Astrophysics Data System (ADS)

Venable, Demetrius D.; Whiteman, David N.; Calhoun, Monique N.; Dirisu, Afusat O.; Connell, Rasheen M.; Landulfo, Eduardo

2011-08-01

We have investigated a technique that allows for the independent determination of the water vapor mixing ratio calibration factor for a Raman lidar system. This technique utilizes a procedure whereby a light source of known spectral characteristics is scanned across the aperture of the lidar system's telescope and the overall optical efficiency of the system is determined. Direct analysis of the temperature-dependent differential scattering cross sections for vibration and vibration-rotation transitions (convolved with narrowband filters) along with the measured efficiency of the system, leads to a theoretical determination of the water vapor mixing ratio calibration factor. A calibration factor was also obtained experimentally from lidar measurements and radiosonde data. A comparison of the theoretical and experimentally determined values agrees within 5%. We report on the sensitivity of the water vapor mixing ratio calibration factor to uncertainties in parameters that characterize the narrowband transmission filters, the temperature-dependent differential scattering cross section, and the variability of the system efficiency ratios as the lamp is scanned across the aperture of the telescope used in the Howard University Raman Lidar system.

Magnesium isotopic evidence for chemical disequilibrium among cumulus minerals in layered mafic intrusion

NASA Astrophysics Data System (ADS)

Chen, Lie-Meng; Teng, Fang-Zhen; Song, Xie-Yan; Hu, Rui-Zhong; Yu, Song-Yue; Zhu, Dan; Kang, Jian

2018-04-01

Magnesium isotopic compositions of olivine, clinopyroxene, and ilmenite from the Baima intrusion, SW China, for the first time, are investigated to constrain the magnitude and mechanisms of Mg isotope fractionation among cumulus minerals in layered mafic intrusions and to evaluate their geological implications. Olivine and clinopyroxene have limited Mg isotope variations, with δ26Mg ranging from -0.33 to +0.05‰ and from -0.29 to -0.13‰, respectively, similar to those of mantle xenolithic peridotites. By contrast, ilmenites display extremely large Mg isotopic variation, with δ26Mg ranging from -0.50 to +1.90‰. The large inter-mineral fractionations of Mg isotopes between ilmenite and silicates may reflect both equilibrium and kinetic processes. A few ilmenites have lighter Mg isotopic compositions than coexisting silicates and contain high MgO contents without compositional zoning, indicating equilibrium fractionation. The implication is that the light Mg isotopic compositions of lunar high-Ti basalts may result from an isotopically light source enriched in cumulate ilmenites. On the other hand, most ilmenites have heavy Mg isotopic compositions, coupled with high MgO concentration and chemical zoning, which can be quantitatively modeled by kinetic Mg isotope fractionations induced by subsolidus Mg-Fe exchange between ilmenite and ferromagnesian silicates during the cooling of the Baima intrusion. The extensive occurrence of kinetic Mg isotope fractionation in ilmenites implies the possibility of widespread compositional disequilibrium among igneous minerals in magma chambers. Consequently, disequilibrium effects need to be considered in studies of basaltic magma evolution, magma chamber processes, and magmatic Fe-Ti oxide ore genesis.

AlGaInAs EML having high extinction ratios fabricated by identical epitaxial layer technique

NASA Astrophysics Data System (ADS)

Deng, Qiufang; Guo, Lu; Liang, Song; Sun, Siwei; Xie, Xiao; Zhu, Hongliang; Wang, Wei

2018-04-01

AlGaInAs electroabsorption-modulated lasers (EMLs) fabricated by identical epitaxial layer technique are demonstrated. The EML device shows an infinite characteristic temperature when the temperature ranges from 20 oC to 30 oC. The integrated modulator has static extinction ratios of larger than 20 dB at a reverse bias voltage of - 2 V. The small signal modulation bandwidth of the modulator is larger than 11 GHz. At 10 Gb/s data modulation, the dynamic extinction ratio is about 9.5 dB in a back to back test configuration. Because only a simple fabrication procedure is needed, our EMLs are promising low cost light sources for optical fiber transmission applications.

The Effect of Educational Disequilibrium in Field Work on Graduate Social Work Students' Self-Concept and Mental Health

ERIC Educational Resources Information Center

Ying, Yu-Wen

2011-01-01

The author used a mixed methods design to assess field work-related educational disequilibrium and its effect on the self-concept and mental health of MSW students. Twenty-eight advanced, fourth-semester MSW students were compared with 37 entering, first-semester MSW students in practice-related sense of accomplishment. Compared with first-year…

Temperature and precipitation records from stalagmites grown under disequilibrium conditions: A model approach.

NASA Astrophysics Data System (ADS)

Mühlinghaus, C.; Scholz, D.; Mangini, A.

2009-04-01

To reconstruct past variations in Earth's climate, a variety of climate archives are studied. During the last decades stalagmites came into focus due to their long, continuous growth and absolute dating techniques. In this study a numerical model was developed, which calculates variations in temperature and precipitation during the growth period of stalagmites grown under isotopic disequilibrium conditions using the isotope profiles both along the growth axis and individual growth layers as well as the growth depth relation. The model is based on the inversion and combination of existing models (Dreybrodt 1999, Kaufmann et al. 2004, Mühlinghaus et al. 2007, Scholz et al. 2008, Mühlinghaus et al. 2008b) and incorporates important parameters describing the cave and the overlying soil. Beside the dependence on temperature and water supply it depends on the isotopic composition of the drip water, the pCO2 pressure of the soil and the cave atmosphere as well as on the mixing coefficient, which describes mixing between the impinging drop and the existing solution layer. To determine the characteristics of temperature and precipitation, in a first step all other parameters are assumed to remain constant over the whole growth period to simplify calculations. This allows to run the model with only two input variables: the isotopic composition ^13C of the drip water and a temperature information at any point of time during the growth period of the stalagmite (e.g. the recent cave temperature). All other parameters are determined by the model. The CSM (Combined Stalagmite Model, Mühlinghaus et al. 2008a) was applied to three stalagmites from the Marcelo Arévalo cave in Southern Patagonia, Chile (Schimpf 2005, Kilian et al. 2006, Schimpf et al. in prep). These stalagmites grew in a small cave next to each other during the last 4500 years. However, their isotopic profiles along the growth axis show different kinetic influences. Despite these conditions, the temperature

Nitrogen Isotopic Disequilibrium in the Cape York III A Iron

NASA Astrophysics Data System (ADS)

Zipfel, J.; Kim, Y.; Marti, K.

1995-09-01

disequilibrium as observed in Cape York include (a) survival of primary isotopic heterogeneities; (b) N loss during secondary processes, e.g., metamorphic heating and shock deformation: (a) Graphite grains within metal of the Acapulco meteorite were identified as carrier of isotopically distinct N and C components and were interpreted as surviving (possibly presolar) grains unaffected by the igneous alteration of the bulk meteorite (5). Obviously such grains exchanged N isotopically with metal and chromite, but not with sulfides and silicates, as these do not carry the light N of metal and chromite (6). The mechanism of this exchange is, however, unclear. No graphite has been observed so far in Cape York. Yet, isotopic heterogeneities in the precursor material of Cape York can not be excluded. During melting of the parent asteroid one would expect homogenization of the nitrogen isotopes. Since chromite and metal crystallize at high temperatures, a probable exchange of N between the S-rich melt and a distinct N reservoir at lower temperature might explain the disequilibrium. (b) Troilite nodules in Cape York indicate a small degree of shock deformation (2,3,5). One might argue that some N was lost and the residue fractionated during this event. However, 107Ag/109Ag ratios from metal and troilite correlate with Pd/Ag ratios, which is not the case in severely shocked magmatic irons (7). In addition, similar isotopic N fractionations are found in the "magmatic" Acapulco meteorite, which shows no indication of shock deformation. Therefore, secondary loss of N preferentially from troilite can be excluded. References: [1] Haak H. and Scott E. (1993) GCA, 57, 3457-3472. [2] Buchwald V. (1975) Handbook of Iron Meteorites, Vols. 1_3, Univ. of California and Arizona State Univ., Berkeley. [3] Kracher A et al. (1977) Geochem. J., 11, 207-217. [4] Murty S. and Marti K. (1994) GCA, 58, 1841-1848. [5] El Goresy A. et al. (1995) Nature, 373, 496-499. [6] Kim Y. et al. (1992) LPS XXIII, 691

Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae).

PubMed

Moraes, M A; Kubota, T Y K; Silva, E C B; Silva, A M; Cambuim, J; Moraes, M L T; Furlani Junior, E; Sebbenn, A M

2016-07-29

Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.

Searching for disease-susceptibility loci by testing for Hardy-Weinberg disequilibrium in a gene bank of affected individuals.

PubMed

Lee, Wen-Chung

2003-09-01

The future of genetic studies of complex human diseases will rely more and more on the epidemiologic association paradigm. The author proposes to scan the genome for disease-susceptibility gene(s) by testing for deviation from Hardy-Weinberg equilibrium in a gene bank of affected individuals. A power formula is presented, which is very accurate as revealed by Monte Carlo simulations. If the disease-susceptibility gene is recessive with an allele frequency of < or = 0.5 or dominant with an allele frequency of > or = 0.5, the number of subjects needed by the present method is smaller than that needed by using a case-parents design (using either the transmission/disequilibrium test or the 2-df likelihood ratio test). However, the method cannot detect genes with a multiplicative mode of inheritance, and the validity of the method relies on the assumption that the source population from which the cases arise is in Hardy-Weinberg equilibrium. Thus, it is prone to produce false positive and false negative results. Nevertheless, the method enables rapid gene hunting in an existing gene bank of affected individuals with no extra effort beyond simple calculations.

Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

PubMed

Wall, Jeffrey D; Stevison, Laurie S

2016-08-09

With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. Copyright © 2016 Wall and Stevison.

Evidence, from family studies, for linkage disequilibrium between TGFA and a gene for nonsyndromic cleft lip with or without cleft palate

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

Feng, Hongshu; Lee, A.; Gasser, D.L.

1994-11-01

The inheritance of alleles of the transforming growth factor alpha (TGFA) locus has been studied in families affected with cleft lip with or without cleft palate (CL/P), by using the transmission/disequilibrium test described by Spielman and colleagues. Only heterozygous parents with an affected child can be included in this test, but within such families a significantly greater frequency of C2 alleles were transmitted to affected children than would be expected by chance. There was no evidence that the total number of C2 alleles transmitted to affected and unaffected children differed significantly from random segregation. These data provide evidence from withinmore » families that a gene for susceptibility to CL/P is in significant linkage disequilibrium with the C2 allele of the TGFA locus. 30 refs., 1 fig., 2 tabs.« less

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-gro...

Sample selection and spatial models of housing price indexes, and, A disequilibrium analysis of the U.S. gasoline market using panel data

NASA Astrophysics Data System (ADS)

Hu, Haixin

This dissertation consists of two parts. The first part studies the sample selection and spatial models of housing price index using transaction data on detached single-family houses of two California metropolitan areas from 1990 through 2008. House prices are often spatially correlated due to shared amenities, or when the properties are viewed as close substitutes in a housing submarket. There have been many studies that address spatial correlation in the context of housing markets. However, none has used spatial models to construct housing price indexes at zip code level for the entire time period analyzed in this dissertation to the best of my knowledge. In this paper, I study a first-order autoregressive spatial model with four different weighing matrix schemes. Four sets of housing price indexes are constructed accordingly. Gatzlaff and Haurin (1997, 1998) study the sample selection problem in housing index by using Heckman's two-step method. This method, however, is generally inefficient and can cause multicollinearity problem. Also, it requires data on unsold houses in order to carry out the first-step probit regression. Maximum likelihood (ML) method can be used to estimate a truncated incidental model which allows one to correct for sample selection based on transaction data only. However, convergence problem is very prevalent in practice. In this paper I adopt Lewbel's (2007) sample selection correction method which does not require one to model or estimate the selection model, except for some very general assumptions. I then extend this method to correct for spatial correlation. In the second part, I analyze the U.S. gasoline market with a disequilibrium model that allows lagged-latent variables, endogenous prices, and panel data with fixed effects. Most existing studies (see the survey of Espey, 1998, Energy Economics) of the gasoline market assume equilibrium. In practice, however, prices do not always adjust fast enough to clear the market

Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon

USDA-ARS?s Scientific Manuscript database

Large datasets containing single nucleotide polymorphisms (SNPs) are used to analyze genome-wide diversity in a robust collection of cultivars from representative accessions, across the world. The extent of linkage disequilibrium (LD) within a population determines the number of markers required fo...

Equilibrium and Disequilibrium of River Basins: Effects on Stream Captures in Serra do Mar and Serra da Mantiqueira, Brazil

NASA Astrophysics Data System (ADS)

DA Silva, L. M.

2015-12-01

Landscapes are mainly driven by river processes that control the dynamic reorganization of networks. Discovering and identifying whether river basins are in geometric equilibrium or disequilibrium requires an analysis of water divides, channels that shift laterally or expand upstream and river captures. Issues specifically discussed include the variation of drainage area change and erosion rates of the basins. In southeastern Brazil there are two main escarpments with extensive geomorphic surfaces: Serra do Mar and Serra da Mantiqueira Mountains. These landscapes are constituted of Neoproterozoic and early Paleozoic rocks, presenting steep escarpments with low-elevation coastal plains and higher elevation interior plateaus. To identify whether river basins and river profiles are in equilibrium or disequilibrium in Serra do Mar and Serra da Mantiqueira Mountains, we used the proxy (χ), evaluating the effect of drainage area change and erosion rates. We selected basins that drain both sides of these two main escarpments (oceanic and continental sides) and have denudation rates derived from pre-existing cosmogenic isotopes data (Rio de Janeiro, Paraná and Minas Gerais). Despite being an ancient and tectonically stable landscape, part of the coastal plain of Serra do Mar Mountain in Rio de Janeiro and Paraná is in geometric disequilibrium, with water divides moving in the direction of higher χ values. To achieve equilibrium, some basins located in the continental side are retracting and disappearing, losing area to the coastal basins. On the contrary, there are some adjacent sub-basins that are close to equilibrium, without strong contrasts in χ values. The same pattern was observed in Serra da Mantiqueira (Minas Gerais state), with stream captures and river network reorganization in its main rivers. The initial results suggest a strong contrast between erosion rates in the continental and the oceanic portions of the escarpments.

Linkage disequilibrium in HLA cannot be explained by selective recombination.

PubMed

Termijtelen, A; D'Amaro, J; van Rood, J J; Schreuder, G M

1995-11-01

Some combinations of HLA-A, -B and -DR antigens occur more frequently than would be expected from their gene frequencies in the population. This phenomenon, referred to as Linkage Disequilibrium (LD) has been the origin of many speculations. One hypothesis to explain LD is that some haplotypes are protected from recombination. A second hypothesis is that these HLA antigens preferentially recombine after cross-over to create an LD haplotype. We tested these 2 hypotheses: from a pool of over 10,000 families typed in our department, we analyzed 126 families in which HLA-A:B or B:DR recombinant offspring was documented. To overcome a possible bias in our material, we used the non-recombined haplotypes from the same 126 families as a control group. Our results show that the number of cross-overs through LD haplotypes is not significantly lower then would be expected if recombination occurred randomly. Also the number of LD haplotypes created upon recombination was not significantly increased.

Delayed, disequilibrium degassing in rhyolite magma: Decompression experiments and implications for explosive volcanism

USGS Publications Warehouse

Mangan, M.; Sisson, T.

2000-01-01

Recent numerical models and analog shock tube experiments show that disequilibrium degassing during magma ascent may lead to violent vesiculation very near the surface. In this study a series of decompression experiments using crystal-free, rhyolite melt were conducted to examine the development of large supersaturations due to delayed, homogenous (spontaneous) bubble nucleation. Melts were saturated at 900??C and 200 MPa with either 5.2 wt% dissolved H2O, or with 4.2 wt% H2O and 640 ppm CO2, and isothermally decompressed at linear rates of either 0.003, 0.025, or 8.5 MPa/s to final pressures between 25 and 175 MPa. Additional isobaric saturation experiments (900??C, 200-25 MPa) using pure H2O or mixed H2O-CO2 fluids establish reference equilibrium solubility curves/values. Homogenous nucleation is triggered in both H2O-only and H2O-CO2 experiments once the supersaturation pressure (??Pss) reaches ?? 120-150 MPa and the melt contains ?? two times its equilibrium water contents. Bubble number density and nucleation rate depend on the supersaturation pressure, with values on the order of 102/cm3 and < 1/cm3/s for ??Pss~120 MPa; 106/cm3 and 103-105/cm3/s for ??Pss??~130-150 MPa; and 107/cm3 and 106/cm3/s for ??Pss??160-175 MPa. Nucleation rates are consistent with classical nucleation theory, and infer an activation energy for nucleation of 1.5 x 10-18 J/nucleus, a critical bubble radius of 2 x 10-9 m, and an effective surface tension for rhyolite at 5.2 wt% H2O and 900??C of 0.10-0.11 N/m. The long nucleation delay limits the time available for subsequent diffusion such that disequilibrium dissolved H2O and CO2 contents persist to the end of our runs. The disequilibrium degassing paths inferred from our experiments contrast markedly with the equilibrium or quasi-equilibrium paths found in other studies where bubble nucleation occurs heterogenously on crystals or other discontinuities in the melt at low ??Pss. Homogenous and heterogenous nucleation rates are

Mercury flux from salt marsh sediments: Insights from a comparison between 224Ra/228Th disequilibrium and core incubation methods

NASA Astrophysics Data System (ADS)

Shi, Xiangming; Mason, Robert P.; Charette, Matthew A.; Mazrui, Nashaat M.; Cai, Pinghe

2018-02-01

In aquatic environments, sediments are the main location of mercury methylation. Thus, accurate quantification of methylmercury (MeHg) fluxes at the sediment-water interface is vital to understanding the biogeochemical cycling of mercury, especially the toxic MeHg species, and their bioaccumulation. Traditional approaches, such as core incubations, are difficult to maintain at in-situ conditions during assays, leading to over/underestimation of benthic fluxes. Alternatively, the 224Ra/228Th disequilibrium method for tracing the transfer of dissolved substances across the sediment-water interface, has proven to be a reliable approach for quantifying benthic fluxes. In this study, the 224Ra/228Th disequilibrium and core incubation methods were compared to examine the benthic fluxes of both 224Ra and MeHg in salt marsh sediments of Barn Island, Connecticut, USA from May to August, 2016. The two methods were comparable for 224Ra but contradictory for MeHg. The radiotracer approach indicated that sediments were always the dominant source of both total mercury (THg) and MeHg. The core incubation method for MeHg produced similar results in May and August, but an opposite pattern in June and July, which suggested sediments were a sink of MeHg, contrary to the evidence of significant MeHg gradients between overlying water and porewater at the sediment-water interface. The potential reasons for such differences are discussed. Overall, we conclude that the 224Ra/228Th disequilibrium approach is preferred for estimating the benthic flux of MeHg and that sediment is indeed an important MeHg source in this marshland, and likely in other shallow coastal waters.

Novel linkage disequilibrium clustering algorithm identifies new lupus genes on meta-analysis of GWAS datasets.

PubMed

Saeed, Mohammad

2017-05-01

Systemic lupus erythematosus (SLE) is a complex disorder. Genetic association studies of complex disorders suffer from the following three major issues: phenotypic heterogeneity, false positive (type I error), and false negative (type II error) results. Hence, genes with low to moderate effects are missed in standard analyses, especially after statistical corrections. OASIS is a novel linkage disequilibrium clustering algorithm that can potentially address false positives and negatives in genome-wide association studies (GWAS) of complex disorders such as SLE. OASIS was applied to two SLE dbGAP GWAS datasets (6077 subjects; ∼0.75 million single-nucleotide polymorphisms). OASIS identified three known SLE genes viz. IFIH1, TNIP1, and CD44, not previously reported using these GWAS datasets. In addition, 22 novel loci for SLE were identified and the 5 SLE genes previously reported using these datasets were verified. OASIS methodology was validated using single-variant replication and gene-based analysis with GATES. This led to the verification of 60% of OASIS loci. New SLE genes that OASIS identified and were further verified include TNFAIP6, DNAJB3, TTF1, GRIN2B, MON2, LATS2, SNX6, RBFOX1, NCOA3, and CHAF1B. This study presents the OASIS algorithm, software, and the meta-analyses of two publicly available SLE GWAS datasets along with the novel SLE genes. Hence, OASIS is a novel linkage disequilibrium clustering method that can be universally applied to existing GWAS datasets for the identification of new genes.

Identification of a psoriasis susceptibility candidate gene by linkage disequilibrium mapping with a localized single nucleotide polymorphism map.

PubMed

Hewett, Duncan; Samuelsson, Lena; Polding, Joanne; Enlund, Fredrik; Smart, Devi; Cantone, Kathryn; See, Chee Gee; Chadha, Sapna; Inerot, Annica; Enerback, Charlotta; Montgomery, Doug; Christodolou, Chris; Robinson, Phil; Matthews, Paul; Plumpton, Mary; Wahlstrom, Jan; Swanbeck, Gunnar; Martinsson, Tommy; Roses, Allen; Riley, John; Purvis, Ian

2002-03-01

Psoriasis is a chronic inflammatory disease of the skin with both genetic and environmental risk factors. Here we describe the creation of a single-nucleotide polymorphism (SNP) map spanning 900-1200 kb of chromosome 3q21, which had been previously recognized as containing a psoriasis susceptibility locus, PSORS5. We genotyped 644 individuals, from 195 Swedish psoriatic families, for 19 polymorphisms. Linkage disequilibrium (LD) between marker and disease was assessed using the transmission/disequilibrium test (TDT). In the TDT analysis, alleles of three of these SNPs showed significant association with disease (P<0.05). A 160-kb interval encompassing these three SNPs was sequenced, and a coding sequence consisting of 13 exons was identified. The predicted protein shares 30-40% homology with the family of cation/chloride cotransporters. A five-marker haplotype spanning the 3' half of this gene is associated with psoriasis to a P value of 3.8<10(-5). We have called this gene SLC12A8, coding for a member of the solute carrier family 12 proteins. It belongs to a class of genes that were previously unrecognized as playing a role in psoriasis pathogenesis.

Divergence between human populations estimated from linkage disequilibrium.

PubMed

Sved, John A; McRae, Allan F; Visscher, Peter M

2008-12-01

Observed linkage disequilibrium (LD) between genetic markers in different populations descended independently from a common ancestral population can be used to estimate their absolute time of divergence, because the correlation of LD between populations will be reduced each generation by an amount that, approximately, depends only on the recombination rate between markers. Although drift leads to divergence in allele frequencies, it has less effect on divergence in LD values. We derived the relationship between LD and time of divergence and verified it with coalescent simulations. We then used HapMap Phase II data to estimate time of divergence between human populations. Summed over large numbers of pairs of loci, we find a positive correlation of LD between African and non-African populations at levels of up to approximately 0.3 cM. We estimate that the observed correlation of LD is consistent with an effective separation time of approximately 1,000 generations or approximately 25,000 years before present. The most likely explanation for such relatively low separation times is the existence of substantial levels of migration between populations after the initial separation. Theory and results from coalescent simulations confirm that low levels of migration can lead to a downward bias in the estimate of separation time.

Evaluation of techniques for handling missing cost-to-charge ratios in the USA Nationwide Inpatient Sample: a simulation study.

PubMed

Yu, Tzy-Chyi; Zhou, Huanxue

2015-09-01

Evaluate performance of techniques used to handle missing cost-to-charge ratio (CCR) data in the USA Healthcare Cost and Utilization Project's Nationwide Inpatient Sample. Four techniques to replace missing CCR data were evaluated: deleting discharges with missing CCRs (complete case analysis), reweighting as recommended by Healthcare Cost and Utilization Project, reweighting by adjustment cells and hot deck imputation by adjustment cells. Bias and root mean squared error of these techniques on hospital cost were evaluated in five disease cohorts. Similar mean cost estimates would be obtained with any of the four techniques when the percentage of missing data is low (<10%). When total cost is the outcome of interest, a reweighting technique to avoid underestimation from dropping observations with missing data should be adopted.

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers.

PubMed

Zhang, Yu; Yan, Haidong; Jiang, Xiaomei; Wang, Xiaoli; Huang, Linkai; Xu, Bin; Zhang, Xinquan; Zhang, Lexin

2016-01-01

To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass ( Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei's gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r 2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 ( P  < 0.01). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

A reliability design method for a lithium-ion battery pack considering the thermal disequilibrium in electric vehicles

NASA Astrophysics Data System (ADS)

Xia, Quan; Wang, Zili; Ren, Yi; Sun, Bo; Yang, Dezhen; Feng, Qiang

2018-05-01

With the rapid development of lithium-ion battery technology in the electric vehicle (EV) industry, the lifetime of the battery cell increases substantially; however, the reliability of the battery pack is still inadequate. Because of the complexity of the battery pack, a reliability design method for a lithium-ion battery pack considering the thermal disequilibrium is proposed in this paper based on cell redundancy. Based on this method, a three-dimensional electric-thermal-flow-coupled model, a stochastic degradation model of cells under field dynamic conditions and a multi-state system reliability model of a battery pack are established. The relationships between the multi-physics coupling model, the degradation model and the system reliability model are first constructed to analyze the reliability of the battery pack and followed by analysis examples with different redundancy strategies. By comparing the reliability of battery packs of different redundant cell numbers and configurations, several conclusions for the redundancy strategy are obtained. More notably, the reliability does not monotonically increase with the number of redundant cells for the thermal disequilibrium effects. In this work, the reliability of a 6 × 5 parallel-series configuration is the optimal system structure. In addition, the effect of the cell arrangement and cooling conditions are investigated.

Cognitive Disequilibrium and Service-Learning in Physical Education Teacher Education: Perceptions of Pre-Service Teachers in a Study Abroad Experience

ERIC Educational Resources Information Center

Ward, Stephen; Pellet, Heidi Henschel; Perez, Mark I.

2017-01-01

Purpose: The purpose of this study was to explore preservice teachers' experiences of cognitive disequilibrium (CD) theory during a service-learning project in a study abroad experience. Method: A case study with 8 participants was used. Data sources consisted of: Formal interviews, videos of planning, videos of teaching, videos of reflection…

High-Aspect-Ratio Ridge Structures Induced by Plastic Deformation as a Novel Microfabrication Technique.

PubMed

Takei, Atsushi; Jin, Lihua; Fujita, Hiroyuki; Takei, A; Fujita, H; Jin, Lihua

2016-09-14

Wrinkles on thin film/elastomer bilayer systems provide functional surfaces. The aspect ratio of these wrinkles is critical to their functionality. Much effort has been dedicated to creating high-aspect-ratio structures on the surface of bilayer systems. A highly prestretched elastomer attached to a thin film has recently been shown to form a high-aspect-ratio structure, called a ridge structure, due to a large strain induced in the elastomer. However, the prestretch requirements of the elastomer during thin film attachment are not compatible with conventional thin film deposition methods, such as spin coating, dip coating, and chemical vapor deposition (CVD). Thus, the fabrication method is complex, and ridge structure formation is limited to planar surfaces. This paper presents a new and simple method for constructing ridge structures on a nonplanar surface using a plastic thin film/elastomer bilayer system. A plastic thin film is attached to a stress-free elastomer, and the resulting bilayer system is highly stretched one- or two-dimensionally. Upon the release of the stretch load, the deformation of the elastomer is reversible, while the plastically deformed thin film stays elongated. The combination of the length mismatch and the large strain induced in the elastomer generates ridge structures. The morphology of the plastic thin film/elastomer bilayer system is experimentally studied by varying the physical parameters, and the functionality and the applicability to a nonplanar surface are demonstrated. Finally, we simulate the effect of plasticity on morphology. This study presents a new technique for generating microscale high-aspect-ratio structures and its potential for functional surfaces.

Th-230 - U-238 series disequilibrium of the Olkaria basalts Gregory Rift Valley, Kenya

NASA Technical Reports Server (NTRS)

Black, S.; Macdonald, R.; Kelly, M.

1993-01-01

U-Th disequilibrium analyses of the Naivasha basalts show a very small (U-238/Th-230) ratios which are lower than any previously analyzed basalts. The broadly positive internal isochron trend from one sample indicates that the basalts may have source heterogeneities, this is supported by earlier work. The Naivasha complex comprises a bimodal suite of basalts and rhyolites. The basalts are divided into two stratigraphic groups each of a transitional nature. The early basalt series (EBS) which were erupted prior to the Group 1 comendites and, the late basalt series (LBS) which erupted temporally between the Broad Acres and the Ololbutot centers. The basalts represent a very small percentage of the overall eruptive volume of material at Naivasha (less than 2 percent). The analyzed samples come from four stratigraphic units in close proximity around Ndabibi, Hell's Gate and Akira areas. The earliest units occur as vesicular flows from the Ndabibi plain. These basalts are olivine-plagioclase phyric with the associated hawaiites being sparsely plagioclase phyric. An absolute age of 0.5Ma was estimated for these basalts. The next youngest basalts flows occur as younger tuft cones in the Ndabibi area and are mainly olivine-plagioclase-clinopyroxcene phyric with one purely plagioclase phyric sample. The final phase of activity at Ndabibi resulted in much younger tuft cones consisting of air fall ashes and lapilli tufts. Many of these contain resorbed plagioclase phenocrysts with sample number 120c also being clinopyroxene phyric. The isotopic evidence for the basalt formation is summarized.

Disequilibrium growth of olivine in mafic magmas revealed by phosphorus zoning patterns of olivine from mafic-ultramafic intrusions

NASA Astrophysics Data System (ADS)

Xing, Chang-Ming; Wang, Christina Yan; Tan, Wei

2017-12-01

Olivine from mafic-ultramafic intrusions rarely displays growth zoning in major and some minor elements, such as Fe, Mg and Ni, due to fast diffusion of these elements at high temperatures. These elements in olivine are thus not useful in deciphering magma chamber processes, such as magma convection, multiple injection and mixing. High-resolution X-ray elemental intensity mapping reveals distinct P zoning patterns of olivine from two mafic-ultramafic intrusions in SW China. Polyhedral olivine grains from lherzolite and dunite of the Abulangdang intrusion show P-rich dendrites similar to those observed in volcanic rocks. Rounded olivine grains from net-textured Fe-Ti oxide ores of the Baima layered intrusion have irregular P-rich patches/bands crosscut and interlocked by P-poor olivine domains. P-rich patches/bands contain 250 to 612 ppm P, much higher than P-poor olivine domains with 123 to 230 ppm P. In electron backscattered diffraction (EBSD) maps, P-rich patches/bands within a single olivine grain have the same crystallographic orientation, indicating that they were remnants of the same crystal. Thus, both P-rich patches/bands and P-poor olivine domains in the same grain show a disequilibrium texture and clearly record two-stage growth. The P-rich patches/bands are likely the remnants of a polyhedral olivine crystal that formed in the first stage, whereas the P-poor olivine domains containing rounded Ti-rich magnetite and Fe-rich melt inclusions may have formed from an Fe-rich ambient melt in the second stage. The complex P zoning of olivine can be attributed to the dissolution of early polyhedral olivine and re-precipitation from the Fe-rich ambient melt. The early polyhedral olivine was in chemical disequilibrium with the ambient melt that may have been developed by silicate liquid immiscibility in a crystal mush. Our study implies that olivine crystals in igneous cumulates with an equilibrium appearance may have experienced disequilibrium growth processes

Small-scale disequilibrium in a magmatic inclusion and its more silicic host

NASA Technical Reports Server (NTRS)

Davidson, Jon P.; Holden, Peter; Halliday, Alex N.; De Silva, Shanaka L.

1990-01-01

An investigation of small-scale isotopic, compositional, and mineralogical variation across the interface of a basaltic-andesite inclusion and its dacitic host from Cerro-Chascon, a Holocene dome in northern Chile, is discussed. Serial sectioning across the interface of the inclusion and its host dacite, complemented by microdrill sampling and detailed microprobe work, has enabled an examination of the scale of mixing and chemical disequilibrium. The composition of the inclusion is found to be relatively homogeneous; the dacite host is heterogeneous on a small scale; the isotopic composition in the marginal zone shows the highest Sr-87/Sr-86 and lowest Nd-143/Nd-144; the large plagioclase crystals in the inclusions and host are xenocrystic. These differences are reconciled with a model of magma evolution in a crustal magma chamber.

Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

PubMed Central

Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

2002-01-01

Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

The Second Economy in Disequilibrium and Shortage Models of Centrally Planned Economies

DTIC Science & Technology

1988-07-01

CPEs 70 IV. The Second Economy in Disequilibrium Models 76 A. General Equilibrium Models with a Second Economy 78 B. The Portes Macroeconomic ...44,~g3 C AC4 v- 44,A0-.’ 3-3. 3 ~ .1 a a 0, a~ 0.a c 63 9 o -o.a- *~~~t a A . 2. 0 V 0 m -6 o 0 *Z 1 0 6Q 446O l ~ 4 ~ ~ ~ 1 0 v 90 3 ~ . 0 6 C a A OA ...A - - A C A A A C - - C * - A AY 0 - - A C A - A A - - ’A - ’A 4 A C A 6- C A ’A A - - .C A - - - - oA A A A 6-C - .C ’AA - A A A CI 4 = A

Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets.

PubMed

Edge, Michael D; Algee-Hewitt, Bridget F B; Pemberton, Trevor J; Li, Jun Z; Rosenberg, Noah A

2017-05-30

Combining genotypes across datasets is central in facilitating advances in genetics. Data aggregation efforts often face the challenge of record matching-the identification of dataset entries that represent the same individual. We show that records can be matched across genotype datasets that have no shared markers based on linkage disequilibrium between loci appearing in different datasets. Using two datasets for the same 872 people-one with 642,563 genome-wide SNPs and the other with 13 short tandem repeats (STRs) used in forensic applications-we find that 90-98% of forensic STR records can be connected to corresponding SNP records and vice versa. Accuracy increases to 99-100% when ∼30 STRs are used. Our method expands the potential of data aggregation, but it also suggests privacy risks intrinsic in maintenance of databases containing even small numbers of markers-including databases of forensic significance.

Comparison of two stable hydrogen isotope-ratio measurement techniques on Antarctic surface-water and ice samples

USGS Publications Warehouse

Hopple, J.A.; Hannon, J.E.; Coplen, T.B.

1998-01-01

A comparison of the new hydrogen isotope-ratio technique of Vaughn et al. ([Vaughn, B.H., White, J.W.C., Delmotte, M., Trolier, M., Cattani, O., Stievenard, M., 1998. An automated system for hydrogen isotope analysis of water. Chem. Geol. (Isot. Geosci. Sect.), 152, 309-319]; the article immediately preceding this article) for the analysis of water samples utilizing automated on-line reduction by elemental uranium showed that 94% of 165 samples of Antarctic snow, ice, and stream water agreed with the ??2H values determined by H2-H2O platinum equilibration, exhibiting a bias of +0.5??? and a 2 - ?? variation of 1.9???. The isotopic results of 10 reduction technique samples, however, gave ??2H values that differed by 3.5??? or more, and were too negative by as much as 5.4??? and too positive by as much as 4.9??? with respect to those determined using the platinum equilibration technique.

Constraints on the origin of Os-isotope disequilibrium in included and interstitial sulfides in mantle peridotites: Implications for the interpretation of Os-isotope signatures in MORB and Abyssal Peridotites

NASA Astrophysics Data System (ADS)

Lassiter, J. C.

2016-12-01

The use of isotope variations in basalts to probe the composition and evolution of the mantle is predicated on the assumption of local (i.e., grain-scale) isotopic equilibrium during mantle melting (Hofmann & Hart, 1978). However, several studies report Os-isotope disequilibrium in distinct populations of sulfides in some peridotites. In principle, grain-scale isotopic heterogeneity could reflect variable radiogenic ingrowth in ancient sulfides with variable Re/Os, or partial re-equilibration of low-Re/Os sulfides with high-Re/Os silicate phases along grain boundaries during mantle melting (e.g., Alard et al., 2005). Both cases require that sulfides fail to maintain isotopic equilibrium with neighboring phases over geologically long ( Ga) time scales. The preservation of Os-isotope disequilibrium in peridotites has been ascribed to the armoring effect of low-[Os] silicates, which limit diffusive exchange between isolated Os-rich phases. This raises the prospect that peridotite-derived melts may not inherit the Os-isotope composition of their source. The timescale required for diffusive equilibration between separate sulfide grains or between Os-rich sulfides and Os-poor silicates is a function of average sulfide size and spacing, Os diffusivity in armoring silicate minerals, and Os partitioning between silicate and sulfide phases. For typical sulfide abundances and sizes in mantle peridotites, neighboring sulfides are expected to re-equilibrate in less than a few 10s of m.y. at adiabatic mantle temperatures, even for very high (>106) sulfide/silicate KD values. Maintenance of disequilibrium requires very large sulfides (>100 um) separated by several mm and diffusion rates (D < 10-20 m2/s) slower than for most other elements in olivine. Equilibration timescales between sulfides and surrounding silicates are similar, so that large-scale isotopic disequilibrium between sulfides and silicates is also unlikely within the convecting mantle. Instead, observed grain

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.

PubMed Central

McKeigue, P M

1997-01-01

Where recent admixture has occurred between two populations that have different disease rates for genetic reasons, family-based association studies can be used to map the genes underlying these differences, if the ancestry of the alleles at each locus examined can be assigned to one of the two founding populations. This article explores the statistical power and design requirements of this approach. Markers suitable for assigning the ancestry of genomic regions could be defined by grouping alleles at closely spaced microsatellite loci into haplotypes, or generated by representational difference analysis. For a given relative risk between populations, the sample size required to detect a disease locus that accounts for this relative risk by linkage-disequilibrium mapping in an admixed population is not critically dependent on assumptions about genotype penetrances or allele frequencies. Using the transmission-disequilibrium test to search the genome for a locus that accounts for a relative risk of between 2 and 3 in a high-risk population, compared with a low-risk population, generally requires between 150 and 800 case-parent pairs of mixed descent. The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture. This approach has greater statistical power than allele-sharing designs and has obvious applications to the genetics of hypertension, non-insulin-dependent diabetes, and obesity. PMID:8981962

Lidar signal-to-noise ratio improvements: Considerations and techniques

NASA Astrophysics Data System (ADS)

Hassebo, Yasser Y.

The primary objective of this study is to improve lidar signal-to-noise ratio (SNR) and hence extend attainable lidar ranges through reduction of the sky background noise (BGP), which dominates other sources of noise in daytime operations. This is particularly important for Raman lidar techniques where the Raman backscattered signal of interest is relatively weak compared with the elastic backscatter lidars. Two approaches for reduction of sky background noise are considered: (1) Improvements in lidar SNR by optimization of the design of the lidar receiver were examined by a series of simulations. This part of the research concentrated on biaxial lidar systems, where overlap between laser beam and receiver field of view (FOV) is an important aspect of noise considerations. The first optimized design evolved is a wedge shaped aperture. While this design has the virtue of greatly reducing background light, it is difficult to implement practically, requiring both changes in area and position with lidar range. A second more practical approach, which preserves some of the advantages of the wedge design, was also evolved. This uses a smaller area circular aperture optimally located in the image plane for desired ranges. Simulated numerical results for a biaxial lidar have shown that the best receiver parameters selection is one using a small circular aperture (field stop) with a small telescope focal length f, to ensure the minimum FOV that accepts all return signals over the entire lidar range while at the same time minimizing detected BGP and hence maximizing lidar SNR and attainable lidar ranges. The improvement in lidar SNR was up to 18%. (2) A polarization selection technique was implemented to reduce sky background signal for linearly polarized monostatic elastic backscatter lidar measurements. The technique takes advantage of naturally occurring polarization properties in scattered sky light, and then ensures that both the lidar transmitter and receiver track and

Evaluation of Pleistocene groundwater flow through fractured tuffs using a U-series disequilibrium approach, Pahute Mesa, Nevada, USA

USGS Publications Warehouse

Paces, James B.; Nichols, Paul J.; Neymark, Leonid A.; Rajaram, Harihar

2013-01-01

Groundwater flow through fractured felsic tuffs and lavas at the Nevada National Security Site represents the most likely mechanism for transport of radionuclides away from underground nuclear tests at Pahute Mesa. To help evaluate fracture flow and matrix–water exchange, we have determined U-series isotopic compositions on more than 40 drill core samples from 5 boreholes that represent discrete fracture surfaces, breccia zones, and interiors of unfractured core. The U-series approach relies on the disruption of radioactive secular equilibrium between isotopes in the uranium-series decay chain due to preferential mobilization of 234U relative to 238U, and U relative to Th. Samples from discrete fractures were obtained by milling fracture surfaces containing thin secondary mineral coatings of clays, silica, Fe–Mn oxyhydroxides, and zeolite. Intact core interiors and breccia fragments were sampled in bulk. In addition, profiles of rock matrix extending 15 to 44 mm away from several fractures that show evidence of recent flow were analyzed to investigate the extent of fracture/matrix water exchange. Samples of rock matrix have 234U/238U and 230Th/238U activity ratios (AR) closest to radioactive secular equilibrium indicating only small amounts of groundwater penetrated unfractured matrix. Greater U mobility was observed in welded-tuff matrix with elevated porosity and in zeolitized bedded tuff. Samples of brecciated core were also in secular equilibrium implying a lack of long-range hydraulic connectivity in these cases. Samples of discrete fracture surfaces typically, but not always, were in radioactive disequilibrium. Many fractures had isotopic compositions plotting near the 230Th-234U 1:1 line indicating a steady-state balance between U input and removal along with radioactive decay. Numerical simulations of U-series isotope evolution indicate that 0.5 to 1 million years are required to reach steady-state compositions. Once attained, disequilibrium 234U/238U

Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes

PubMed Central

Lam, Tze Hau; Tay, Matthew Zirui; Wang, Bei; Xiao, Ziwei; Ren, Ee Chee

2015-01-01

Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases. PMID:26593880

Linkage disequilibrium interval mapping of quantitative trait loci.

PubMed

Boitard, Simon; Abdallah, Jihad; de Rochambeau, Hubert; Cierco-Ayrolles, Christine; Mangin, Brigitte

2006-03-16

For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods. Under a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations. Our method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates.

Characteristic vector analysis of inflection ratio spectra: New technique for analysis of ocean color data

NASA Technical Reports Server (NTRS)

Grew, G. W.

1985-01-01

Characteristic vector analysis applied to inflection ratio spectra is a new approach to analyzing spectral data. The technique applied to remote data collected with the multichannel ocean color sensor (MOCS), a passive sensor, simultaneously maps the distribution of two different phytopigments, chlorophyll alpha and phycoerythrin, the ocean. The data set presented is from a series of warm core ring missions conducted during 1982. The data compare favorably with a theoretical model and with data collected on the same mission by an active sensor, the airborne oceanographic lidar (AOL).

Disequilibrium in the uranium and actinium series in oil scale samples.

PubMed

Landsberger, S; Tamalis, D; Leblanc, C; Yoho, M D

2017-01-01

We have investigated the disequilibrium of the uranium and actinium series and have found both 226 Ra (90,200 ± 4300 Bq/kg) and 228 Ra have activity concentrations orders of magnitude higher that 238 U (1.83 ± 0.36 Bq/kg) and 232 Th (7.0 ± 0.4) which are at the head of the decay series. As well the activity concentration of 210 Pb (24,400 ± 1200 Bg/kg) was about 3.6 times less than 226 Ra. Once an efficiency curve was constructed summing corrections for specific isotopes in the decay change also needed to be taken in consideration. Furthermore, self-attenuation of the photons especially the 46.5 keV belonging to 210 Pb was calculated to be 78% since the scale had elevated elemental concentrations of high-Z elements such as barium and strontium. Copyright © 2016 Elsevier Ltd. All rights reserved.

Consequence of oxidant to monomer ratio on optical and structural properties of Polypyrrole thin film deposited by oxidation polymerization technique

NASA Astrophysics Data System (ADS)

Jatratkar, Aviraj A.; Yadav, Jyotiprakash B.; Kamat, Sandip V.; Patil, Vaishali S.; Mahadik, D. B.; Barshilia, Harish C.; Puri, Vijaya; Puri, R. K.

2015-05-01

This paper reports the effect of oxidant to monomer (O/M) ratio on optical and structural properties of Polypyrrole (PPy) thin film deposited by chemical oxidation polymerization technique. Noticeable changes have observed in the properties of PPy thin films with O/M ratio. Cauliflower structure have been observed in FE-SEM images, wherein grain size is observed to decrease with increase in O/M ratio. AFM results are in good agreement with FE-SEM results. From FTIR spectra it is found that, PPy is in highly oxidized form at low O/M ratio but oxidation decreased with increase in O/M ratio. Also C-C stretching vibrations of PPy ring is decreased whereas C=C stretching is increased with ratio. Absorption peak around 450 nm corresponds to π-π* transition and around 800 nm for polarons and bipolarons. The intensity of such peaks confirms the conductivity of PPy, which is observed maximum at low O/M ratio and found to decrease with increase in ratio. Optical band gap (BG) is found to increase from 2.07 eV to 2.11 eV with increase in the O/M ratio.

Diagnosis of 25 genotypes of human papillomaviruses for their physical statuses in cervical precancerous/cancerous lesions: a comparison of E2/E6E7 ratio-based vs. multiple E1-L1/E6E7 ratio-based detection techniques.

PubMed

Zhang, Rong; He, Yi-feng; Chen, Mo; Chen, Chun-mei; Zhu, Qiu-jing; Lu, Huan; Wei, Zhen-hong; Li, Fang; Zhang, Xiao-xin; Xu, Cong-jian; Yu, Long

2014-10-02

Cervical lesions caused by integrated human papillomavirus (HPV) infection are highly dangerous because they can quickly develop into invasive cancers. However, clinicians are currently hampered by the lack of a quick, convenient and precise technique to detect integrated/mixed infections of various genotypes of HPVs in the cervix. This study aimed to develop a practical tool to determine the physical status of different HPVs and evaluate its clinical significance. The target population comprised 1162 women with an HPV infection history of > six months and an abnormal cervical cytological finding. The multiple E1-L1/E6E7 ratio analysis, a novel technique, was developed based on determining the ratios of E1/E6E7, E2/E6E7, E4E5/E6E7, L2/E6E7 and L1/E6E7 within the viral genome. Any imbalanced ratios indicate integration. Its diagnostic and predictive performances were compared with those of E2/E6E7 ratio analysis. The detection accuracy of both techniques was evaluated using the gold-standard technique "detection of integrated papillomavirus sequences" (DIPS). To realize a multigenotypic detection goal, a primer and probe library was established. The integration rate of a particular genotype of HPV was correlated with its tumorigenic potential and women with higher lesion grades often carried lower viral loads. The E1-L1/E6E7 ratio analysis achieved 92.7% sensitivity and 99.0% specificity in detecting HPV integration, while the E2/E6E7 ratio analysis showed a much lower sensitivity (75.6%) and a similar specificity (99.3%). Interference due to episomal copies was observed in both techniques, leading to false-negative results. However, some positive results of E1-L1/E6E7 ratio analysis were missed by DIPS due to its stochastic detection nature. The E1-L1/E6E7 ratio analysis is more efficient than E2/E6E7 ratio analysis and DIPS in predicting precancerous/cancerous lesions, in which both positive predictive values (36.7%-82.3%) and negative predictive values (75

New theoretical models and ratio imaging techniques associated with the NASA earth resources spectral information system

NASA Technical Reports Server (NTRS)

Vincent, R. K.

1974-01-01

Four independent investigations are reported; in general these are concerned with improving and utilizing the correlation between the physical properties of natural materials as evidenced in laboratory spectra and spectral data collected by multispectral scanners. In one investigation, two theoretical models were devised that permit the calculation of spectral emittance spectra for rock and mineral surfaces of various particle sizes. The simpler of the two models can be used to qualitatively predict the effect of texture on the spectral emittance of rocks and minerals; it is also potentially useful as an aid in predicting the identification of natural atmospheric aerosol constituents. The second investigation determined, via an infrared ratio imaging technique, the best pair of infrared filters for silicate rock-type discrimination. In a third investigation, laboratory spectra of natural materials were compressed into 11-digit ratio codes for use in feature selection, in searches for false alarm candidates, and eventually for use as training sets in completely automatic data processors. In the fourth investigation, general outlines of a ratio preprocessor and an automatic recognition map processor are developed for on-board data processing in the space shuttle era.

Re-evaluation of the H+/site ratio of mitochondrial electron transport with the oxygen pulse technique.

PubMed

Brand, M D; Reynafarje, B; Lehninger, A L

1976-09-25

The number of protons ejected per pair of electrons passing each energy-conserving site in the electron transport chain (the H+/site ratio) has been investigated in rat liver mitochondria by means of the oxygen pulse technique introduced by Mitchell and Moyle (1967) (Biochem. J. 105, 1147-1162). The usual H+/site values of 2.0 observed by this method were found to be substantially underestimated as a result of the influx of phosphate into the mitochondria. This was shown by three different kinds of experiments. 1. Addition of N-ethylmaleimide or mersalyl, inhibitors of mitochondrial phosphate transport, increased the H+/site ratio from 2.0 to 3.0. The dependence of this effect on the concentration of either inhibitor was identical with that for inhibition of phosphate transport. Added phosphate diminished the H+/site ratio to values below 2.0 in the absence of N-ethylmaleimide. N-Ethylmaleimide protected the elevated H+/site ratio of 3.0 against the deleterious effect of added phosphate, but did not prevent a lowering effect of weak acid anions such as 3-hydroxybutyrate. 2. Prior washing of mitochondria to remove the endogenous phosphate that leaks out during the anaerobic preincubation led to H+/site ratios near 3.0, which were not increased by N-ethylmaleimide. Addition of low concentrations of phosphate to such phosphate-depleted mitochondria decreased the H+/site ratio to 2.0; addition of N-ethylmaleimide returned the ratio to 3.0. 3. Lowering the temperature to 5 degrees, which slows down phosphate transport, led to H+/site values of 3.0 even in the absence of N-ethylmaleimide. The H+/site ratio of 3.0 observed in the absence of phosphate movements was not dependent on any narrowly limited set of experimental conditions. It occurred with either Ca2+ or K+ (in the presence of valinomycin) as mobile permeant cation. It was independent of the concentration of succinate, oxygen, mitochondria, or rotenone, additions of Ca2+, Li+, or Na+ and was independent of

Polarization-discrimination technique to maximize the lidar signal-to-noise ratio for daylight operations.

PubMed

Hassebo, Yasser Y; Gross, Barry; Oo, Min; Moshary, Fred; Ahmed, Samir

2006-08-01

The impact and potential of a polarization-selection technique to reduce the sky background signal for linearly polarized monostatic elastic backscatter lidar measurements are examined. Taking advantage of naturally occurring polarization properties in scattered skylight, we devised a polarization-discrimination technique in which both the lidar transmitter and the receiver track and minimize detected sky background noise while maintaining maximum lidar signal throughput. Lidar elastic backscatter measurements, carried out continuously during daylight hours at 532 nm, show as much as a factor of square root 10 improvement in the signal-to-noise ratio (SNR) over conventional unpolarized schemes. For vertically pointing lidars, the largest improvements are limited to the early morning and late afternoon hours, while for lidars scanning azimuthally and in elevation at angles other than vertical, significant improvements are achievable over more extended time periods with the specific times and improvement factors depending on the specific angle between the lidar and the solar axes. The resulting diurnal variations in SNR improvement sometimes show an asymmetry with the solar angle that analysis indicates can be attributed to changes in observed relative humidity that modifies the underlying aerosol microphysics and observed optical depth.

Polarization-discrimination technique to maximize the lidar signal-to-noise ratio for daylight operations

NASA Astrophysics Data System (ADS)

Hassebo, Yasser Y.; Gross, Barry; Oo, Min; Moshary, Fred; Ahmed, Samir

2006-08-01

The impact and potential of a polarization-selection technique to reduce the sky background signal for linearly polarized monostatic elastic backscatter lidar measurements are examined. Taking advantage of naturally occurring polarization properties in scattered skylight, we devised a polarization-discrimination technique in which both the lidar transmitter and the receiver track and minimize detected sky background noise while maintaining maximum lidar signal throughput. Lidar elastic backscatter measurements, carried out continuously during daylight hours at 532 nm, show as much as a factor of square root 10 improvement in the signal-to-noise ratio (SNR) over conventional unpolarized schemes. For vertically pointing lidars, the largest improvements are limited to the early morning and late afternoon hours, while for lidars scanning azimuthally and in elevation at angles other than vertical, significant improvements are achievable over more extended time periods with the specific times and improvement factors depending on the specific angle between the lidar and the solar axes. The resulting diurnal variations in SNR improvement sometimes show an asymmetry with the solar angle that analysis indicates can be attributed to changes in observed relative humidity that modifies the underlying aerosol microphysics and observed optical depth.

Linkage disequilibrium between STRPs and SNPs across the human genome.

PubMed

Payseur, Bret A; Place, Michael; Weber, James L

2008-05-01

Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this idea, we measured associations between short-tandem-repeat polymorphisms (STRPs), which can mutate rapidly and recurrently, and SNPs in 721 regions across the human genome. We directly compared STRP-SNP LD with SNP-SNP LD from the same genomic regions in the human HapMap populations. The intensity of STRP-SNP LD, measured by the average of D', was reduced, consistent with the action of recurrent mutation. Nevertheless, a higher fraction of STRP-SNP pairs than SNP-SNP pairs showed significant LD, on both short (up to 50 kb) and long (cM) scales. These results reveal the substantial effects of mutational processes on LD at STRPs and provide important measures of the potential of STRPs for association mapping of disease genes.

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the...

Detecting isotopic ratio outliers

NASA Astrophysics Data System (ADS)

Bayne, C. K.; Smith, D. H.

An alternative method is proposed for improving isotopic ratio estimates. This method mathematically models pulse-count data and uses iterative reweighted Poisson regression to estimate model parameters to calculate the isotopic ratios. This computer-oriented approach provides theoretically better methods than conventional techniques to establish error limits and to identify outliers.

Dual sources of water overprinting on the low zircon δ18O metamorphic country rocks: Disequilibrium constrained through inverse modelling of partial reequilibration

PubMed Central

Wei, Chun-Sheng; Zhao, Zi-Fu

2017-01-01

Since water is only composed of oxygen and hydrogen, δ18O and δ2H values are thus utilized to trace the origin of water(s) and quantify the water-rock interactions. While Triassic high pressure (HP) and ultrahigh pressure (UHP) metamorphic rocks across the Dabie-Sulu orogen in central-eastern China have been well documented, postcollisional magmatism driven hydrothermal systems are little known. Here we show that two sources of externally derived water interactions were revealed by oxygen isotopes for the gneissic country rocks intruded by the early Cretaceous postcollisional granitoids. Inverse modellings indicate that the degree of disequilibrium (doD) of meteoric water interactions was more evident than that of magmatic one (−65 ± 1o vs. −20 ± 2°); the partial reequilibration between quartz and alkali feldspar oxygen isotopes with magmatic water was achieved at 340 °C with a water/rock (W/R) ratio of about 1.2 for an open-hydrothermal system; two-stage meteoric water interactions were unraveled with reequilibration temperatures less than 300 °C and W/R ratios around 0.4. The lifetime of fossil magmatic hydrothermal system overprinted on the low zircon δ18O orthogneissic country rocks was estimated to maintain up to 50 thousand years (Kyr) through oxygen exchange modellings. Four-stage isotopic evolutions were proposed for the magmatic water interacted gneiss. PMID:28091552

Applying a low energy HPGe detector gamma ray spectrometric technique for the evaluation of Pu/Am ratio in biological samples.

PubMed

Singh, I S; Mishra, Lokpati; Yadav, J R; Nadar, M Y; Rao, D D; Pradeepkumar, K S

2015-10-01

The estimation of Pu/(241)Am ratio in the biological samples is an important input for the assessment of internal dose received by the workers. The radiochemical separation of Pu isotopes and (241)Am in a sample followed by alpha spectrometry is a widely used technique for the determination of Pu/(241)Am ratio. However, this method is time consuming and many times quick estimation is required. In this work, Pu/(241)Am ratio in the biological sample was estimated with HPGe detector based measurements using gamma/X-rays emitted by these radionuclides. These results were compared with those obtained from alpha spectroscopy of sample after radiochemical analysis and found to be in good agreement. Copyright © 2015 Elsevier Ltd. All rights reserved.

Trace element zoning as a record of chemical disequilibrium during garnet growth

NASA Astrophysics Data System (ADS)

Chernoff, Carlotta B.; Carlson, William D.

1999-06-01

Trace element concentrations in pelitic garnets from the Picuris Range of New Mexico display precipitous changes coincident with abrupt variations in Ca concentration. These patterns probably arise from the transitory participation of different trace element enriched phases in the garnet forming reaction. Changes in the reactant and product assemblages occur at different times during the reaction history for crystals of different size, so they cannot be the result of any event affecting the entire rock, such as a change in pressure, temperature, or fluid composition. Instead, they reflect kinetic factors that cause Ca, Y, Yb, P, Ti, Sc, Zr, Hf, Sr, Na, and Li to fail to achieve chemical equilibrium during garnet growth. Caution is needed to avoid misinterpreting excursions in the concentration of these elements as event markers recording simultaneous rockwide changes in intensive parameters, when in fact they may record transient disequilibrium states that are local in scope, and not contemporaneous.

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

PubMed Central

Loh, Po-Ru; Lipson, Mark; Patterson, Nick; Moorjani, Priya; Pickrell, Joseph K.; Reich, David; Berger, Bonnie

2013-01-01

Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese. PMID:23410830

First Look at the Upper Tropospheric Ozone Mixing Ratio from OMI Estimated using the Cloud Slicing Technique

NASA Technical Reports Server (NTRS)

Bhartia, Pawan K.; Ziemke, Jerry; Chandra, Sushil; Joiner, Joanna; Vassilkov, Alexandra; Taylor, Steven; Yang, Kai; Ahn, Chang-Woo

2004-01-01

The Cloud Slicing technique has emerged as a powerful tool for the study of ozone in the upper troposphere. In this technique one looks at the variation with cloud height of the above-cloud column ozone derived from the backscattered ultraviolet instruments, such as TOMS, to determine the ozone mixing ratio. For this technique to work properly one needs an instrument with relatively good horizontal resolution with very good signal to noise in measuring above-cloud column ozone. In addition, one needs the (radiatively) effective cloud pressure rather than the cloud-top pressure, for the ultraviolet photons received by a satellite instrument are scattered from inside the cloud rather than from the top. For this study we use data from the OMI sensor, which was recently launched on the EOS Aura satellite. OMI is a W-Visible backscattering instrument with a nadir pixel size of 13 x 24 km. The effective cloud pressure is derived from a new algorithm based on Rotational Raman Scattering and O2-O2, absorption in the 340-400 nm band of OMI.

Optimized demineralization technique for the measurement of stable isotope ratios of nonexchangeable H in soil organic matter.

PubMed

Ruppenthal, Marc; Oelmann, Yvonne; Wilcke, Wolfgang

2013-01-15

To make use of the isotope ratio of nonexchangeable hydrogen (δ(2)H(n (nonexchangeable))) of bulk soil organic matter (SOM), the mineral matrix (containing structural water of clay minerals) must be separated from SOM and samples need to be analyzed after H isotope equilibration. We present a novel technique for demineralization of soil samples with HF and dilute HCl and recovery of the SOM fraction solubilized in the HF demineralization solution via solid-phase extraction. Compared with existing techniques, organic C (C(org)) and organic N (N(org)) recovery of demineralized SOM concentrates was significantly increased (C(org) recovery using existing techniques vs new demineralization method: 58% vs 78%; N(org) recovery: 60% vs 78%). Chemicals used for the demineralization treatment did not affect δ(2)H(n) values as revealed by spiking with deuterated water. The new demineralization method minimized organic matter losses and thus artificial H isotope fractionation, opening up the opportunity to use δ(2)H(n) analyses of SOM as a new tool in paleoclimatology or geospatial forensics.

The linkage disequilibrium pattern of the angiotensin converting enzyme gene in Arabic and Asian population groups.

PubMed

Kharrat, Najla; Abdelmouleh, Wafa; Abdelhedi, Rania; Alfadhli, Suad; Rebai, Ahmed

2012-01-01

DNA variations within the Angiotensin-Converting Enzyme (ACE) gene have been shown to be involved in the aetiology of several common diseases and the therapeutic response. This study reports a comparison of haplotype analysis of five SNPs in the ACE gene region using a sample of 100 healthy subjects derived from five different populations (Tunisian, Iranian, Kuwaiti, Bahraini and Indian). Strong linkage disequilibrium was found among all SNPs studied for all populations. Two SNPs (rs1800764 and rs4340) were identified as key SNPs for all populations. These SNPs will be valuable for future effective association studies of the ACE gene polymorphisms in Arab and Asian populations.

Measurement of the distribution of ventilation-perfusion ratios in the human lung with proton MRI: comparison with the multiple inert-gas elimination technique.

PubMed

Sá, Rui Carlos; Henderson, A Cortney; Simonson, Tatum; Arai, Tatsuya J; Wagner, Harrieth; Theilmann, Rebecca J; Wagner, Peter D; Prisk, G Kim; Hopkins, Susan R

2017-07-01

We have developed a novel functional proton magnetic resonance imaging (MRI) technique to measure regional ventilation-perfusion (V̇ A /Q̇) ratio in the lung. We conducted a comparison study of this technique in healthy subjects ( n = 7, age = 42 ± 16 yr, Forced expiratory volume in 1 s = 94% predicted), by comparing data measured using MRI to that obtained from the multiple inert gas elimination technique (MIGET). Regional ventilation measured in a sagittal lung slice using Specific Ventilation Imaging was combined with proton density measured using a fast gradient-echo sequence to calculate regional alveolar ventilation, registered with perfusion images acquired using arterial spin labeling, and divided on a voxel-by-voxel basis to obtain regional V̇ A /Q̇ ratio. LogSDV̇ and LogSDQ̇, measures of heterogeneity derived from the standard deviation (log scale) of the ventilation and perfusion vs. V̇ A /Q̇ ratio histograms respectively, were calculated. On a separate day, subjects underwent study with MIGET and LogSDV̇ and LogSDQ̇ were calculated from MIGET data using the 50-compartment model. MIGET LogSDV̇ and LogSDQ̇ were normal in all subjects. LogSDQ̇ was highly correlated between MRI and MIGET (R = 0.89, P = 0.007); the intercept was not significantly different from zero (-0.062, P = 0.65) and the slope did not significantly differ from identity (1.29, P = 0.34). MIGET and MRI measures of LogSDV̇ were well correlated (R = 0.83, P = 0.02); the intercept differed from zero (0.20, P = 0.04) and the slope deviated from the line of identity (0.52, P = 0.01). We conclude that in normal subjects, there is a reasonable agreement between MIGET measures of heterogeneity and those from proton MRI measured in a single slice of lung. NEW & NOTEWORTHY We report a comparison of a new proton MRI technique to measure regional V̇ A /Q̇ ratio against the multiple inert gas elimination technique (MIGET). The study reports good relationships

Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains.

PubMed

Kim, Yunjung; Feng, Sheng; Zeng, Zhao-Bang

2008-05-01

A map of the background levels of disequilibrium between nearby markers can be useful for association mapping studies. In order to assess the background levels of linkage disequilibrium (LD), multilocus LD measures are more advantageous than pairwise LD measures because the combined analysis of pairwise LD measures is not adequate to detect simultaneous allele associations among multiple markers. Various multilocus LD measures based on haplotypes have been proposed. However, most of these measures provide a single index of association among multiple markers and does not reveal the complex patterns and different levels of LD structure. In this paper, we employ non-homogeneous, multiple order Markov Chain models as a statistical framework to measure and partition the LD among multiple markers into components due to different orders of marker associations. Using a sliding window of multiple markers on phased haplotype data, we compute corresponding likelihoods for different Markov Chain (MC) orders in each window. The log-likelihood difference between the lowest MC order model (MC0) and the highest MC order model in each window is used as a measure of the total LD or the overall deviation from the gametic equilibrium for the window. Then, we partition the total LD into lower order disequilibria and estimate the effects from two-, three-, and higher order disequilibria. The relationship between different orders of LD and the log-likelihood difference involving two different orders of MC models are explored. By applying our method to the phased haplotype data in the ENCODE regions of the HapMap project, we are able to identify high/low multilocus LD regions. Our results reveal that the most LD in the HapMap data is attributed to the LD between adjacent pairs of markers across the whole region. LD between adjacent pairs of markers appears to be more significant in high multilocus LD regions than in low multilocus LD regions. We also find that as the multilocus total LD

Mapping the Rust Resistant Loci MXC3 and MER in P. trichocarpa and Assessing the Intermarker Linkage Disequilibrium in MXC3 Region

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

Yin, Tongming; Difazio, Stephen P.; Gunter, Lee E

In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa, we have mapped two resistance loci, MXC3 and MER, and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations. We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3. The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16more » kb, respectively. The MXC3 region also contained six disease-resistance candidate genes. The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker-aided selection.« less

Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.).

PubMed

Chen, Haofeng; Morrell, Peter L; de la Cruz, Marlene; Clegg, Michael T

2008-01-01

Resequencing studies provide the ultimate resolution of genetic diversity because they identify all mutations in a gene that are present within the sampled individuals. We report a resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado. The sample includes 21 wild accessions from Mexico, Costa Rica, Ecuador, and the Dominican Republic. Estimated levels of nucleotide polymorphism and linkage disequilibrium (LD) are obtained from fully resolved haplotype data from 4 nuclear loci that span 5960 nucleotide sites. Results show that, although avocado is a subtropical tree crop and a predominantly outcrossing plant, the overall level of genetic variation is not exceptionally high (nucleotide diversity at silent sites, pi(sil) = 0.0102) compared with available estimates from temperate plant species. Intralocus LD decays rapidly to half the initial value within about 1 kb. Estimates of recombination rate (based on the sequence data) show that the rate is not exceptionally high when compared with annual plants such as wild barley or maize. Interlocus LD is significant owing to substantial population structure induced by mixing of the 3 botanical races of avocado.

Semi-Empirical Validation of the Cross-Band Relative Absorption Technique for the Measurement of Molecular Mixing Ratios

NASA Technical Reports Server (NTRS)

Pliutau, Denis; Prasad, Narasimha S

2013-01-01

Studies were performed to carry out semi-empirical validation of a new measurement approach we propose for molecular mixing ratios determination. The approach is based on relative measurements in bands of O2 and other molecules and as such may be best described as cross band relative absorption (CoBRA). . The current validation studies rely upon well verified and established theoretical and experimental databases, satellite data assimilations and modeling codes such as HITRAN, line-by-line radiative transfer model (LBLRTM), and the modern-era retrospective analysis for research and applications (MERRA). The approach holds promise for atmospheric mixing ratio measurements of CO2 and a variety of other molecules currently under investigation for several future satellite lidar missions. One of the advantages of the method is a significant reduction of the temperature sensitivity uncertainties which is illustrated with application to the ASCENDS mission for the measurement of CO2 mixing ratios (XCO2). Additional advantages of the method include the possibility to closely match cross-band weighting function combinations which is harder to achieve using conventional differential absorption techniques and the potential for additional corrections for water vapor and other interferences without using the data from numerical weather prediction (NWP) models.

Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

PubMed

Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

2015-09-01

Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis.

PubMed

Verardi, A; Lucchini, V; Randi, E

2006-09-01

Occasional crossbreeding between free-ranging domestic dogs and wild wolves (Canis lupus) has been detected in some European countries by mitochondrial DNA sequencing and genotyping unlinked microsatellite loci. Maternal and unlinked genomic markers, however, might underestimate the extent of introgressive hybridization, and their impacts on the preservation of wild wolf gene pools. In this study, we genotyped 220 presumed Italian wolves, 85 dogs and 7 known hybrids at 16 microsatellites belonging to four different linkage groups (plus four unlinked microsatellites). Population clustering and individual assignments were performed using a Bayesian procedure implemented in structure 2.1, which models the gametic disequilibrium arising between linked loci during admixtures, aiming to trace hybridization events further back in time and infer the population of origin of chromosomal blocks. Results indicate that (i) linkage disequilibrium was higher in wolves than in dogs; (ii) 11 out of 220 wolves (5.0%) were likely admixed, a proportion that is significantly higher than one admixed genotype in 107 wolves found previously in a study using unlinked markers; (iii) posterior maximum-likelihood estimates of the recombination parameter r revealed that introgression in Italian wolves is not recent, but could have continued for the last 70 (+/- 20) generations, corresponding to approximately 140-210 years. Bayesian clustering showed that, despite some admixture, wolf and dog gene pools remain sharply distinct (the average proportions of membership to wolf and dog clusters were Q(w) = 0.95 and Q(d) = 0.98, respectively), suggesting that hybridization was not frequent, and that introgression in nature is counteracted by behavioural or selective constraints.

Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

PubMed

Jiang, Y; Slager, S L; Huang, J

2001-01-01

We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

Generalized disequilibrium test for association in qualitative traits incorporating imprinting effects based on extended pedigrees.

PubMed

Li, Jian-Long; Wang, Peng; Fung, Wing Kam; Zhou, Ji-Yuan

2017-10-16

For dichotomous traits, the generalized disequilibrium test with the moment estimate of the variance (GDT-ME) is a powerful family-based association method. Genomic imprinting is an important epigenetic phenomenon and currently, there has been increasing interest of incorporating imprinting to improve the test power of association analysis. However, GDT-ME does not take imprinting effects into account, and it has not been investigated whether it can be used for association analysis when the effects indeed exist. In this article, based on a novel decomposition of the genotype score according to the paternal or maternal source of the allele, we propose the generalized disequilibrium test with imprinting (GDTI) for complete pedigrees without any missing genotypes. Then, we extend GDTI and GDT-ME to accommodate incomplete pedigrees with some pedigrees having missing genotypes, by using a Monte Carlo (MC) sampling and estimation scheme to infer missing genotypes given available genotypes in each pedigree, denoted by MCGDTI and MCGDT-ME, respectively. The proposed GDTI and MCGDTI methods evaluate the differences of the paternal as well as maternal allele scores for all discordant relative pairs in a pedigree, including beyond first-degree relative pairs. Advantages of the proposed GDTI and MCGDTI test statistics over existing methods are demonstrated by simulation studies under various simulation settings and by application to the rheumatoid arthritis dataset. Simulation results show that the proposed tests control the size well under the null hypothesis of no association, and outperform the existing methods under various imprinting effect models. The existing GDT-ME and the proposed MCGDT-ME can be used to test for association even when imprinting effects exist. For the application to the rheumatoid arthritis data, compared to the existing methods, MCGDTI identifies more loci statistically significantly associated with the disease. Under complete and incomplete

Extreme isotopologue disequilibrium in molecular SIMS species during SHRIMP geochronology

NASA Astrophysics Data System (ADS)

Magee, Charles W., Jr.; Danišík, Martin; Mernagh, Terry

2017-12-01

The current limitation in the accuracy and precision of inter-element analysis in secondary ion mass spectrometry (SIMS) is the ability to find measurable quantities that allow relative differences in ionization and transmission efficiency of secondary ions to be normalized. In uranium-thorium-lead geochronology, the ability to make these corrections, or "calibrate" the data, results in an accuracy limit of approximately 1 %. This study looks at the ionization of uranium and thorium oxide species, which are traditionally used in U-Pb calibration, to explore the conditions under which isotopologues, or molecular species whose composition differs only in the isotopic composition of one or more atoms in the molecule, remain in or deviate from equilibrium. Isotopologue deficits of up to 0.2 (200 ‰) below ideal mixing are observed in UO2+ species during SIMS gechronological analyses using the SHRIMP IIe SIMS instrument. These are identified by bombarding natural U-bearing minerals with an 18O2- primary beam. The large anomalies are associated with repeat analyses down a single SIMS sputtering crater (Compston et al., 1984), analysis of high-uranium, radiation-damaged zircon, and analysis of baddeleyite. Analysis of zircon under routine conditions yield UO2+ isotopologue anomalies generally within a few percent of equilibrium. The conditions under which the isotopologue anomalies are observed are also conditions in which the UOx-based corrections, or calibration, for relative U vs. Pb ionization efficiencies fail. The existence of these isotopologue anomalies suggest that failure of the various UOx species to equilibrate with each other is the reason that none of them will successfully correct the U  / Pb ratio. No simple isotopologue-based correction is apparent. However, isotopologue disequilibrium appears to be a more sensitive tool for detecting high-U calibration breakdowns than Raman spectroscopy, which showed sharper peaks for ˜ 37 Ma high

Localization of an ataxia-telangiectasia gene by linkage disequilibrium in the Costa Rican population

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

Uhrhammer, N.A.; Lange, E.; Gatti, R.A.

1994-09-01

Linkage disequilibrium (LD) was studied in 27 Costa Rican families with ataxia-telangiectasia. Previous studies indicate that the ATA and ATC gene(s) are on chromosome 11q22.3, between D11S1819 and D11S927. We studied the ordered loci D11-S1816, S1817, S1343, S1819, S384, S535, S1295, S1818, S927, S1300 and S1004 by PCR and Southern blotting. We noted moderate LD at the more distant markers S1816, S1300, and S1004. LD was higher at markers closer to A-T, and also where A-T was associated with rarer alleles. This broad region of disequilibrium did not by itself contribute to further localization of the A-T gene(s). We analyzedmore » 54 affected chromosomal haplotypes. The most common haplotype occurred 34 times, including some that had recombined outside the known A-T region. Other haplotypes occurred seven times, five times, two occurred twice, and the four remaining were unique. The most common haplotype had `broken` at S927 in five different patients, placing A-T proximal to this marker. We looked for recombination events in 15 of the families to further localize A-T. We observed one family with a recombination event placing A-T distal to S1819. A second family appears to either not link to 11q22.3 or to have a double-crossover between the markers S384 and S927; two affected sibs share haplotypes for the entire region studied, and a normal sib shared the same two haplotypes. Since all or part of this A-T haplotype occurs in 32 other, unrelated, Costa Rican patients, we anticipate a double-crossover in the 1600 kb between the informative flanking markers. All other families show segregation patterns consistent with placing A-T at 11q22.3. These results demonstrate that the major A-T gene in the Costa Rican population is located between S1819 and S927 at 11q22.3.« less

Forcing lateral electron disequilibrium to spare lung tissue: a novel technique for stereotactic body radiation therapy of lung cancer

NASA Astrophysics Data System (ADS)

Disher, Brandon; Hajdok, George; Gaede, Stewart; Mulligan, Matthew; Battista, Jerry J.

2013-10-01

Stereotactic body radiation therapy (SBRT) has quickly become a preferred treatment option for early-stage lung cancer patients who are ineligible for surgery. This technique uses tightly conformed megavoltage (MV) x-ray beams to irradiate a tumour with ablative doses in only a few treatment fractions. Small high energy x-ray fields can cause lateral electron disequilibrium (LED) to occur within low density media, which can reduce tumour dose. These dose effects may be challenging to predict using analytic dose calculation algorithms, especially at higher beam energies. As a result, previous authors have suggested using low energy photons (<10 MV) and larger fields (>5 × 5 cm2) for lung cancer patients to avoid the negative dosimetric effects of LED. In this work, we propose a new form of SBRT, described as LED-optimized SBRT (LED-SBRT), which utilizes radiotherapy (RT) parameters designed to cause LED to advantage. It will be shown that LED-SBRT creates enhanced dose gradients at the tumour/lung interface, which can be used to manipulate tumour dose, and/or normal lung dose. To demonstrate the potential benefits of LED-SBRT, the DOSXYZnrc (National Research Council of Canada, Ottawa, ON) Monte Carlo (MC) software was used to calculate dose within a cylindrical phantom and a typical lung patient. 6 MV or 18 MV x-ray fields were focused onto a small tumour volume (diameter ˜1 cm). For the phantom, square fields of 1 × 1 cm2, 3 × 3 cm2, or 5 × 5 cm2 were applied. However, in the patient, 3 × 1 cm2, 3 × 2 cm2, 3 × 2.5 cm2, or 3 × 3 cm2 field sizes were used in simulations to assure target coverage in the superior-inferior direction. To mimic a 180° SBRT arc in the (symmetric) phantom, a single beam profile was calculated, rotated, and beams were summed at 1° segments to accumulate an arc dose distribution. For the patient, a 360° arc was modelled with 36 equally weighted (and spaced) fields focused on the tumour centre. A planning target volume (PTV) was

Uranium-series disequilibrium in tuffs from Yucca Mountain, Nevada, as evidence of pore-fluid flow over the last million years

USGS Publications Warehouse

Gascoyne, M.; Miller, N.H.; Neymark, L.A.

2002-01-01

Samples of tuff from boreholes drilled into fault zones in the Exploratory Studies Facility (ESF) and relatively unfractured rock of the Cross Drift tunnels, at Yucca Mountain, Nevada, have been analysed by U-series methods. This work is part of a project to verify the finding of fast flow-paths through the tuff to ESF level, indicated by the presence of 'bomb' 36Cl in pore fluids. Secular radioactive equilibrium in the U decay series, (i.e. when the radioactivity ratios 234U/238U, 230Th/234U and 226Ra/230Th all equal 1.00) might be expected if the tuff samples have not experienced radionuclide loss due to rock-water interaction occurring within the last million years. However, most fractured and unfractured samples were found to have a small deficiency of 234U (weighted mean 234U/238U=0.95??0.01) and a small excess of 230Th (weighted mean 230Th/234U 1.10??0.02). The 226Ra/230Th ratios are close to secular equilibrium (weighted mean = 0.94??0.07). These data indicate that 234U has been removed from the rock samples in the last ???350 ka, probably by pore fluids. Within the precision of the measurement, it would appear that 226Ra has not been mobilized and removed from the tuff, although there may be some localised 226Ra redistribution as suggested by a few ratio values that are significantly different from 1.0. Because both fractured and unfractured tuffs show approximately the same deficiency of 234U, this indicates that pore fluids are moving equally through fractured and unfractured rock, More importantly, fractured rock appears not to be a dominant pathway for groundwater flow (otherwise the ratio would be more strongly affected and the Th and Ra isotopic ratios would likely also show disequilibrium). Application of a simple mass-balance model suggests that surface infiltration rate is over an order of magnitude greater than the rate indicated by other infiltration models and that residence time of pore fluids at ESF level is about 400 a. Processes of U

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

PubMed Central

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod. PMID:22428056

Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers.

PubMed

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardes, Laëtitia; Xia, Ling; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

2012-01-01

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.

Non-heuristic automatic techniques for overcoming low signal-to-noise-ratio bias of localization microscopy and multiple signal classification algorithm.

PubMed

Agarwal, Krishna; Macháň, Radek; Prasad, Dilip K

2018-03-21

Localization microscopy and multiple signal classification algorithm use temporal stack of image frames of sparse emissions from fluorophores to provide super-resolution images. Localization microscopy localizes emissions in each image independently and later collates the localizations in all the frames, giving same weight to each frame irrespective of its signal-to-noise ratio. This results in a bias towards frames with low signal-to-noise ratio and causes cluttered background in the super-resolved image. User-defined heuristic computational filters are employed to remove a set of localizations in an attempt to overcome this bias. Multiple signal classification performs eigen-decomposition of the entire stack, irrespective of the relative signal-to-noise ratios of the frames, and uses a threshold to classify eigenimages into signal and null subspaces. This results in under-representation of frames with low signal-to-noise ratio in the signal space and over-representation in the null space. Thus, multiple signal classification algorithms is biased against frames with low signal-to-noise ratio resulting into suppression of the corresponding fluorophores. This paper presents techniques to automatically debias localization microscopy and multiple signal classification algorithm of these biases without compromising their resolution and without employing heuristics, user-defined criteria. The effect of debiasing is demonstrated through five datasets of invitro and fixed cell samples.

New Examination of the Traditional Raman Lidar Technique II: Temperature Dependence Aerosol Scattering Ratio and Water Vapor Mixing Ratio Equations

NASA Technical Reports Server (NTRS)

Whiteman, David N.; Abshire, James B. (Technical Monitor)

2002-01-01

In a companion paper, the temperature dependence of Raman scattering and its influence on the Raman water vapor signal and the lidar equations was examined. New forms of the lidar equation were developed to account for this temperature sensitivity. Here we use those results to derive the temperature dependent forms of the equations for the aerosol scattering ratio, aerosol backscatter coefficient, extinction to backscatter ratio and water vapor mixing ratio. Pertinent analysis examples are presented to illustrate each calculation.

Extended Linkage Disequilibrium Surrounding the Hemoglobin E Variant Due to Malarial Selection

PubMed Central

Ohashi, Jun ; Naka, Izumi ; Patarapotikul, Jintana ; Hananantachai, Hathairad ; Brittenham, Gary ; Looareesuwan, Sornchai ; Clark, Andrew G. ; Tokunaga, Katsushi 

2004-01-01

The hemoglobin E variant (HbE; β26Glu→Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240–4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection. PMID:15114532

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.

PubMed

Ohashi, Jun; Naka, Izumi; Patarapotikul, Jintana; Hananantachai, Hathairad; Brittenham, Gary; Looareesuwan, Sornchai; Clark, Andrew G; Tokunaga, Katsushi

2004-06-01

The hemoglobin E variant (HbE; ( beta )26Glu-->Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240-4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection.

Peak-to-average power ratio reduction in orthogonal frequency division multiplexing-based visible light communication systems using a modified partial transmit sequence technique

NASA Astrophysics Data System (ADS)

Liu, Yan; Deng, Honggui; Ren, Shuang; Tang, Chengying; Qian, Xuewen

2018-01-01

We propose an efficient partial transmit sequence technique based on genetic algorithm and peak-value optimization algorithm (GAPOA) to reduce high peak-to-average power ratio (PAPR) in visible light communication systems based on orthogonal frequency division multiplexing (VLC-OFDM). By analysis of hill-climbing algorithm's pros and cons, we propose the POA with excellent local search ability to further process the signals whose PAPR is still over the threshold after processed by genetic algorithm (GA). To verify the effectiveness of the proposed technique and algorithm, we evaluate the PAPR performance and the bit error rate (BER) performance and compare them with partial transmit sequence (PTS) technique based on GA (GA-PTS), PTS technique based on genetic and hill-climbing algorithm (GH-PTS), and PTS based on shuffled frog leaping algorithm and hill-climbing algorithm (SFLAHC-PTS). The results show that our technique and algorithm have not only better PAPR performance but also lower computational complexity and BER than GA-PTS, GH-PTS, and SFLAHC-PTS technique.

Financial Ratio Analysis Comes to Nonprofits.

ERIC Educational Resources Information Center

Chabotar, Kent John

1989-01-01

To evaluate their financial health, a growing number of colleges, universities, and other nonprofit organizations are using financial ratio analysis, a technique used in business. The strengths and weaknesses of ratio analysis are assessed and suggestions are made on how nonprofits can use it most effectively. (Author/MLW)

The changing distribution of a major surgical procedure across hospitals: were supply shifts and disequilibrium important?

PubMed

Friedman, B; Elixhauser, A

1995-01-01

This paper describes and analyzes the changing distribution across hospitals in the U.S. of total hip replacement surgery (THR) for the period 1980-1987. THR is one of the most costly single procedures contributing to health care expenses. Also, the use of THR exhibits a particularly high degree of geographic variation. Recent research pointed to shifts in demand as one plausible economic explanation for increasing use of THR. This paper questions whether shifts in supply may have been large enough to explain changes in patient mix and the relationship of patient mix to the number of procedures performed at a particular hospital. In addition, the relationship between total use of THR and the local availability of orthopaedic surgeons as well as the average allowable Medicare fee for standardized physician services is analyzed. These relationships might yield evidence to support a scenario of induced demand beyond the optimum for patients' welfare, or evidence of supply increase within a disequilibrium scenario. This study, using data for all THR patients in a large sample of hospitals, tends to reject the formulation of a market with independent supply and demand shifts where the supply shifts were the dominant forces. Hospitals with a larger number of THRs performed did not see a higher percentage of older, sicker, and lower income patients. It was more likely that demand shifts generated increases in capacity for surgical services. Moreover, there was little evidence for a persistent disequilibrium and only weak evidence for inducement. Also, we found little evidence that hospitals responded to financial incentives inherent in the Medicare payment system after 1983 to select among THR candidates in favour of those with below average expected cost. We did observe increased concentration over time of THR procedures in facilities with high volume--suggesting plausible demand shifts towards hospitals with a priori quality and cost advantages or who obtained those

DC-to-AC inverter ratio failure detector

NASA Technical Reports Server (NTRS)

Ebersole, T. J.; Andrews, R. E.

1975-01-01

Failure detection technique is based upon input-output ratios, which is independent of inverter loading. Since inverter has fixed relationship between V-in/V-out and I-in/I-out, failure detection criteria are based on this ratio, which is simply inverter transformer turns ratio, K, equal to primary turns divided by secondary turns.

Chromosome-wide linkage disequilibrium as a consequence of meiotic drive

PubMed Central

Dyer, Kelly A.; Charlesworth, Brian; Jaenike, John

2007-01-01

Adaptation by natural selection proceeds most efficiently when alleles compete solely on the basis of their effects on the survival and reproduction of their carriers. A major condition for this is equal Mendelian segregation, but meiotic drive can short-circuit this process. The evolution of drive often involves multiple, interacting genetic components, together with enhancers and suppressors of drive. Chromosomal inversions that suppress crossing over are also frequently associated with drive systems. This study investigates the effects of these processes on patterns of molecular evolution in the fly Drosophila recens, which is polymorphic for a driving X chromosome (XD). Whereas standard wild-type chromosomes exhibit high levels of polymorphism at multiple loci, all of the XD chromosomes effectively carry a single multilocus haplotype that spans at least 130 cM. The XD is associated with a complex set of inversions that completely suppresses recombination between the standard wild-type chromosome and XD in heterozygous females, which maintain nonrandom associations among loci that presumably interact epistatically for the expression of drive. The long-term costs of foregoing recombination may be substantial; in combination with its low equilibrium frequency, this makes the XD chromosome susceptible to the accumulation of deleterious mutations. Consistent with this, XD chromosomes are apparently fixed for a recessive mutation that causes female sterility. Thus, the XD in D. recens appears to be in chromosome-wide linkage disequilibrium and in the early stages of mutational degradation. PMID:17242362

Accounting for linkage disequilibrium in association analysis of diverse populations.

PubMed

Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

2014-04-01

The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases. © 2014 WILEY PERIODICALS, INC.

A potential dating technique using 228Th/228Ra ratio for tracing the chronosequence of elemental concentrations in plants.

PubMed

Chao, J H; Niu, H; Chiu, C Y; Lin, C

2007-06-01

We propose a radiometric method based on measurement of the radioactivity of the naturally occurring radionuclides (228)Ra and 228)Th and the derived (228)Th/(228)Ra ratios in plant samples to estimate plant age and the corresponding nutritional conditions in a field-growing fern, Dicranopteris linearis. Plant age (tissue age) was associated with the (228)Th/(228)Ra ratio in fronds, which implies the accumulation time of immobile elements in the plant tissue or the life span of the fronds. Results indicated that the accumulation of alkaline earth elements in D. linearis is relatively constant with increased age, while the K concentration is reversed with age because of translocation among plant tissues. Estimation of dating uncertainty based on measurement conditions revealed that the radiometric technique can be applied to trace chronosequential changes of elemental concentrations and environmental pollutants in plants with ages of less than 10-15 years.

Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.

PubMed

Sved, John A; Cameron, Emilie C; Gilchrist, A Stuart

2013-01-01

There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The Ne estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The 'Burrows composite index' is introduced in a novel way with a 'composite haplotype table'. We show that in a sample of diploid size S, the mean value of x2 or r2 from the composite haplotype table is biased by a factor of 1-1/(2S-1)2, rather than the usual factor 1+1/(2S-1) for a conventional haplotype table. But analysis of population data using these formulae leads to Ne estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low Ne estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to r2, and find that this factor leads to a bias in the Ne estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered r2 with lower variance than the original r2, and one that is also insensitive to null alleles. The resulting formulae are used to provide Ne estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent Ne expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated Ne values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

PubMed

He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

2015-01-01

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

Using Object Oriented Bayesian Networks to Model Linkage, Linkage Disequilibrium and Mutations between STR Markers

PubMed Central

Kling, Daniel; Egeland, Thore; Mostad, Petter

2012-01-01

In a number of applications there is a need to determine the most likely pedigree for a group of persons based on genetic markers. Adequate models are needed to reach this goal. The markers used to perform the statistical calculations can be linked and there may also be linkage disequilibrium (LD) in the population. The purpose of this paper is to present a graphical Bayesian Network framework to deal with such data. Potential LD is normally ignored and it is important to verify that the resulting calculations are not biased. Even if linkage does not influence results for regular paternity cases, it may have substantial impact on likelihood ratios involving other, more extended pedigrees. Models for LD influence likelihoods for all pedigrees to some degree and an initial estimate of the impact of ignoring LD and/or linkage is desirable, going beyond mere rules of thumb based on marker distance. Furthermore, we show how one can readily include a mutation model in the Bayesian Network; extending other programs or formulas to include such models may require considerable amounts of work and will in many case not be practical. As an example, we consider the two STR markers vWa and D12S391. We estimate probabilities for population haplotypes to account for LD using a method based on data from trios, while an estimate for the degree of linkage is taken from the literature. The results show that accounting for haplotype frequencies is unnecessary in most cases for this specific pair of markers. When doing calculations on regular paternity cases, the markers can be considered statistically independent. In more complex cases of disputed relatedness, for instance cases involving siblings or so-called deficient cases, or when small differences in the LR matter, independence should not be assumed. (The networks are freely available at http://arken.umb.no/~dakl/BayesianNetworks.) PMID:22984448

speed-ne: Software to simulate and estimate genetic effective population size (Ne ) from linkage disequilibrium observed in single samples.

PubMed

Hamilton, Matthew B; Tartakovsky, Maria; Battocletti, Amy

2018-05-01

The genetic effective population size, N e , can be estimated from the average gametic disequilibrium (r2^) between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed-ne is a suite of matlab computer code functions to estimate Ne^ from r2^ with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed-ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of Ne^ estimators under various population genetic scenarios. speed-ne was validated with data simulated under both time-forward and time-backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on Ne^, how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact Ne^. Estimators differed greatly in precision in the scenarios examined, and a widely employed Ne^ estimator exhibited the largest variances among replicate data sets. speed-ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed-ne provides an open-source extensible tool for estimation of Ne^ from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare Ne^ estimators. © 2018 John Wiley & Sons Ltd.

Extreme U-Th disequilibrium in rift-related basalts, rhyolites and granophyric granite and the timescale of rhyolite generation, intrusion and crystallization at Alid volcanic center, Eritrea

USGS Publications Warehouse

Lowenstern, J. B.; Charlier, B.L.A.; Clynne, M.A.; Wooden, J.L.

2006-01-01

Rhyolite pumices and co-erupted granophyric (granite) xenoliths yield evidence for rapid magma generation and crystallization prior to their eruption at 15·2 ± 2·9 ka at the Alid volcanic center in the Danikil Depression, Eritrea. Whole-rock U and Th isotopic analyses show 230Th excesses up to 50% in basalts <10 000 years old from the surrounding Oss lava fields. The 15 ka rhyolites also have 30–40% 230Th excesses. Similarity in U–Th disequilibrium, and in Sr, Nd, and Pb isotopic values, implies that the rhyolites are mostly differentiated from the local basaltic magma. Given the (230Th/232Th) ratio of the young basalts, and presumably the underlying mantle, the (230Th/232Th) ratio of the rhyolites upon eruption could be generated by in situ decay in about 50 000 years. Limited (∼5%) assimilation of old crust would hasten the lowering of (230Th/232Th) and allow the process to take place in as little as 30 000 years. Final crystallization of the Alid granophyre occurred rapidly and at shallow depths at ∼20–25 ka, as confirmed by analyses of mineral separates and ion microprobe data on individual zircons. Evidently, 30 000–50 000 years were required for extraction of basalt from its mantle source region, subsequent crystallization and melt extraction to form silicic magmas, and final crystallization of the shallow intrusion. The granophyre was then ejected during eruption of the comagmatic rhyolites.

Resolved 12CH2D2 and 13CH3D in CH4 as Sensitive Indicators of Disequilibrium and Equilibrium during Microbial Methane Cycling

NASA Astrophysics Data System (ADS)

Ash, J. L.; Egger, M.; Slomp, C. P.; Kohl, I. E.; Treude, T.; Rumble, D.; Young, E. D.

2016-12-01

The ability to measure the relative concentrations of at least two doubly-substituted rare isotopologues of gases with biogeochemical relevance provides new constraints on sources and sinks of these gases. In particular, as shown recently for O2, the use of two independent, rare isotopologues allows for detection of thermodynamic intra-species equilibrium and disequilibrium. Here, we report the first measurements of fully resolved 13CH3D and 12CH2D2 from natural samples of microbial methane gas. A suite of sedimentary methane samples from the Bornholm Basin in the Baltic Sea was collected during IODP Exp. 347. Sample depths range from 2-20 meters below seafloor (mbsf). Methane concentrations decrease with depth, and mcrA (a marker for methanogenesis and methanotropy) is present throughout. See Figure. Both Δ13CH3D and Δ12CH2D2 increase with depth as methane concentrations decrease with the shallowest samples exhibiting disequilibrium by up to 2‰ in Δ13CH3D and 13‰ in Δ12CH2D2 while the deepest samples approach isotopic thermodynamic equilibrium (marked by grey bars in Figure). The Fe-mediated anaerobic oxidation of methane (Fe-AOM) has been inferred in these sediments by geochemical modeling . Slow methane cycling by methanogensis and methanotrophy is likely responsible for the approach to isotopic bond order equilibrium in CH4 with depth, consistent with Fe-AOM. While axenic culturing experiments generate methane with large deficits in 12CH2D2 (reported at this meeting), these data from the Baltic Sea demonstrate that isotopic equilibrium can be achieved during microbial recycling of methane. In the absence of Δ12CH2D2, the Δ13CH3D values alone could be misinterpreted as representing gradients in temperature due perhaps to exothermic organic matter degradation. The combination of both mass-18 rare isotopologues of methane provides the means to distinguish equilibrium from disequilibrium and probe microbial methane cycling even where Δ13CH3D suggests

The ratio of lead-210 to polonium-210 in U.K. diet.

PubMed

Smith-Briggs, J L; Bradley, E J; Potter, M D

1986-10-01

The levels of the natural radionuclides, 210Pb and 210Po, in U.K. diet have been measured previously. However, in the earlier measurements, the samples were sufficiently aged for 210Pb and 210Po to have attained secular equilibrium. In order to determine the extent of disequilibrium between these radionuclides in fresh food, measurements have been made on recently collected dietary samples. Disequilibrium has been observed in five food groups. The activity per unit mass of 210Pb was found to be greater than that of 210Po in bread, cereals, sugar and preserves, whereas the opposite was found to be true for eggs and beverages. When account is taken of consumption rates, however, the total intakes of 210Pb and 210Po from these food groups are approximately the same. The annual effective dose equivalents from the ingestion of 210Pb and 210Po have been re-estimated at 41 and 12 mu Sv, respectively.

Linkage disequilibrium compared between five populations of domestic sheep.

PubMed

Meadows, Jennifer R S; Chan, Eva K F; Kijas, James W

2008-09-30

The success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation. High density SNP arrays are currently in development for the sheep genome, however little is known about the behaviour of LD in this livestock species. This study examined the behaviour of LD within five sheep populations using two LD metrics, D' and x2'. Four economically important Australian sheep flocks, three pure breeds (White Faced Suffolk, Poll Dorset, Merino) and a crossbred population (Merino x Border Leicester), along with an inbred Australian Merino museum flock were analysed. Short range LD (0 - 5 cM) was observed in all five populations, however the persistence with increasing distance and magnitude of LD varied considerably between populations. Average LD (x2') for markers spaced up to 20 cM exceeded the non-syntenic average within the White Faced Suffolk, Poll Dorset and Macarthur Merino. LD decayed faster within the Merino and Merino x Border Leicester, with LD below or consistent with observed background levels. Using marker-marker LD as a guide to the behaviour of marker-QTL LD, estimates of minimum marker spacing were made. For a 95% probability of detecting QTL, a microsatellite marker would be required every 0.1 - 2.5 centimorgans, depending on the population used. Sheep populations were selected which were inbred (Macarthur Merino), highly heterogeneous (Merino) or intermediate between these two extremes. This facilitated analysis and comparison of LD (x2') between populations. The strength and magnitude of LD was found to differ markedly between breeds and aligned closely with both observed levels of genetic diversity and expectations based on breed history. This confirmed that breed specific information is likely to be important for genome wide selection and during the design of successful genome scans where tens of thousands of markers will be required.

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

Detection of linkage disequilibrium between the myotonic dystrophy locus and a new polymorphic DNA marker.

PubMed Central

Harley, H G; Brook, J D; Floyd, J; Rundle, S A; Crow, S; Walsh, K V; Thibault, M C; Harper, P S; Shaw, D J

1991-01-01

We have examined the linkage of two new polymorphic DNA markers (D19S62 and D19S63) and a previously unreported polymorphism with an existing DNA marker (ERCC1) to the myotonic dystrophy (DM) locus. In addition, we have used pulsed-field gel electrophoresis to obtain a fine-structure map of this region. The detection of linkage disequilibrium between DM and one of these markers (D19S63) is the first demonstration of this phenomenon in a heterogeneous DM population. The results suggest that at least 58% of DM patients in the British population, as well as those in a French-Canadian subpopulation, are descended from the same ancestral DM mutation. We discuss the implications of this finding in terms of strategies for cloning the DM gene, for a possible role in modification of risk for prenatal and presymptomatic testing, and we speculate on the origin and number of existing mutations which may result in a DM phenotype. PMID:2063878

Heat transfer to two-phase air/water mixtures flowing in small tubes with inlet disequilibrium

NASA Technical Reports Server (NTRS)

Janssen, J. M.; Florschuetz, L. W.; Fiszdon, J. P.

1986-01-01

The cooling of gas turbine components was the subject of considerable research. The problem is difficult because the available coolant, compressor bleed air, is itself quite hot and has relatively poor thermophysical properties for a coolant. Injecting liquid water to evaporatively cool the air prior to its contact with the hot components was proposed and studied, particularly as a method of cooling for contingency power applications. Injection of a small quantity of cold liquid water into a relatively hot coolant air stream such that evaporation of the liquid is still in process when the coolant contacts the hot component was studied. No approach was found whereby heat transfer characteristics could be confidently predicted for such a case based solely on prior studies. It was not clear whether disequilibrium between phases at the inlet to the hot component section would improve cooling relative to that obtained where equilibrium was established prior to contact with the hot surface.

Mineral disequilibrium in lavas explained by convective self-mixing in open magma chambers.

PubMed

Couch, S; Sparks, R S; Carroll, M R

2001-06-28

Characteristic features of many porphyritic andesite and dacite lavas are that they are rich in crystals and display a range of disequilibrium features, including reversely zoned crystals, resorption surfaces, wide ranges of mineral compositions and minerals which are not in equilibrium with the surrounding rock matrix. These features are often interpreted as evidence of the mixing of magmas of contrasting composition, temperature and origin. Here, however, we propose that such features can also be caused by convection within a magma body with a single composition, that is heated from below and cooled from above. We describe petrological observations of andesite lava erupted at the Soufrière Hills volcano, Montserrat, which indicate a heating event and the intermingling of crystals that have very different thermal histories. We present experimental data on a representative groundmass composition of this lava, which indicate that it is difficult to explain the calcic compositions of plagioclase overgrowth rims and microphenocrysts unless parts of the magma were at temperatures much higher than the inferred average temperature. The concept of convective self-mixing allows us to explain the occurrence of compositions of minerals that apparently cannot coexist under equilibrium conditions.

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array

PubMed Central

Kawakami, Takeshi; Backström, Niclas; Burri, Reto; Husby, Arild; Olason, Pall; Rice, Amber M; Ålund, Murielle; Qvarnström, Anna; Ellegren, Hans

2014-01-01

With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system. PMID:24784959

Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

PubMed Central

Miller, Joshua M; Poissant, Jocelyn; Malenfant, René M; Hogg, John T; Coltman, David W

2015-01-01

Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D′, and χ′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible. PMID:26380673

Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations.

PubMed

Slate, J; Phua, S H

2003-03-01

Mitochondrial DNA (mtDNA) is a widely employed molecular tool in phylogeography, in the inference of human evolutionary history, in dating the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages. The recent demonstration that linkage disequilibrium (LD) declines as a function of distance between polymorphic sites in hominid mitochondrial genomes has been interpreted as evidence of recombination between mtDNA haplotypes, and hence nonclonal inheritance. However, critics of mtDNA recombination have suggested that this association is an artefact of an inappropriate measure of LD or of sequencing error, and subsequent studies of other populations have failed to replicate the initial finding. Here we report the analysis of 16 ruminant populations and present evidence that LD significantly declines with distance in five of them. A meta-analysis of the data indicates a nonsignificant trend of LD declining with distance. Most of the earlier criticisms of patterns between LD and distance in hominid mtDNA are not applicable to this data set. Our results suggest that either ruminant mtDNA is not strictly clonal or that compensatory selection has influenced patterns of variation at closely linked sites within the mitochondrial control region. The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies.

Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes.

PubMed

Long, Ji-Rong; Zhao, Lan-Juan; Liu, Peng-Yuan; Lu, Yan; Dvornyk, Volodymyr; Shen, Hui; Liu, Yong-Jun; Zhang, Yuan-Yuan; Xiong, Dong-Hai; Xiao, Peng; Deng, Hong-Wen

2004-05-24

The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. We examined the patterns of LD and haplotype distribution in eight candidate genes for osteoporosis and/or obesity using 31 SNPs in 1,873 subjects. These eight genes are apolipoprotein E (APOE), type I collagen alpha1 (COL1A1), estrogen receptor-alpha (ER-alpha), leptin receptor (LEPR), parathyroid hormone (PTH)/PTH-related peptide receptor type 1 (PTHR1), transforming growth factor-beta1 (TGF-beta1), uncoupling protein 3 (UCP3), and vitamin D (1,25-dihydroxyvitamin D3) receptor (VDR). Yin yang haplotypes, two high-frequency haplotypes composed of completely mismatching SNP alleles, were examined. To quantify LD patterns, two common measures of LD, D' and r2, were calculated for the SNPs within the genes. The haplotype distribution varied in the different genes. Yin yang haplotypes were observed only in PTHR1 and UCP3. D' ranged from 0.020 to 1.000 with the average of 0.475, whereas the average r2 was 0.158 (ranging from 0.000 to 0.883). A decay of LD was observed as the intermarker distance increased, however, there was a great difference in LD characteristics of different genes or even in different regions within gene. The differences in haplotype distributions and LD patterns among the genes underscore the importance of characterizing genomic regions of interest prior to association studies.

Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

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

Escamilla, M.A.; Reus, V.I.; Smith, L.B.

1996-05-31

Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP). As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, should be suitable for LD mapping; this assertion is supported by reconstruction of extended haplotypes shared by distantly related individuals in this population suffering low-frequency hearing loss (LFHL1), which has previously been mapped by linkage analysis. A sampling strategy is described for applying LD methods to map genes for BP, andmore » clinical and demographic characteristics of an initially collected sample are discussed. This sample will provide a complement to a previously collected set of Costa Rican BP families which is under investigation using standard linkage analysis. 42 refs., 4 figs., 2 tabs.« less

Atmospheric Dynamics and Disequilibrium CO/CH4 Chemistry in the Atmosphere of the Transiting Planet HD 209458b

NASA Astrophysics Data System (ADS)

Cooper, C. S.; Showman, A. P.

2005-08-01

Chemical equilibrium considerations predict that carbon will be present in the atmosphere of HD 209458b as either CO or CH4. Assuming a solar abundance distribution of elements, the concentrations of these species are controlled by temperature and pressure only. In cooler regions, however, vigorous mass transport can occur on time scales shorter than the time scale for interconversion between CO and CH4. This results in excess [CO]/[CH4] relative to the concentrations attained in chemical equilibrium. In this work, we adapt the model of HD 209458b's meteorology used in Cooper & Showman (2005) to treat the disequilibrium chemistry of carbon. Cooper & Showman (2005) show that high-speed winds ( ˜ 4 km s-1) and large temperature contrasts ( ˜ 500 K) are plausible near the photosphere. We model CO and CH4 as passive tracers; i.e., they follow but do not disturb the fluid dynamics of the system. Our simulations will yield maps of the distribution of CO and CH4 to help guide efforts to detect the presence of carbon on this planet. Though CO was not detected on HD 209458b (Deming et al. 2005) by transmission spectroscopy, its presence in the atmosphere cannot be ruled out. For example, CO could be present over much of the dayside hemisphere but depleted near the limbs. The distribution of CO in the atmosphere is diagnostic of temperature at the pressure levels probed by various CO absorption features (Bézard & Lellouch 2002). A positive CO detection would also rule out the hypothesis that the ratio C/O > 1 on this extrasolar planet (e.g., Fortney et al. 2005). This research is supported by NSF grant AST-0307664 and NASA GSRP NGT5-50462.

CYP21A2 polymorphisms in patients with autoimmune Addison's disease, and linkage disequilibrium to HLA risk alleles.

PubMed

Brønstad, Ingeborg; Skinningsrud, Beate; Bratland, Eirik; Løvås, Kristian; Undlien, Dag; Sverre Husebye, Eystein; Wolff, Anette Susanne Bøe

2014-12-01

Steroid 21-hydroxylase, encoded by CYP21A2, is the major autoantigen in autoimmune Addison's disease (AAD). CYP21A2 is located in the region of the HLA complex on chromosome 6p21.3, which harbours several risk alleles for AAD. The objective was to investigate whether CYP21A2 gene variants confer risk of AAD independently of other risk alleles in the HLA loci. DNA samples from 381 Norwegian patients with AAD and 340 healthy controls (HC) previously genotyped for the HLA-A, -B, -DRB1, and -DQB1 and MICA loci were used for genotyping of CYP21A2. Genotyping of CYP21A2 was carried out by direct sequencing. Linkage of CYP21A2 to the HLA loci was assessed using UNPHASED version 3.0.10 and PHASE version 2.1. Heterozygotes of the single-nucleotide polymorphisms (SNPs) rs397515394, rs6467, rs6474, rs76565726 and rs6473 were detected significantly more frequently in AAD patients compared with HC (P<0.005), but all SNPs were in a linkage disequilibrium (LD) with high-risk HLA-DRB1 haplotypes. rs6472C protected against AAD (odds ratio=0.15, 95% CI (0.08-0.30), P=3.8×10(-10)). This SNP was not in an LD with HLA loci (P=0.02), but did not increase protection when considering the effect of HLA-DRB1 alleles. Mutations causing congenital adrenal hyperplasia were found in heterozygosity in <1.5% of the cases in both groups. Genetic variants of CYP21A2 associated to AAD are in LD with the main AAD risk locus HLA-DRB1, and CYP21A2 does not constitute an independent susceptibility locus. © 2014 European Society of Endocrinology.

Performance of the Bowen ratio systems on a 22 deg slope

NASA Technical Reports Server (NTRS)

Nie, D.; Flitcroft, I.; Kanemasu, E. T.

1990-01-01

The Bowen ratio energy balance technique was used to assess the energy fluxes on inclined surfaces during the First ISLSCP Field Experiment (FIFE). Since air flow over sloping surface may differ from that over flat terrain, it is important to examine whether Bowen ratio measurements taken on sloping surfaces are valid. In this study, the suitability of using the Bowen ratio technique on sloping surfaces was tested by examining the assumptions that the technique requires for valid measurements. This was accomplished by studying the variation of Bowen ratio measurements along a selected slope at the FIFE site. In September 1988, four Bowen ratio systems were set up in a line along the 22 degree north-facing slope with northerly air flow (wind went up the slope). In July of 1989, six Bowen ratio systems were similarly installed with southerly air flow (the wind went down slope). Results indicated that, at distances between 10 to 40 meters from the top of the slope, no temperature or vapor pressure gradient parallel to the slope was detected. Uniform Bowen ratio values were obtained on the slope, and thus the sensible or latent heat flux should be similar along the slope. This indicates that the assumptions for valid flux measurements are reasonably met at the slope. The Bowen ratio technique should give the best estimates of the energy fluxes on slopes similar to that in this study.

Enhanced techniques for the measurement of ultra-low level (pg and fg) actinide analysis by ICP-MS for forensic and geologic applications

NASA Astrophysics Data System (ADS)

Pollington, A. D.; Kinman, W.; Hanson, S. K.

2014-12-01

Recent advances in mass spectrometry have led to an improved ability to measure high precision isotope ratios at increasingly low analyte concentrations. Combining techniques for enhanced ionization with better counting of small ion beams, we routinely measure isotope ratios on 100's of pg uranium samples and ≤10 pg plutonium samples with relative standard deviations of 1‰ on major isotope ratios and 10‰ on minor ratios achievable. With slightly larger samples (≤1 ng total U), these precisions can be as low as 0.01‰ (10 ppm) and 1‰ respectively. These techniques can be applied to both nuclear forensics questions where only a small amount of sample is available, as well as geologic questions such as U-Pb or U-Th disequilibrium geochronology from either single small crystals, or microsampled domains from within a heterogeneous sample. The analytical setup is a Cetac Aridus II desolvating nebulizer interfaced with a ThermoScientific Neptune Plus equipped with a jet-type sample cone and x-type skimmer cone. The combination of the desolvating nebulizer with the enhanced cone setup leads to an increase in sensitivity on the order of 10x that of a standard glass spray chamber (~1000V/ppm U). The Neptune Plus is equipped with 9 Faraday cups and 5 electron multipliers (two behind RPQ energy filters for improved abundance sensitivtiy). This allows for the simultaneous collection of all isotopes of either U or Pu with a combination of Faraday cups (e.g., 235U and 238U) and electron multipliers (e.g., 234U and 236U) with other configurations also available (e.g., 235U and 238U can instead be measured on electron multipliers in small samples). As sample sizes get small, the contributions from environmental blanks, as well as interfering species, become increasing concerns. In this study, we will present data on efforts to minimize the contribution of environmental U using scaled down chemical procedures as well as the effect of polyatomic species on the precision

Bubble fusion: Preliminary estimates

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

Krakowski, R.A.

1995-02-01

The collapse of a gas-filled bubble in disequilibrium (i.e., internal pressure {much_lt} external pressure) can occur with a significant focusing of energy onto the entrapped gas in the form of pressure-volume work and/or acoustical shocks; the resulting heating can be sufficient to cause ionization and the emission of atomic radiations. The suggestion that extreme conditions necessary for thermonuclear fusion to occur may be possible has been examined parametrically in terms of the ratio of initial bubble pressure relative to that required for equilibrium. In this sense, the disequilibrium bubble is viewed as a three-dimensional ``sling shot`` that is ``loaded`` tomore » an extent allowed by the maximum level of disequilibrium that can stably be achieved. Values of this disequilibrium ratio in the range 10{sup {minus}5}--10{sup {minus}6} are predicted by an idealized bubble-dynamics model as necessary to achieve conditions where nuclear fusion of deuterium-tritium might be observed. Harmonic and aharmonic pressurizations/decompressions are examined as means to achieve the required levels of disequilibrium required to create fusion conditions. A number of phenomena not included in the analysis reported herein could enhance or reduce the small levels of nuclear fusions predicted.« less

Skewed sex ratios in India: "physician, heal thyself".

PubMed

Patel, Archana B; Badhoniya, Neetu; Mamtani, Manju; Kulkarni, Hemant

2013-06-01

Sex selection, a gender discrimination of the worst kind, is highly prevalent across all strata of Indian society. Physicians have a crucial role in this practice and implementation of the Indian Government's Pre-Natal Diagnostic Techniques Act in 1996 to prevent the misuse of ultrasound techniques for the purpose of prenatal sex determination. Little is known about family preferences, let alone preferences among families of physicians. We investigated the sex ratios in 946 nuclear families with 1,624 children, for which either one or both parents were physicians. The overall child sex ratio was more skewed than the national average of 914. The conditional sex ratios decreased with increasing number of previous female births, and a previous birth of a daughter in the family was associated with a 38 % reduced likelihood of a subsequent female birth. The heavily skewed sex ratios in the families of physicians are indicative of a deeply rooted social malady that could pose a critical challenge in correcting the sex ratios in India.

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances.

PubMed

Li, X; Yang, S; Dong, K; Tang, Z; Li, K; Fan, B; Wang, Z; Liu, B

2017-10-01

Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

PubMed Central

Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

PubMed

Greenberg, David A; Zhang, Junying; Shmulewitz, Dvora; Strug, Lisa J; Zimmerman, Regina; Singh, Veena; Marathe, Sudhir

2005-12-30

The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. 2) To observe the effect on genetic analysis and gene discovery of a complex set of gene x gene interactions. 3) To allow comparison of microsatellite vs. large-scale single-nucleotide polymorphism (SNP) data. 4) To allow testing of association to identify the disease gene and the effect of moderate marker x marker linkage disequilibrium. 5) To observe the effect of different ascertainment/disease definition schemes on the analysis. Data was distributed in two forms. Data distributed to participants contained about 1,000 SNPs and 400 microsatellite markers. Internet-obtainable data consisted of a finer 10,000 SNP map, which also contained data on controls. While disease characteristics and parameters were constant, four "studies" used varying ascertainment schemes based on differing beliefs about disease characteristics. One of the studies contained multiplex two- and three-generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different phenotypes, which were themselves heterogeneous. The population parameters were calibrated so that the major genes could be discovered by linkage analysis in most datasets. The association evidence was more difficult to calibrate but was designed to find statistically significant association in 50% of datasets. We also

Opposite extremes in ethylene/nitric oxide ratio induce cell death in suspension culture and root apices of tomato exposed to salt stress.

PubMed

Poór, P; Borbély, P; Kovács, Judit; Papp, Anita; Szepesi, Ágnes; Takács, Z; Tari, Irma

2014-12-01

The plant hormone ethylene or the gaseous signalling molecule nitric oxide (NO) may enhance salt stress tolerance by maintaining ion homeostasis, first of all K+/Na+ ratio of tissues. Ethylene and NO accumulation increased in the root apices and suspension culture cells of tomato at sublethal salt stress caused by 100 mM NaCl, however, the induction phase of programmed cell death (PCD) was different at lethal salt concentration. The production of ethylene by root apices and the accumulation of NO in the cells of suspension culture did not increase during the initiation of PCD after 250 mM NaCl treatment. Moreover, cells in suspension culture accumulated higher amount of reactive oxygen species which, along with NO deficiency contributed to cell death induction. The absence of ethylene in the apical root segments and the absence of NO accumulation in the cell suspension resulted in similar ion disequilibrium, namely K+/Na+ ratio of 1.41 ± 0.1 and 1.68 ± 0.3 in intact plant tissues and suspension culture cells, respectively that was not tolerated by tomato.

Improvement of the tetrachloromercurate absorption technique for measuring low atmospheric SO2 mixing ratios

NASA Astrophysics Data System (ADS)

Jaeschke, W.; Beltz, N.; Haunold, W.; Krischke, U.

1997-07-01

During the Gas-Phase Sulfur Intercomparison Experiment (GASIE) in 1994 an analytical system for measuring sulfur dioxide mixing ratios at low parts per trillion (pptv) levels was employed. It is based on the absorption of SO2 on a tetrachloromercurate(II)-impregnated filter. The subsequent analysis uses a chemiluminescence reaction by treating the resulting disulfitomercurate(II) complex with an acidic cerium sulfate solution. An improved sampling device has been introduced that increases the maximum sampling volume from 200 L to 500 L. It is also possible to determine the blank value accurately for each sample. The absorption efficiency of the sampling system is 98.7±6.4% at a nominal flow rate of 10 L/min. The calculated (3σ) detection limit is 3±1 pptv SO2. The sample solution is stable for up to 30 days, which allows the samples to be safely stored or shipped before analysis. This permits the use of a sensitive, compact, and reliable sampling system in the field with subsequent analysis under optimal conditions in the laboratory. A continuous flow chemiluminescence (CFCL) analyzer for on-line measurements is also presented. The system is based on the same chemical principles as the described filter technique.

Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Cheng, Ching-Yu; Wong, Tien Yin; Quake, Stephen R; Burkholder, William F

2014-06-03

Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity was detected around several L1 insertions. This finding suggests that some of these L1 insertions may have been the target of recent positive selection.

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

PubMed Central

Siol, Mathieu; Jacquin, Françoise; Chabert-Martinello, Marianne; Smýkal, Petr; Le Paslier, Marie-Christine; Aubert, Grégoire; Burstin, Judith

2017-01-01

Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions, gathering elite cultivars, landraces, and wild relatives using an array of ∼13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types, and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. LD decreases steeply as genetic distance increases. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter, and spring pea, respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions. PMID:28611254

Dosage Transmission Disequilibrium Test (dTDT) for Linkage and Association Detection

PubMed Central

Zhang, Zhehao; Wang, Jen-Chyong; Howells, William; Lin, Peng; Agrawal, Arpana; Edenberg, Howard J.; Tischfield, Jay A.; Schuckit, Marc A.; Bierut, Laura J.; Goate, Alison; Rice, John P.

2013-01-01

Both linkage and association studies have been successfully applied to identify disease susceptibility genes with genetic markers such as microsatellites and Single Nucleotide Polymorphisms (SNPs). As one of the traditional family-based studies, the Transmission/Disequilibrium Test (TDT) measures the over-transmission of an allele in a trio from its heterozygous parents to the affected offspring and can be potentially useful to identify genetic determinants for complex disorders. However, there is reduced information when complete trio information is unavailable. In this study, we developed a novel approach to “infer” the transmission of SNPs by combining both the linkage and association data, which uses microsatellite markers from families informative for linkage together with SNP markers from the offspring who are genotyped for both linkage and a Genome-Wide Association Study (GWAS). We generalized the traditional TDT to process these inferred dosage probabilities, which we name as the dosage-TDT (dTDT). For evaluation purpose, we developed a simulation procedure to assess its operating characteristics. We applied the dTDT to the simulated data and documented the power of the dTDT under a number of different realistic scenarios. Finally, we applied our methods to a family study of alcohol dependence (COGA) and performed individual genotyping on complete families for the top signals. One SNP (rs4903712 on chromosome 14) remained significant after correcting for multiple testing Methods developed in this study can be adapted to other platforms and will have widespread applicability in genomic research when case-control GWAS data are collected in families with existing linkage data. PMID:23691058

Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

PubMed

Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

2016-08-01

The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda

PubMed Central

Westbrook, Jared W.; Chhatre, Vikram E.; Wu, Le-Shin; Chamala, Srikar; Neves, Leandro Gomide; Muñoz, Patricio; Martínez-García, Pedro J.; Neale, David B.; Kirst, Matias; Mockaitis, Keithanne; Nelson, C. Dana; Peter, Gary F.; Echt, Craig S.

2015-01-01

A consensus genetic map for Pinus taeda (loblolly pine) and Pinus elliottii (slash pine) was constructed by merging three previously published P. taeda maps with a map from a pseudo-backcross between P. elliottii and P. taeda. The consensus map positioned 3856 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.6 cM and total map length was 2305 cM. Functional predictions of mapped genes were improved by aligning expressed sequence tags used for marker discovery to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 3305 scaffold sequences onto 12 linkage groups. The consensus genetic map was used to compare the genome-wide linkage disequilibrium in a population of distantly related P. taeda individuals (ADEPT2) used for association genetic studies and a multiple-family pedigree used for genomic selection (CCLONES). The prevalence and extent of LD was greater in CCLONES as compared to ADEPT2; however, extended LD with LGs or between LGs was rare in both populations. The average squared correlations, r2, between SNP alleles less than 1 cM apart were less than 0.05 in both populations and r2 did not decay substantially with genetic distance. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association mapping and genomic selection in P. taeda and P. elliottii. PMID:26068575

Combined slope ratio analysis and linear-subtraction: An extension of the Pearce ratio method

NASA Astrophysics Data System (ADS)

De Waal, Sybrand A.

1996-07-01

A new technique, called combined slope ratio analysis, has been developed by extending the Pearce element ratio or conserved-denominator method (Pearce, 1968) to its logical conclusions. If two stoichiometric substances are mixed and certain chemical components are uniquely contained in either one of the two mixing substances, then by treating these unique components as conserved, the composition of the substance not containing the relevant component can be accurately calculated within the limits allowed by analytical and geological error. The calculated composition can then be subjected to rigorous statistical testing using the linear-subtraction method recently advanced by Woronow (1994). Application of combined slope ratio analysis to the rocks of the Uwekahuna Laccolith, Hawaii, USA, and the lavas of the 1959-summit eruption of Kilauea Volcano, Hawaii, USA, yields results that are consistent with field observations.

Disequilibrium after Traumatic Brain Injury: Vestibular Mechanisms

DTIC Science & Technology

2012-09-01

potentially modifiable factors. 0078 Chiropractic Sacro Occipital Technique (SOT) and Cranial Treatment Model for Traumatic Brain Injury Along with...model incorporating laboratory testing to evaluate neurotrans- mitter balance and chiropractic cranial care for the treatment of a patient with traumatic...Approach She has been under care for three years, which consisted of chiropractic sacro occipital technique (SOT) and cranial treat- ment. Within the

Genetic Structure, Linkage Disequilibrium and Association Mapping of Verticillium Wilt Resistance in Elite Cotton (Gossypium hirsutum L.) Germplasm Population

PubMed Central

Zhao, Yunlei; Wang, Hongmei; Chen, Wei; Li, Yunhai

2014-01-01

Understanding the population structure and linkage disequilibrium in an association panel can effectively avoid spurious associations and improve the accuracy in association mapping. In this study, one hundred and fifty eight elite cotton (Gossypium hirsutum L.) germplasm from all over the world, which were genotyped with 212 whole genome-wide marker loci and phenotyped with an disease nursery and greenhouse screening method, were assayed for population structure, linkage disequilibrium, and association mapping of Verticillium wilt resistance. A total of 480 alleles ranging from 2 to 4 per locus were identified from all collections. Model-based analysis identified two groups (G1 and G2) and seven subgroups (G1a–c, G2a–d), and differentiation analysis showed that subgroup having a single origin or pedigree was apt to differentiate with those having a mixed origin. Only 8.12% linked marker pairs showed significant LD (P<0.001) in this association panel. The LD level for linked markers is significantly higher than that for unlinked markers, suggesting that physical linkage strongly influences LD in this panel, and LD level was elevated when the panel was classified into groups and subgroups. The LD decay analysis for several chromosomes showed that different chromosomes showed a notable change in LD decay distances for the same gene pool. Based on the disease nursery and greenhouse environment, 42 marker loci associated with Verticillium wilt resistance were identified through association mapping, which widely were distributed among 15 chromosomes. Among which 10 marker loci were found to be consistent with previously identified QTLs and 32 were new unreported marker loci, and QTL clusters for Verticillium wilt resistanc on Chr.16 were also proved in our study, which was consistent with the strong linkage in this chromosome. Our results would contribute to association mapping and supply the marker candidates for marker-assisted selection of Verticillium wilt

Single-Specimen Technique to Establish the J-Resistance of Linear Viscoelastic Solids with Constant Poisson's Ratio

NASA Technical Reports Server (NTRS)

Gutierrez-Lemini, Danton; McCool, Alex (Technical Monitor)

2001-01-01

A method is developed to establish the J-resistance function for an isotropic linear viscoelastic solid of constant Poisson's ratio using the single-specimen technique with constant-rate test data. The method is based on the fact that, for a test specimen of fixed crack size under constant rate, the initiation J-integral may be established from the crack size itself, the actual external load and load-point displacement at growth initiation, and the relaxation modulus of the viscoelastic solid, without knowledge of the complete test record. Since crack size alone, of the required data, would be unknown at each point of the load-vs-load-point displacement curve of a single-specimen test, an expression is derived to estimate it. With it, the physical J-integral at each point of the test record may be established. Because of its basis on single-specimen testing, not only does the method not require the use of multiple specimens with differing initial crack sizes, but avoids the need for tracking crack growth as well.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

PubMed

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

PubMed Central

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

Estimating TCP Packet Loss Ratio from Sampled ACK Packets

NASA Astrophysics Data System (ADS)

Yamasaki, Yasuhiro; Shimonishi, Hideyuki; Murase, Tutomu

The advent of various quality-sensitive applications has greatly changed the requirements for IP network management and made the monitoring of individual traffic flows more important. Since the processing costs of per-flow quality monitoring are high, especially in high-speed backbone links, packet sampling techniques have been attracting considerable attention. Existing sampling techniques, such as those used in Sampled NetFlow and sFlow, however, focus on the monitoring of traffic volume, and there has been little discussion of the monitoring of such quality indexes as packet loss ratio. In this paper we propose a method for estimating, from sampled packets, packet loss ratios in individual TCP sessions. It detects packet loss events by monitoring duplicate ACK events raised by each TCP receiver. Because sampling reveals only a portion of the actual packet loss, the actual packet loss ratio is estimated statistically. Simulation results show that the proposed method can estimate the TCP packet loss ratio accurately from a 10% sampling of packets.

Novel Oversampling Technique for Improving Signal-to-Quantization Noise Ratio on Accelerometer-Based Smart Jerk Sensors in CNC Applications.

PubMed

Rangel-Magdaleno, Jose J; Romero-Troncoso, Rene J; Osornio-Rios, Roque A; Cabal-Yepez, Eduardo

2009-01-01

Jerk monitoring, defined as the first derivative of acceleration, has become a major issue in computerized numeric controlled (CNC) machines. Several works highlight the necessity of measuring jerk in a reliable way for improving production processes. Nowadays, the computation of jerk is done by finite differences of the acceleration signal, computed at the Nyquist rate, which leads to low signal-to-quantization noise ratio (SQNR) during the estimation. The novelty of this work is the development of a smart sensor for jerk monitoring from a standard accelerometer, which has improved SQNR. The proposal is based on oversampling techniques that give a better estimation of jerk than that produced by a Nyquist-rate differentiator. Simulations and experimental results are presented to show the overall methodology performance.

Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis.

PubMed

Silva-Junior, Orzenil B; Grattapaglia, Dario

2015-11-01

We used high-density single nucleotide polymorphism (SNP) data and whole-genome pooled resequencing to examine the landscape of population recombination (ρ) and nucleotide diversity (ϴw ), assess the extent of linkage disequilibrium (r(2) ) and build the highest density linkage maps for Eucalyptus. At the genome-wide level, linkage disequilibrium (LD) decayed within c. 4-6 kb, slower than previously reported from candidate gene studies, but showing considerable variation from absence to complete LD up to 50 kb. A sharp decrease in the estimate of ρ was seen when going from short to genome-wide inter-SNP distances, highlighting the dependence of this parameter on the scale of observation adopted. Recombination was correlated with nucleotide diversity, gene density and distance from the centromere, with hotspots of recombination enriched for genes involved in chemical reactions and pathways of the normal metabolic processes. The high nucleotide diversity (ϴw = 0.022) of E. grandis revealed that mutation is more important than recombination in shaping its genomic diversity (ρ/ϴw = 0.645). Chromosome-wide ancestral recombination graphs allowed us to date the split of E. grandis (1.7-4.8 million yr ago) and identify a scenario for the recent demographic history of the species. Our results have considerable practical importance to Genome Wide Association Studies (GWAS), while indicating bright prospects for genomic prediction of complex phenotypes in eucalypt breeding. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Heritability and Familiality of Temperament and Character Dimensions in Korean Families with Schizophrenic Linkage Disequilibrium.

PubMed

Lee, Byung Dae; Park, Je Min; Lee, Young Min; Moon, Eunsoo; Jeong, Hee Jeong; Chung, Young In; Yi, Young Mi

2016-05-31

Categorical syndromes such as schizophrenia may represent complexes of many continuous psychological structural phenotypes along several dimensions of personality development/degeneration. The present study investigated the heritability and familiality of personality dimensions in Korean families with schizophrenic linkage disequilibrium (LD). We recruited 179 probands (with schizophrenia) as well as, whenever possible, their parents and siblings. We used the Temperament and Character Inventory (TCI) to measure personality and symptomatic dimensions. The heritability of personality dimensions in a total of 472 family members was estimated using Sequential Oligogenic Linkage Analysis Routines (SOLAR). To measure familiality, we compared the personality dimensions of family members with those of 336 healthy unrelated controls using analysis of variance (ANOVA) analysis. Three of the seven TCI variables were significantly heritable and were included in subsequent analyses. The three groups (control, unaffected first-degree relative, case) were found to significantly differ from one another, with the expected order of average group scores, for all heritable dimensions. Despite several study limitations with respect to family recruitment and phenotyping, our results show that aberrations in several personality dimensions related to genetic-environment coactions or interactions may underlie the complexity of the schizophrenic syndrome.

Spectral ratio techniques as a tool for soil-structure interaction assessment

NASA Astrophysics Data System (ADS)

Ladina, C.; Lovati, S.; Marzorati, S.; Massa, M.

2009-04-01

structure, is built on lithological units characterized by alluvial deposits. All noise measurements, characterized by a minimum duration of 30 minutes (sampling rate 100 Hz), were performed using a Lennartz LE3D-5s seismometer (flat response 0.2 - 40 Hz) coupled with a 24 bits Reftek 130/01 digital recorder. To investigate the dynamic characterization of buildings both standard spectral ratio (SSR) and horizontal to vertical spectral ratio (HVNR) techniques were applied to the recorded data; in the first case two simultaneous measures, computed at the bottom and at the top of the structure were considered. For the stations where earthquakes recordings were available, the results from ambients noise were compared, to those obtained from earthquakes (HVSR). For all records the linear trend and the instrumental response were removed and a band-pass Butterworth 4 poles filter between 0.2 and 25 Hz was applied. Then each component of noise was windowed in time series of 120 s length (cosine taper 5%), the horizontal components were rotated between 0° and 175° with step of 5° and the power spectral density (PSD) were calculated using a Konno and Ohmachi (1998) window (b=20). Finally, for each considered azimuth average HVNRs were computed calculating for each time window the spectral ratio between the spectrum of the radial component over the spectrum of the vertical one. For earthquake the data processing were performed as described for noise but considering different portion of signal: 5 s and 15 s of S waves, starting 0.5 s before the S-waves picking, and 20 s of coda were selected. Also in this case for each selected window HVSR were calculated through a directional analysis as that described for HVNR. The results highlight the fundamental role of the installation. For BAG8 and AUL, where the sensors are directly installed on rock, the vibrations of the structure do not affect HVNR at the bottom, which show flat responses in the whole frequency range: in both cases the

The Isotopologue Record of Repeat Vital Effect Offenders: Tracking (Dis)equilibrium Effects in Sea Urchins and Nannofossil Using Clumped Isotopes

NASA Astrophysics Data System (ADS)

John, C. M.; Davies, A.; Drury, A. J.

2016-12-01

Vital effects vary between species and affect various isotopic systems in unequal proportion. The magnitude of the response of different isotopic systems might thus be key in understanding biologically-mediated disequilibrium, especially in groups that show a tendency to be "repeat offenders" with regards to vital effects. Here we present carbon, oxygen, and clumped isotope data from echinoderm calcite and nannofossil ooze, both of which exhibit strong vital effects in bulk isotopes. Our study is the first to investigate the clumped isotope (dis)equilibrium of echinoids. Results from two echinoids, three marine gastropods and a bivalve mollusk from modern beach deposits of Bali, Indonesia, highlight a significant offset in clumped isotopes of a regular echinoid test from expected values, interpreted as evidence of a similar "vital effect" as observed in surface corals. This is in contrast to the test of an irregular "sand dollar" echinoid, with clumped isotope values within error of expected sea surface temperature. Furthermore, data on the inter-skeletal variability in the clumped isotopic composition of two regular echinoid species shows that the spines of the echinoids are in equilibrium with seawater with respect to clumped isotopes, but the test is not. For the nannofossil material, no clumped isotope vital effects are observed, consistent with previously published studies but at odds with strong vital effects in carbon and oxygen isotopes, often correlated with cell-size. In addition, we reveal that the <63 micron fraction of deep-sea ooze could constitute useful material for clumped isotope studies. An intriguing result of our study is that vital effects are mostly absent in clumped isotopes, even in phylums known for important isotopic effects. It remains to be explained why some parts of the echinoids show clear vital effects, notably enrichment in clumped isotopes of urchin tests. Mechanisms that could explain this include pH effects during calcification

Sample preparation techniques for the determination of natural 15N/14N variations in amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS).

PubMed

Hofmann, D; Gehre, M; Jung, K

2003-09-01

In order to identify natural nitrogen isotope variations of biologically important amino acids four derivatization reactions (t-butylmethylsilylation, esterification with subsequent trifluoroacetylation, acetylation and pivaloylation) were tested with standard mixtures of 17 proteinogenic amino acids and plant (moss) samples using GC-C-IRMS. The possible fractionation of the nitrogen isotopes, caused for instance by the formation of multiple reaction products, was investigated. For biological samples, the esterification of the amino acids with subsequent trifluoroacetylation is recommended for nitrogen isotope ratio analysis. A sample preparation technique is described for the isotope ratio mass spectrometric analysis of amino acids from the non-protein (NPN) fraction of terrestrial moss. 14N/15N ratios from moss (Scleropodium spec.) samples from different anthropogenically polluted areas were studied with respect to ecotoxicologal bioindication.

Marker selection for the transmission/disequilibrium test, in recently admixed populations.

PubMed Central

Kaplan, N L; Martin, E R; Morris, R W; Weir, B S

1998-01-01

Recent admixture between genetically differentiated populations can result in high levels of association between alleles at loci that are <=10 cM apart. The transmission/disequilibrium test (TDT) proposed by Spielman et al. (1993) can be a powerful test of linkage between disease and marker loci in the presence of association and therefore could be a useful test of linkage in admixed populations. The degree of association between alleles at two loci depends on the differences in allele frequencies, at the two loci, in the founding populations; therefore, the choice of marker is important. For a multiallelic marker, one strategy that may improve the power of the TDT is to group marker alleles within a locus, on the basis of information about the founding populations and the admixed population, thereby collapsing the marker into one with fewer alleles. We have examined the consequences of collapsing a microsatellite into a two-allele marker, when two founding populations are assumed for the admixed population, and have found that if there is random mating in the admixed population, then typically there is a collapsing for which the power of the TDT is greater than that for the original microsatellite marker. A method is presented for finding the optimal collapsing that has minimal dependence on the disease and that uses estimates either of marker allele frequencies in the two founding populations or of marker allele frequencies in the current, admixed population and in one of the founding populations. Furthermore, this optimal collapsing is not always the collapsing with the largest difference in allele frequencies in the founding populations. To demonstrate this strategy, we considered a recent data set, published previously, that provides frequency estimates for 30 microsatellites in 13 populations. PMID:9497257

The evolution of sex ratio distorter suppression affects a 25 cM genomic region in the butterfly Hypolimnas bolina.

PubMed

Hornett, Emily A; Moran, Bruce; Reynolds, Louise A; Charlat, Sylvain; Tazzyman, Samuel; Wedell, Nina; Jiggins, Chris D; Hurst, Greg D D

2014-12-01

Symbionts that distort their host's sex ratio by favouring the production and survival of females are common in arthropods. Their presence produces intense Fisherian selection to return the sex ratio to parity, typified by the rapid spread of host 'suppressor' loci that restore male survival/development. In this study, we investigated the genomic impact of a selective event of this kind in the butterfly Hypolimnas bolina. Through linkage mapping, we first identified a genomic region that was necessary for males to survive Wolbachia-induced male-killing. We then investigated the genomic impact of the rapid spread of suppression, which converted the Samoan population of this butterfly from a 100:1 female-biased sex ratio in 2001 to a 1:1 sex ratio by 2006. Models of this process revealed the potential for a chromosome-wide effect. To measure the impact of this episode of selection directly, the pattern of genetic variation before and after the spread of suppression was compared. Changes in allele frequencies were observed over a 25 cM region surrounding the suppressor locus, with a reduction in overall diversity observed at loci that co-segregate with the suppressor. These changes exceeded those expected from drift and occurred alongside the generation of linkage disequilibrium. The presence of novel allelic variants in 2006 suggests that the suppressor was likely to have been introduced via immigration rather than through de novo mutation. In addition, further sampling in 2010 indicated that many of the introduced variants were lost or had declined in frequency since 2006. We hypothesize that this loss may have resulted from a period of purifying selection, removing deleterious material that introgressed during the initial sweep. Our observations of the impact of suppression of sex ratio distorting activity reveal a very wide genomic imprint, reflecting its status as one of the strongest selective forces in nature.

Parameter estimation in astronomy through application of the likelihood ratio. [satellite data analysis techniques

NASA Technical Reports Server (NTRS)

Cash, W.

1979-01-01

Many problems in the experimental estimation of parameters for models can be solved through use of the likelihood ratio test. Applications of the likelihood ratio, with particular attention to photon counting experiments, are discussed. The procedures presented solve a greater range of problems than those currently in use, yet are no more difficult to apply. The procedures are proved analytically, and examples from current problems in astronomy are discussed.

High-precision determination of 18O/16O ratios of silver phosphate by EA-pyrolysis-IRMS continuous flow technique.

PubMed

Lécuyer, Christophe; Fourel, François; Martineau, François; Amiot, Romain; Bernard, Aurélien; Daux, Valérie; Escarguel, Gilles; Morrison, John

2007-01-01

A high-precision, and rapid on-line method for oxygen isotope analysis of silver phosphate is presented. The technique uses high-temperature elemental analyzer (EA)-pyrolysis interfaced in continuous flow (CF) mode to an isotopic ratio mass spectrometer (IRMS). Calibration curves were generated by synthesizing silver phosphate with a 13 per thousand spread in delta(18)O values. Calibration materials were obtained by reacting dissolved potassium dihydrogen phosphate (KH(2)PO(4)) with water samples of various oxygen isotope compositions at 373 K. Validity of the method was tested by comparing the on-line results with those obtained by classical off-line sample preparation and dual inlet isotope measurement. In addition, silver phosphate precipitates were prepared from a collection of biogenic apatites with known delta(18)O values ranging from 12.8 to 29.9 per thousand (V-SMOW). Reproducibility of +/- 0.2 per thousand was obtained by the EA-Py-CF-IRMS method for sample sizes in the range 400-500 microg. Both natural and synthetic samples are remarkably well correlated with conventional (18)O/(16)O determinations. Silver phosphate is a very stable material and easy to degas and, thus, could be considered as a good candidate to become a reference material for the determination of (18)O/(16)O ratios of phosphate by high-temperature pyrolysis. Copyright 2006 John Wiley & Sons, Ltd.

Automated Measurement of P- and S-Wave Differential Times for Imaging Spatial Distributions of Vp/Vs Ratio, with Moving-Window Cross-Correlation Technique

NASA Astrophysics Data System (ADS)

Taira, T.; Kato, A.

2013-12-01

A high-resolution Vp/Vs ratio estimate is one of the key parameters to understand spatial variations of composition and physical state within the Earth. Lin and Shearer (2007, BSSA) recently developed a methodology to obtain local Vp/Vs ratios in individual similar earthquake clusters, based on P- and S-wave differential times. A waveform cross-correlation approach is typically employed to measure those differential times for pairs of seismograms from similar earthquakes clusters, at narrow time windows around the direct P and S waves. This approach effectively collects P- and S-wave differential times and however requires the robust P- and S-wave time windows that are extracted based on either manually or automatically picked P- and S-phases. We present another technique to estimate P- and S-wave differential times by exploiting temporal properties of delayed time as a function of elapsed time on the seismograms with a moving-window cross-correlation analysis (e.g., Snieder, 2002, Phys. Rev. E; Niu et al. 2003, Nature). Our approach is based on the principle that the delayed time for the direct S wave differs from that for the direct P wave. Two seismograms aligned by the direct P waves from a pair of similar earthquakes yield that delayed times become zero around the direct P wave. In contrast, delayed times obtained from time windows including the direct S wave have non-zero value. Our approach, in principle, is capable of measuring both P- and S-wave differential times from single-component seismograms. In an ideal case, the temporal evolution of delayed time becomes a step function with its discontinuity at the onset of the direct S wave. The offset in the resulting step function would be the S-wave differential time, relative to the P-wave differential time as the two waveforms are aligned by the direct P wave. We apply our moving-window cross-correlation technique to the two different data sets collected at: 1) the Wakayama district, Japan and 2) the Geysers

Cloud and Aerosol 1064nm Lidar Ratio Retrievals from the CATS Instrument

NASA Astrophysics Data System (ADS)

Pauly, R.; Yorks, J. E.; McGill, M. J.; Hlavka, D. L.; Midzak, N.

2017-12-01

The extinction to backscatter ratio or lidar ratio is an essential value in order to derive the optical properties of cloud and aerosol layers from standard elastic backscatter lidar data. For these instruments, the lidar ratio can sometimes be determined from lidar data utilizing the transmission loss or "constrained" technique. The best situations for deploying this technique involve clearly defined layers with clear sky underneath for 1-3 km. In situations where the lidar ratio cannot be calculated, look-up tables exist for various cloud and aerosol types. There is a vast data record of derived lidar ratios for various cloud and aerosol types using 532nm from an array of instruments (i.e. HSRL, CALIOP, CPL, Aeronet, MPLNET). To date, because the 1064nm molecular signal is so small, lidar ratios at 1064nm have been mostly determined from 532nm lidar ratios using angstrom exponents, color ratios and ground based non-lidar measurements, as HSRL measurements at that wavelength do not exist. Due to the better signal quality at 1064nm compared to the 532nm signal, the CATS laser was thermally tuned to increase the 1064nm output energy. Therefore, the 1064nm channel is used in nearly all CATS layer data processing, making the accurate determination of 1064nm lidar ratio imperative. The CATS 1064nm signal allows for the unique capability to determine 1064nm lidar ratios better than previous instruments. The statistical and case study results of the CATS derived smoke and dust lidar ratios will be presented. Results have shown that the previously assumed 1064nm lidar ratios for dust need to be lowered. In addition to 1064nm lidar ratio results from the traditional transmission loss technique, results for aerosol layers above opaque water clouds from a method utilizing the depolarization ratio of the opaque cloud will be discussed. Incorporating this method into the CATS algorithms should increase the number of aerosol layers with constrained lidar ratio.

EVALUATION OF A NON-LETHAL SAMPLING TECHNIQUE FOR THE MEASUREMENT OF MERCURY (HG) CONCENTRATIONS AND STABLE-NITROGEN (15N/14N) ISOTOPE RATIOS IN LARGE MOUTH BASS (MICROPTERUS SALMOIDES)

EPA Science Inventory

Contaminant bioaccumulation studies often rely on fish muscle filets as the tissue of choice for the measurement of nitrogen stable isotope ratios ( 15N) and mercury (Hg). Lethal sampling techniques may not be suitable for studies on limited populations from smaller sized aquati...

Quantifying asymmetry: ratios and alternatives.

PubMed

Franks, Erin M; Cabo, Luis L

2014-08-01

Traditionally, the study of metric skeletal asymmetry has relied largely on univariate analyses, utilizing ratio transformations when the goal is comparing asymmetries in skeletal elements or populations of dissimilar dimensions. Under this approach, raw asymmetries are divided by a size marker, such as a bilateral average, in an attempt to produce size-free asymmetry indices. Henceforth, this will be referred to as "controlling for size" (see Smith: Curr Anthropol 46 (2005) 249-273). Ratios obtained in this manner often require further transformations to interpret the meaning and sources of asymmetry. This model frequently ignores the fundamental assumption of ratios: the relationship between the variables entered in the ratio must be isometric. Violations of this assumption can obscure existing asymmetries and render spurious results. In this study, we examined the performance of the classic indices in detecting and portraying the asymmetry patterns in four human appendicular bones and explored potential methodological alternatives. Examination of the ratio model revealed that it does not fulfill its intended goals in the bones examined, as the numerator and denominator are independent in all cases. The ratios also introduced strong biases in the comparisons between different elements and variables, generating spurious asymmetry patterns. Multivariate analyses strongly suggest that any transformation to control for overall size or variable range must be conducted before, rather than after, calculating the asymmetries. A combination of exploratory multivariate techniques, such as Principal Components Analysis, and confirmatory linear methods, such as regression and analysis of covariance, appear as a promising and powerful alternative to the use of ratios. © 2014 Wiley Periodicals, Inc.

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

PubMed Central

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J.; Hunt, Sarah; Deloukas, Panos; Bentley, David R.; Morton, Newton E.

2004-01-01

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences. PMID:15604137

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

PubMed

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

2004-12-28

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.

PubMed Central

Rossi, Monica; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Rau, Domenico; Attene, Giovanna; Papa, Roberto

2009-01-01

Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes. PMID:25567895

Nestling sex ratio in the Southwestern Willow Flycatcher

USGS Publications Warehouse

Paxton, E.H.; Sogge, M.K.; McCarthey, T.D.; Keim, P.

2002-01-01

Using molecular-genetic techniques, we determined the gender of 202 Southwestern Willow Flycatcher (Empidonax traillii extimus) nestlings from 95 nests sampled over a five-year period. Overall nestling sex ratio did not vary significantly from 50:50 among years, by clutch order, or by mating strategy (monogamous vs. polygamous pairings). However, we did observe significant differences among the four sites sampled, with sex ratios biased either toward males or females at the different sites. Given the small population sizes and geographic isolation of many of the endangered subspecies' breeding populations, sex-ratio differences may have localized negative impacts. ?? The Cooper Ornithological Society 2002.

Nestling sex ratios in the southwestern willow flycatcher

USGS Publications Warehouse

Paxton, E.H.; Sogge, M.K.; McCarthey, Tracy; Keim, Paul

2002-01-01

Using molecular-genetic techniques, we determined the gender of 202 Southwestern Willow Flycatcher (Empidonax traillii extimus) nestlings from 95 nests sampled over a five-year period. Overall nestling sex ratio did not vary significantly from 50:50 among years, by clutch order, or by mating strategy (monogamous vs. polygamous pairings). However, we did observe significant differences among the four sites sampled, with sex ratios biased either toward males or females at the different sites. Given the small population sizes and geographic isolation of many of the endangered subspecies' breeding populations, sex-ratio differences may have localized negative impacts.

Method for nanomachining high aspect ratio structures

DOEpatents

Yun, Wenbing; Spence, John; Padmore, Howard A.; MacDowell, Alastair A.; Howells, Malcolm R.

2004-11-09

A nanomachining method for producing high-aspect ratio precise nanostructures. The method begins by irradiating a wafer with an energetic charged-particle beam. Next, a layer of patterning material is deposited on one side of the wafer and a layer of etch stop or metal plating base is coated on the other side of the wafer. A desired pattern is generated in the patterning material on the top surface of the irradiated wafer using conventional electron-beam lithography techniques. Lastly, the wafer is placed in an appropriate chemical solution that produces a directional etch of the wafer only in the area from which the resist has been removed by the patterning process. The high mechanical strength of the wafer materials compared to the organic resists used in conventional lithography techniques with allows the transfer of the precise patterns into structures with aspect ratios much larger than those previously achievable.

Linear signal noise summer accurately determines and controls S/N ratio

NASA Technical Reports Server (NTRS)

Sundry, J. L.

1966-01-01

Linear signal noise summer precisely controls the relative power levels of signal and noise, and mixes them linearly in accurately known ratios. The S/N ratio accuracy and stability are greatly improved by this technique and are attained simultaneously.

Effect of pH, application technique, and chlorine-to-nitrogen ratio on disinfectant activity of inorganic chloramines with pure culture bacteria.

PubMed Central

Ward, N R; Wolfe, R L; Olson, B H

1984-01-01

The influence of pH, application technique, and chlorine-to-nitrogen weight ratio on the bactericidal activity of inorganic chloramine compounds was determined with stock and environmental strains of Escherichia coli, Salmonella spp., Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterobacter cloacae. The rate of inactivation increased from 1.5 to 2 times as the chlorine-to-nitrogen weight ratio was adjusted from 2:1 to 5:1, 5 to 6 times as the pH was decreased from 8 to 6, and 5 to 6 times as the concentration was increased from 1 to 5 mg/liter. Separate additions of free chlorine and ammonia (concurrent addition and preammoniation) into seeded water at or below pH 7.5 resulted in killing comparable to that observed with free chlorine (99% inactivation in less than 20 s). At pH 8, inactivation by separate additions was considerably slower and was comparable to that by prereacted chloramine compounds (99% inactivation in 25 to 26 min). Determination of the effectiveness of inorganic chloramine compounds as primary disinfectants for drinking water must consider the method of application, pH and concentrations of chlorine and ammonia. PMID:6437328

The Power to Detect Linkage Disequilibrium with Quantitative Traits in Selected Samples

PubMed Central

Abecasis, Gonçalo R.; Cookson, William O. C.; Cardon, Lon R.

2001-01-01

Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and the imminent availability of a dense diallelic marker map, the families are likely to be used in allelic-association as well as linkage studies. However, optimal selection strategies for linkage may not be equally powerful for association. We examine the power to detect linkage disequilibrium for quantitative traits after phenotypic selection. The results encompass six selection strategies that are in widespread use, including single selection (two designs), affected sib pairs, concordant and discordant pairs, and the extreme-concordant and -discordant design. Selection of sibships on the basis of one extreme proband with high or low trait scores provides as much power as discordant sib pairs but requires the screening and phenotyping of substantially fewer initial families from which to select. Analysis of the role of allele frequencies within each selection design indicates that common trait alleles generally offer the most power, but similarities between the marker- and trait-allele frequencies are much more important than the trait-locus frequency alone. Some of the most widespread selection designs, such as single selection, yield power gains only when both the marker and quantitative trait loci (QTL) are relatively rare in the population. In contrast, discordant pairs and the extreme-proband design provide power for the broadest range of QTL–marker-allele frequency differences. Overall, proband selection from either tail provides the best balance of power, robustness, and simplicity of ascertainment for family-based association analysis. PMID:11349228

Simultaneous fabrication of very high aspect ratio positive nano- to milliscale structures.

PubMed

Chen, Long Qing; Chan-Park, Mary B; Zhang, Qing; Chen, Peng; Li, Chang Ming; Li, Sai

2009-05-01

A simple and inexpensive technique for the simultaneous fabrication of positive (i.e., protruding), very high aspect (>10) ratio nanostructures together with micro- or millistructures is developed. The method involves using residual patterns of thin-film over-etching (RPTO) to produce sub-micro-/nanoscale features. The residual thin-film nanopattern is used as an etching mask for Si deep reactive ion etching. The etched Si structures are further reduced in size by Si thermal oxidation to produce amorphous SiO(2), which is subsequently etched away by HF. Two arrays of positive Si nanowalls are demonstrated with this combined RPTO-SiO(2)-HF technique. One array has a feature size of 150 nm and an aspect ratio of 26.7 and another has a feature size of 50 nm and an aspect ratio of 15. No other parallel reduction technique can achieve such a very high aspect ratio for 50-nm-wide nanowalls. As a demonstration of the technique to simultaneously achieve nano- and milliscale features, a simple Si nanofluidic master mold with positive features with dimensions varying continuously from 1 mm to 200 nm and a highest aspect ratio of 6.75 is fabricated; the narrow 200-nm section is 4.5 mm long. This Si master mold is then used as a mold for UV embossing. The embossed open channels are then closed by a cover with glue bonding. A high aspect ratio is necessary to produce unblocked closed channels after the cover bonding process of the nanofluidic chip. The combined method of RPTO, Si thermal oxidation, and HF etching can be used to make complex nanofluidic systems and nano-/micro-/millistructures for diverse applications.

Modulated-splitting-ratio fiber-optic temperature sensor

NASA Technical Reports Server (NTRS)

Beheim, Glenn; Anthan, Donald J.; Rys, John R.; Fritsch, Klaus; Ruppe, Walter A.

1988-01-01

A fiber-optic temperature sensor is described, which uses a small silicon beamsplitter whose splitting ratio varies as a function of temperature. A four-beam technique is used to measure the sensor's temperature-indicating splitting ratio. This referencing method provides a measurement that is largely independent of the transmission properties of the sensor's optical fiber link. A significant advantage of this sensor, relative to other fiber-optic sensors, is its high stability, which permits the fiber-optic components to be readily substituted, thereby simplifying the sensor's installation and maintenance.

The ratioed image film thickness meter

NASA Astrophysics Data System (ADS)

Husen, Nicholas M.; Liu, Tianshu; Sullivan, John P.

2018-06-01

A technique for measuring the thickness of a fluorescent oil film is presented. Incident light is cast upon the oil film and the intensity of the luminescent signal from the fluorescent dye is ratioed with the intensity of the incident light which is scattered from the surface of the model. The quotient is independent of the intensity of the incident light and proportional to the film thickness. Experiments are presented supporting that for sufficiently thin films the ratio is independent of the intensity of the incident light as well as independent of the angle from which the experiment is imaged and the angle from which the incident light is cast.

A quantum framework for likelihood ratios

NASA Astrophysics Data System (ADS)

Bond, Rachael L.; He, Yang-Hui; Ormerod, Thomas C.

The ability to calculate precise likelihood ratios is fundamental to science, from Quantum Information Theory through to Quantum State Estimation. However, there is no assumption-free statistical methodology to achieve this. For instance, in the absence of data relating to covariate overlap, the widely used Bayes’ theorem either defaults to the marginal probability driven “naive Bayes’ classifier”, or requires the use of compensatory expectation-maximization techniques. This paper takes an information-theoretic approach in developing a new statistical formula for the calculation of likelihood ratios based on the principles of quantum entanglement, and demonstrates that Bayes’ theorem is a special case of a more general quantum mechanical expression.

Linkage disequilibrium between polymorphisms of ABCB1 and ABCC2 to predict the treatment outcome of Malaysians with complex partial seizures on treatment with carbamazepine mono-therapy at the Kuala Lumpur Hospital.

PubMed

Subenthiran, Soobitha; Abdullah, Noor Rain; Joseph, Joyce Pauline; Muniandy, Prem Kumar; Mok, Boon Teck; Kee, Chee Cheong; Ismail, Zakiah; Mohamed, Zahurin

2013-01-01

Carbamazepine (CBZ) is used as the first line of treatment of Complex Partial Seizures (CPS) in the Epilepsy Clinic, Neurology Department of Kuala Lumpur Hospital (KLH). More than 30% of the patients remain drug resistant to CBZ mono-therapy. CBZ is transported by the P-glycoprotein (P-gp). The P-gp encoded by the ABCB1 and ABCC2 genes are expressed in drug resistant patients with epilepsy. A few studies have shown significant association between CBZ resistant epilepsy and Linkage Disequilibrium (LD) with adjacent polymorphisms of these genes. Our study is aimed at determining the correlation between patients' response to CBZ mono-therapy to Single Nucleotide Polymorphisms G2677T and C3435T of the ABCB1 gene as well as G1249A and -24C>T of the ABCC2 gene. 314 patients with CPS were recruited from the Neurology Department of the KLH based on stringent inclusion and exclusion criteria, of whom 152 were responders and the other 162 were non-responders. DNA was extracted from their blood samples and Taqman technology for allelic discrimination was performed. Results were described as genotype frequencies. The SHEsis analysis platform was used to calculate linkage disequilibrium index and infer haplotype frequencies. Haploview was used to do permutation test to obtain a corrected p-value. Resistance to treatment with CBZ mono-therapy was significantly associated with the 2677TT and the 3435TT genotypes while it was not significantly associated with the G1249A and -24C>T polymorphisms. The GCGC haplotype combination of the 2677G>T, 3435C>T, 1249G>A and -24C>T respectively was found to be extremely significant (p = 1.10e-20) with good drug response to CBZ mono-therapy. Linkage disequilibrium between the 2677G>T, 3435C>T, 1249G>A and -24C>T SNPs may be used as a reliable screening marker to determine the treatment outcome of CBZ mono-therapy with CPS irrespective of race or gender.

An intercomparison of nitric oxide measurement techniques

NASA Technical Reports Server (NTRS)

Hoell, J. M., Jr.; Gregory, G. L.; Mcdougal, D. S.; Carroll, M. A.; Mcfarland, M.; Ridley, B. A.; Davis, D. D.; Bradshaw, J.; Rodgers, M. O.; Torres, A. L.

1985-01-01

Results from an intercomparison of techniques to measure tropospheric levels of nitric oxide (NO) are discussed. The intercomparison was part of the National Aeronautics and Space Administration's Global Tropospheric Experiment and was conducted at Wallops Island, VA, in July 1983. Instruments intercompared included a laser-induced fluorescence system and two chemiluminescence instruments. The intercomparisons were performed with ambient air at NO mixing ratios ranging from 10 to 60 pptv and NO-enriched ambient air at mixing ratios from 20 to 170 pptv. All instruments sampled from a common manifold. The techniques exhibited a high degree of correlation among themselves and with changes in the NO mixing ratio. Agreement among the three techniques was placed at approximately + or - 30 percent. Within this level of agreement, no artifacts or species interferences were identified.

Defining window-boundaries for genomic analyses using smoothing spline techniques

DOE PAGES

Beissinger, Timothy M.; Rosa, Guilherme J.M.; Kaeppler, Shawn M.; ...

2015-04-17

High-density genomic data is often analyzed by combining information over windows of adjacent markers. Interpretation of data grouped in windows versus at individual locations may increase statistical power, simplify computation, reduce sampling noise, and reduce the total number of tests performed. However, use of adjacent marker information can result in over- or under-smoothing, undesirable window boundary specifications, or highly correlated test statistics. We introduce a method for defining windows based on statistically guided breakpoints in the data, as a foundation for the analysis of multiple adjacent data points. This method involves first fitting a cubic smoothing spline to the datamore » and then identifying the inflection points of the fitted spline, which serve as the boundaries of adjacent windows. This technique does not require prior knowledge of linkage disequilibrium, and therefore can be applied to data collected from individual or pooled sequencing experiments. Moreover, in contrast to existing methods, an arbitrary choice of window size is not necessary, since these are determined empirically and allowed to vary along the genome.« less

New Examination of the Traditional Raman Lidar Technique II: Evaluating the Ratios for Water Vapor and Aerosols

NASA Technical Reports Server (NTRS)

Whiteman, David N.

2003-01-01

In a companion paper, the temperature dependence of Raman scattering and its influence on the Raman and Rayleigh-Mie lidar equations was examined. New forms of the lidar equation were developed to account for this temperature sensitivity. Here those results are used to derive the temperature dependent forms of the equations for the water vapor mixing ratio, aerosol scattering ratio, aerosol backscatter coefficient, and extinction to backscatter ratio (Sa). The error equations are developed, the influence of differential transmission is studied and different laser sources are considered in the analysis. The results indicate that the temperature functions become significant when using narrowband detection. Errors of 5% and more can be introduced in the water vapor mixing ratio calculation at high altitudes and errors larger than 10% are possible for calculations of aerosol scattering ratio and thus aerosol backscatter coefficient and extinction to backscatter ratio.

Stable oxygen and hydrogen isotopes of brines - comparing isotope ratio mass spectrometry and isotope ratio infrared spectroscopy

NASA Astrophysics Data System (ADS)

Ahrens, Christian; Koeniger, Paul; van Geldern, Robert; Stadler, Susanne

2013-04-01

Today's standard analytical methods for high precision stable isotope analysis of fluids are gas-water equilibration and high temperature pyrolysis coupled to isotope ratio mass spectrometers (IRMS). In recent years, relatively new laser-based analytical instruments entered the market that are said to allow high isotope precision data on nearly every media. This optical technique is referred to as isotope ratio infrared spectroscopy (IRIS). The objective of this study is to evaluate the capability of this new instrument type for highly saline solutions and a comparison of the analytical results with traditional IRMS analysis. It has been shown for the equilibration method that the presence of salts influences the measured isotope values depending on the salt concentration (see Lécuyer et al, 2009; Martineau, 2012). This so-called 'isotope salt effect' depends on the salt type and salt concentration. These factors change the activity in the fluid and therefore shift the isotope ratios measured by the equilibration method. Consequently, correction factors have to be applied to these analytical data. Direct conversion techniques like pyrolysis or the new laser instruments allow the measurement of the water molecule from the sample directly and should therefore not suffer from the salt effect, i.e. no corrections of raw values are necessary. However, due to high salt concentrations this might cause technical problems with the analytical hardware and may require labor-intensive sample preparation (e.g. vacuum distillation). This study evaluates the salt isotope effect for the IRMS equilibration technique (Thermo Gasbench II coupled to Delta Plus XP) and the laser-based IRIS instruments with liquid injection (Picarro L2120-i). Synthetic salt solutions (NaCl, KCl, CaCl2, MgCl2, MgSO4, CaSO4) and natural brines collected from the Stassfurt Salt Anticline (Germany; Stadler et al., 2012) were analysed with both techniques. Salt concentrations ranged from seawater salinity

Isotope Ratios Reveal Trickery in the Produce Aisle

ERIC Educational Resources Information Center

Journal of Chemical Education, 2007

2007-01-01

A new technique for the proper checking and banning of organic food items is proposed. The analysis of the nitrogen isotope ratio present in the food is found to be a perfect standard for the organic checking of the food products.

On virial analysis at low aspect ratio

DOE PAGES

Bongard, Michael W.; Barr, Jayson L.; Fonck, Raymond J.; ...

2016-07-28

The validity of virial analysis to infer global MHD equilibrium poloidal beta β p and internal inductance ℓ i from external magnetics measurements is examined for low aspect ratio configurations with A < 2. Numerical equilibrium studies at varied aspect ratio are utilized to validate the technique at finite aspect ratio. The effect of applying high-A approximations to low-A experimental data is quantified and demonstrates significant over-estimation of stored energy (factors of 2–10) in spherical tokamak geometry. Experimental approximations to equilibrium-dependent volume integral terms in the analysis are evaluated at low-A. Highly paramagnetic configurations are found to be inadequately representedmore » through the virial mean radius parameter R T. Alternate formulations for inferring β p and ℓ i that are independent of R T to avoid this difficulty are presented for the static isotropic limit. Lastly, these formulations are suitable for fast estimation of tokamak stored energy components at low aspect ratio using virial analysis.« less

Two-Oxide Disequilibrium: A New Geospeedometer Based on Diffusion in Ilmenite

NASA Astrophysics Data System (ADS)

Williams, K. B.; Krawczynski, M. J.; Van Orman, J. A.

2016-12-01

Diffusion-annealing experiments were conducted in a 0.5" piston cylinder apparatus to investigate diffusivity of Fe2+, Mg2+, and Mn2+ in ilmenite solid solutions between 800ºC and 1000ºC. Polycrystalline ilmenite (FeTiO3) was juxtaposed against either an oriented geikielite (MgTiO3) single crystal or polycrystalline Mn-bearing (5 mol% Mn) ilmenite, in a "diffusion-couple" geometry. Geikielite single crystals were synthesized at Los Alamos National Laboratory, cut into 1 mm edge-length cubes, and polished either perpendicular or parallel to the c-axis. Polycrystalline ilmenite starting materials were synthesized by mixing high purity reagent-grade oxides (FeO, MnO, and TiO2) and sintering in a piston cylinder apparatus, then cut into wafers and polished. Experimental run products were analyzed by electron microprobe at Washington University in St. Louis. Microprobe analyses were obtained perpendicularly across the diffusion interface for each experiment. Experimental diffusion profiles create smooth curves that, when fit with an error function, define Fe-Mg and Fe-Mn interdiffusion coefficients in ilmenite. The diffusion coefficients do not appear compositionally dependent, but do show significant anisotropy. Preliminary results suggest diffusion activation energies are lower in ilmenite than in titanomagnetite [1]. Ilmenite-titanomagnetite equilibria define pre-eruptive temperatures and oxygen fugacities. However, oxides often exist out of equilibrium [2]. We use the cation diffusion data for ilmenite and existing data on titanomagnetite to establish two-oxide disequilibrium as a geospeedometer. Our data constrain oxide-oxide re-equilibration timescales at Mt. Unzen to months, consistent with estimates from zoned, single crystals of magnetite [3,4]. Future experiments will examine the effect of oxygen fugacity on diffusivity in ilmenite solid solutions. References:[1] Van Orman & Crispin (2010) RiMG 72, 757-825.[2] Bacon & Hirschmann (1988) Am. Min. 73, 57

Estimating crustal thickness and Vp/Vs ratio with joint constraints of receiver function and gravity data

NASA Astrophysics Data System (ADS)

Shi, Lei; Guo, Lianghui; Ma, Yawei; Li, Yonghua; Wang, Weilai

2018-05-01

The technique of teleseismic receiver function H-κ stacking is popular for estimating the crustal thickness and Vp/Vs ratio. However, it has large uncertainty or ambiguity when the Moho multiples in receiver function are not easy to be identified. We present an improved technique to estimate the crustal thickness and Vp/Vs ratio by joint constraints of receiver function and gravity data. The complete Bouguer gravity anomalies, composed of the anomalies due to the relief of the Moho interface and the heterogeneous density distribution within the crust, are associated with the crustal thickness, density and Vp/Vs ratio. According to their relationship formulae presented by Lowry and Pérez-Gussinyé, we invert the complete Bouguer gravity anomalies by using a common algorithm of likelihood estimation to obtain the crustal thickness and Vp/Vs ratio, and then utilize them to constrain the receiver function H-κ stacking result. We verified the improved technique on three synthetic crustal models and evaluated the influence of selected parameters, the results of which demonstrated that the novel technique could reduce the ambiguity and enhance the accuracy of estimation. Real data test at two given stations in the NE margin of Tibetan Plateau illustrated that the improved technique provided reliable estimations of crustal thickness and Vp/Vs ratio.

Linkage disequilibrium between polymorphisms at the 5{prime} untranslated region and intron 5 (Dde I) of the antithrombin III (ATIII) gene in the Chinese

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

Tay, J.S.H.; Liu, Y.; Low, P.S.

A length polymorphism at the 5{prime} untranslated region of exon 1 and an RFLP (Dde I) in intron 5 (nt 160) of the ATIII gene were amplified by polymerase chain reaction with primers of published sequences. DNA fragments were size-fractionated by agarose gel electrophoresis (3% NuSieve and 1% Seakem GTG) and photographed over a UV transilluminator. A strong linkage disequilibrium was observed between these two polymorphisms of the ATIII gene in the Chinese ({chi}{sup 2} = 63.7; {triangle} 0.42, P < 0.001). The estimated frequencies of the three haplotypes were found to be 0.37 for SD+, 0.40 for LD+ andmore » 0.23 for LD-.« less

MEASUREMENT OF BI-DIRECTIONAL AMMONIA FLUXES OVER SOYBEAN USING MODIFIED BOWEN-RATIO TECHNIQUE

EPA Science Inventory

Measurements of bi-directional ammonia exchange over a fertilized soybean canopy are presented for an 8-week period during the summer of 2002. The modified Bowne-ratio approach was used to determine fluxes from vertical NH3 and temperature gradients in combination with eddy covar...

Study of signal-to-noise ratio in digital mammography

NASA Astrophysics Data System (ADS)

Kato, Yuri; Fujita, Naotoshi; Kodera, Yoshie

2009-02-01

Mammography techniques have recently advanced from those using analog systems (the screen-film system) to those using digital systems; for example, computed radiography (CR) and flat-panel detectors (FPDs) are nowadays used in mammography. Further, phase contrast mammography (PCM)-a digital technique by which images with a magnification of 1.75× can be obtained-is now available in the market. We studied the effect of the air gap in PCM and evaluated the effectiveness of an antiscatter x-ray grid in conventional mammography (CM) by measuring the scatter fraction ratio (SFR) and relative signal-to-noise ratio (rSNR) and comparing them between PCM and the digital CM. The results indicated that the SFRs for the CM images obtained with a grid were the lowest and that these ratios were almost the same as those for the PCM images. In contrast, the rSNRs for the PCM images were the highest, which means that the scattering of x-rays was sufficiently reduced by the air gap without the loss of primary x-rays.

Refined mapping of a gene responsible for Fukuyama-type congenital muscular dystrophy: Evidence for strong linkage disequilibrium

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

Toda, Tatsushi; Ikegawa, Shiro; Okui, Keiko

1994-11-01

Fukuyama-type congenital muscular dystrophy (FCMD), the second most common form of childhood muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy associated with an anomaly of the brain. After our initial mapping of the FCMD locus to chromosome 9q31-33, we further defined the locus within a region of {approximately}5 cM between loci D9S127 and CA246, by homozygosity mapping in patients born to consanguineous marriages and by recombination analyses in other families. We also found evidence for strong linkage disequilibrium between FCMD and a polymorphic microsatellite marker, mfd220, which showed no recombination and a lod score of (Z) 17.49.more » A {open_quotes}111-bp{close_quotes} allele for the mfd220 was observed in 22 (34%) of 64 FCMD chromosomes, but it was present in only 1 of 120 normal chromosomes. This allelic association with FCMD was highly significant ({chi}{sup 2} = 50.7; P < .0001). Hence, we suspect that the FCMD gene could lie within a few hundred kilobases of the mfd220 locus. 32 refs., 2 figs., 2 tabs.« less

High-aspect ratio magnetic nanocomposite polymer cilium

NASA Astrophysics Data System (ADS)

Rahbar, M.; Tseng, H. Y.; Gray, B. L.

2014-03-01

This paper presents a new fabrication technique to achieve ultra high-aspect ratio artificial cilia micro-patterned from flexible highly magnetic rare earth nanoparticle-doped polymers. We have developed a simple, inexpensive and scalable fabrication method to create cilia structures that can be actuated by miniature electromagnets, that are suitable to be used for lab-on-a chip (LOC) and micro-total-analysis-system (μ-TAS) applications such as mixers and flow-control elements. The magnetic cilia are fabricated and magnetically polarized directly in microfluidic channels or reaction chambers, allowing for easy integration with complex microfluidic systems. These cilia structures can be combined on a single chip with other microfluidic components employing the same permanently magnetic nano-composite polymer (MNCP), such as valves or pumps. Rare earth permanent magnetic powder, (Nd0.7Ce0.3)10.5Fe83.9B5.6, is used to dope polydimethylsiloxane (PDMS), resulting in a highly flexible M-NCP of much higher magnetization and remanence [1] than ferromagnetic polymers typically employed in magnetic microfluidics. Sacrificial poly(ethylene-glycol) (PEG) is used to mold the highly magnetic polymer into ultra high-aspect ratio artificial cilia. Cilia structures with aspect ratio exceeding 8:0.13 can be easily fabricated using this technique and are actuated using miniature electromagnets to achieve a high range of motion/vibration.

Sex ratio variation in Iberian pigs.

PubMed

Toro, M A; Fernández, A; García-Cortés, L A; Rodrigáñez, J; Silió, L

2006-06-01

Within the area of sex allocation, one of the topics that has attracted a lot of attention is the sex ratio problem. Fisher (1930) proposed that equal numbers of males and females have been promoted by natural selection and it has an adaptive significance. But the empirical success of Fisher's theory remains doubtful because a sex ratio of 0.50 is also expected from the chromosomal mechanism of sex determination. Another way of approaching the subject is to consider that Fisher's argument relies on the underlying assumption that offspring inherit their parent's tendency in biased sex ratio and therefore that genetic variance for this trait exists. Here, we analyzed sex ratio data of 56,807 piglets coming from 550 boars and 1893 dams. In addition to classical analysis of heterogeneity we performed analyses fitting linear and threshold animal models in a Bayesian framework using Gibbs sampling techniques. The marginal posterior mean of heritability was 2.63 x 10(-4) under the sire linear model and 9.17 x 10(-4) under the sire threshold model. The probability of the hypothesis p(h(2) = 0) fitting the last model was 0.996. Also, we did not detect any trend in sex ratio related to maternal age. From an evolutionary point of view, the chromosomal sex determination acts as a constraint that precludes control of offspring sex ratio in vertebrates and it should be included in the general theory of sex allocation. From a practical view that means that the sex ratio in domestic species is hardly susceptible to modification by artificial selection.

Inflammatory Disequilibrium in Stroke

PubMed Central

Petrovic-Djergovic, Danica; Goonewardena, Sascha N.; Pinsky, David J.

2016-01-01

Over the past several decades, there have been substantial advances in our knowledge of the pathophysiology of stroke. Understanding the benefits of timely reperfusion has led to the development of thrombolytic therapy as the cornerstone of current management of ischemic stroke, but there remains much to be learned about mechanisms of neuronal ischemic and reperfusion injury and associated inflammation. For ischemic stroke, novel therapeutic targets have continued to remain elusive. When considering modern molecular biologic techniques, advanced translational stroke models, and clinical studies, a consistent pattern emerges, implicating perturbation of the immune equilibrium by stroke in both central nervous system injury and repair responses. Stroke triggers activation of the neuroimmune axis, comprised of multiple cellular constituents of the immune system resident within the parenchyma of the brain, leptomeninges, and vascular beds, as well as through secretion of biological response modifiers and recruitment of immune effector cells. This neuroimmune activation can directly impact the initiation, propagation, and resolution phases of ischemic brain injury. In order to leverage a potential opportunity to modulate local and systemic immune responses to favorably affect the stroke disease curve, it is necessary to expand our mechanistic understanding of the neuroimmune axis in ischemic stroke. This review explores the frontiers of current knowledge of innate and adaptive immune responses in the brain and how these responses together shape the course of ischemic stroke. PMID:27340273

Forest soil carbon oxidation state and oxidative ratio responses to elevated CO 2

DOE PAGES

Hockaday, William C.; Gallagher, Morgan E.; Masiello, Caroline A.; ...

2015-09-21

The oxidative ratio (OR) of the biosphere is the stoichiometric ratio (O 2/CO 2) of gas exchange by photosynthesis and respiration a key parameter in budgeting calculations of the land and ocean carbon sinks. Carbon cycle-climate feedbacks could alter the OR of the biosphere by affecting the quantity and quality of organic matter in plant biomass and soil carbon pools. Here, this study considers the effect of elevated atmospheric carbon dioxide concentrations ([CO 2]) on the OR of a hardwood forest after nine growing seasons of Free-Air CO 2 Enrichment. We measured changes in the carbon oxidation state (C ox)more » of biomass and soil carbon pools as a proxy for the ecosystem OR. The OR of net primary production, 1.039, was not affected by elevated [CO 2]. However, the C ox of the soil carbon pool was 40% higher at elevated [CO 2], and the estimated OR values for soil respiration increased from 1.006 at ambient [CO 2] to 1.054 at elevated [CO 2]. A biochemical inventory of the soil organic matter ascribed the increases in C ox and OR to faster turnover of reduced substrates, lignin and lipids, at elevated [CO 2]. This implicates the heterotrophic soil community response to elevated [CO 2] as a driver of disequilibrium in the ecosystem OR. The oxidation of soil carbon pool constitutes an unexpected terrestrial O 2 sink. Carbon budgets constructed under the assumption of OR equilibrium would equate such a terrestrial O 2 sink to CO 2 uptake by the ocean. We find that the potential for climate-driven disequilibriua in the cycling of O 2 and CO 2 warrants further investigation.« less

Quantifying Void Ratio in Granular Materials Using Voronoi Tessellation

NASA Technical Reports Server (NTRS)

Alshibli, Khalid A.; El-Saidany, Hany A.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Voronoi technique was used to calculate the local void ratio distribution of granular materials. It was implemented in an application-oriented image processing and analysis algorithm capable of extracting object edges, separating adjacent particles, obtaining the centroid of each particle, generating Voronoi polygons, and calculating the local void ratio. Details of the algorithm capabilities and features are presented. Verification calculations included performing manual digitization of synthetic images using Oda's method and Voronoi polygon system. The developed algorithm yielded very accurate measurements of the local void ratio distribution. Voronoi tessellation has the advantage, compared to Oda's method, of offering a well-defined polygon generation criterion that can be implemented in an algorithm to automatically calculate local void ratio of particulate materials.

Derivation of sideband gain ratio for Herschel/HIFI

NASA Astrophysics Data System (ADS)

Kester, Do; Higgins, Ronan; Teyssier, David

2017-03-01

Context. Heterodyne mixers are commonly used for high-resolution spectroscopy at radio telescopes. When used as a double sideband system, the accurate flux calibration of spectral lines acquired by those detectors is highly dependent on the system gains in the respective mixer sidebands via the so-called sideband gain ratio (SBR). As such, the SBR was one of the main contributors to the calibration uncertainty budget of the Herschel/HIFI instrument. Aims: We want to determine the HIFI instrument sideband gain ratio for all bands on a fine frequency grid and within an accuracy of a few percent. Methods: We introduce a novel technique involving in-orbit HIFI data that is bootstrapped onto standard methods involving laboratory data measurements of the SBR. We deconvolved the astronomical data to provide a proxy of the expected signal at every frequency channel, and extracted the sideband gain ratios from the residuals of that process. Results: We determine the HIFI sideband gain ratio to an accuracy varying between 1 and 4%, with degraded accuracy in higher frequency ranges, and at places where the reliability of the technique is lower. These figures were incorporated into the HIFI data processing pipeline and improved the overall flux uncertainty of the legacy data from this instrument. Conclusions: We demonstrate that a modified sideband deconvolution algorithm, using astronomical data in combination with gas cell measurements, can be used to generate an accurate and fine-granularity picture of the sideband gain ratio behaviour of a heterodyne receiver. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

Effects of must concentration techniques on wine isotopic parameters.

PubMed

Guyon, Francois; Douet, Christine; Colas, Sebastien; Salagoïty, Marie-Hélène; Medina, Bernard

2006-12-27

Despite the robustness of isotopic methods applied in the field of wine control, isotopic values can be slightly influenced by enological practices. For this reason, must concentration technique effects on wine isotopic parameters were studied. The two studied concentration techniques were reverse osmosis (RO) and high-vacuum evaporation (HVE). Samples (must and extracted water) have been collected in various French vineyards. Musts were microfermented at the laboratory, and isotope parameters were determined on the obtained wine. Deuterium and carbon-13 isotope ratios were studied on distilled ethanol by nuclear magnetic resonance (NMR) and isotope ratio mass spectrometry (IRMS), respectively. The oxygen-18 ratio was determined on extracted and wine water using IRMS apparatus. The study showed that the RO technique has a very low effect on isotopic parameters, indicating that this concentration technique does not create any isotopic fractionation, neither at sugar level nor at water level. The effect is notable for must submitted to HVE concentration: water evaporation leads to a modification of the oxygen-18 ratio of the must and, as a consequence, ethanol deuterium concentration is also modified.

Laser two focus techniques

NASA Astrophysics Data System (ADS)

Schodl, R.

The development of the laser two focus velocimetry are reviewed. The fundamentals of this nonintrusive fluid flow velocity measurement technique are described. Emphasis is placed upon the advances of this technique. Results of measurements in a very small flow channel and in a small turbocharger compressor rotor are presented. The influence of beam diameter - beam separation ratio on the measuring accuracy and on the measuring time is treated. A multicolor two dimensional system with selectable beam separation is presented. The laser Doppler and the laser two focus techniques are compared.

On-demand drawing of high aspect-ratio, microsphere-tipped elastomeric micropillars

NASA Astrophysics Data System (ADS)

Li, Qiang; Kim, Jaeyoun

2017-08-01

High aspect-ratio elastomeric micropillars are widely used in a plethora of applications, such as functional surfaces, actuators, and sensors. Their fabrication at arbitrary positions on non-planar substrates, however, has rarely been reported. Here we demonstrate a new technique for facile fabrication of high aspect-ratio, microsphere-tipped elastomeric micropillars on structures with uncommon geometries. As a proof-of-concept exemplary application, a fiber optic contact sensor is realized by integrating a micropillar onto the end facet of an optical fiber. Overall, both the fabrication technique and the resulting outcomes of this work will add new tools to the toolbox of soft-MEMS and softrobotics.

Measuring demand for flat water recreation using a two-stage/disequilibrium travel cost model with adjustment for overdispersion and self-selection

NASA Astrophysics Data System (ADS)

McKean, John R.; Johnson, Donn; Taylor, R. Garth

2003-04-01

An alternate travel cost model is applied to an on-site sample to estimate the value of flat water recreation on the impounded lower Snake River. Four contiguous reservoirs would be eliminated if the dams are breached to protect endangered Pacific salmon and steelhead trout. The empirical method applies truncated negative binomial regression with adjustment for endogenous stratification. The two-stage decision model assumes that recreationists allocate their time among work and leisure prior to deciding among consumer goods. The allocation of time and money among goods in the second stage is conditional on the predetermined work time and income. The second stage is a disequilibrium labor market which also applies if employers set work hours or if recreationists are not in the labor force. When work time is either predetermined, fixed by contract, or nonexistent, recreationists must consider separate prices and budgets for time and money.

Fronto-orbital feminization technique. A surgical strategy using fronto-orbital burring with or without eggshell technique to optimize the risk/benefit ratio.

PubMed

Villepelet, A; Jafari, A; Baujat, B

2018-05-04

The demand for facial feminization is increasing in transsexual patients. Masculine foreheads present extensive supraorbital bossing with a more acute glabellar angle, whereas female foreheads show softer features. The aim of this article is to describe our surgical technique for fronto-orbital feminization. The mask-lift technique is an upper face-lift. It provides rejuvenation by correcting collapsed features, and fronto-orbital feminization through burring of orbital rims and lateral canthopexies. Depending on the size of the frontal sinus and the thickness of its anterior wall, frontal remodeling is achieved using simple burring or by means of the eggshell technique. Orbital remodeling comprises a superolateral orbital opening, a reduction of ridges and a trough at the lateral orbital rim to support the lateral canthopexy. Frontal, corrugator and procerus myectomies, plus minimal scalp excision, complete the surgery. Our technique results in significant, natural-looking feminization. No complications were observed in our series of patients. The eggshell technique is an alternative to bone flap on over-pneumatized sinus. Fronto-orbital feminization fits into a wider surgical strategy. It can be associated to rhinoplasty, genioplasty, mandibular angle remodeling, face lift and laryngoplasty. Achieving facial feminization in 2 or 3 stages improves psychological and physiological tolerance. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.

PubMed

De La Vega, Francisco M; Isaac, Hadar I; Scafe, Charles R

2006-01-01

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan SNP Genotyping Assays or the SNPlex Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.

Optimisation of phase ratio in the triple jump using computer simulation.

PubMed

Allen, Sam J; King, Mark A; Yeadon, M R Fred

2016-04-01

The triple jump is an athletic event comprising three phases in which the optimal proportion of each phase to the total distance jumped, termed the phase ratio, is unknown. This study used a whole-body torque-driven computer simulation model of all three phases of the triple jump to investigate optimal technique. The technique of the simulation model was optimised by varying torque generator activation parameters using a Genetic Algorithm in order to maximise total jump distance, resulting in a hop-dominated technique (35.7%:30.8%:33.6%) and a distance of 14.05m. Optimisations were then run with penalties forcing the model to adopt hop and jump phases of 33%, 34%, 35%, 36%, and 37% of the optimised distance, resulting in total distances of: 13.79m, 13.87m, 13.95m, 14.05m, and 14.02m; and 14.01m, 14.02m, 13.97m, 13.84m, and 13.67m respectively. These results indicate that in this subject-specific case there is a plateau in optimum technique encompassing balanced and hop-dominated techniques, but that a jump-dominated technique is associated with a decrease in performance. Hop-dominated techniques are associated with higher forces than jump-dominated techniques; therefore optimal phase ratio may be related to a combination of strength and approach velocity. Copyright © 2016 Elsevier B.V. All rights reserved.

Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

PubMed

Vitart, Veronique; Carothers, Andrew D; Hayward, Caroline; Teague, Peter; Hastie, Nicholas D; Campbell, Harry; Wright, Alan F

2005-05-01

Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

Isotopic Ratio, Isotonic Ratio, Isobaric Ratio and Shannon Information Uncertainty

NASA Astrophysics Data System (ADS)

Ma, Chun-Wang; Wei, Hui-Ling

2014-11-01

The isoscaling and the isobaric yield ratio difference (IBD) probes, both of which are constructed by yield ratio of fragment, provide cancelation of parameters. The information entropy theory is introduced to explain the physical meaning of the isoscaling and IBD probes. The similarity between the isoscaling and IBD results is found, i.e., the information uncertainty determined by the IBD method equals to β - α determined by the isoscaling (α (β) is the parameter fitted from the isotopic (isotonic) yield ratio).

Ratio maps of iron ore deposits Atlantic City district, Wyoming

NASA Technical Reports Server (NTRS)

Vincent, R. K.

1973-01-01

Preliminary results of a spectral rationing technique are shown for a region at the southern end of the Wind River Range, Wyoming. Digital ratio graymaps and analog ratio images have been produced for the test site, but ground truth is not yet available for thorough interpretation of these products. ERTS analog ratio images were found generally better than either ERTS single-channel images or high altitude aerial photos for the discrimination of vegetation from non-vegetation in the test site region. Some linear geological features smaller than the ERTS spatial resolution are seen as well in ERTS ratio and single-channel images as in high altitude aerial photography. Geochemical information appears to be extractable from ERTS data. Good preliminary quantitative agreement between ERTS-derived ratios and laboratory-derived reflectance ratios of rocks and minerals encourage plans to use lab data as training sets for a simple ratio gating logic approach to automatic recognition maps.

Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium

PubMed Central

Ramstein, Guillaume P.; Evans, Joseph; Kaeppler, Shawn M.; Mitchell, Robert B.; Vogel, Kenneth P.; Buell, C. Robin; Casler, Michael D.

2016-01-01

Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs. PMID:26869619

Visualization of Secondary Flow Development in High Aspect Ratio Channels with Curvature

NASA Technical Reports Server (NTRS)

Meyer, Michael L.; Giuliani, James E.

1994-01-01

The results of an experimental project to visually examine the secondary flow structure that develops in curved, high aspect-ratio rectangular channels are presented. The results provide insight into the fluid dynamics within high aspect ratio channels. A water flow test rig constructed out of plexiglass, with an adjustable aspect ratio, was used for these experiments. Results were obtained for a channel geometry with a hydraulic diameter of 10.6 mm (0.417 in.), an aspect ratio of 5.0, and a hydraulic radius to curvature radius ratio of 0.0417. Flow conditions were varied to achieve Reynolds numbers up to 5,100. A new particle imaging velocimetry technique was developed which could resolve velocity information from particles entering and leaving the field of view. Time averaged secondary flow velocity vectors, obtained using this velocimetry technique, are presented for 30 degrees, 60 degrees, and 90 degrees into a 180 degrees bend and at a Reynolds number of 5,100. The secondary flow results suggest the coexistence of both the classical curvature induced vortex pair flow structure and the eddies seen in straight turbulent channel flow.

Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road.

PubMed

Branscomb, Elbert; Russell, Michael J

2013-02-01

The Submarine Hydrothermal Alkaline Spring Theory for the emergence of life holds that it is the ordered delivery of hydrogen and methane in alkaline hydrothermal solutions at a spontaneously precipitated inorganic osmotic and catalytic membrane to the carbon dioxide and other electron acceptors in the earliest acidulous cool ocean that, through these gradients, drove life into being. That such interactions between hydrothermal fuels and potential oxidants have so far not been accomplished in the lab is because some steps along the necessary metabolic pathways are endergonic and must therefore be driven by being coupled to thermodynamically larger exergonic processes. But coupling of this kind is far from automatic and it is not enough to merely sum the ΔGs of two supposedly coupled reactions and show their combined thermodynamic viability. An exergonic reaction will not drive an endergonic one unless 'forced' to do so by being tied to it mechanistically via an organized "engine" of "Free Energy Conversion" (FEC). Here we discuss the thermodynamics of FEC and advance proposals regarding the nature and roles of the FEC devices that could, in principle, have arisen spontaneously in the alkaline hydrothermal context and have forced the onset of a protometabolism. The key challenge is to divine what these initial engines of life were in physicochemical terms and as part of that, what structures provided the first "turnstile-like" mechanisms needed to couple the partner processes in free energy conversion; in particular to couple the dissipation of geochemically given gradients to, say, the reduction of CO(2) to formate and the generation of a pyrophosphate disequilibrium. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Linkage disequilibrium with HLA-DRB1-DQB1 haplotypes explains the association of TNF-308G>A variant with type 1 diabetes in a Brazilian cohort.

PubMed

Patente, Thiago A; Monteiro, Maria B; Vieira, Suzana M; Rossi da Silva, Maria E; Nery, Márcia; Queiroz, Márcia; Azevedo, Mirela J; Canani, Luis H; Parisi, Maria C; Pavin, Elizabeth J; Mainardi, Débora; Javor, Juraj; Velho, Gilberto; Coimbra, Cássio N; Corrêa-Giannella, Maria Lúcia

2015-08-15

A functional variant in the promoter region of the gene encoding tumor necrosis factor (TNF; rs1800629, -308G>A) showed to confer susceptibility to T1D. However, TNF rs1800629 was found, in several populations, to be in linkage disequilibrium with HLA susceptibility haplotypes to T1D. We evaluated the association of TNF rs1800629 with T1D in a cohort of Brazilian subjects, and assessed the impact of HLA susceptibility haplotypes in this association. 659 subjects with T1D and 539 control subjects were genotyped for TNF-308G>A variant. HLA-DRB1 and HLA-DQB1 genes were genotyped in a subset of 313 subjects with T1D and 139 control subjects. Associations with T1D were observed for the A-allele of rs1800629 (OR 1.69, 95% CI 1.33-2.15, p<0.0001, in a codominant model) and for 3 HLA haplotypes: DRB1*03:01-DQB1*02:01 (OR 5.37, 95% CI 3.23-8.59, p<0.0001), DRB1*04:01-DQB1*03:02 (OR 2.95, 95% CI 1.21-7.21, p=0.01) and DRB1*04:02-DQB1*03:02 (OR 2.14, 95% CI 1.02-4.50, p=0.04). Linkage disequilibrium was observed between TNF rs1800629 and HLA-DRB1 and HLA-DQB1 alleles. In a stepwise regression analysis HLA haplotypes, but not TNF rs1800629, remained independently associated with T1D. Our results do not support an independent effect of allelic variations of TNF in the genetic susceptibility to T1D. Copyright © 2015 Elsevier B.V. All rights reserved.

Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis).

PubMed

Huynh, L Y; Maney, D L; Thomas, J W

2011-04-01

Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2(m)) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2(m) polymorphism is a complex inversion spanning > 100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2(m) polymorphism, we generated sequence from 8 ZAL2(m) and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2(m), resulting in uniformly high levels of genetic differentiation (F(ST)=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ~104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2(m) homozygotes are exceedingly rare in the population, occurring at a frequency of < 1%, we detected evidence of historical recombination between ZAL2(m) chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.

Disequilibrium dihedral angles in layered intrusions: the microstructural record of fractionation

NASA Astrophysics Data System (ADS)

Holness, Marian; Namur, Olivier; Cawthorn, Grant

2013-04-01

The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only rarely in textural equilibrium in gabbros from km-scale crustal layered intrusions. The median of a population of these disequilibrium angles, Θcpp, varies systematically within individual layered intrusions, remaining constant over large stretches of stratigraphy with significant increases or decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The step-wise changes in Θcpp are present in Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard Intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of Θcpp, dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the step-wise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the interstitial liquid inferred to be present in the crystal mush. Step-wise changes in the rate of change in enthalpy with temperature (ΔH) of the cooling and crystallizing magma correspond to the observed variation of Θcpp, with increases of both ΔH and Θcpp associated with the addition of another liquidus phase, and decreases of both associated with the removal of a liquidus phase. The replacement of one phase by another (e.g. olivine ⇔ orthpyroxene) has little effect on ΔH and no discernible effect on Θcpp. An increase of ΔH is manifest by an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also results in an increase in the amount crystallized in each incremental temperature drop (the crystal productivity). An increased fractional latent heat and crystal productivity result in an increased rate of plagioclase growth compared to that of augite during the final stages of solidification

Bayes Factor based on the Trend Test Incorporating Hardy-Weinberg Disequilibrium: More Powerful to Detect Genetic Association

PubMed Central

Xu, Jinfeng; Yuan, Ao; Zheng, Gang

2012-01-01

Summary In the analysis of case-control genetic association, the trend test and Pearson’s test are the two most commonly used tests. In genome-wide association studies (GWAS), Bayes factor is a useful tool to support significant p-values, and a better measure than p-value when results are compared across studies with different sample sizes. When reporting the p-value of the trend test, we propose a Bayes factor directly based on the trend test. To improve the power to detect association under recessive or dominant genetic models, we propose a Bayes factor based on the trend test and incorporating Hardy-Weinberg disequilibrium in cases. When the true model is unknown, or both the trend test and Pearson’s test or other robust tests are applied in genome-wide scans, we propose a joint Bayes factor, combining the previous two Bayes factors. All three Bayes factors studied in this paper have closed forms and are easy to compute without integrations, so they can be reported along with p-values, especially in GWAS. We discuss how to use each of them and how to specify priors. Simulation studies and applications to three GWAS are provided to illustrate their usefulness to detect non-additive gene susceptibility in practice. PMID:22607017

Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies (L.) Karst

PubMed Central

Heuertz, Myriam; De Paoli, Emanuele; Källman, Thomas; Larsson, Hanna; Jurman, Irena; Morgante, Michele; Lascoux, Martin; Gyllenstrand, Niclas

2006-01-01

DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico–Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively. PMID:17057229

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

Survey Of Lossless Image Coding Techniques

NASA Astrophysics Data System (ADS)

Melnychuck, Paul W.; Rabbani, Majid

1989-04-01

Many image transmission/storage applications requiring some form of data compression additionally require that the decoded image be an exact replica of the original. Lossless image coding algorithms meet this requirement by generating a decoded image that is numerically identical to the original. Several lossless coding techniques are modifications of well-known lossy schemes, whereas others are new. Traditional Markov-based models and newer arithmetic coding techniques are applied to predictive coding, bit plane processing, and lossy plus residual coding. Generally speaking, the compression ratio offered by these techniques are in the area of 1.6:1 to 3:1 for 8-bit pictorial images. Compression ratios for 12-bit radiological images approach 3:1, as these images have less detailed structure, and hence, their higher pel correlation leads to a greater removal of image redundancy.

Hepatoblastoma Biology Using Isotope Ratio Mass Spectrometry: Utility of a Unique Technique for the Analysis of Oncological Specimens.

PubMed

Taran, Katarzyna; Frączek, Tomasz; Sitkiewicz, Anna; Sikora-Szubert, Anita; Kobos, Józef; Paneth, Piotr

2016-07-07

Hepatoblastoma is the most common primary liver tumor in children. However, it occurs rarely, with an incidence of 0.5-1.5 cases per million children. There is no clear explanation of the relationship between clinicopathologic features, therapy, and outcome in hepatoblastoma cases, so far. One of the most widely accepted prognostic factors in hepatoblastoma is histology of the tumor. The aim of the study was to determine the potential differences in biology of hepatoblastoma histological subtypes at the atomic level using the unique method of isotope ratio mass spectrometry, which is especially valuable in examination of small groups of biological samples. Twenty-four measurements of nitrogen stable isotope ratio, carbon stable isotope ratio and total carbon to nitrogen mass ratio in fetal and embryonal hepatoblastoma tissue were performed using a Sercon 20-22 Continuous Flow Isotope Ratio Mass Spectrometer (CF-IRMS) coupled with a Sercon SL elemental analyzer for simultaneous carbon-nitrogen-sulfur (NCS) analysis. A difference of about 1.781‰ in stable nitrogen isotope 15N/14N ratio was found between examined hepatoblastoma histological subtypes. The prognosis in liver tumors cases in children may be challenging particularly because of the lack of versatile methods of its evaluation. Isotope ratio mass spectrometry allows one to determine the difference between hepatoblastoma histological subtypes and clearly indicates the cases with the best outcome.

Forensic analysis of explosives using isotope ratio mass spectrometry (IRMS)--part 1: instrument validation of the DELTAplusXP IRMS for bulk nitrogen isotope ratio measurements.

PubMed

Benson, Sarah J; Lennard, Christopher J; Hill, David M; Maynard, Philip; Roux, Claude

2010-01-01

A significant amount of research has been conducted into the use of stable isotopes to assist in determining the origin of various materials. The research conducted in the forensic field shows the potential of isotope ratio mass spectrometry (IRMS) to provide a level of discrimination not achievable utilizing traditional forensic techniques. Despite the research there have been few, if any, publications addressing the validation and measurement uncertainty of the technique for forensic applications. This study, the first in a planned series, presents validation data for the measurement of bulk nitrogen isotope ratios in ammonium nitrate (AN) using the DELTA(plus)XP (Thermo Finnigan) IRMS instrument equipped with a ConFlo III interface and FlashEA 1112 elemental analyzer (EA). Appropriate laboratory standards, analytical methods and correction calculations were developed and evaluated. A validation protocol was developed in line with the guidelines provided by the National Association of Testing Authorities, Australia (NATA). Performance characteristics including: accuracy, precision/repeatability, reproducibility/ruggedness, robustness, linear range, and measurement uncertainty were evaluated for the measurement of nitrogen isotope ratios in AN. AN (99.5%) and ammonium thiocyanate (99.99+%) were determined to be the most suitable laboratory standards and were calibrated against international standards (certified reference materials). All performance characteristics were within an acceptable range when potential uncertainties, including the manufacturer's uncertainty of the technique and standards, were taken into account. The experiments described in this article could be used as a model for validation of other instruments for similar purposes. Later studies in this series will address the more general issue of demonstrating that the IRMS technique is scientifically sound and fit-for-purpose in the forensic explosives analysis field.

Simultaneous spectrophotometric determination of indacaterol and glycopyrronium in a newly approved pharmaceutical formulation using different signal processing techniques of ratio spectra

NASA Astrophysics Data System (ADS)

Abdel Ghany, Maha F.; Hussein, Lobna A.; Magdy, Nancy; Yamani, Hend Z.

2016-03-01

Three spectrophotometric methods have been developed and validated for determination of indacaterol (IND) and glycopyrronium (GLY) in their binary mixtures and novel pharmaceutical dosage form. The proposed methods are considered to be the first methods to determine the investigated drugs simultaneously. The developed methods are based on different signal processing techniques of ratio spectra namely; Numerical Differentiation (ND), Savitsky-Golay (SG) and Fourier Transform (FT). The developed methods showed linearity over concentration range 1-30 and 10-35 (μg/mL) for IND and GLY, respectively. The accuracy calculated as percentage recoveries were in the range of 99.00%-100.49% with low value of RSD% (< 1.5%) demonstrating an excellent accuracy of the proposed methods. The developed methods were proved to be specific, sensitive and precise for quality control of the investigated drugs in their pharmaceutical dosage form without the need for any separation process.

Dual temperature effects on oxygen isotopic ratio of shallow-water coral skeleton: Consequences on seasonal and interannual records

NASA Astrophysics Data System (ADS)

Juillet-Leclerc, A.; Reynaud, S.

2009-04-01

Oxygen isotopic ratio from coral skeleton is regarded for a long time as promising climate archives at seasonal scale. Although in isotopic disequilibrium relative to seawater, it is supposed to obey to the isotope thermometer. Indeed, coral oxygen isotopic records are strongly temperature dependent, but d18O-temperature calibrations derived from different corals are highly variable. The isotope thermometer assumption does not take into account vital effects due to biogenic origin of the mineral. Corals are animals living in symbiosis with algae (zooxanthellae). Interactions between symbiont photosynthesis and coral skeleton carbonation have been abundantly observed but they remain poorly understood and the effects of photosynthesis on coral growth and skeleton oxygen ratio are ignored. Coral cultured under two light conditions enabled to relate metabolic parameters and oxygen isotopic variability with photosynthetic activity. By examining responses provided by each colony they revealed that photosynthesis significantly affected d18O, by an opposite sense compared with the sole temperature influence. Since temperature and light changes are associated during seasonal variations, this complicates the interpretation of seasonal record. Additionally, this complexity is amplified because photosynthetic activity is also directly impacted by temperature variability. Thus, the annual isotopic amplitude due to the "physical" temperature influence is partly compensated through photosynthesis. Similar opposite effect is also shown by extension rate of the cultured colonies. First, we will examine and quantify consequences of photosynthesis on growth rate and oxygen isotopic signature, from cultured corals. Second, we will consider the consequences of this vital effect on data series, at seasonal and interannual time scales.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

PubMed

Sudrajad, P; Seo, D W; Choi, T J; Park, B H; Roh, S H; Jung, W Y; Lee, S S; Lee, J H; Kim, S; Lee, S H

2017-02-01

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. © 2016 Stichting International Foundation for Animal Genetics.

Dynamic Responses of Flexible Cylinders with Low Mass Ratio

NASA Astrophysics Data System (ADS)

Olaoye, Abiodun; Wang, Zhicheng; Triantafyllou, Michael

2017-11-01

Flexible cylinders with low mass ratios such as composite risers are attractive in the offshore industry because they require lower top tension and are less likely to buckle under self-weight compared to steel risers. However, their relatively low stiffness characteristics make them more vulnerable to vortex induced vibrations. Additionally, numerical investigation of the dynamic responses of such structures based on realistic conditions is limited by high Reynolds number, complex sheared flow profile, large aspect ratio and low mass ratio challenges. In the framework of Fourier spectral/hp element method, the current technique employs entropy-viscosity method (EVM) based large-eddy simulation approach for flow solver and fictitious added mass method for structure solver. The combination of both methods can handle fluid-structure interaction problems at high Reynolds number with low mass ratio. A validation of the numerical approach is provided by comparison with experiments.

Residual strain effects on large aspect ratio micro-diaphragms

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

Hijab, R.S.; Muller, R.S.

1988-09-30

Highly compliant, large aspect ratio diaphragms for use in low-pressure, capacitive-readout sensors, have been investigated. In such structures, unrelaxed strain in the diaphragms can radically alter mechanical behavior. Although strain can be reduced by thermal annealing, it usually reaches a remnant irreducible minimum. The purpose of this paper is to describe techniques that result in low-strain materials and that reduce the effects of residual strain in micro-diaphragms. Square polysilicon grilles and perforated diaphragms made from both single and double polysilicon layers and from single-crystal silicon, with aspect ratios (side/thickness) of up to 1000 and very low compressive strain ({approx}6 {times}more » 10{sup {minus}5}), have been fabricated. Strain reduction is achieved by combining thermal annealing with one of two mechanical design techniques. The first technique makes use of a series of cantilever beams to support the diaphragms. In a second procedure, corrugated surfaces in thinned membranes of single-crystal silicon are formed. The corrugations result from the use of boron doping and anisotropic silicon etching. In both of these techniques to produce low-strain diaphragms, an etched cavity is purposely formed in the substrate crystal below them. Only one-sided processing of wafers is employed, thus aiding reproducibility and providing ease of compatibility with an MOS process. A fast-etching sacrificial-support layer (phosphorus-doped CVD oxide) is used. 4 refs., 10 figs.« less

Evaluation of the 3D spatial distribution of the Calcium/Phosphorus ratio in bone using computed-tomography dual-energy analysis.

PubMed

Hadjipanteli, A; Kourkoumelis, N; Fromme, P; Huang, J; Speller, R D

2016-01-01

The Calcium/Phosphorus (Ca/P) ratio was shown to vary between healthy bones and bones with osteoporotic symptoms. The relation of the Ca/P ratio to bone quality remains under investigation. To study this relation and determine if the ratio can be used to predict bone fractures, a non-invasive 3D imaging technique is required. The first aim of this study was to test the effectiveness of a computed-tomography dual-energy analysis (CT-DEA) technique developed to assess the Ca/P ratio in bone apatite (collagen-free bone) in identifying differences between healthy and inflammation-mediated osteoporotic (IMO) bones. The second aim was to extend the above technique for its application to a more complex structure, intact bone, that could potentially lead to clinical use. For the first aim, healthy and IMO rabbit cortical bone apatite samples were assessed. For the second aim, some changes were made to the technique, which was applied to healthy and IMO intact bone samples. Statistically significant differences between healthy and IMO bone apatite were found for the bulk Ca/P ratio, low Ca/P ratio proportion and interconnected low Ca/P ratio proportion. For the intact bone samples, the bulk Ca/P ratio was found to be significantly different between healthy and IMO. Results show that the CT-DEA technique can be used to identify differences in the Ca/P ratio between healthy and osteoporotic, in both bone apatite and intact bone. With quantitative imaging becoming an increasingly important advancement in medical imaging, CT-DEA for bone decomposition could potentially have several applications. Copyright © 2015. Published by Elsevier Ltd.

Elevation-relief ratio, hypsometric integral, and geomorphic area-altitude analysis.

NASA Technical Reports Server (NTRS)

Pike, R. J.; Wilson, S. E.

1971-01-01

Mathematical proof establishes identity of hypsometric integral and elevation-relief ratio, two quantitative topographic descriptors developed independently of one another for entirely different purposes. Operationally, values of both measures are in excellent agreement for arbitrarily bounded topographic samples, as well as for low-order fluvial watersheds. By using a point-sampling technique rather than planimetry, elevation-relief ratio (defined as mean elevation minus minimum elevation divided by relief) is calculated manually in about a third of the time required for the hypsometric integral.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Accuracy of genomic prediction in switchgrass ( Panicum virgatum L.) improved by accounting for linkage disequilibrium

DOE PAGES

Ramstein, Guillaume P.; Evans, Joseph; Kaeppler, Shawn M.; ...

2016-02-11

Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height,more » and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Furthermore, some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.« less

Investigation of previously implicated genetic variants in chronic tic disorders: a transmission disequilibrium test approach.

PubMed

Abdulkadir, Mohamed; Londono, Douglas; Gordon, Derek; Fernandez, Thomas V; Brown, Lawrence W; Cheon, Keun-Ah; Coffey, Barbara J; Elzerman, Lonneke; Fremer, Carolin; Fründt, Odette; Garcia-Delgar, Blanca; Gilbert, Donald L; Grice, Dorothy E; Hedderly, Tammy; Heyman, Isobel; Hong, Hyun Ju; Huyser, Chaim; Ibanez-Gomez, Laura; Jakubovski, Ewgeni; Kim, Young Key; Kim, Young Shin; Koh, Yun-Joo; Kook, Sodahm; Kuperman, Samuel; Leventhal, Bennett; Ludolph, Andrea G; Madruga-Garrido, Marcos; Maras, Athanasios; Mir, Pablo; Morer, Astrid; Müller-Vahl, Kirsten; Münchau, Alexander; Murphy, Tara L; Plessen, Kerstin J; Roessner, Veit; Shin, Eun-Young; Song, Dong-Ho; Song, Jungeun; Tübing, Jennifer; van den Ban, Els; Visscher, Frank; Wanderer, Sina; Woods, Martin; Zinner, Samuel H; King, Robert A; Tischfield, Jay A; Heiman, Gary A; Hoekstra, Pieter J; Dietrich, Andrea

2018-04-01

Genetic studies in Tourette syndrome (TS) are characterized by scattered and poorly replicated findings. We aimed to replicate findings from candidate gene and genome-wide association studies (GWAS). Our cohort included 465 probands with chronic tic disorder (93% TS) and both parents from 412 families (some probands were siblings). We assessed 75 single nucleotide polymorphisms (SNPs) in 465 parent-child trios; 117 additional SNPs in 211 trios; and 4 additional SNPs in 254 trios. We performed SNP and gene-based transmission disequilibrium tests and compared nominally significant SNP results with those from a large independent case-control cohort. After quality control 71 SNPs were available in 371 trios; 112 SNPs in 179 trios; and 3 SNPs in 192 trios. 17 were candidate SNPs implicated in TS and 2 were implicated in obsessive-compulsive disorder (OCD) or autism spectrum disorder (ASD); 142 were tagging SNPs from eight monoamine neurotransmitter-related genes (including dopamine and serotonin); 10 were top SNPs from TS GWAS; and 13 top SNPs from attention-deficit/hyperactivity disorder, OCD, or ASD GWAS. None of the SNPs or genes reached significance after adjustment for multiple testing. We observed nominal significance for the candidate SNPs rs3744161 (TBCD) and rs4565946 (TPH2) and for five tagging SNPs; none of these showed significance in the independent cohort. Also, SLC1A1 in our gene-based analysis and two TS GWAS SNPs showed nominal significance, rs11603305 (intergenic) and rs621942 (PICALM). We found no convincing support for previously implicated genetic polymorphisms. Targeted re-sequencing should fully appreciate the relevance of candidate genes.

Accuracy of genomic prediction in switchgrass ( Panicum virgatum L.) improved by accounting for linkage disequilibrium

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

Ramstein, Guillaume P.; Evans, Joseph; Kaeppler, Shawn M.

Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height,more » and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Furthermore, some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.« less

Measurement of isotope ratios on transient signals by MC-ICP-MS.

PubMed

Günther-Leopold, Ines; Wernli, Beat; Kopajtic, Zlatko; Günther, Detlef

2004-01-01

Precise and accurate isotope ratio measurements are an important task in many applications such as isotope-dilution mass spectrometry, bioavailability studies, or the determination of isotope variations in geological or nuclear samples. The technique of MC-ICP-MS has attracted much attention because it permits the precise measurement of isotope compositions for a wide range of elements combined with excellent detection limits due to high ionisation efficiencies. However, the results are based mainly on measurements using continuous sample introduction. In the present study the determination of isotope ratios on various transient signals with a time duration of 30 to 60 s has been achieved by coupling high-performance liquid chromatography to a multicollector inductively coupled plasma mass spectrometer. In order to investigate the origin of ratio drifts across the transient signals for this hyphenated technique, measurements with the same standard solutions were also carried out using a flow-injection device for sample introduction. As a result of this application it could be concluded that the main source of the bias in the measured isotope ratios is within the ICP-MS instead of fractionation effects on the chromatographic column material. Preliminary studies on short transient signals of gaseous samples (dry plasma) showed a reverse fractionation effect compared with wet plasma conditions (flow injection and HPLC).

Intermediate-mass-ratio black-hole binaries: numerical relativity meets perturbation theory.

PubMed

Lousto, Carlos O; Nakano, Hiroyuki; Zlochower, Yosef; Campanelli, Manuela

2010-05-28

We study black-hole binaries in the intermediate-mass-ratio regime 0.01≲q≲0.1 with a new technique that makes use of nonlinear numerical trajectories and efficient perturbative evolutions to compute waveforms at large radii for the leading and nonleading (ℓ, m) modes. As a proof-of-concept, we compute waveforms for q=1/10. We discuss applications of these techniques for LIGO and VIRGO data analysis and the possibility that our technique can be extended to produce accurate waveform templates from a modest number of fully nonlinear numerical simulations.

Evaluation of optimum roughage to concentrate ratio in maize stover based complete rations for efficient microbial biomass production using in vitro gas production technique.

PubMed

Reddy, Y Ramana; Kumari, N Nalini; Monika, T; Sridhar, K

2016-06-01

A study was undertaken to evaluate the optimum roughage to concentrate ratio in maize stover (MS) based complete diets for efficient microbial biomass production (EMBP) using in vitro gas production technique. MS based complete diets with roughage to concentrate ratio of 100:0, 90:10, 80:20, 70:30, 60:40, 50:50, 40:60, and 30:70 were formulated, and 200 mg of oven-dried sample was incubated in water bath at 39°C along with media (rumen liquor [RL] - buffer) in in vitro gas syringes to evaluate the gas production. The gas produced was recorded at 8 and 24 h of incubation. In vitro organic matter digestibility (IVOMD), metabolizable energy (ME), truly digestible organic matter (TDOM), partitioning factor (PF), and EMBP were calculated using appropriate formulae. Ammonia nitrogen and total volatile fatty acids (TVFAs) production were analyzed in RL fluid-media mixture after 24 h of incubation. In vitro gas production (ml) at 24 h incubation, IVOMD, ME, TDOM, TVFA concentration, and ammonia nitrogen production were increased (p<0.01) in proportion to the increase in the level of concentrate in the diet. Significantly (p<0.01) higher PF and EMBP was noticed in total mixed ration with roughage to concentrate ratio of 60:40 and 50:50 followed by 70:30 and 40:60. Based on the results, it was concluded that the MS can be included in complete rations for ruminants at the level of 50-60% for better microbial biomass synthesis which in turn influences the performance of growing sheep.

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

PubMed Central

Goicoechea, P G; Herrán, A; Durand, J; Bodénès, C; Plomion, C; Kremer, A

2015-01-01

We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the ‘species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory. PMID:25515016

Influence of Ga doping ratio on the saturable absorption mechanism in Ga doped ZnO thin solid films processed by sol-gel spin coating technique

NASA Astrophysics Data System (ADS)

Sandeep, K. M.; Bhat, Shreesha; Dharmaprakash, S. M.; Byrappa, K.

2017-03-01

In the present study, the nonlinear optical properties of sol-gel spin coated gallium doped zinc oxide (GZO) thin solid films are explored with nanosecond laser pulses using the z-scan technique. The higher doping ratios of Ga result in a large redshift of the energy gap (0.38 eV) due to the existence of enhanced grain boundary defects in GZO films. A positive nonlinear absorption coefficient is observed in undoped 1 at.wt.% GZO and 2 at.wt.% GZO films, and a negative nonlinear absorption coefficient in 3 at.wt.% GZO film. Fewer defects in undoped 1% GZO and 2% GZO films resulted in reverse saturable absorption (RSA), whereas a saturable absorption (SA) mechanism is observed in 3% GZO films and is attributed to the enhanced defect concentration in the band structure of GZO. However, all the films showed a self-defocusing mechanism, derived by a closed aperture z-scan technique. The present work sheds light on the defect mechanism involved in the observed nonlinear properties of GZO films.

Three-Signal Method for Accurate Measurements of Depolarization Ratio with Lidar

NASA Technical Reports Server (NTRS)

Reichardt, Jens; Baumgart, Rudolf; McGee, Thomsa J.

2003-01-01

A method is presented that permits the determination of atmospheric depolarization-ratio profiles from three elastic-backscatter lidar signals with different sensitivity to the state of polarization of the backscattered light. The three-signal method is insensitive to experimental errors and does not require calibration of the measurement, which could cause large systematic uncertainties of the results, as is the case in the lidar technique conventionally used for the observation of depolarization ratios.

Linkage disequilibrium analysis in young populations: Pseudo-vitamin D-deficiency rickets and the founder effect in French Canadians

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

Labuda, M.; Glorieux, F.H.; Labuda, D.

1996-09-01

Pseudo-vitamin D-deficiency rickets (PDDR) was mapped close to D12S90 and between proximal D12S312 and distal (D12S305, D12S104) microsatellites that were subsequently found on a single YAC clone. Analysis of a complex haplotype in linkage disequilibrium (LD) with the disease discriminated among distinct founder effects in French Canadian populations in Acadia and in Charlevoix-Saguenay-Lac-Saint-Jean (Ch-SLSJ), as well as an earlier one in precolonial Europe. A simple demographic model suggested the historical age of the founder effect in Ch-SLSJ to be {approximately}12 generations. The corresponding LD data are consistent with this figure when they are analyzed within the framework of Luria-Delbruck model,more » which takes into account the population growth. Population sampling due to a limited number of first settlers and the rapid demographic expansion appear to have played a major role in the founding of PDDR in Ch-SLSJ and, presumably, other genetic disorders endemic to French Canada. Similarly, the founder effect in Ashkenazim, coinciding with their early settlement in medieval Poland and subsequent expansion eastward, could explain the origin of frequent genetic diseases in this population. 48 refs., 5 figs., 2 tabs.« less

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis

PubMed Central

Song, Bao-Hua; Windsor, Aaron J.; Schmid, Karl J.; Ramos-Onsins, Sebastian; Schranz, M. Eric; Heidel, Andrew J.; Mitchell-Olds, Thomas

2009-01-01

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have ∼45% higher recombination per kilobase than outcrossing A. lyrata. PMID:19104077

Experimental thrust performance of a high-area-ratio rocket nozzle

NASA Technical Reports Server (NTRS)

Pavli, Albert J.; Kacynski, Kenneth J.; Smith, Tamara A.

1987-01-01

An experimental investigation was conducted to determine the thrust performance attainable from high-area-ratio rocket nozzles. A modified Rao-contoured nozzle with an expansion area of 1030 was test fired with hydrogen-oxygen propellants at altitude conditions. The nozzle was also tested as a truncated nozzle, at an expansion area ratio of 428. Thrust coefficient and thrust coefficient efficiency values are presented for each configuration at various propellant mixture ratios (oxygen/fuel). Several procedural techniques were developed permitting improved measurement of nozzle performance. The more significant of these were correcting the thrust for the aneroid effects, determining the effective chamber pressure, and referencing differential pressure transducers to a vacuum reference tank.

Experimental thrust performance of a high area-ratio rocket nozzle

NASA Technical Reports Server (NTRS)

Pavli, A. J.; Kacynski, K. J.; Smith, T. A.

1986-01-01

An experimental investigation was conducted to determine the thrust performance attainable from high-area-ratio rocket nozzles. A modified Rao-contoured nozzle with an expansion area of 1030 was test fired with hydrogen-oxygen propellants at altitude conditions. The nozzle was also tested as a truncated nozzle, at an expansion area ratio of 428. Thrust coefficient and thrust coefficient efficiency values are presented for each configuration at various propellant mixture ratios (oxygen/fuel). Several procedural techniques were developed permitting improved measurement of nozzle performance. The more significant of these were correcting the thrust for the aneroid effects, determining the effective chamber pressure, and referencing differential pressure transducers to a vacuum reference tank.

The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

PubMed

Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

2012-01-01

The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

234Th: 238U disequilibrium as an indicator of sediment resuspension in Thermaikos Gulf, northwestern Aegean Sea

NASA Astrophysics Data System (ADS)

Muir, G. K. P.; Pates, J. M.; Karageorgis, A. P.; Kaberi, H.

2005-12-01

234Th: 238U disequilibria have been used extensively as tracers of particle dynamics in marine environments. 234Th ( t1/2=24.1 days) can be used as "proxy" for particle reactive pollutants, due to their similar rapid rate of scavenging onto particles and subsequent removal from the water column, to the sediments. Radioactive disequilibrium can be exploited to determine the rates and time-scales of processes occurring over days to months; in this instance the residence times of dissolved and particulate species with the benthic nepheloid layer (BNL). Three sampling cruises were undertaken in Thermaikos Gulf (NW Aegean Sea) during contrasting periods, to examine the impact of natural and anthropogenic activity on sediment resuspension. September and October 2001 represented background and trawling periods, respectively; January 2002 represented a mixed period, of trawling and storms. Dissolved 234Th is scavenged actively at the BNL, in the presence of suspended particulate material (SPM), with a mean residence time of 16 days. There is a weak inverse correlation between dissolved 234Th residence time and SPM concentration in the BNL, with the shortest residence times occurring during October 2001. No relationship was observed between particulate 234Th activities and SPM concentrations, indicating that particles are rapidly removed from the system, either by sinking or advection. The mean particulate 234Th residence time is 5 days.

Determination of electron temperature in a penning discharge by the helium line ratio method

NASA Technical Reports Server (NTRS)

Richardson, R. W.

1975-01-01

The helium line ratio technique was used to determine electron temperatures in a toroidal steady-state Penning discharge operating in helium. Due to the low background pressure, less than .0001 torr, and the low electron density, the corona model is expected to provide a good description of the excitation processes in this discharge. In addition, by varying the Penning discharge anode voltage and background pressure, it is possible to vary the electron temperature as measured by the line ratio technique over a wide range (10 to 100+ eV). These discharge characteristics allow a detailed comparison of electron temperatures measured from different possible line ratios over a wide range of temperatures and under reproducible steady-state conditions. Good agreement is found between temperatures determined from different neutral line ratios, but use of the helium ion line results in a temperature systematically 10 eV high compared to that from the neutral lines.

Stable hydrogen and carbon isotope ratios of extractable hydrocarbons in the Murchison meteorite

NASA Technical Reports Server (NTRS)

Krishnamurthy, R. V.; Epstein, S.; Pizzarello, S.; Cronin, J. R.; Yuen, G. U.

1991-01-01

A fairly fool-proof method to ensure that the compounds isolated from meteorites are truly part of the meteorites and not an artifact introduced by exposure to the terrestrial environment, storage, or handling is presented. The stable carbon and hydrogen isotope ratios in several of the chemical compounds extracted from the Murchison meteorite were measured. The results obtained by studying the amino acids in this meteorite gave very unusual hydrogen and carbon isotope ratios. The technique was extended to the different classes of hydrocarbons and the hydrocarbons were isolated using a variety of separation techniques. The results and methods used in this investigation are described in this two page paper.

Spectral ratio imaging methods for geological remote sensing from aircraft and satellites

NASA Technical Reports Server (NTRS)

Vincent, R. K. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The production of ratio images from multispectral scanner data is described and several examples of ratio images from aircraft and ERTS-1 data are given for visible, reflective infrared, and thermal infrared wavelengths. The application of photogrammetric techniques to ratio images, defined for this paper as ratio scannergrammetry, is considerably aided by the lesser dependence of ratio images on atmospheric and solar illumination variations, compared with single channel scanner imagery or aerial photos. Ratio scannergrammetry is further aided by the proportionality between ratios of a target deduced from ratio images and ratios of reflectances calculated from laboratory spectra of samples from the target area. Consequently, ratios calculated from laboratory data can be used to predict which ratios are best for discriminating a given rock or mineral, to predict what other rocks or minerals will be confused with it, and finally, to place ratio scannergrammetry on an absolute basis, within an estimated standard error on the order of 5% to 10%. Examples of relative agreement between laboratory data and ratio images are given from two iron oxides, hematite and magnetite.

The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes.

PubMed

Porto-Neto, Laercio R; Kijas, James W; Reverter, Antonio

2014-03-24

The extent of linkage disequilibrium (LD) between molecular markers impacts genome-wide association studies and implementation of genomic selection. The availability of high-density single nucleotide polymorphism (SNP) genotyping platforms makes it possible to investigate LD at an unprecedented resolution. In this work, we characterised LD decay in breeds of beef cattle of taurine, indicine and composite origins and explored its variation across autosomes and the X chromosome. In each breed, LD decayed rapidly and r2 was less than 0.2 for marker pairs separated by 50 kb. The LD decay curves clustered into three groups of similar LD decay that distinguished the three main cattle types. At short distances between markers (<10 kb), taurine breeds showed higher LD (r2=0.45) than their indicine (r2=0.25) and composite (r2=0.32) counterparts. This higher LD in taurine breeds was attributed to a smaller effective population size and a stronger bottleneck during breed formation. Using all SNPs on only the X chromosome, the three cattle types could still be distinguished. However for taurine breeds, the LD decay on the X chromosome was much faster and the background level much lower than for indicine breeds and composite populations. When using only SNPs that were polymorphic in all breeds, the analysis of the X chromosome mimicked that of the autosomes. The pattern of LD mirrored some aspects of the history of breed populations and showed a sharp decay with increasing physical distance between markers. We conclude that the availability of the HD chip can be used to detect association signals that remained hidden when using lower density genotyping platforms, since LD dropped below 0.2 at distances of 50 kb.

Extent of Linkage Disequilibrium in the Domestic Cat, Felis silvestris catus, and Its Breeds

PubMed Central

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A.

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r 2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits. PMID:23308248

Carbon and oxygen isotopic disequilibrium during calcification of Globigerina bulloides in the Southern ocean

NASA Astrophysics Data System (ADS)

K, P.; Ghosh, P.; N, A.

2015-12-01

Oxygen and carbon isotopes in planktonic foraminifera Globigerina bulloides recovered from the water column of 0-1000 m depth across the meridional transect i.e. 10°N to 53°S of Indian ocean were compared with the available data from the core-top samples across the same transect. We also recorded in situ temperatures of the water column based on probe (CTD) profiles. The δ18O and δ13C values measured in the core top samples matches with the tow results. The equilibrium δ18O of calcite calculated from known temperature and δ18O of water column allowed us to compare the observed δ18O of formaminieral shell with the expected equilibrium values. Our comparison of carbonate composition in the samples between 10°N till 40°S showed excellent match with the expected equilibrium δ18O values established from the water collected at depth range of ~75-200m, however beyond 40°S the disequilibrium was pronounced with heavier δ18O (enriched by ~1.5‰) recorded in the carbonate as compared with the expected equilibrium δ18O values established from water. This observation was further verified with δ13C measurement of shell carbonates comparing with the equilibrium δ13C of calcite calculated with known temperature and δ13C of dissolved inorganic carbon in the water column. The δ13C of the shell carbonate was found heavier as compared to the expected equilibrium δ13C. Both δ18O and δ13C showed simultaneous enrichment signature in the region beyond 40°S suggesting role of processes such as leaching along with dissolution of shell carbonate in a relatively acidic condition.

Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

PubMed

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A; Gandolfi, Barbara; Mullikin, James C; Cole, Shelley A; Gruffydd-Jones, Timothy J; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

Ratio of sequential chromatograms for quantitative analysis and peak deconvolution: Application to standard addition method and process monitoring

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

Synovec, R.E.; Johnson, E.L.; Bahowick, T.J.

1990-08-01

This paper describes a new technique for data analysis in chromatography, based on taking the point-by-point ratio of sequential chromatograms that have been base line corrected. This ratio chromatogram provides a robust means for the identification and the quantitation of analytes. In addition, the appearance of an interferent is made highly visible, even when it coelutes with desired analytes. For quantitative analysis, the region of the ratio chromatogram corresponding to the pure elution of an analyte is identified and is used to calculate a ratio value equal to the ratio of concentrations of the analyte in sequential injections. For themore » ratio value calculation, a variance-weighted average is used, which compensates for the varying signal-to-noise ratio. This ratio value, or equivalently the percent change in concentration, is the basis of a chromatographic standard addition method and an algorithm to monitor analyte concentration in a process stream. In the case of overlapped peaks, a spiking procedure is used to calculate both the original concentration of an analyte and its signal contribution to the original chromatogram. Thus, quantitation and curve resolution may be performed simultaneously, without peak modeling or curve fitting. These concepts are demonstrated by using data from ion chromatography, but the technique should be applicable to all chromatographic techniques.« less

LIBS analysis of hydroxyapatite extracted from bovine bone for Ca/P ratio measurements

NASA Astrophysics Data System (ADS)

Tariq, Usman; Haider, Zuhaib; Hussain, Rafaqat; Tufail, Kashif; Ali, Jalil

2017-03-01

Hydroxyapatite has been extensively used as a potential biocompatible ceramic in many orhtopedic applications. Hydroxyapatite is one of the members of calcium phosphate family and been used extensively as a bone substitute. The mechanical properties of hydroxyapatite itself, ceramics and bone cements prepared from hydroxyapatite vary greatly with slight variation in its Ca/P ratio. At present EDX, XRD, XRF and ICP-OES are being used for the determination of Ca/P ratio in hydroxyapatite. These techniques require special sample preparation, may also use toxic chemicals and usually are not very fast in giving the measurements. We report LIBS as a rapid alternative technique for calculation of Ca/P ratio in hydroxyapatite extracted from bovine bone (BHA). Ca/P ratio in laboratory prepared HA is calculated using LIBS and the results are validated against EDX results Ca/P ratio of the hydroxyapatite was calculated as 1.54±0.19 using LIBS while 1.63±0.03 using EDX. Ca/P ratio calculated by LIBS and EDX and showed comparable results with a difference of 5.5%. Moreover, plasma temperature and the ratio of the calcium (ion) line to calcium (atomic) line did not show significant variation in plasma conditions during measurements. The present study has demonstrated that LIBS can also be used for the determination of Ca/P ratio of hydroxyapatite and other calcium phosphates. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 24 May 2017.

On the cross-sensitivity between water vapor mixing ratio and stable isotope measurements of in-situ analyzers

NASA Astrophysics Data System (ADS)

Parkes, Stephen; Wang, Lixin; McCabe, Matthew

2015-04-01

In recent years there has been an increasing amount of water vapor stable isotope data collected using in-situ instrumentation. A number of papers have characterized the performance of these in-situ analyzers and suggested methods for calibrating raw measurements. The cross-sensitivity of the isotopic measurements on the mixing ratio has been shown to be a major uncertainty and a variety of techniques have been suggested to characterize this inaccuracy. However, most of these are based on relating isotopic ratios to water vapor mixing ratios from in-situ analyzers when the mixing ratio is varied and the isotopic composition kept constant. An additional correction for the span of the isotopic ratio scale is then applied by measuring different isotopic standards. Here we argue that the water vapor cross-sensitivity arises from different instrument responses (span and offset) of the parent H2O isotope and the heavier isotopes, rather than spectral overlap that could cause a true variation in the isotopic ratio with mixing ratio. This is especially relevant for commercial laser optical instruments where absorption lines are well resolved. Thus, the cross-sensitivity determined using more conventional techniques is dependent on the isotopic ratio of the standard used for the characterization, although errors are expected to be small. Consequently, the cross-sensitivity should be determined by characterizing the span and zero offset of each isotope mixing ratio. In fact, this technique makes the span correction for the isotopic ratio redundant. In this work we model the impact of changes in the span and offset of the heavy and light isotopes and illustrate the impact on the cross-sensitivity of the isotopic ratios on water vapor. This clearly shows the importance of determining the zero offset for the two isotopes. The cross-sensitivity of the isotopic ratios on water vapor is then characterized by determining the instrument response for the individual isotopes for a

RATIO_TOOL - SOFTWARE FOR COMPUTING IMAGE RATIOS

NASA Technical Reports Server (NTRS)

Yates, G. L.

1994-01-01

Geological studies analyze spectral data in order to gain information on surface materials. RATIO_TOOL is an interactive program for viewing and analyzing large multispectral image data sets that have been created by an imaging spectrometer. While the standard approach to classification of multispectral data is to match the spectrum for each input pixel against a library of known mineral spectra, RATIO_TOOL uses ratios of spectral bands in order to spot significant areas of interest within a multispectral image. Each image band can be viewed iteratively, or a selected image band of the data set can be requested and displayed. When the image ratios are computed, the result is displayed as a gray scale image. At this point a histogram option helps in viewing the distribution of values. A thresholding option can then be used to segment the ratio image result into two to four classes. The segmented image is then color coded to indicate threshold classes and displayed alongside the gray scale image. RATIO_TOOL is written in C language for Sun series computers running SunOS 4.0 and later. It requires the XView toolkit and the OpenWindows window manager (version 2.0 or 3.0). The XView toolkit is distributed with Open Windows. A color monitor is also required. The standard distribution medium for RATIO_TOOL is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation is included on the program media. RATIO_TOOL was developed in 1992 and is a copyrighted work with all copyright vested in NASA. Sun, SunOS, and OpenWindows are trademarks of Sun Microsystems, Inc. UNIX is a registered trademark of AT&T Bell Laboratories.

Dose ratio proton radiography using the proximal side of the Bragg peak

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

Doolan, P. J., E-mail: paul.doolan.09@ucl.ac.uk; Royle, G.; Gibson, A.

Purpose: In recent years, there has been a movement toward single-detector proton radiography, due to its potential ease of implementation within the clinical environment. One such single-detector technique is the dose ratio method in which the dose maps from two pristine Bragg peaks are recorded beyond the patient. To date, this has only been investigated on the distal side of the lower energy Bragg peak, due to the sharp falloff. The authors investigate the limits and applicability of the dose ratio method on the proximal side of the lower energy Bragg peak, which has the potential to allow a muchmore » wider range of water-equivalent thicknesses (WET) to be imaged. Comparisons are made with the use of the distal side of the Bragg peak. Methods: Using the analytical approximation for the Bragg peak, the authors generated theoretical dose ratio curves for a range of energy pairs, and then determined how an uncertainty in the dose ratio would translate to a spread in the WET estimate. By defining this spread as the accuracy one could achieve in the WET estimate, the authors were able to generate lookup graphs of the range on the proximal side of the Bragg peak that one could reliably use. These were dependent on the energy pair, noise level in the dose ratio image and the required accuracy in the WET. Using these lookup graphs, the authors investigated the applicability of the technique for a range of patient treatment sites. The authors validated the theoretical approach with experimental measurements using a complementary metal oxide semiconductor active pixel sensor (CMOS APS), by imaging a small sapphire sphere in a high energy proton beam. Results: Provided the noise level in the dose ratio image was 1% or less, a larger spread of WETs could be imaged using the proximal side of the Bragg peak (max 5.31 cm) compared to the distal side (max 2.42 cm). In simulation, it was found that, for a pediatric brain, it is possible to use the technique to image a region

Developing an economical and reliable test for measuring the resilient modulus and Poisson's ratio of subgrade.

DOT National Transportation Integrated Search

2010-11-01

The resilient modulus and Poissons ratio of base and sublayers in highway use are : important parameters in design and quality control process. The currently used techniques : include CBR (California Bearing Ratio) test, resilient modulus test,...

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

PubMed Central

De La Vega, Francisco M.; Isaac, Hadar; Collins, Andrew; Scafe, Charles R.; Halldórsson, Bjarni V.; Su, Xiaoping; Lippert, Ross A.; Wang, Yu; Laig-Webster, Marion; Koehler, Ryan T.; Ziegle, Janet S.; Wogan, Lewis T.; Stevens, Junko F.; Leinen, Kyle M.; Olson, Sheri J.; Guegler, Karl J.; You, Xiaoqing; Xu, Lily H.; Hemken, Heinz G.; Kalush, Francis; Itakura, Mitsuo; Zheng, Yi; de Thé, Guy; O'Brien, Stephen J.; Clark, Andrew G.; Istrail, Sorin; Hunkapiller, Michael W.; Spier, Eugene G.; Gilbert, Dennis A.

2005-01-01

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies. PMID:15781572

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

PubMed

Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Tortorici, Lina; Sardina, Maria Teresa; Portolano, Baldassare

2014-10-10

The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed. This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

PubMed Central

2012-01-01

Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have similar nucleotide diversity

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene.

PubMed

Yang, Ming; Yang, Bin; Yan, Xueming; Ouyang, Jing; Zeng, Weihong; Ai, Huashui; Ren, Jun; Huang, Lusheng

2012-07-13

MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima'D, and Fu and Li's D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Chinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4

Rapakivi texture formation via disequilibrium melting in a contact partial melt zone, Antarctica

NASA Astrophysics Data System (ADS)

Currier, R. M.

2017-12-01

In the McMurdo Dry Valleys of Antarctica, a Jurassic aged dolerite sill induced partial melting of granite in the shallow crust. The melt zone can be traced in full, from high degrees of melting (>60%) along the dolerite contact, to no apparent signs of melting, 10s of meters above the contact. Within this melt zone, the well-known rapakivi texture is found, arrested in various stages of development. High above the contact, and at low degrees of melting, K-feldspar crystals are slightly rounded and unmantled. In the lower half of the melt zone, mantles of cellular textured plagioclase appear on K-feldspar, and thicken towards the contact heat source. At the highest degrees of melting, cellular-textured plagioclase completely replaces restitic K-feldspar. Because of the complete exposure and intact context, the leading models of rapakivi texture formation can be tested against this system. The previously proposed mechanisms of subisothermal decompression, magma-mixing, and hydrothermal exsolution all fail to adequately describe rapakivi generation in this melt zone. Preferred here is a closed system model that invokes the production of a heterogeneous, disequilibrium melt through rapid heating, followed by calcium and sodium rich melt reacting in a peritectic fashion with restitic K-feldspar crystals. This peritectic reaction results in the production of plagioclase of andesine-oligoclase composition—which is consistent with not just mantles in the melt zone, but globally as well. The thickness of the mantle is diffusion limited, and thus a measure of the diffusive length scale of sodium and calcium over the time scale of melting. Thermal modeling provides a time scale of melting that is consistent with the thickness of observed mantles. Lastly, the distribution of mantled feldspars is highly ordered in this melt zone, but if it were mobilized and homogenized—mixing together cellular plagioclase, mantled feldspars, and unmantled feldspars—the result would be

Determination of element/Ca ratios in foraminifera and corals using cold- and hot-plasma techniques in inductively coupled plasma sector field mass spectrometry

NASA Astrophysics Data System (ADS)

Lo, Li; Shen, Chuan-Chou; Lu, Chia-Jung; Chen, Yi-Chi; Chang, Ching-Chih; Wei, Kuo-Yen; Qu, Dingchuang; Gagan, Michael K.

2014-02-01

We have developed a rapid and precise procedure for measuring multiple elements in foraminifera and corals by inductively coupled plasma sector field mass spectrometry (ICP-SF-MS) with both cold- [800 W radio frequency (RF) power] and hot- (1200 W RF power) plasma techniques. Our quality control program includes careful subsampling protocols, contamination-free workbench spaces, and refined plastic-ware cleaning process. Element/Ca ratios are calculated directly from ion beam intensities of 24Mg, 27Al, 43Ca, 55Mn, 57Fe, 86Sr, and 138Ba, using a standard bracketing method. A routine measurement time is 3-5 min per dissolved sample. The matrix effects of nitric acid, and Ca and Sr levels, are carefully quantified and overcome. There is no significant difference between data determined by cold- and hot-plasma methods, but the techniques have different advantages. The cold-plasma technique offers a more stable plasma condition and better reproducibility for ppm-level elements. Long-term 2-sigma relative standard deviations (2-RSD) for repeat measurements of an in-house coral standard are 0.32% for Mg/Ca and 0.43% for Sr/Ca by cold-plasma ICP-SF-MS, and 0.69% for Mg/Ca and 0.51% for Sr/Ca by hot-plasma ICP-SF-MS. The higher sensitivity and enhanced measurement precision of the hot-plasma procedure yields 2-RSD precision for μmol/mol trace elements of 0.60% (Mg/Ca), 9.9% (Al/Ca), 0.68% (Mn/Ca), 2.7% (Fe/Ca), 0.50% (Sr/Ca), and 0.84% (Ba/Ca) for an in-house foraminiferal standard. Our refined ICP-SF-MS technique, which has the advantages of small sample size (2-4 μg carbonate consumed) and fast sample throughput (5-8 samples/hour), should open the way to the production of high precision and high resolution geochemical records for natural carbonate materials.

Uncertainty importance analysis using parametric moment ratio functions.

PubMed

Wei, Pengfei; Lu, Zhenzhou; Song, Jingwen

2014-02-01

This article presents a new importance analysis framework, called parametric moment ratio function, for measuring the reduction of model output uncertainty when the distribution parameters of inputs are changed, and the emphasis is put on the mean and variance ratio functions with respect to the variances of model inputs. The proposed concepts efficiently guide the analyst to achieve a targeted reduction on the model output mean and variance by operating on the variances of model inputs. The unbiased and progressive unbiased Monte Carlo estimators are also derived for the parametric mean and variance ratio functions, respectively. Only a set of samples is needed for implementing the proposed importance analysis by the proposed estimators, thus the computational cost is free of input dimensionality. An analytical test example with highly nonlinear behavior is introduced for illustrating the engineering significance of the proposed importance analysis technique and verifying the efficiency and convergence of the derived Monte Carlo estimators. Finally, the moment ratio function is applied to a planar 10-bar structure for achieving a targeted 50% reduction of the model output variance. © 2013 Society for Risk Analysis.

Mills' ratio

NASA Astrophysics Data System (ADS)

Baricz, Árpád

2008-04-01

In this paper we study the monotonicity properties of some functions involving the Mills' ratio of the standard normal law. From these we deduce some new functional inequalities involving the Mills' ratio, and we show that the Mills' ratio is strictly completely monotonic. At the end of this paper we present some Turán-type inequalities for Mills' ratio.

Isotope ratio analysis of individual sub-micrometer plutonium particles with inductively coupled plasma mass spectrometry.

PubMed

Esaka, Fumitaka; Magara, Masaaki; Suzuki, Daisuke; Miyamoto, Yutaka; Lee, Chi-Gyu; Kimura, Takaumi

2010-12-15

Information on plutonium isotope ratios in individual particles is of great importance for nuclear safeguards, nuclear forensics and so on. Although secondary ion mass spectrometry (SIMS) is successfully utilized for the analysis of individual uranium particles, the isobaric interference of americium-241 to plutonium-241 makes difficult to obtain accurate isotope ratios in individual plutonium particles. In the present work, an analytical technique by a combination of chemical separation and inductively coupled plasma mass spectrometry (ICP-MS) is developed and applied to isotope ratio analysis of individual sub-micrometer plutonium particles. The ICP-MS results for individual plutonium particles prepared from a standard reference material (NBL SRM-947) indicate that the use of a desolvation system for sample introduction improves the precision of isotope ratios. In addition, the accuracy of the (241)Pu/(239)Pu isotope ratio is much improved, owing to the chemical separation of plutonium and americium. In conclusion, the performance of the proposed ICP-MS technique is sufficient for the analysis of individual plutonium particles. Copyright © 2010 Elsevier B.V. All rights reserved.

Practical Guidance for Conducting Mediation Analysis With Multiple Mediators Using Inverse Odds Ratio Weighting

PubMed Central

Nguyen, Quynh C.; Osypuk, Theresa L.; Schmidt, Nicole M.; Glymour, M. Maria; Tchetgen Tchetgen, Eric J.

2015-01-01

Despite the recent flourishing of mediation analysis techniques, many modern approaches are difficult to implement or applicable to only a restricted range of regression models. This report provides practical guidance for implementing a new technique utilizing inverse odds ratio weighting (IORW) to estimate natural direct and indirect effects for mediation analyses. IORW takes advantage of the odds ratio's invariance property and condenses information on the odds ratio for the relationship between the exposure (treatment) and multiple mediators, conditional on covariates, by regressing exposure on mediators and covariates. The inverse of the covariate-adjusted exposure-mediator odds ratio association is used to weight the primary analytical regression of the outcome on treatment. The treatment coefficient in such a weighted regression estimates the natural direct effect of treatment on the outcome, and indirect effects are identified by subtracting direct effects from total effects. Weighting renders treatment and mediators independent, thereby deactivating indirect pathways of the mediators. This new mediation technique accommodates multiple discrete or continuous mediators. IORW is easily implemented and is appropriate for any standard regression model, including quantile regression and survival analysis. An empirical example is given using data from the Moving to Opportunity (1994–2002) experiment, testing whether neighborhood context mediated the effects of a housing voucher program on obesity. Relevant Stata code (StataCorp LP, College Station, Texas) is provided. PMID:25693776

Nitrogen isotopic analyses by isotope-ratio-monitoring gas chromatography/mass spectrometry

NASA Technical Reports Server (NTRS)

Merritt, D. A.; Hayes, J. M.

1994-01-01

Amino acids containing natural-abundance levels of 15N were derivatized and analyzed isotopically using a technique in which individual compounds are separated by gas chromatography, combusted on-line, and the product stream sent directly to an isotope-ratio mass spectrometer. For samples of N2 gas, standard deviations of ratio measurement were better than 0.1% (Units for delta are parts per thousand or per million (%).) for samples larger than 400 pmol and better than 0.5% for samples larger than 25 pmol (0.1% 15N is equivalent to 0.00004 atom % 15N). Results duplicated those of conventional, batchwise analyses to within 0.05%. For combustion of organic compounds yielding CO2/N2 ratios between 14 and 28, in particular for N-acetyl n-propyl derivatives of amino acids, delta values were within 0.25% of results obtained using conventional techniques and standard deviations were better than 0.35%. Pooled data for measurements of all amino acids produced an accuracy and precision of 0.04 and 0.23%, respectively, when 2 nmol of each amino acid was injected on column and 20% of the stream of combustion products was delivered to the mass spectrometer.

Air/fuel ratio visualization in a diesel spray

NASA Astrophysics Data System (ADS)

Carabell, Kevin David

1993-01-01

To investigate some features of high pressure diesel spray ignition, we have applied a newly developed planar imaging system to a spray in an engine-fed combustion bomb. The bomb is designed to give flow characteristics similar to those in a direct injection diesel engine yet provide nearly unlimited optical access. A high pressure electronic unit injector system with on-line manually adjustable main and pilot injection features was used. The primary scalar of interest was the local air/fuel ratio, particularly near the spray plumes. To make this measurement quantitative, we have developed a calibration LIF technique. The development of this technique is the key contribution of this dissertation. The air/fuel ratio measurement was made using biacetyl as a seed in the air inlet to the engine. When probed by a tripled Nd:YAG laser the biacetyl fluoresces, with a signal proportional to the local biacetyl concentration. This feature of biacetyl enables the fluorescent signal to be used as as indicator of local fuel vapor concentration. The biacetyl partial pressure was carefully controlled, enabling estimates of the local concentration of air and the approximate local stoichiometry in the fuel spray. The results indicate that the image quality generated with this method is sufficient for generating air/fuel ratio contours. The processes during the ignition delay have a marked effect on ignition and the subsequent burn. These processes, vaporization and pre-flame kinetics, very much depend on the mixing of the air and fuel. This study has shown that poor mixing and over-mixing of the air and fuel will directly affect the type of ignition. An optimal mixing arrangement exists and depends on the swirl ratio in the engine, the number of holes in the fuel injector and the distribution of fuel into a pilot and main injection. If a short delay and a diffusion burn is desired, the best mixing parameters among those surveyed would be a high swirl ratio, a 4-hole nozzle and a

A technique to detect microclimatic inhomogeneities in historical temperature records

NASA Astrophysics Data System (ADS)

Runnalls, K. E.; Oke, T. R.

2003-04-01

A technique to identify inhomogeneities in historical temperature records caused by microclimatic changes to the surroundings of a climate station (e.g. minor instrument relocations, vegetation growth/removal, construction of houses, roads, runways) is presented. The technique uses daily maximum and minimum temperatures to estimate the magnitude of nocturnal cooling. The test station is compared to a nearby reference station by constructing time series of monthly "cooling ratios". It is argued that the cooling ratio is a particularly sensitive measure of microclimatic differences between neighbouring climate stations. Firstly, because microclimatic character is best expressed at night in stable conditions. Secondly, because larger-scale climatic influences common to both stations are removed by the use of a ratio and, because the ratio can be shown to be invariant in the mean with weather variables such as wind and cloud. Inflections (change points) in time series of cooling ratios therefore signal microclimatic change in one of the station records. Hurst rescaling is applied to the time series to aid in the identification of change points, which can then be compared to documented station history events, if sufficient metatdata is available. Results for a variety of air temperature records, ranging from rural to urban stations, are presented to illustrate the applicability of the technique.

Micropowder collecting technique for stable isotope analysis of carbonates.

PubMed

Sakai, Saburo; Kodan, Tsuyoshi

2011-05-15

Micromilling is a conventional technique used in the analysis of the isotopic composition of geological materials, which improves the spatial resolution of sample collection for analysis. However, a problem still remains concerning the recovery ratio of the milled sample. We constructed a simple apparatus consisting of a vacuum pump, a sintered metal filter, electrically conductive rubber stopper and a stainless steel tube for transferring the milled powder into a reaction vial. In our preliminary experiments on carbonate powder, we achieved a rapid recovery of 5 to 100 µg of carbonate with a high recovery ratio (>90%). This technique shortens the sample preparation time, improves the recovery ratio, and homogenizes the sample quantity, which, in turn, improves the analytical reproducibility. Copyright © 2011 John Wiley & Sons, Ltd.

Simultaneous measurement of the Young's modulus and the Poisson ratio of thin elastic layers.

PubMed

Gross, Wolfgang; Kress, Holger

2017-02-07

The behavior of cells and tissue is greatly influenced by the mechanical properties of their environment. For studies on the interactions between cells and soft matrices, especially those applying traction force microscopy the characterization of the mechanical properties of thin substrate layers is essential. Various techniques to measure the elastic modulus are available. Methods to accurately measure the Poisson ratio of such substrates are rare and often imply either a combination of multiple techniques or additional equipment which is not needed for the actual biological studies. Here we describe a novel technique to measure both parameters, the Youngs's modulus and the Poisson ratio in a single experiment. The technique requires only a standard inverted epifluorescence microscope. As a model system, we chose cross-linked polyacrylamide and poly-N-isopropylacrylamide hydrogels which are known to obey Hooke's law. We place millimeter-sized steel spheres on the substrates which indent the surface. The data are evaluated using a previously published model which takes finite thickness effects of the substrate layer into account. We demonstrate experimentally for the first time that the application of the model allows the simultaneous determination of both the Young's modulus and the Poisson ratio. Since the method is easy to adapt and comes without the need of special equipment, we envision the technique to become a standard tool for the characterization of substrates for a wide range of investigations of cell and tissue behavior in various mechanical environments as well as other samples, including biological materials.

Masking in three pinnipeds: underwater, low-frequency critical ratios.

PubMed

Southall, B L; Schusterman, R J; Kastak, D

2000-09-01

Behavioral techniques were used to determine underwater masked hearing thresholds for a northern elephant seal (Mirounga angustirostris), a harbor seal (Phoca vitulina), and a California sea lion (Zalophus californianus). Octave-band white noise maskers were centered at five test frequencies ranging from 200 to 2500 Hz; a slightly wider noise band was used for testing at 100 Hz. Critical ratios were calculated at one masking noise level for each test frequency. Above 200 Hz, critical ratios increased with frequency. This pattern is similar to that observed in most animals tested, and indicates that these pinnipeds lack specializations for detecting low-frequency tonal sounds in noise. However, the individual pinnipeds in this study, particularly the northern elephant seal, detected signals at relatively low signal-to-noise ratios. These results provide a means of estimating zones of auditory masking for pinnipeds exposed to anthropogenic noise sources.

[Extended middle fossa approach in treatment of vestibular schwannoma--technique of surgery and postoperative complications].

PubMed

Jamróz, Barbara; Niemczyk, Kazimierz; Morawski, Krzysztof; Bartoszewicz, Robert

2010-06-01

The main tumor of cerebellopontine angle are vestibular schwannoma (80-90%). According to National Institute of Health Consensus Development Conference the best treatment method is microsurgery. There are three principal surgical approaches: translabyrinthin, retrosigmoid and middle fossa. Only the latter two approaches provide the possibility of hearing preservation. Technique of surgery and postoperative morbidity after MFA. 39 patients (40 tumor) suffered from tumor of cerebellopontine angle, operated by using middle fossa approach in years 1998-2007. We evaluate hearing preservation and function of facial nerve and others postoperative morbidity. 22.5% of patients has hearing impairment and 32.5% has facial weakness. By individual cases we observed: CSF leak, meningitis, corneal ulceration, ischialgia, wound bleeding and venue thrombosis. 1/3 of patients suffered from headache and disequilibrium and 1/6 suffered from tinnitus. According to NIH middle fossa approach is one of three possible approaches in microsurgery of cerebellopontine angle tumors. There is possible total tumor removal with hearing preservation. Monitoring of facial and cochlear nerve during operation is recommended.

Detection of counterfeit antiviral drug Heptodin and classification of counterfeits using isotope amount ratio measurements by multicollector inductively coupled plasma mass spectrometry (MC-ICPMS) and isotope ratio mass spectrometry (IRMS).

PubMed

Santamaria-Fernandez, Rebeca; Hearn, Ruth; Wolff, Jean-Claude

2009-06-01

Isotope ratio mass spectrometry (IRMS) and multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) are highly important techniques that can provide forensic evidence that otherwise would not be available. MC-ICP-MS has proved to be a very powerful tool for measuring high precision and accuracy isotope amount ratios. In this work, the potential of combining isotope amount ratio measurements performed by MC-ICP-MS and IRMS for the detection of counterfeit pharmaceutical tablets has been investigated. An extensive study for the antiviral drug Heptodin has been performed for several isotopic ratios combining MC-ICP-MS and an elemental analyser EA-IRMS for stable isotope amount ratio measurements. The study has been carried out for 139 batches of the antiviral drug and analyses have been performed for C, S, N and Mg isotope ratios. Authenticity ranges have been obtained for each isotopic system and combined to generate a unique multi-isotopic pattern only present in the genuine tablets. Counterfeit tablets have then been identified as those tablets with an isotopic fingerprint outside the genuine isotopic range. The combination of those two techniques has therefore great potential for pharmaceutical counterfeit detection. A much greater power of discrimination is obtained when at least three isotopic systems are combined. The data from these studies could be presented as evidence in court and therefore methods need to be validated to support their credibility. It is also crucial to be able to produce uncertainty values associated to the isotope amount ratio measurements so that significant differences can be identified and the genuineness of a sample can be assessed.

Mapping the benefit-cost ratios of interventions against bovine trypanosomosis in Eastern Africa.

PubMed

Shaw, A P M; Wint, G R W; Cecchi, G; Torr, S J; Mattioli, R C; Robinson, T P

2015-12-01

This study builds upon earlier work mapping the potential benefits from bovine trypanosomosis control and analysing the costs of different approaches. Updated costs were derived for five intervention techniques: trypanocides, targets, insecticide-treated cattle, aerial spraying and the release of sterile males. Two strategies were considered: continuous control and elimination. For mapping the costs, cattle densities, environmental constraints, and the presence of savannah or riverine tsetse species were taken into account. These were combined with maps of potential benefits to produce maps of benefit-cost ratios. The results illustrate a diverse picture, and they clearly indicate that no single technique or strategy is universally profitable. For control using trypanocide prophylaxis, returns are modest, even without accounting for the risk of drug resistance but, in areas of low cattle densities, this is the only approach that yields a positive return. Where cattle densities are sufficient to support it, the use of insecticide-treated cattle stands out as the most consistently profitable technique, widely achieving benefit-cost ratios above 5. In parts of the high-potential areas such as the mixed farming, high-oxen-use zones of western Ethiopia, the fertile crescent north of Lake Victoria and the dairy production areas in western and central Kenya, all tsetse control strategies achieve benefit-cost ratios from 2 to over 15, and for elimination strategies, ratios from 5 to over 20. By contrast, in some areas, notably where cattle densities are below 20per km(2), the costs of interventions against tsetse match or even outweigh the benefits, especially for control scenarios using aerial spraying or the deployment of targets where both savannah and riverine flies are present. If the burden of human African trypanosomosis were factored in, the benefit-cost ratios of some of the low-return areas would be considerably increased. Comparatively, elimination strategies

A study of FM threshold extension techniques

NASA Technical Reports Server (NTRS)

Arndt, G. D.; Loch, F. J.

1972-01-01

The characteristics of three postdetection threshold extension techniques are evaluated with respect to the ability of such techniques to improve the performance of a phase lock loop demodulator. These techniques include impulse-noise elimination, signal correlation for the detection of impulse noise, and delta modulation signal processing. Experimental results from signal to noise ratio data and bit error rate data indicate that a 2- to 3-decibel threshold extension is readily achievable by using the various techniques. This threshold improvement is in addition to the threshold extension that is usually achieved through the use of a phase lock loop demodulator.

Orbital Transfer Vehicle Engine Technology High Velocity Ratio Diffusing Crossover

NASA Technical Reports Server (NTRS)

Lariviere, Brian W.

1992-01-01

High speed, high efficiency head rise multistage pumps require continuous passage diffusing crossovers to effectively convey the pumped fluid from the exit of one impeller to the inlet of the next impeller. On Rocketdyne's Orbital Transfer Vehicle (OTV), the MK49-F, a three stage high pressure liquid hydrogen turbopump, utilizes a 6.23 velocity ratio diffusing crossover. This velocity ratio approaches the diffusion limits for stable and efficient flow over the operating conditions required by the OTV system. The design of the high velocity ratio diffusing crossover was based on advanced analytical techniques anchored by previous tests of stationary two-dimensional diffusers with steady flow. To secure the design and the analytical techniques, tests were required with the unsteady whirling characteristics produced by an impeller. A tester was designed and fabricated using a 2.85 times scale model of the MK49-F turbopumps first stage, including the inducer, impeller, and the diffusing crossover. Water and air tests were completed to evaluate the large scale turbulence, non-uniform velocity, and non-steady velocity on the pump and crossover head and efficiency. Suction performance tests from 80 percent to 124 percent of design flow were completed in water to assess these pump characteristics. Pump and diffuser performance from the water and air tests were compared with the actual MK49-F test data in liquid hydrogen.

HLA-DR4 as a risk allele for autism acting in mothers of probands possibly during pregnancy.

PubMed

Johnson, William G; Buyske, Steven; Mars, Audrey E; Sreenath, Madhura; Stenroos, Edward S; Williams, Tanishia A; Stein, Rosanne; Lambert, George H

2009-06-01

To test whether HLA-DR4 acts in the mother, possibly during pregnancy, to contribute to the phenotype of autistic disorder in her fetus. Transmission disequilibrium testing in case mothers and maternal grandparents. Previous studies have consistently shown increased frequency of HLA-DR4 in probands with autism and their mothers, but not their fathers. However, this has been documented only in case-control studies and not by a more direct study design to determine whether HLA-DR4 acts in mothers during pregnancy to contribute to autism in their affected offspring. We genotyped for HLA-DR alleles in members of 31 families with parents and maternal grandparents. Probands with autism were tested using the Autism Diagnostic Observation Schedule-Western Psychological Services and Autism Diagnostic Interview, Revised. There was 80% power to detect an odds ratio of 3.6. Participants were all families from New Jersey and were similar in number to earlier studies of autism and HLA-DR4. Analysis was by standard transmission disequilibrium testing. As a secondary test we examined the possibility of maternal imprinting. Significant transmission disequilibrium for HLA-DR4 was seen (odds ratio, 4.67; 95% confidence interval, 1.34-16.24; P = .008) for transmissions from maternal grandparents to mothers of probands, supporting a role for HLA-DR4 as an autism risk factor acting in mothers during pregnancy. Transmission disequilibrium was not seen for HLA-DR4 transmissions from parents to probands or from mothers to probands. The HLA-DR4 gene may act in mothers of children with autism during pregnancy to contribute to autism in their offspring. Further studies are required to confirm these findings.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

PubMed

Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

PubMed Central

Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

Adaptive critic learning techniques for engine torque and air-fuel ratio control.

PubMed

Liu, Derong; Javaherian, Hossein; Kovalenko, Olesia; Huang, Ting

2008-08-01

A new approach for engine calibration and control is proposed. In this paper, we present our research results on the implementation of adaptive critic designs for self-learning control of automotive engines. A class of adaptive critic designs that can be classified as (model-free) action-dependent heuristic dynamic programming is used in this research project. The goals of the present learning control design for automotive engines include improved performance, reduced emissions, and maintained optimum performance under various operating conditions. Using the data from a test vehicle with a V8 engine, we developed a neural network model of the engine and neural network controllers based on the idea of approximate dynamic programming to achieve optimal control. We have developed and simulated self-learning neural network controllers for both engine torque (TRQ) and exhaust air-fuel ratio (AFR) control. The goal of TRQ control and AFR control is to track the commanded values. For both control problems, excellent neural network controller transient performance has been achieved.

Non-invasive acoustic-based monitoring of uranium in solution and H/D ratio

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

Pantea, Cristian; Beedle, Christopher Craig; Sinha, Dipen N.

The primary objective of this project is to adapt existing non-invasive acoustic techniques (Swept-Frequency Acoustic Interferometry and Gaussian-pulse acoustic technique) for the purpose of demonstrating the ability to quantify U or H/D ratios in solution. Furthermore, a successful demonstration will provide an easily implemented, low cost, and non-invasive method for remote and unattended uranium mass measurements for International Atomic Energy Agency (IAEA).

210Po/210Pb Activity Ratios as a Possible `Dating Tool' of Ice Cores and Ice-rafted Sediments from the Western Arctic Ocean - Preliminary Results

NASA Astrophysics Data System (ADS)

Krupp, K.; Baskaran, M. M.

2016-02-01

We have collected and analyzed a suite of surface snow samples, ice cores, ice-rafted sediments (IRS) and aerosol samples from the Western Arctic for Po-210 and Pb-210 to examine the extent of disequilibrium between this pair to possibly use 210Po/210Pb activity ratio to date different layers of ice cores and time of incorporation of ice-rafted sediments into the sea ice. We have earlier reported that the activity concentrations of 210Pb in IRS vary over an order of magnitude and it is 1-2 orders of magnitude higher than that of the benthic sediments (1-2 dpm/g in benthic sediments compared to 25 to 300 dpm/g in IRS). In this study, we have measured 210Po/210Pb activity ratios in aerosols from the Arctic Ocean to constrain the initial 210Po/210Pb ratio at the time of deposition during precipitation. The 210Po activity concentration in recent snow is compared to surface ice samples. The `age' of IRS incorporation can be calculated as follows: [210Po]measured = [210Po]initial + [210Pb] (1 - exp(-λt)) (1) where λ is the decay constant of 210Po, 138.4 days, and `t' is the in-growth time period. From this equation, `t' can be calculated as follows: t = (-1/λ) [ln (1- ((210Po/210Pb)measured - (210Po/210Pb)initial)] (2) The assumption involved in this approach are: i) there is no preferential uptake of 210Po (highly biogenic - S group); and iii) both 210Po and 210Pb remain as closed system. The calculated age using equation (2) will be discussed and presented.

Hepatic MR imaging for in vivo differentiation of steatosis, iron deposition and combined storage disorder: single-ratio in/opposed phase analysis vs. dual-ratio Dixon discrimination.

PubMed

Bashir, Mustafa R; Merkle, Elmar M; Smith, Alastair D; Boll, Daniel T

2012-02-01

To assess whether in vivo dual-ratio Dixon discrimination can improve detection of diffuse liver disease, specifically steatosis, iron deposition and combined disease over traditional single-ratio in/opposed phase analysis. Seventy-one patients with biopsy-proven (17.7 ± 17.0 days) hepatic steatosis (n = 16), iron deposition (n = 11), combined deposition (n = 3) and neither disease (n = 41) underwent MR examinations. Dual-echo in/opposed-phase MR with Dixon water/fat reconstructions were acquired. Analysis consisted of: (a) single-ratio hepatic region-of-interest (ROI)-based assessment of in/opposed ratios; (b) dual-ratio hepatic ROI assessment of in/opposed and fat/water ratios; (c) computer-aided dual-ratio assessment evaluating all hepatic voxels. Disease-specific thresholds were determined; statistical analyses assessed disease-dependent voxel ratios, based on single-ratio (a) and dual-ratio (b and c) techniques. Single-ratio discrimination succeeded in identifying iron deposition (I/O(Ironthreshold)<0.88) and steatosis (I/O(Fatthreshold>1.15)) from normal parenchyma, sensitivity 70.0%; it failed to detect combined disease. Dual-ratio discrimination succeeded in identifying abnormal hepatic parenchyma (F/W(Normalthreshold)>0.05), sensitivity 96.7%; logarithmic functions for iron deposition (I/O(Irondiscriminator)e((F/W(Fat)-0.01)/0.48)) differentiated combined from isolated diseases, sensitivity 100.0%; computer-aided dual-ratio analysis was comparably sensitive but less specific, 90.2% vs. 97.6%. MR two-point-Dixon imaging using dual-ratio post-processing based on in/opposed and fat/water ratios improved in vivo detection of hepatic steatosis, iron deposition, and combined storage disease beyond traditional in/opposed analysis. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Faulty serotonin--DHEA interactions in autism: results of the 5-hydroxytryptophan challenge test.

PubMed

Croonenberghs, Jan; Spaas, Kristien; Wauters, Annick; Verkerk, Robert; Scharpe, Simon; Deboutte, Dirk; Maes, Michael

2008-06-01

Autism is accompanied by peripheral and central disorders in the metabolism of serotonin (5-HT). The present study examines plasma dehydroepiandrosterone-sulphate (DHEA-S) and the cortisol/DHEA-S ratio following administration of L-5-hydroxytryptophan (5-HTP), the direct precursor of 5-HT, to autistic patients. Plasma DHEA-S levels were determined both before and after administration of 5-HTP or placebo, on two consecutive days in a single blind order in 18 male autistic patients and 22 matched healthy controls. The 5-HTP-induced DHEA-S responses were significantly higher in autistic patients than in controls. In baseline conditions, the cortisol/DHEA-S ratio was significantly higher in autistic patients than in controls. The results suggest that autism is accompanied by a major disequilibrium in the serotonergic system. The increased Cortisol (neurotoxic) versus DHEA-S (neuroprotective) ratio suggests that an increased neurotoxic potential occurs in autism. It is concluded that a disequilibrium in the peripheral and central turnover of serotonin and an increased neurotoxic capacity by glucocorticoids are important pathways in autism.

Experimental determination of U and Th partitioning between clinopyroxene and natural and synthetic basaltic liquid

NASA Technical Reports Server (NTRS)

Latourrette, T. Z.; Burnett, D. S.

1992-01-01

Experimental measurements of U and the partition coefficients between clinopyroxene and synthetic and natural basaltic liquid are presented. The results demonstrate that crystal-liquid U-Th fractionation is fO2-dependent and that U in terrestrial magmas is not entirely tetravalent. During partial melting, the liquid will have a Th/U ratio less than the clinopyroxene in the source. The observed U-238 - Th-230 disequilibrium in MORB requires that the partial melt should have a U/Th ratio greater than the bulk source and therefore cannot result from clinopyroxene-liquid partitioning. Further, the magnitudes of the measured partition coefficients are too small to generate significant U-Th fractionation in either direction. Assuming that clinopyroxene contains the bulk of the U and Th in the MORB source, the results indicate that U-238 - Th-230 disequilibrium in MORB may not be caused by partial melting at all.

An in-depth Monte Carlo study of lateral electron disequilibrium for small fields in ultra-low density lung: implications for modern radiation therapy

NASA Astrophysics Data System (ADS)

Disher, Brandon; Hajdok, George; Gaede, Stewart; Battista, Jerry J.

2012-03-01

Modern radiation therapy techniques such as intensity-modulated radiation therapy (IMRT) and stereotactic body radiation therapy (SBRT) use tightly conformed megavoltage x-ray fields to irradiate a tumour within lung tissue. For these conditions, lateral electron disequilibrium (LED) may occur, which systematically perturbs the dose distribution within tumour and nearby lung tissues. The goal of this work is to determine the combination of beam and lung density parameters that cause significant LED within and near the tumour. The Monte Carlo code DOSXYZnrc (National Research Council of Canada, Ottawa, ON) was used to simulate four 20 × 20 × 25 cm3 water-lung-water slab phantoms, which contained lung tissue only, or one of three different centrally located small tumours (sizes: 1 × 1 × 1, 3 × 3 × 3, 5 × 5 × 5 cm3). Dose calculations were performed using combinations of six beam energies (Co-60 up to 18 MV), five field sizes (1 × 1 cm2 up to 15 × 15 cm2), and 12 lung densities (0.001 g cm-3 up to 1 g cm-3) for a total of 1440 simulations. We developed the relative depth-dose factor (RDDF), which can be used to characterize the extent of LED (RDDF <1.0). For RDDF <0.7 severe LED occurred, and both lung and tumour dose were drastically reduced. For example, a 6 MV (3 × 3 cm2) field was used to irradiate a 1 cm3 tumour embedded in lung with ultra-low density of 0.001 g cm-3 (RDDF = 0.2). Dose in up-stream lung and tumour centre were reduced by as much as 80% with respect to the water density calculation. These reductions were worse for smaller tumours irradiated with high energy beams, small field sizes, and low lung density. In conclusion, SBRT trials based on dose calculations in homogeneous tissue are misleading as they do not reflect the actual dosimetric effects due to LED. Future clinical trials should only use dose calculation engines that can account for electron scatter, with special attention given to patients with low lung density (i.e. emphysema

Investigating a dynamic gas hydrate system in disequilibrium in the Danube Delta, Black Sea

NASA Astrophysics Data System (ADS)

Hillman, Jess; Bialas, Joerg; Klaucke, Ingo; Feldman, Howard; Drexler, Tina

2017-04-01

Gas hydrates are known to be extensive across the Danube Delta, as indicated by the presence of bottom simulating reflections (BSRs). The shelf break in this region is characterised by several incised submarine canyons, the largest of which is the Viteaz Canyon, and numerous slope failures. BSRs often coincide with submarine landslides, and it has been proposed that hydrates may play a role in triggering, or facilitating such events. This study focuses on a seafloor canyon (the S2 Canyon) to the north-east of the main Viteaz Canyon, where geophysical survey data and sediment cores were acquired in 2014. Active venting from the seafloor is known to be occurring at this site as multiple flares were been imaged in the water column. The location of these flares coincides with a significant slope failure adjacent to the canyon, and some can be correlated to subsurface gas chimneys, indicating a complex 'plumbing system' of gas migration pathways. This site is of particular interest as the 'present-day' BSR imaged in seismic data is not at equilibrium with the present-day seafloor conditions. Using high resolution 2D seismic data, a P-cable 3D seismic volume and ocean bottom seismometer data we investigate potential gas migration pathways and the complex gas hydrate system in the vicinity of the S2 Canyon. In addition, we use stratigraphic interpretation based on regional 2D seismic lines to constrain the relative ages of the channel levee systems. Through detailed mapping of the BSR, possible paleo-seafloor surfaces and gas migration features we are able to provide estimates of equilibrium conditions for the hydrate system, and examine the controlling factors affecting gas migration pathways and hydrate formation. The results of this study provide new insight into a geologically complex setting with a dynamic hydrate system. Characterising the hydrate system here may help to explain why it is in disequilibrium with the present day seafloor, and provide a better

X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations

PubMed Central

Laan, Maris; Wiebe, Victor; Khusnutdinova, Elza; Remm, Maido; Pääbo, Svante

2005-01-01

Linkage disequilibrium structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225-DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25-40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasise the importance of understanding the history, structure and variation of a study population. PMID:15657606

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers.

PubMed

Pavy, N; Namroud, M-C; Gagnon, F; Isabel, N; Bousquet, J

2012-03-01

In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r(2) value was 0.19 (s.d.=0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r(2)=0.28), and a second group of 38 genes had weaker LD (mean r(2)=0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

Further Delineation of the Clinical Phenotype of Cerebellar Ataxia, Mental Retardation, and Disequilibrium Syndrome Type 4

PubMed Central

Alsahli, Saud; Alrifai, Muhammad Talal; Al Tala, Saeed; Mutairi, Fuad Al; Alfadhel, Majid

2018-01-01

Background: Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) is a heterogeneous group of genetic disorders that have been grouped by shared clinical features; all of these features are transmitted via an autosomal recessive mechanism. Four variants of this syndrome have been identified so far, and each one differs in terms of both clinical and genotypical features. CAMRQ4 is a rare genetic disorder characterized by mental retardation, ataxia or an inability to walk, dysarthria and, in some patients, quadrupedal gait. Methods: We investigated three Saudi families with CAMRQ4. Blood samples were collected from the affected patients, their parents, and healthy siblings. DNA was extracted from whole blood, and whole-exome sequencing was performed. Findings were confirmed by segregation analysis, which was performed on other family members. Results: Thus far, 17 patients have been affected by CAMRQ4. Genetic analysis of all patients, including our current patients, showed a mutation in the aminophospholipid transporter, class I, type 8A, member 2 gene (ATP8A2). A series of common phenotypical features have been reported in these patients, with few exceptions. Ataxia, mental retardation, and hypotonia were present in all patients, consanguinity in 90% and abnormal movements in 50%. Moreover, 40% achieved ambulation at least once in their lifetime, 40% had microcephaly, whereas 30% were mute. Magnetic resonance imaging (MRI) of the brain was normal in 60% of patients. Conclusions: We described the largest cohort of patients with CAMRQ4 syndrome and identified three novel mutations. CAMRQ4 syndrome should be suspected in patients presenting with ataxia, intellectual disability, hypotonia, microcephaly, choreoathetoid movements, ophthalmoplegia, and global developmental delay, even if brain MRI appears normal. PMID:29531481

Further Delineation of the Clinical Phenotype of Cerebellar Ataxia, Mental Retardation, and Disequilibrium Syndrome Type 4.

PubMed

Alsahli, Saud; Alrifai, Muhammad Talal; Al Tala, Saeed; Mutairi, Fuad Al; Alfadhel, Majid

2018-01-01

Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) is a heterogeneous group of genetic disorders that have been grouped by shared clinical features; all of these features are transmitted via an autosomal recessive mechanism. Four variants of this syndrome have been identified so far, and each one differs in terms of both clinical and genotypical features. CAMRQ4 is a rare genetic disorder characterized by mental retardation, ataxia or an inability to walk, dysarthria and, in some patients, quadrupedal gait. We investigated three Saudi families with CAMRQ4. Blood samples were collected from the affected patients, their parents, and healthy siblings. DNA was extracted from whole blood, and whole-exome sequencing was performed. Findings were confirmed by segregation analysis, which was performed on other family members. Thus far, 17 patients have been affected by CAMRQ4. Genetic analysis of all patients, including our current patients, showed a mutation in the aminophospholipid transporter, class I, type 8A, member 2 gene ( ATP8A2 ). A series of common phenotypical features have been reported in these patients, with few exceptions. Ataxia, mental retardation, and hypotonia were present in all patients, consanguinity in 90% and abnormal movements in 50%. Moreover, 40% achieved ambulation at least once in their lifetime, 40% had microcephaly, whereas 30% were mute. Magnetic resonance imaging (MRI) of the brain was normal in 60% of patients. We described the largest cohort of patients with CAMRQ4 syndrome and identified three novel mutations. CAMRQ4 syndrome should be suspected in patients presenting with ataxia, intellectual disability, hypotonia, microcephaly, choreoathetoid movements, ophthalmoplegia, and global developmental delay, even if brain MRI appears normal.

Activity disequilibrium between 234U and 238U isotopes in natural environment.

PubMed

Boryło, Alicja; Skwarzec, Bogdan

The aim of this work was to calculate the values of the 234 U/ 238 U activity ratio in natural environment (water, sediments, Baltic organisms and marine birds from various regions of the southern Baltic Sea; river waters (the Vistula and the Oder River); plants and soils collected near phosphogypsum waste heap in Wiślinka (Northern Poland) and deer-like animals from Northern Poland. On the basis of the studies it was found that the most important processes of uranium geochemical migration in the southern Baltic Sea ecosystem are the sedimentation of suspended material and the vertical diffusion from the sediments into the bottom water. Considerable values of the 234 U/ 238 U are characterized for the Vistula and Oder Rivers and its tributaries. The values of the 234 U/ 238 U activity ratio in different tissues and organs of the Baltic organisms, sea birds and wild deer are varied. Such a large variation value of obtained activity ratios indicates different behavior of uranium isotopes in the tissues and organisms of sea birds and wild animals. This value shows that uranium isotopes can be disposed at a slower or faster rate. The values of the 234 U/ 238 U activity ratio in the analyzed plants, soils and mosses collected in the vicinity of phosphogypsum dumps in Wiślinka are close to one and indicate the phosphogypsum origin of the analyzed nuclides. Uranium isotopes 234 U and 238 U are not present in radioactive equilibrium in the aquatic environment, which indicates that their activities are not equal. The inverse relationship is observed in the terrestrial environment, where the value of the of the 234 U/ 238 U activity ratio really oscillates around unity.

Evaluation of the equivalence ratio of the reacting mixture using intensity ratio of chemiluminescence in laminar partially premixed CH{sub 4}-air flames

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

Jeong, Yong Ki; Jeon, Chung Hwan; Chang, Young June

An experimental study was performed to investigate the effects of partially premixing, varying the equivalence ratios from 0.79 to 9.52, on OH*, CH* and C{sub 2}* in laminar partially premixed flames. The signals from the electronically excited states of OH*, CH* and C{sub 2}* were detected through interference filters using a photo multiplier tube, which were processed to the intensity ratios (C{sub 2}*/CH*, C{sub 2}*/OH* and CH*/OH*) to determine a correlation with the local equivalence ratios. Furthermore, the consistency between the results of the tomographic reconstruction; Abel inversion technique, image with CCD (Couple Charged Detector) camera and the local radicalmore » intensity with PMT was investigated. The results demonstrated that (1) the flames at F=<1.36 exhibited classical double flame structure, at F>=4.76, the flames exhibited non-premixed-like flame structure and the intermediate flames at 1.36ratio of CH*/OH* was nearly proportional to 1/F for the 1 dimensional results with PMT, with a correlation coefficient of 0.99 at the equivalence ratios of 0.79-9.52. These results are in good agreement with those obtained from the two dimensional results with ICCD. However, it is difficult to predict the relationships between the equivalence ratios and intensity ratios of C{sub 2}*/CH* and C{sub 2}*/OH*. (author)« less

Energy Balance Bowen Ratio (EBBR) Handbook

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

Cook, D. R.

2016-01-01

The Energy Balance Bowen Ratio (EBBR) system produces 30-minute estimates of the vertical fluxes of sensible and latent heat at the local surface. Flux estimates are calculated from observations of net radiation, soil surface heat flux, and the vertical gradients of temperature and relative humidity (RH). Meteorological data collected by the EBBR are used to calculate bulk aerodynamic fluxes, which are used in the Bulk Aerodynamic Technique (BA) EBBR value-added product (VAP) to replace sunrise and sunset spikes in the flux data. A unique aspect of the system is the automatic exchange mechanism (AEM), which helps to reduce errors frommore » instrument offset drift.« less

High signal-to-noise ratio acoustic sensor using phase shifted gratings interrogated by the Pound-Drever-Hall technique

NASA Astrophysics Data System (ADS)

Kung, Peter; Comanici, Maria I.

2015-03-01

Optical fiber is made of glass, an insulator, and thus it is immune to strong electromagnetic interference. Therefore, fiber optics is a technology ideally suitable for sensing of partial discharge (PD) both in transformers and generators. Extensive efforts have been used to develop a cost effective solution for detecting partial discharge, which generates acoustic emission, with signals ranging from 30 kHz to 200 kHz. The requirement is similar to fiber optics Hydro Phone, but at higher frequencies. There are several keys to success: there must be at least 60 dB signal-to-noise ratio (SNR) performance, which will ensure not only PD detection but later on provide diagnostics and also the ability to locate the origin of the events. Defects that are stationary would gradually degrade the insulation and result in total breakdown. Transformers currently need urgent attention: most of them are oil filled and are at least 30 to 50 years old, close to the end of life. In this context, an issue to be addressed is the safety of the personnel working close to the assets and collateral damage that could be caused by a tank explosion (with fire spilling over the whole facility). This paper will describe the latest achievement in fiber optics PD sensor technology: the use of phase shifted-fiber gratings with a very high speed interrogation method that uses the Pound-Drever-Hall technique. More importantly, this is based on a technology that could be automated, easy to install, and, eventually, available at affordable prices.

High signal-to-noise ratio acoustic sensor using phase-shifted gratings interrogated by the Pound-Drever-Hall technique

NASA Astrophysics Data System (ADS)

Kung, Peter; Comanici, Maria I.

2014-06-01

Optical fiber is made of glass, an insulator, and thus it is immune to strong electromagnetic interference. Therefore, fiber optics is a technology ideally suitable for sensing of partial discharge (PD) both in transformers and generators. Extensive efforts have been used to develop a cost effective solution for detecting partial discharge, which generates acoustic emission, with signals ranging from 30 kHz to 200 kHz. The requirement is similar to fiber optics Hydro Phone, but at higher frequencies. There are several keys to success: there must be at least 60 dB signal-to-noise ratio (SNR) performance, which will ensure not only PD detection but later on provide diagnostics and also the ability to locate the origin of the events. Defects that are stationary would gradually degrade the insulation and result in total breakdown. Transformers currently need urgent attention: most of them are oil filled and are at least 30 to 50 years old, close to the end of life. In this context, an issue to be addressed is the safety of the personnel working close to the assets and collateral damage that could be caused by a tank explosion (with fire spilling over the whole facility). This paper will describe the latest achievement in fiber optics PD sensor technology: the use of phase shifted-fiber gratings with a very high speed interrogation method that uses the Pound-Drever-Hall technique. More importantly, this is based on a technology that could be automated, easy to install, and, eventually, available at affordable prices

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

PubMed Central

Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca e; Mundim, Gabriel Borges

2016-01-01

Abstract The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis. PMID:27007903

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits.

PubMed

Paes, Geísa Pinheiro; Viana, José Marcelo Soriano; Silva, Fabyano Fonseca E; Mundim, Gabriel Borges

2016-03-01

The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

Signal-to-noise ratio estimation in digital computer simulation of lowpass and bandpass systems with applications to analog and digital communications, volume 3

NASA Technical Reports Server (NTRS)

Tranter, W. H.; Turner, M. D.

1977-01-01

Techniques are developed to estimate power gain, delay, signal-to-noise ratio, and mean square error in digital computer simulations of lowpass and bandpass systems. The techniques are applied to analog and digital communications. The signal-to-noise ratio estimates are shown to be maximum likelihood estimates in additive white Gaussian noise. The methods are seen to be especially useful for digital communication systems where the mapping from the signal-to-noise ratio to the error probability can be obtained. Simulation results show the techniques developed to be accurate and quite versatile in evaluating the performance of many systems through digital computer simulation.

Proposed method of hydrogeochemical exploration for salt deposits using ClBr ratios, Eastern Province, Kingdom of Saudi Arabia

USGS Publications Warehouse

Smith, C.L.

1991-01-01

Despite the value of the salt (NaCl) and brine used by the chemical industry, geochemical prospecting techniques are not customarily employed in the search for these raw materials. In this study, Br geochemistry is used as the basis for a proposed hydrogeochemical prospecting technique that was designed to search for shallow halite beds in the Eastern Province of the Kingdom of Saudi Arabia. Near-surface brine samples were collected at Sabkhah Jayb Uwayyid, both directly above and distant from a buried salt bed. Brine samples collected both directly above and offset to the north-west of the salt bed had ClBr ratios > 8000. The regional background ClBr ratio of fresh nonmarime ground water is ???300. The large range in ClBr ratios and the association of high ClBr ratios with the buried salt body suggest that the ratio can be useful in hydrogeochemical prospecting for sibakh-associated, shallow salt bodies. ?? 1991.

A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

PubMed

Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

2015-09-01

Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

Practical guidance for conducting mediation analysis with multiple mediators using inverse odds ratio weighting.

PubMed

Nguyen, Quynh C; Osypuk, Theresa L; Schmidt, Nicole M; Glymour, M Maria; Tchetgen Tchetgen, Eric J

2015-03-01

Despite the recent flourishing of mediation analysis techniques, many modern approaches are difficult to implement or applicable to only a restricted range of regression models. This report provides practical guidance for implementing a new technique utilizing inverse odds ratio weighting (IORW) to estimate natural direct and indirect effects for mediation analyses. IORW takes advantage of the odds ratio's invariance property and condenses information on the odds ratio for the relationship between the exposure (treatment) and multiple mediators, conditional on covariates, by regressing exposure on mediators and covariates. The inverse of the covariate-adjusted exposure-mediator odds ratio association is used to weight the primary analytical regression of the outcome on treatment. The treatment coefficient in such a weighted regression estimates the natural direct effect of treatment on the outcome, and indirect effects are identified by subtracting direct effects from total effects. Weighting renders treatment and mediators independent, thereby deactivating indirect pathways of the mediators. This new mediation technique accommodates multiple discrete or continuous mediators. IORW is easily implemented and is appropriate for any standard regression model, including quantile regression and survival analysis. An empirical example is given using data from the Moving to Opportunity (1994-2002) experiment, testing whether neighborhood context mediated the effects of a housing voucher program on obesity. Relevant Stata code (StataCorp LP, College Station, Texas) is provided. © The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks.

PubMed

Zhao, Huiying; Nyholt, Dale R; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

2017-06-14

Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path .

Towards absolute laser spectroscopic CO2 isotope ratio measurements

NASA Astrophysics Data System (ADS)

Anyangwe Nwaboh, Javis; Werhahn, Olav; Ebert, Volker

2017-04-01

Knowledge of isotope composition of carbon dioxide (CO2) in the atmosphere is necessary to identify sources and sinks of this key greenhouse gas. In the last years, laser spectroscopic techniques such as cavity ring-down spectroscopy (CRDS) and tunable diode laser absorption spectroscopy (TDLAS) have been shown to perform accurate isotope ratio measurements for CO2 and other gases like water vapour (H2O) [1,2]. Typically, isotope ratios are reported in literature referring to reference materials provided by e.g. the International Atomic Energy Agency (IAEA). However, there could be some benefit if field deployable absolute isotope ratio measurement methods were developed to address issues such as exhausted reference material like the Pee Dee Belemnite (PDB) standard. Absolute isotope ratio measurements would be particularly important for situations where reference materials do not even exist. Here, we present CRDS and TDLAS-based absolute isotope ratios (13C/12C ) in atmospheric CO2. We demonstrate the capabilities of the used methods by measuring CO2 isotope ratios in gas standards. We compare our results to values reported for the isotope certified gas standards. Guide to the expression of uncertainty in measurement (GUM) compliant uncertainty budgets on the CRDS and TDLAS absolute isotope ratio measurements are presented, and traceability is addressed. We outline the current impediments in realizing high accuracy absolute isotope ratio measurements using laser spectroscopic methods, propose solutions and the way forward. Acknowledgement Parts of this work have been carried out within the European Metrology Research Programme (EMRP) ENV52 project-HIGHGAS. The EMRP is jointly funded by the EMRP participating countries within EURAMET and the European Union. References [1] B. Kühnreich, S. Wagner, J. C. Habig,·O. Möhler, H. Saathoff, V. Ebert, Appl. Phys. B 119:177-187 (2015). [2] E. Kerstel, L. Gianfrani, Appl. Phys. B 92, 439-449 (2008).

Sex Ratio Elasticity Influences the Selection of Sex Ratio Strategy.

PubMed

Wang, Yaqiang; Wang, Ruiwu; Li, Yaotang; Sam Ma, Zhanshan

2016-12-23

There are three sex ratio strategies (SRS) in nature-male-biased sex ratio, female-biased sex ratio and, equal sex ratio. It was R. A. Fisher who first explained why most species in nature display a sex ratio of ½. Consequent SRS theories such as Hamilton's local mate competition (LMC) and Clark's local resource competition (LRC) separately explained the observed deviations from the seemingly universal 1:1 ratio. However, to the best of our knowledge, there is not yet a unified theory that accounts for the mechanisms of the three SRS. Here, we introduce the price elasticity theory in economics to define sex ratio elasticity (SRE), and present an analytical model that derives three SRSs based on the following assumption: simultaneously existing competitions for both resources A and resources B influence the level of SRE in both sexes differently. Consequently, it is the difference (between two sexes) in the level of their sex ratio elasticity that leads to three different SRS. Our analytical results demonstrate that the elasticity-based model not only reveals a highly plausible mechanism that explains the evolution of SRS in nature, but also offers a novel framework for unifying two major classical theories (i.e., LMC &LRC) in the field of SRS research.

Sex Ratio Elasticity Influences the Selection of Sex Ratio Strategy

NASA Astrophysics Data System (ADS)

Wang, Yaqiang; Wang, Ruiwu; Li, Yaotang; (Sam) Ma, Zhanshan

2016-12-01

There are three sex ratio strategies (SRS) in nature—male-biased sex ratio, female-biased sex ratio and, equal sex ratio. It was R. A. Fisher who first explained why most species in nature display a sex ratio of ½. Consequent SRS theories such as Hamilton’s local mate competition (LMC) and Clark’s local resource competition (LRC) separately explained the observed deviations from the seemingly universal 1:1 ratio. However, to the best of our knowledge, there is not yet a unified theory that accounts for the mechanisms of the three SRS. Here, we introduce the price elasticity theory in economics to define sex ratio elasticity (SRE), and present an analytical model that derives three SRSs based on the following assumption: simultaneously existing competitions for both resources A and resources B influence the level of SRE in both sexes differently. Consequently, it is the difference (between two sexes) in the level of their sex ratio elasticity that leads to three different SRS. Our analytical results demonstrate that the elasticity-based model not only reveals a highly plausible mechanism that explains the evolution of SRS in nature, but also offers a novel framework for unifying two major classical theories (i.e., LMC & LRC) in the field of SRS research.

Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD:sulfate ratios in a UASB reactor.

PubMed

Hirasawa, Julia Sumiko; Sarti, Arnaldo; Del Aguila, Nora Katia Saavedra; Varesche, Maria Bernadete A

2008-10-01

In this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0+/-0.7 mg O2 l(-1)) were analyzed using molecular biology techniques. The granules were provided by an upflow anaerobic sludge blanket (UASB) operated over 469 days and fed with synthetic substrate. Ethanol and sulfate were added to obtain different COD/SO4(2-) ratios (3.0, 2.0, and 1.6). The results of fluorescent in situ hybridization (FISH) analyses showed that archaeal cells, detected by the ARC915 probe, accounted for 77%, 84%, and 75% in the COD/SO(4)(2-) ratios (3.0, 2.0, and 1.6, respectively). Methanosaeta sp. was the predominant acetoclastic archaea observed by optical microscopy and FISH analyses, and confirmed by sequencing of the excised bands of the DGGE gel with a similarity of 96%. The sulfate-reducing bacterium Desulfovibrio vulgaris subsp. vulgaris (similarity of 99%) was verified by sequencing of the DGGE band. Others identified microorganism were similar to Shewanella sp. and Desulfitobacterium hafniense, with similarities of 95% and 99%, respectively. These results confirmed that the presence of oxygen did not severely affect the metabolism of microorganisms that are commonly considered strictly anaerobic. We obtained mean efficiencies of organic matter conversion and sulfate reducing higher than 74%.

Statistical modeling and MAP estimation for body fat quantification with MRI ratio imaging

NASA Astrophysics Data System (ADS)

Wong, Wilbur C. K.; Johnson, David H.; Wilson, David L.

2008-03-01

We are developing small animal imaging techniques to characterize the kinetics of lipid accumulation/reduction of fat depots in response to genetic/dietary factors associated with obesity and metabolic syndromes. Recently, we developed an MR ratio imaging technique that approximately yields lipid/{lipid + water}. In this work, we develop a statistical model for the ratio distribution that explicitly includes a partial volume (PV) fraction of fat and a mixture of a Rician and multiple Gaussians. Monte Carlo hypothesis testing showed that our model was valid over a wide range of coefficient of variation of the denominator distribution (c.v.: 0-0:20) and correlation coefficient among the numerator and denominator (ρ 0-0.95), which cover the typical values that we found in MRI data sets (c.v.: 0:027-0:063, ρ: 0:50-0:75). Then a maximum a posteriori (MAP) estimate for the fat percentage per voxel is proposed. Using a digital phantom with many PV voxels, we found that ratio values were not linearly related to PV fat content and that our method accurately described the histogram. In addition, the new method estimated the ground truth within +1.6% vs. +43% for an approach using an uncorrected ratio image, when we simply threshold the ratio image. On the six genetically obese rat data sets, the MAP estimate gave total fat volumes of 279 +/- 45mL, values 21% smaller than those from the uncorrected ratio images, principally due to the non-linear PV effect. We conclude that our algorithm can increase the accuracy of fat volume quantification even in regions having many PV voxels, e.g. ectopic fat depots.

An Image Processing Technique for Achieving Lossy Compression of Data at Ratios in Excess of 100:1

DTIC Science & Technology

1992-11-01

5 Lempel , Ziv , Welch (LZW) Compression ............... 7 Lossless Compression Tests Results ................. 9 Exact...since IBM holds the patent for this technique. Lempel , Ziv , Welch (LZW) Compression The LZW compression is related to two compression techniques known as... compression , using the input stream as data . This step is possible because the compression algorithm always outputs the phrase and character components of a

The High Accuracy Measurement of CO2 Mixing Ratio Profiles Using Ground Based 1.6 μm CO2-DIAL with Temperature Measurement Techniques in the Lower-Atmosphere

NASA Astrophysics Data System (ADS)

Abo, M.; Shibata, Y.; Nagasawa, C.

2017-12-01

We have developed a ground based direct detection three-wavelength 1.6 μm differential absorption lidar (DIAL) to achieve measurements of vertical CO2 concentration and temperature profiles in the atmosphere. As the spectra of absorption lines of any molecules are influenced basically by the temperature and pressure in the atmosphere, it is important to measure them simultaneously so that the better accuracy of the DIAL measurement is realized. Conventionally, we have obtained the vertical profile of absorption cross sections using the atmospheric temperature profile by the objective analysis and the atmospheric pressure profile calculated by the pressure height equation. Comparison of atmospheric pressure profiles calculated from this equation and those obtained from radiosonde observations at Tateno, Japan is consistent within 0.2 % below 3 km altitude. But the temperature dependency of the CO2 density is 0.25 %/°C near the surface. Moreover, the CO2 concentration is often evaluated by the mixing ratio. Because the air density is related by the ideal gas law, the mixing ratio is also related by the atmospheric temperature. Therefore, the temperature affects not only accuracy of CO2 concentration but the CO2 mixing ratio. In this paper, some experimental results of the simultaneous measurement of atmospheric temperature profiles and CO2 mixing ratio profiles are reported from 0.4 to 2.5 km altitude using the three-wavelength 1.6 μm DIAL system. Temperature profiles of CO2 DIAL measurement were sometimes different from those of objective analysis below 1.5 km altitude. These differences are considered to be due to regionality at the lidar site. The temperature difference of 5.0 °C corresponds to a CO2 mixing ratio difference of 8.0 ppm at 500 m altitude. This cannot be ignored in estimates of regional sources and sinks of CO2. This three-wavelength CO2 DIAL technique can estimate accurately temporal behavior of CO2 mixing ratio profiles in the lower atmosphere

A Three-dimensional Polymer Scaffolding Material Exhibiting a Zero Poisson's Ratio.

PubMed

Soman, Pranav; Fozdar, David Y; Lee, Jin Woo; Phadke, Ameya; Varghese, Shyni; Chen, Shaochen

2012-05-14

Poisson's ratio describes the degree to which a material contracts (expands) transversally when axially strained. A material with a zero Poisson's ratio does not transversally deform in response to an axial strain (stretching). In tissue engineering applications, scaffolding having a zero Poisson's ratio (ZPR) may be more suitable for emulating the behavior of native tissues and accommodating and transmitting forces to the host tissue site during wound healing (or tissue regrowth). For example, scaffolding with a zero Poisson's ratio may be beneficial in the engineering of cartilage, ligament, corneal, and brain tissues, which are known to possess Poisson's ratios of nearly zero. Here, we report a 3D biomaterial constructed from polyethylene glycol (PEG) exhibiting in-plane Poisson's ratios of zero for large values of axial strain. We use digital micro-mirror device projection printing (DMD-PP) to create single- and double-layer scaffolds composed of semi re-entrant pores whose arrangement and deformation mechanisms contribute the zero Poisson's ratio. Strain experiments prove the zero Poisson's behavior of the scaffolds and that the addition of layers does not change the Poisson's ratio. Human mesenchymal stem cells (hMSCs) cultured on biomaterials with zero Poisson's ratio demonstrate the feasibility of utilizing these novel materials for biological applications which require little to no transverse deformations resulting from axial strains. Techniques used in this work allow Poisson's ratio to be both scale-independent and independent of the choice of strut material for strains in the elastic regime, and therefore ZPR behavior can be imparted to a variety of photocurable biomaterial.

Comparison of gas chromatography/isotope ratio mass spectrometry and liquid chromatography/isotope ratio mass spectrometry for carbon stable-isotope analysis of carbohydrates.

PubMed

Moerdijk-Poortvliet, Tanja C W; Schierbeek, Henk; Houtekamer, Marco; van Engeland, Tom; Derrien, Delphine; Stal, Lucas J; Boschker, Henricus T S

2015-07-15

We compared gas chromatography/isotope ratio mass spectrometry (GC/IRMS) and liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) for the measurement of δ(13)C values in carbohydrates. Contrary to GC/IRMS, no derivatisation is needed for LC/IRMS analysis of carbohydrates. Hence, although LC/IRMS is expected to be more accurate and precise, no direct comparison has been reported. GC/IRMS with the aldonitrile penta-acetate (ANPA) derivatisation method was compared with LC/IRMS without derivatisation. A large number of glucose standards and a variety of natural samples were analysed for five neutral carbohydrates at natural abundance as well as at (13)C-enriched levels. Gas chromatography/chemical ionisation mass spectrometry (GC/CIMS) was applied to check for incomplete derivatisation of the carbohydrate, which would impair the accuracy of the GC/IRMS method. The LC/IRMS technique provided excellent precision (±0.08‰ and ±3.1‰ at natural abundance and enrichment levels, respectively) for the glucose standards and this technique proved to be superior to GC/IRMS (±0.62‰ and ±19.8‰ at natural abundance and enrichment levels, respectively). For GC/IRMS measurements the derivatisation correction and the conversion of carbohydrates into CO2 had a considerable effect on the measured δ(13)C values. However, we did not find any significant differences in the accuracy of the two techniques over the full range of natural δ(13)C abundances and (13)C-labelled glucose. The difference in the performance of GC/IRMS and LC/IRMS diminished when the δ(13)C values were measured in natural samples, because the chromatographic performance and background correction became critical factors, particularly for LC/IRMS. The derivatisation of carbohydrates for the GC/IRMS method was complete. Although both LC/IRMS and GC/IRMS are reliable techniques for compound-specific stable carbon isotope analysis of carbohydrates (provided that derivatisation is complete and the

Synthesis of high aspect ratio ZnO nanowires with an inexpensive handcrafted electrochemical setup

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

Taheri, Ali, E-mail: at1361@aut.ac.ir, E-mail: atahery@aeoi.org.ir; Saramad, Shahyar; Setayeshi, Saeed

In this work, high aspect ratio zinc oxide nanowires are synthesized using templated one-step electrodeposition technique. Electrodeposition of the nanowires is done using a handcrafted electronic system. Nuclear track-etched polycarbonate membrane is used as a template to form the high aspect ratio nanowires. The result of X-ray diffraction and scanning electron microscopy shows that nanowires with a good crystallinity and an aspect ratio of more than 30 can be achieved in a suitable condition. The height of electrodeposited nanowires reaches to about 11 μm. Based on the obtained results, high aspect ratio ZnO nanowires can be formed using inexpensive electrodepositionmore » setup with an acceptable quality.« less

A review on the determination of isotope ratios of boron with mass spectrometry.

PubMed

Aggarwal, Suresh Kumar; You, Chen-Feng

2017-07-01

The present review discusses different mass spectrometric techniques-viz, thermal ionization mass spectrometry (TIMS), inductively coupled plasma mass spectrometry (ICPMS), and secondary ion mass spectrometry (SIMS)-used to determine 11 B/ 10 B isotope ratio, and concentration of boron required for various applications in earth sciences, marine geochemistry, nuclear technology, environmental, and agriculture sciences, etc. The details of the techniques-P-TIMS, which uses Cs 2 BO 2 + , N-TIMS, which uses BO 2 - , and MC-ICPMS, which uses B + ions for bulk analysis or B - and B + ions for in situ micro-analysis with SIMS-are highlighted. The capabilities, advantages, limitations, and problems in each mass spectrometric technique are summarized. The results of international interlaboratory comparison experiments conducted at different times are summarized. The certified isotopic reference materials available for boron are also listed. Recent developments in laser ablation (LA) ICPMS and QQQ-ICPMS for solids analysis and MS/MS analysis, respectively, are included. The different aspects of sample preparation and analytical chemistry of boron are summarized. Finally, the future requirements of boron isotope ratios for future applications are also given. Presently, MC-ICPMS provides the best precision and accuracy (0.2-0.4‰) on isotope ratio measurements, whereas N-TIMS holds the potential to analyze smallest amount of boron, but has the issue of bias (+2‰ to 4‰) which needs further investigations. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:499-519, 2017. © 2016 Wiley Periodicals, Inc.

Calibration Technique for Polarization-Sensitive Lidars

NASA Technical Reports Server (NTRS)

Alvarez, J. M.; Vaughan, M. A.; Hostetler, C. A.; Hung, W. H.; Winker, D. M.

2006-01-01

Polarization-sensitive lidars have proven to be highly effective in discriminating between spherical and non-spherical particles in the atmosphere. These lidars use a linearly polarized laser and are equipped with a receiver that can separately measure the components of the return signal polarized parallel and perpendicular to the outgoing beam. In this work we describe a technique for calibrating polarization-sensitive lidars that was originally developed at NASA s Langley Research Center (LaRC) and has been used continually over the past fifteen years. The procedure uses a rotatable half-wave plate inserted into the optical path of the lidar receiver to introduce controlled amounts of polarization cross-talk into a sequence of atmospheric backscatter measurements. Solving the resulting system of nonlinear equations generates the system calibration constants (gain ratio, G, and offset angle, theta) required for deriving calibrated measurements of depolarization ratio from the lidar signals. In addition, this procedure also determines the mean depolarization ratio within the region of the atmosphere that is analyzed. Simulations and error propagation studies show the method to be both reliable and well behaved. Operational details of the technique are illustrated using measurements obtained as part of Langley Research Center s participation in the First ISCCP Regional Experiment (FIRE).

Does the Mother or Father Determine the Offspring Sex Ratio? Investigating the Relationship between Maternal Digit Ratio and Offspring Sex Ratio

PubMed Central

Kim, Tae Beom; Oh, Jin Kyu; Kim, Kwang Taek; Yoon, Sang Jin; Kim, Soo Woong

2015-01-01

Objective In mammals, high parental testosterone levels present around the time of conception are thought to skew offspring sex ratio toward sons. The second to fourth digit ratio (digit ratio) is now widely accepted as a negative correlate of prenatal testosterone. Thus, we investigated the association between digit ratio and offspring sex ratio. Methods A total of 508 Korean patients (257 males and 251 females) less than 60 years old who had one or more offspring were prospectively enrolled. The lengths of the 2nd and 4th digits of the right hand were measured by a single investigator using a digital vernier calliper. Next, the patients’ lifetime offspring birth sex ratios were investigated. Results Maternal (rather than paternal) digit ratio was significantly associated with the number of sons (r = -0.153, p = 0.015), number of daughters (r = 0.130, p = 0.039), and offspring sex ratio (r = -0.171, p = 0.007). And, the maternal digit ratio was a significant factor for predicting offspring sex ratio (B = -1.620, p = 0.008) on multiple linear regression analysis. The female patients with a lower digit ratio (< 0.95) were found to have a higher offspring sex ratio (0.609 versus 0.521, p = 0.046) compared to those with a higher digit ratio (≥ 0.95). Furthermore, females in the low digit ratio group have a probability 1.138 greater of having sons than females in the high digit ratio group. Conclusions Maternal digit ratio was negatively associated with offspring sex ratio. Females with a lower digit ratio were more likely to have more male offspring compared to those with a higher digit ratio. Thus, our results suggest that the sex of offspring might be more influenced by maternal rather than paternal factors. PMID:26575995

Manufacture of high aspect ratio micro-pillar wall shear stress sensor arrays

NASA Astrophysics Data System (ADS)

Gnanamanickam, Ebenezer P.; Sullivan, John P.

2012-12-01

In the field of experimental fluid mechanics the measurement of unsteady, distributed wall shear stress has proved historically challenging. Recently, sensors based on an array of flexible micro-pillars have shown promise in carrying out such measurements. Similar sensors find use in other applications such as cellular mechanics. This work presents a manufacturing technique that can manufacture micro-pillar arrays of high aspect ratio. An electric discharge machine (EDM) is used to manufacture a micro-drilling tool. This micro-drilling tool is used to form holes in a wax sheet which acts as the mold for the micro-pillar array. Silicone rubber is cast in these molds to yield a micro-pillar array. Using this technique, micro-pillar arrays with a maximum aspect ratio of about 10 have been manufactured. Manufacturing issues encountered, steps to alleviate them and the potential of the process to manufacture similar micro-pillar arrays in a time-efficient manner are also discussed.

Ratioed scatter diagrams - An erotetic method for phase identification on complex surfaces using scanning Auger microscopy

NASA Technical Reports Server (NTRS)

Browning, R.

1984-01-01

By ratioing multiple Auger intensities and plotting a two-dimensional occupational scatter diagram while digitally scanning across an area, the number and elemental association of surface phases can be determined. This can prove a useful tool in scanning Auger microscopic analysis of complex materials. The technique is illustrated by results from an anomalous region on the reaction zone of a SiC/Ti-6Al-4V metal matrix composite material. The anomalous region is shown to be a single phase associated with sulphur and phosphorus impurities. Imaging of a selected phase from the ratioed scatter diagram is possible and may be a useful technique for presenting multiple scanning Auger images.

Effect of aspect ratio and deformability on nanoparticle extravasation through nanopores.

PubMed

Kersey, Farrell R; Merkel, Timothy J; Perry, Jillian L; Napier, Mary E; DeSimone, Joseph M

2012-06-12

We describe the fabrication of filamentous hydrogel nanoparticles using a unique soft lithography based particle molding process referred to as PRINT (particle replication in nonwetting templates). The nanoparticles possess a constant width of 80 nm, and we varied their lengths ranging from 180 to 5000 nm. In addition to varying the aspect ratio of the particles, the deformability of the particles was tuned by varying the cross-link density within the particle matrix. Size characteristics such as hydrodynamic diameter and persistence length of the particles were analyzed using dynamic light scattering and electron microscopy techniques, respectively, while particle deformability was assessed by atomic force microscopy. Additionally, the ability of the particles to pass through membranes containing 0.2 μm pores was assessed by means of a simple filtration technique, and particle recovery was determined using fluorescence spectroscopy. The results show that particle recovery is mostly independent of aspect ratio at all cross-linker concentrations utilized, with the exception of 96 wt % PEG diacrylate 80 × 5000 nm particles, which showed the lowest percent recovery.

Measurement of the absorption coefficient using the sound-intensity technique

NASA Technical Reports Server (NTRS)

Atwal, M.; Bernhard, R.

1984-01-01

The possibility of using the sound intensity technique to measure the absorption coefficient of a material is investigated. This technique measures the absorption coefficient by measuring the intensity incident on the sample and the net intensity reflected by the sample. Results obtained by this technique are compared with the standard techniques of measuring the change in the reverberation time and the standing wave ratio in a tube, thereby, calculating the random incident and the normal incident adsorption coefficient.

Techniques and results of nongame bird monitoring in North America

USGS Publications Warehouse

Robbins, C.S.; Bystrak, D.; Geissler, P.H.; Oelke, H.

1980-01-01

Long-term bird population trends based on accumulated ratios (proportional change) sometimes give a very misleading view of population change. Alternate methods of representing population change, based on the weighted means for the individual years, avoid the dangers of using ratios. Some advantages and disadvantages of various weighting techniques are discussed.

Y-chromosome specific alleles and haplotypes in European and Asian populations: linkage disequilibrium and geographic diversity.

PubMed

Mitchell, R J; Earl, L; Fricke, B

1997-10-01

Variation on the Y chromosome may permit our understanding the evolution of the human paternal lineage and male gene flow. This study reports upon the distribution and non random association of alleles at four Y-chromosome specific loci in four populations, three Caucasoid (Italian, Greek and Slav) and one Asian. The markers include insertion/deletion (p12f), point mutation (92R7 and pY alpha I), and repeat sequence (p21A1) polymorphisms. Our data confirm that the p12f/TaqI 8 kb allele is a Caucasoid marker and that Asians are monomorphic at three of the loci (p12f, 92R7, and pY alpha I). The alleles at 92R7 and pY alpha I were found to be in complete disequilibrium in Europeans. Y-haplotype diversity was highly significant between Asians and all three European groups (P < 0.001), but the Greeks and Italians were also significantly different with respect to some alleles and haplotypes (P < 0.02). We find strong evidence that the p12f/TaqI 8 kb allele may have arisen only once, as a deletion event, and, additionally, that the present-day frequency distribution of Y chromosomes carrying the p12f/8 kb allele suggests that it may have been spread by colonising sea-faring peoples from the Near East, possibly the Phoenicians, rather than by expansion of Neolithic farmers into continental Europe. The p12f deletion is the key marker of a unique Y chromosome, found only in Caucasians to date, labelled 'Mediterranean' and this further increases the level of Y-chromosome diversity seen among Caucasoids when compared to the other major population groups.

Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers

PubMed Central

Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

2011-01-01

Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r2>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5–10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5∼25 cM) compared to landraces (<5∼15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources. PMID:21365016

Towards a framework for testing general relativity with extreme-mass-ratio-inspiral observations

NASA Astrophysics Data System (ADS)

Chua, A. J. K.; Hee, S.; Handley, W. J.; Higson, E.; Moore, C. J.; Gair, J. R.; Hobson, M. P.; Lasenby, A. N.

2018-07-01

Extreme-mass-ratio-inspiral observations from future space-based gravitational-wave detectors such as LISA will enable strong-field tests of general relativity with unprecedented precision, but at prohibitive computational cost if existing statistical techniques are used. In one such test that is currently employed for LIGO black hole binary mergers, generic deviations from relativity are represented by N deformation parameters in a generalized waveform model; the Bayesian evidence for each of its 2N combinatorial submodels is then combined into a posterior odds ratio for modified gravity over relativity in a null-hypothesis test. We adapt and apply this test to a generalized model for extreme-mass-ratio inspirals constructed on deformed black hole spacetimes, and focus our investigation on how computational efficiency can be increased through an evidence-free method of model selection. This method is akin to the algorithm known as product-space Markov chain Monte Carlo, but uses nested sampling and improved error estimates from a rethreading technique. We perform benchmarking and robustness checks for the method, and find order-of-magnitude computational gains over regular nested sampling in the case of synthetic data generated from the null model.

Towards a framework for testing general relativity with extreme-mass-ratio-inspiral observations

NASA Astrophysics Data System (ADS)

Chua, A. J. K.; Hee, S.; Handley, W. J.; Higson, E.; Moore, C. J.; Gair, J. R.; Hobson, M. P.; Lasenby, A. N.

2018-04-01

Extreme-mass-ratio-inspiral observations from future space-based gravitational-wave detectors such as LISA will enable strong-field tests of general relativity with unprecedented precision, but at prohibitive computational cost if existing statistical techniques are used. In one such test that is currently employed for LIGO black-hole binary mergers, generic deviations from relativity are represented by N deformation parameters in a generalised waveform model; the Bayesian evidence for each of its 2N combinatorial submodels is then combined into a posterior odds ratio for modified gravity over relativity in a null-hypothesis test. We adapt and apply this test to a generalised model for extreme-mass-ratio inspirals constructed on deformed black-hole spacetimes, and focus our investigation on how computational efficiency can be increased through an evidence-free method of model selection. This method is akin to the algorithm known as product-space Markov chain Monte Carlo, but uses nested sampling and improved error estimates from a rethreading technique. We perform benchmarking and robustness checks for the method, and find order-of-magnitude computational gains over regular nested sampling in the case of synthetic data generated from the null model.

Predicting intrapartum fetal compromise using the fetal cerebro-umbilical ratio.

PubMed

Sabdia, S; Greer, R M; Prior, T; Kumar, S

2015-05-01

The aim of this study was to explore the association between the cerebro-umbilical ratio measured at 35-37 weeks and intrapartum fetal compromise. This retrospective cross sectional study was conducted at the Mater Mothers' Hospital in Brisbane, Australia. Maternal demographics and fetal Doppler indices at 35-37 weeks gestation for 1381 women were correlated with intrapartum and neonatal outcomes. Babies born by caesarean section or instrumental delivery for fetal compromise had the lowest median cerebro-umbilical ratio 1.60 (IQR 1.22-2.08) compared to all other delivery groups (vaginal delivery, emergency delivery for failure to progress, emergency caesarean section for other reasons or elective caesarean section). The percentage of infants with a cerebro-umbilical ratio <10th centile that required emergency delivery (caesarean section or instrumental delivery) for fetal compromise was 22%, whereas only 7.3% of infants with a cerebro-umbilical ratio between the 10th-90th centile and 9.6% of infants with a cerebro-umbilical ratio > 90th centile required delivery for the same indication (p < 0.001). A lower cerebro-umbilical ratio was associated with an increased risk of emergency delivery for fetal compromise, OR 2.03 (95% CI 1.41-2.92), p < 0.0001. This study suggests that a low fetal cerebro-umbilical ratio measured at 35-37 weeks is associated with a greater risk of intrapartum compromise. This is a relatively simple technique which could be used to risk stratify women in diverse healthcare settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Precise and accurate isotope ratio measurements by ICP-MS.

PubMed

Becker, J S; Dietze, H J

2000-09-01

The precise and accurate determination of isotope ratios by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) is important for quite different application fields (e.g. for isotope ratio measurements of stable isotopes in nature, especially for the investigation of isotope variation in nature or age dating, for determining isotope ratios of radiogenic elements in the nuclear industry, quality assurance of fuel material, for reprocessing plants, nuclear material accounting and radioactive waste control, for tracer experiments using stable isotopes or long-lived radionuclides in biological or medical studies). Thermal ionization mass spectrometry (TIMS), which used to be the dominant analytical technique for precise isotope ratio measurements, is being increasingly replaced for isotope ratio measurements by ICP-MS due to its excellent sensitivity, precision and good accuracy. Instrumental progress in ICP-MS was achieved by the introduction of the collision cell interface in order to dissociate many disturbing argon-based molecular ions, thermalize the ions and neutralize the disturbing argon ions of plasma gas (Ar+). The application of the collision cell in ICP-QMS results in a higher ion transmission, improved sensitivity and better precision of isotope ratio measurements compared to quadrupole ICP-MS without the collision cell [e.g., for 235U/238U approximately 1 (10 microg x L(-1) uranium) 0.07% relative standard deviation (RSD) vs. 0.2% RSD in short-term measurements (n = 5)]. A significant instrumental improvement for ICP-MS is the multicollector device (MC-ICP-MS) in order to obtain a better precision of isotope ratio measurements (with a precision of up to 0.002%, RSD). CE- and HPLC-ICP-MS are used for the separation of isobaric interferences of long-lived radionuclides and stable isotopes by determination of spallation nuclide abundances in an irradiated tantalum target.

Effects of modification of in vitro fertilization techniques on the sex ratio of the resultant bovine embryos.

PubMed

Iwata, H; Shiono, H; Kon, Y; Matsubara, K; Kimura, K; Kuwayama, T; Monji, Y

2008-05-01

The duration of sperm-oocyte co-incubation has been observed to affect the sex ratio of in vitro produced bovine embryos. The purpose of this study was to investigate some factors that may be responsible for the skewed sex ratio. The factors studied were selected combinations of the duration of co-incubation, the presence or absence of cumulus cells, and the level of hyaluronic acid (HA) in the culture medium. Experiment 1 examined the effect of selected combinations of different factors during the fertilization phase of in vitro oocyte culture. The factors were the nature of the sperm or its treatment, the duration of the sperm-oocyte co-incubation, and the level of hyaluronic acid in the culture medium. In experiment 2, the capacitation of frozen-thawed-Percoll-washed sperm (control), pre-incubated, and non-binding sperm was evaluated by the zona pellucida (ZP) binding assay and the hypo-osmotic swelling test (HOST). The purpose of experiment 3 was to determine the oocyte cleavage rate and sex ratio of the embryos (>5 cells) produced as a consequence of the 10 treatments used in experiment 1. In treatments 1-3 (experiments 1 and 3) COC were co-cultured with sperm for 1, 5 or 18 h. Polyspermic fertilization rose as the co-incubation period increased (1 h 6.5%, 5 h 15.9%, 18 h 41.8%; P<0.05), and the highest rate of normal fertilization was observed for 5h culture (73.4%; P<0.05). The sex ratio was significantly (P<0.05) skewed from the expected 50:50 towards males following 1 h (64.4%) and 5 h (67.3%) co-incubation, but was not affected by 18 h incubation (52.3%). In treatment 4, sperm was pre-incubated for 1h and cultured with COC for 5 h. Relative to control sperm, pre-incubation of sperm increased ZP binding (116 versus 180 per ZP; P<0.05) and decreased the proportion of HOST positive sperm (65.8-48.6%; P<0.05; experiment 2). Pre-incubation did not affect the rates of polyspermy, normal fertilization or the sex ratio of the embryos (experiments 1 and 3). The

Effects of acidification on the isotopic ratios of Neotropical otter tooth dentin.

PubMed

Carrasco, Thayara S; Botta, Silvina; Machado, Rodrigo; Colares, Elton P; Secchi, Eduardo R

2018-05-30

Stable carbon and nitrogen isotope ratios are widely used in ecological studies providing important information on the trophic ecology and habitat use of consumers. However, some factors may lead to isotopic variability, which makes difficult the interpretation of data, such as the presence of inorganic carbon in mineralized tissues. In order to remove the inorganic carbon, acidification is a commonly used treatment. The effects of two methods of acidification were tested: (i) dentin acidification with 10% HCl using the 'drop-by-drop' technique, and (ii) dentin acidification in an 'HCl atmosphere', by exposing the dentin to vaporous 30% hydrochloric acid. Results were compared with untreated subsamples. The stable carbon and nitrogen ratios of untreated and acidified subsamples were measured using an elemental analyzer coupled to an isotope ratio mass spectrometer. The nitrogen isotopic ratios were statistically different between the two acidification treatments, but no significant changes in carbon isotopic ratios were found in acidified and untreated samples. The results indicated that acidification had no effect on carbon isotopic ratios of Neotropical otter tooth dentin, while introducing a source of error in nitrogen isotopic ratios. Therefore, we conclude that acidification is an unnecessary step for C and N stable isotope analysis. Copyright © 2018 John Wiley & Sons, Ltd.

Fourier-transform infrared derivative spectroscopy with an improved signal-to-noise ratio.

PubMed

Fetterman, M R

2005-09-01

Infrared derivative spectroscopy is a useful technique for finding peaks hidden in broad spectral features. A data acquisition technique is shown that will improve the signal-to-noise ratio (SNR) of Fourier-transform infrared (FTIR) derivative spectroscopy. Typically, in a FTIR measurement one samples each point for the same time interval. The effect of using a graded time interval is studied. The simulations presented show that the SNR of first-derivative FTIR spectroscopy will improve by 15% and that the SNR of second-derivative FTIR will improve by 34%.

Comparison of dual and single exposure techniques in dual-energy chest radiography.

PubMed

Ho, J T; Kruger, R A; Sorenson, J A

1989-01-01

Conventional chest radiography is the most effective tool for lung cancer detection and diagnosis; nevertheless, a high percentage of lung cancer tumors are missed because of the overlap of lung nodule image contrast with bone image contrast in a chest radiograph. Two different energy subtraction strategies, dual exposure and single exposure techniques, were studied for decomposing a radiograph into bone-free and soft tissue-free images to address this problem. For comparing the efficiency of these two techniques in lung nodule detection, the performances of the techniques were evaluated on the basis of residual tissue contrast, energy separation, and signal-to-noise ratio. The evaluation was based on both computer simulation and experimental verification. The dual exposure technique was found to be better than the single exposure technique because of its higher signal-to-noise ratio and greater residual tissue contrast. However, x-ray tube loading and patient motion are problems.

What Happens When a Teacher's Science Belief Structure Is in Disequilibrium? Entangled Nature of Beliefs and Practice

NASA Astrophysics Data System (ADS)

Martin, Anita; Park, Soonhye; Hand, Brian

2017-08-01

This qualitative case study examined the process of change in an experienced elementary teacher's belief structure during implementation of an inquiry-based science program. Difficulties generally associated with ascertaining beliefs were minimized by using Leatham's (Journal of Mathematics Teacher Education, 9, 91-102 (2006) Sensible System Framework, enabling researchers to obtain rich descriptions of the teacher's belief structure by focusing on words (professed beliefs), intentions (intended beliefs), and actions (enacted beliefs). Models were constructed of the teacher's belief structure before and after implementation of the Science Writing Heuristic (SWH) approach (Hand et al. International Journal of Science Education, 26(2), 131-149, 2004), an inquiry-based approach to teaching science. Key beliefs for this teacher were related to how students learn, goals for teaching science, focus of instruction, and roles of teacher and student. Ultimately, the teacher shifted her professed, intended, and enacted beliefs resulting in a shift from a teacher-centered to a student-centered classroom. Findings support Thagard's Coherence Theory of Justification (2002), positing that change in one belief creates a state of disequilibrium that must be alleviated by changing/realigning other beliefs in order to re-establish coherence in the overall belief structure. This research focus is distinct from the general trend in teacher beliefs research in important ways. Most significant is that this study was not focused on the traditional two lists—those beliefs that were consistent with practice and those that were inconsistent with practice—but instead focused on the entwined nature of beliefs and practice and have shown that a teacher's practice can be viewed as their enacted beliefs, an integral part of the teacher's overall belief structure.

Identification of a Linkage Disequilibrium Block in Chromosome 1q Associated With BMD in Premenopausal White Women

PubMed Central

Ichikawa, Shoji; Koller, Daniel L; Curry, Leah R; Lai, Dongbing; Xuei, Xiaoling; Pugh, Elizabeth W; Tsai, Ya-Yu; Doheny, Kimberly F; Edenberg, Howard J; Hui, Siu L; Foroud, Tatiana; Peacock, Munro; Econs, Michael J

2008-01-01

Osteoporosis is a complex disease with both genetic and environmental risk factors. A major determinant of osteoporotic fractures is peak BMD obtained during young adulthood. We previously reported linkage of chromosome 1q (LOD = 4.3) with variation in spinal areal BMD in healthy premenopausal white women. In this study, we used a two-stage genotyping approach to identify genes in the linked region that contributed to the variation of femoral neck and lumbar spine areal BMD. In the first stage, 654 SNPs across the linked region were genotyped in a sample of 1309 premenopausal white women. The most significant evidence of association for lumbar spine (p = 1.3 × 10−6) was found with rs1127091 in the GATAD2B gene. In the second stage, 52 SNPs around this candidate gene were genotyped in an expanded sample of 1692 white women. Significant evidence of association with spinal BMD (p < 10−5), and to a lesser extent with femoral neck BMD, was observed with eight SNPs within a single 230-kb linkage disequilibrium (LD) block. The most significant SNP (p = 3.4 × 10−7) accounted for >2.5% of the variation in spinal BMD in these women. The 230-kb LD block contains 11 genes, but because of the extensive LD, the specific gene(s) contributing to the variation in BMD could not be determined. In conclusion, the significant association between spinal BMD and SNPs in the 230-kb LD block in chromosome 1q indicates that genetic factor(s) in this block plays an important role in peak spinal BMD in healthy premenopausal white women. PMID:18505370

Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

PubMed Central

Farmer, Andrew D.; Huang, Wei; Ambachew, Daniel; Penmetsa, R. Varma; Carrasquilla-Garcia, Noelia; Assefa, Teshale; Cannon, Steven B.

2018-01-01

Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel. A whole genome genetic map was created that covered all eleven linkage groups (LG). The LGs were linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length in total was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as the use of gene-based markers. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters. LD levels were found to be stronger within the Mesoamerican genepool and decay more rapidly within the Andean genepool. The recombination rate across the genome was 2.13 cM / Mb but R was found to be highly repressed around centromeres and frequent outside peri-centromeric regions. These results have important implications for association and genetic mapping or crop improvement in common bean. PMID:29522524

An Association Between Functional Polymorphisms of the Interleukin 1 Gene Complex and Schizophrenia Using Transmission Disequilibrium Test.

PubMed

Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Pawlak, Joanna; Dmitrzak-Weglarz, Monika; Szczepankiewicz, Aleksandra; Zaremba, Dorota; Twarowska-Hauser, Joanna

2016-12-01

IL1 gene complex has been implicated in the etiology of schizophrenia. To assess whether IL1 gene complex is associated with susceptibility to schizophrenia in Polish population we conducted family-based study. Functional polymorphisms from IL1A (rs1800587, rs17561, rs11677416), IL1B (rs1143634, rs1143643, rs16944, rs4848306, rs1143623, rs1143633, rs1143627) and IL1RN (rs419598, rs315952, rs9005, rs4251961) genes were genotyped in 143 trio with schizophrenia. Statistical analysis was performed using transmission disequilibrium test. We have found a trend toward an association of rs1143627, rs16944, rs1143623 in IL1B gene with the risk of schizophrenia. Our results show a protective effect of allele T of rs4251961 in IL1RN against schizophrenia. We also performed haplotype analysis of IL1 gene complex and found a trend toward an association with schizophrenia of GAGG haplotype (rs1143627, rs16944, rs1143623, rs4848306) in IL1B gene, haplotypes: TG (rs315952, rs9005) and TT (rs4251961, rs419598) in IL1RN. Haplotype CT (rs4251961, rs419598) in IL1RN was found to be associated with schizophrenia. After correction for multiple testing associations did not reach significance level. Our results might support theory that polymorphisms of interleukin 1 complex genes (rs1143627, rs16944, rs1143623, rs4848306 in IL1B gene and rs4251961, rs419598, rs315952, rs9005 in IL1RN gene) are involved in the pathogenesis of schizophrenia, however, none of the results reach significance level after correction for multiple testing.

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

PubMed Central

Nimmakayala, Padma; Abburi, Venkata L.; Saminathan, Thangasamy; Almeida, Aldo; Davenport, Brittany; Davidson, Joshua; Reddy, C. V. Chandra Mohan; Hankins, Gerald; Ebert, Andreas; Choi, Doil; Stommel, John; Reddy, Umesh K.

2016-01-01

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9–2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers. PMID:27857720

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms.

PubMed

Nimmakayala, Padma; Abburi, Venkata L; Saminathan, Thangasamy; Almeida, Aldo; Davenport, Brittany; Davidson, Joshua; Reddy, C V Chandra Mohan; Hankins, Gerald; Ebert, Andreas; Choi, Doil; Stommel, John; Reddy, Umesh K

2016-01-01

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum , indicating a population bottleneck during domestication of C. baccatum . In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum , 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index ( F ST ) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9-2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.

Evaluation of neonatal brain myelination using the T1- and T2-weighted MRI ratio.

PubMed

Soun, Jennifer E; Liu, Michael Z; Cauley, Keith A; Grinband, Jack

2017-09-01

To validate the T1- and T2-weighted (T1w/T2w) MRI ratio technique in evaluating myelin in the neonatal brain. T1w and T2w MR images of 10 term neonates with normal-appearing brain parenchyma were obtained from a single 1.5 Tesla MRI and retrospectively analyzed. T1w/T2w ratio images were created with a postprocessing pipeline and qualitatively compared with standard clinical sequences (T1w, T2w, and apparent diffusion coefficient [ADC]). Quantitative assessment was also performed to assess the ratio technique in detecting areas of known myelination (e.g., posterior limb of the internal capsule) and very low myelination (e.g., optic radiations) using linear regression analysis and the Michelson Contrast equation, a measure of luminance contrast intensity. The ratio image provided qualitative improvements in the ability to visualize regional variation in myelin content of neonates. Linear regression analysis demonstrated a significant inverse relationship between the ratio intensity values and ADC values in the posterior limb of the internal capsule and the optic radiations (R 2  = 0.96 and P < 0.001). The Michelson Contrast equation showed that contrast differences between these two regions for the ratio images were 1.6 times higher than T1w, 2.6 times higher than T2w, and 1.8 times higher than ADC (all P < 0.001). Finally, the ratio improved visualization of the corticospinal tract, one of the earliest myelinated pathways. The T1w/T2w ratio accentuates contrast between myelinated and less myelinated structures and may enhance our diagnostic ability to detect myelination patterns in the neonatal brain. 2 Technical Efficacy: Stage2 J. MAGN. RESON. IMAGING 2017;46:690-696. © 2016 International Society for Magnetic Resonance in Medicine.

Genetic diversity and linkage disequilibrium in the chemokine receptor CCR2-CCR5 region among individuals and populations

PubMed Central

Lawhorn, Collene; Yuferov, Vadim; Randesi, Matthew; Ho, Ann; Morgello, Susan; Kreek, Mary Jeanne; Levran, Orna

2013-01-01

Background Chemokine receptors CCR2 and CCR5 play a key role in immune and inflammatory responses and have been associated with several diseases, including AIDS. In order to comprehend health disparities it is important to understand the nature of genetic variation in specific genes of interest in different populations. Current studies of the CCR2 and CCR5 receptor genes are primarily focused on the CCR5-Δ32, and CCR2-V64I SNPs. Methods Sanger sequencing was used to sequence the regions containing 16 SNPs in the adjacent CCR2 and CCR5 genes (including CCR5-Δ32, and CCR2-V64I) in 249 subjects of African, European and Hispanic ancestry. Linkage disequilibrium (LD) and haplotypes were determined using Haploview. Results The data revealed large differences in allele frequencies of several SNPs and LD patterns among the ethnic groups, including SNPs that were restricted to Africans or Europeans. Seven known CCR5 haplotypes and six novel CCR2 haplotypes were identified. A rare case of an HIV+ subject with the CCR5-Δ32/Δ32 was identified. Conclusions These data demonstrate a LD between CCR2 and CCR5 at several loci and provide new information about CCR2 that contributes to our understanding of its population-specific genetic variability. The data indicate that in addition to CCR5-Δ32 and CCR2-V64I, other SNPs and haplotypes may be important genetic determinants of disease and should be investigated. PMID:24011637

Prevalence odds ratio versus prevalence ratio: choice comes with consequences.

PubMed

Tamhane, Ashutosh R; Westfall, Andrew O; Burkholder, Greer A; Cutter, Gary R

2016-12-30

Odds ratio, risk ratio, and prevalence ratio are some of the measures of association which are often reported in research studies quantifying the relationship between an independent variable and the outcome of interest. There has been much debate on the issue of which measure is appropriate to report depending on the study design. However, the literature on selecting a particular category of the outcome to be modeled and/or change in reference group for categorical independent variables and the effect on statistical significance, although known, is scantly discussed nor published with examples. In this article, we provide an example of a cross-sectional study wherein prevalence ratio was chosen over (Prevalence) odds ratio and demonstrate the analytic implications of the choice of category to be modeled and choice of reference level for independent variables. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

On the Composition of Young, Directly Imaged Giant Planets

NASA Technical Reports Server (NTRS)

Moses, J. I.; Marley, M. S.; Zahnle, K.; Line, M. R.; Fortney, J. J.; Barman, T. S.; Visscher, C.; Lewis, N. K.; Wolff, M. J.

2016-01-01

The past decade has seen significant progress on the direct detection and characterization of young, self-luminous giant planets at wide orbital separations from their host stars. Some of these planets show evidence for disequilibrium processes like transport-induced quenching in their atmospheres; photochemistry may also be important, despite the typically large orbital distances. Disequilibrium chemical processes such as these can alter the expected composition, spectral behavior, thermal structure, and cooling history of the planets, and can potentially confuse determinations of bulk elemental ratios, which provide important insights into planet-formation mechanisms. Using a thermo/photochemical kinetics and transport model, we investigate the extent to which disequilibrium chemical processes affect the composition and spectra of directly imaged giant exoplanets. Results for specific "young Jupiters" such as HR 8799 b and c and 51 Eri b are presented, as are general trends as a function of planetary effective temperature, surface gravity, incident ultraviolet flux, and strength of deep atmospheric convection. We find that quenching is very important on young Jupiters, leading to CO/CH4 and N2/NH3 ratios much greater than; and H2O mixing ratios a factor of a few less than chemical equilibrium predictions. Photochemistry can also be important on such planets, with CO2 and HCN being key photochemical products. Carbon dioxide becomes a particularly major constituent when stratospheric temperatures are low and recycling of water following H2O photolysis becomes stifled. Young Jupiters with effective temperatures less than 700 degrees Kelvin are in a particularly interesting photochemical regime that differs from both transiting hot Jupiters and our own solar-system giant planets.

Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

PubMed

Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J; Xiao, Yingjie; Liu, Kede

2016-01-01

High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.

Drop Axis Ratio Distributions in Stratiform and Convective Rain

NASA Technical Reports Server (NTRS)

Thurai, M.; Bringi, V. N.; Petersen, W. A.; Schultz, C.

2010-01-01

A fully calibrated low profile 2D video disdrometer (2DVD) has been recording many different rainfall events in Northern Alabama (USA) since June 2007. An earlier publication reported drop shapes and axis ratio distributions determined for some of the events. For one of the cases examined, a noticeable shift in the 3.5 - 3.75 mm drop axis ratio distribution was noted. In this paper, we extend the earlier work by separating the 2DVD measurements into stratiform and convective rain. The separation is made possible by using the minute-by-minute drop size distribution (DSD) measured by the 2DVD. The 1-minute DSDs are fitted to a gamma distribution, and using a simple indexing technique which involves two of the fitted parameters, periods of convective and stratiform rain are separated for a given event. The output of the DSD indexing technique is qualitatively confirmed by comparing with simultaneous time series observations from a co-located UHF profiler which continuously records height profiles of reflectivity, Doppler mean and spectral width, all of which enable the identification of bright-band periods and, furthermore, periods of moderate and deep convection. Excellent consistency is found between the output of the DSD-based separation method and the profiler observations. Next, we utilize the output of DSD index-based separation method to flag the periods of severe convection for a given event. Drop axis ratios during the flagged periods are derived and compared with those during stratiform rain periods. Five cases have been considered. Axis ratio distributions do not show appreciable differences between stratiform and convective periods for four of the cases. The fifth case (the same case as reported earlier) shows a shift in the 3.5 - 3.75 mm drop axis ratios during a prolonged period of convection. The contoured shapes for these drops determined from the 2DVD camera data indicate the possibility of non-axisymmetric oscillations, compared with the contoured

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep.

PubMed

Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric

2015-11-24

Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This

Energy Balance Bowen Ratio Station (EBBR) Handbook

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

Cook, DR

2011-02-23

The energy balance Bowen ratio (EBBR) system produces 30-minute estimates of the vertical fluxes of sensible and latent heat at the local surface. Flux estimates are calculated from observations of net radiation, soil surface heat flux, and the vertical gradients of temperature and relative humidity (RH). Meteorological data collected by the EBBR are used to calculate bulk aerodynamic fluxes, which are used in the Bulk Aerodynamic Technique (BA) EBBR value-added product (VAP) to replace sunrise and sunset spikes in the flux data. A unique aspect of the system is the automatic exchange mechanism (AEM), which helps to reduce errors frommore » instrument offset drift.« less

Non-linearity of the response accommodative convergence to accommodation ratio.

PubMed

Johnston, Miriam S; Firth, Alison Y

2013-09-01

Previous studies have reported variation in stimulus accommodative convergence to accommodation (AC/A) ratio across differing accommodative stimuli. Response AC/A ratio was assessed across 4 accommodative demands to determine if these differences could be due to accommodative inaccuracies to stimuli. Twenty-three student participants aged 18 to 26 years (mean age 20.3 ± 1.7 years) successfully completed all testing conditions. The modified Thorington technique was used at 4 m to measure heterophoria. The Shin Nippon SRW 5000 infrared autorefractor was used to determine accommodative change to -1.50, -3.00, -4.50, and -6.00D lens stimuli. Significant differences were found in response AC/A ratio between different minus lens stimulated accommodative demands (p < 0.001). Mean AC/A ratio values were 3.11 ± 1.29 with the -1.50D lens stimulus; 4.03 ± 2.11 with -3.00D; 4.14 ± 1.40 with -4.50D; and 4.48 ± 1.56 with -6.00D. No differences in linearity were noted between myopes and non-myopic participants, but myopes tended to have higher response AC/A ratios than non-myopes, mean 4.88 ± 1.89 for myopes vs 3.61 ± 1.47 for non-myopes (p = 0.045). Response AC/A ratio did not display linearity across 4 minus lens accommodative stimuli, but tended to increase with accommodative demand. Significant variability in response AC/A ratio was found, both within individuals to different accommodative demands, and between individuals across the data set.

Evaluation of Clipping Based Iterative PAPR Reduction Techniques for FBMC Systems

PubMed Central

Kollár, Zsolt

2014-01-01

This paper investigates filter bankmulticarrier (FBMC), a multicarrier modulation technique exhibiting an extremely low adjacent channel leakage ratio (ACLR) compared to conventional orthogonal frequency division multiplexing (OFDM) technique. The low ACLR of the transmitted FBMC signal makes it especially favorable in cognitive radio applications, where strict requirements are posed on out-of-band radiation. Large dynamic range resulting in high peak-to-average power ratio (PAPR) is characteristic of all sorts of multicarrier signals. The advantageous spectral properties of the high-PAPR FBMC signal are significantly degraded if nonlinearities are present in the transceiver chain. Spectral regrowth may appear, causing harmful interference in the neighboring frequency bands. This paper presents novel clipping based PAPR reduction techniques, evaluated and compared by simulations and measurements, with an emphasis on spectral aspects. The paper gives an overall comparison of PAPR reduction techniques, focusing on the reduction of the dynamic range of FBMC signals without increasing out-of-band radiation. An overview is presented on transmitter oriented techniques employing baseband clipping, which can maintain the system performance with a desired bit error rate (BER). PMID:24558338

Critical Concentration Ratio for Solar Thermoelectric Generators

NASA Astrophysics Data System (ADS)

ur Rehman, Naveed; Siddiqui, Mubashir Ali

2016-10-01

A correlation for determining the critical concentration ratio (CCR) of solar concentrated thermoelectric generators (SCTEGs) has been established, and the significance of the contributing parameters is discussed in detail. For any SCTEG, higher concentration ratio leads to higher temperatures at the hot side of modules. However, the maximum value of this temperature for safe operation is limited by the material properties of the modules and should be considered as an important design constraint. Taking into account this limitation, the CCR can be defined as the maximum concentration ratio usable for a particular SCTEG. The established correlation is based on factors associated with the material and geometric properties of modules, thermal characteristics of the receiver, installation site attributes, and thermal and electrical operating conditions. To reduce the number of terms in the correlation, these factors are combined to form dimensionless groups by applying the Buckingham Pi theorem. A correlation model containing these groups is proposed and fit to a dataset obtained by simulating a thermodynamic (physical) model over sampled values acquired by applying the Latin hypercube sampling (LHS) technique over a realistic distribution of factors. The coefficient of determination and relative error are found to be 97% and ±20%, respectively. The correlation is validated by comparing the predicted results with literature values. In addition, the significance and effects of the Pi groups on the CCR are evaluated and thoroughly discussed. This study will lead to a wide range of opportunities regarding design and optimization of SCTEGs.

The Golden Ratio

ERIC Educational Resources Information Center

Hyde, Hartley

2004-01-01

The Golden Ratio is sometimes called the "Golden Section" or the "Divine Proportion", in which three points: A, B, and C, divide a line in this proportion if AC/AB = AB/BC. "Donald in Mathmagicland" includes a section about the Golden Ratio and the ratios within a five-pointed star or pentagram. This article presents two computing exercises that…

Isotope ratio mass spectrometry in nutrition research

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

Luke, A.H.

Many of the biochemical pathways and processes that form the foundation of modern nutrition research was elucidated using stable isotopes as physiological tracers. Since the discovery of stable isotopes, improvements and innovations in mass spectrometry and chromatography have led to greatly expanded applications. This research project was designed to evaluate gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) as a tool for isotopic tracer studies and to delineate the operational parameters for the analysis of {sup 13}C-labeled cholesterol, leucine and {alpha}-ketoisocaproate. The same isotope ratio mass spectrometer was then used as the base instrument for the ratio mass spectrometer was then usedmore » as the base instrument for the development of two additional inlet systems: a continuous-flow inlet for the analyses of {sup 13}C and {sup 18}O as CO{sub 2} and a filament inlet for on-line combustion and isotopic analysis of non-volatile organic compounds. Each of these three inlets was evaluated and their utility in nutrition research illustrated. GC/C/IRMS was used to analyze cholesterol, leucine and {alpha}-ketoisocaproate with good accuracy, precision and little isotopic memory. For all three compounds the detection limits achieved well surpassed currently used technologies. For compounds that can be well separated by GC, GC/C/IRMS is a valuable analytical tool. The continuous-flow inlet provided good accuracy and precision for measurements of {sup 13}CO{sub 2} from breath tests and {sup 18}O as CO{sub 2} from total energy expenditure tests. Most importantly, the continuous-flow inlet increased sample throughput by at least a factor of three over conventional analytical techniques. The filament inlet provided accurate and precise {sup 13}C ratio measurements of both natural abundance and enriched standards of non-volatile organic compounds of physiological interest.« less

Demonstrating the limitations of line ratio temperature diagnostic using Fe X and Fe XIV spectral line intensity observations

NASA Technical Reports Server (NTRS)

Brickhouse, Nancy; Esser, Ruth; Habbal, Shadia R.

1995-01-01

The electron temperature in the inner corona can be derived from spectral line intensity measurements by comparing the ratio of the measured intensities of two spectral lines to the ratio calculated from theoretical models. In a homogeneous plasma the line ratio technique can be used for any two lines if the ratio of the intensities is independent of the density. The corona, however, is far from homogeneous. Even large coronal holes present at the solar poles at solar minimum can be partly or completely obscured by emission from hotter and denser surrounding regions. In this paper we investigate the effect of these surrounding regions on coronal hole temperatures. using daily intensity measurements at 1.15 Rs of the Fe XIV 5303 A and Fe X 6374 A spectral lines carried out at the National Solar Observatory at Sacramento Peak. We show that the temperatures derived using the line ratio technique for these two spectral lines can vary by more than 0.8 x 10(exp 6) K due to the contribution from surrounding regions. This example demonstrates the inadequacy of spectral lines with widely separate peak temperatures for temperature diagnostic.

Global remote sensing of water-chlorophyll ratio in terrestrial plant leaves.

PubMed

Kushida, Keiji

2012-10-01

I evaluated the use of global remote sensing techniques for estimating plant leaf chlorophyll a + b (C(ab); μg cm(-2)) and water (C(w); mg cm(-2)) concentrations as well as the ratio of C(w)/C(ab) with the PROSAIL model under possible distributions for leaf and soil spectra, leaf area index (LAI), canopy geometric structure, and leaf size. First, I estimated LAI from the normalized difference vegetation index. I found that, at LAI values <2, C(ab), C(w), and C(w)/C(ab) could not be reliably estimated. At LAI values >2, C(ab) and C(w) could be estimated for only restricted ranges of the canopy structure; however, the ratio of C(w)/C(ab) could be reliably estimated for a variety of possible canopy structures with coefficients of determination (R(2)) ranging from 0.56 to 0.90. The remote estimation of the C(w)/C(ab) ratio from satellites offers information on plant condition at a global scale.

Two sampling techniques for game meat.

PubMed

van der Merwe, Maretha; Jooste, Piet J; Hoffman, Louw C; Calitz, Frikkie J

2013-03-20

A study was conducted to compare the excision sampling technique used by the export market and the sampling technique preferred by European countries, namely the biotrace cattle and swine test. The measuring unit for the excision sampling was grams (g) and square centimetres (cm2) for the swabbing technique. The two techniques were compared after a pilot test was conducted on spiked approved beef carcasses (n = 12) that statistically proved the two measuring units correlated. The two sampling techniques were conducted on the same game carcasses (n = 13) and analyses performed for aerobic plate count (APC), Escherichia coli and Staphylococcus aureus, for both techniques. A more representative result was obtained by swabbing and no damage was caused to the carcass. Conversely, the excision technique yielded fewer organisms and caused minor damage to the carcass. The recovery ratio from the sampling technique improved 5.4 times for APC, 108.0 times for E. coli and 3.4 times for S. aureus over the results obtained from the excision technique. It was concluded that the sampling methods of excision and swabbing can be used to obtain bacterial profiles from both export and local carcasses and could be used to indicate whether game carcasses intended for the local market are possibly on par with game carcasses intended for the export market and therefore safe for human consumption.

A joint technique for sidelobe suppression and peak-to-average power ratio reduction in non-contiguous OFDM-based cognitive radio networks

NASA Astrophysics Data System (ADS)

Sivadas, Namitha Arackal; Mohammed, Sameer Saheerudeen

2017-02-01

In non-contiguous orthogonal frequency division multiplexing (NC-OFDM)-based interweave cognitive radio networks, the sidelobe power of secondary users (SUs) must be strictly controlled to avoid the interference between the SUs and the primary users (PUs) of the adjacent bands. Similarly, the inherent issue of high peak-to-average power ratio (PAPR) of the OFDM signal is another drawback of the cognitive radio communication system based on the NC-OFDM technology. A few methods are available in the literature to solve either of these problems individually, while in this paper, we propose a new method for the joint minimisation of sidelobe power and PAPR in NC-OFDM-based cognitive radio networks using Zadoff-Chu (ZC) sequence. In this method, the sidelobe power suppression of SUs is benefited by PUs and the PAPR is reduced for SUs. We modelled a new optimisation problem for minimising the sidelobe power with a constraint on the maximum tolerable PAPR and sidelobe power. The proper selection of ZC sequence, which is crucial for minimising both the issues simultaneously, is achieved by solving the proposed optimisation problem. The proposed technique is shown to provide 7 dB and 20 dB reduction in PAPR and sidelobe power, respectively, without causing any signal distortion along with the improvement in bit error rate (BER) performance.

An improved technique for the 2H/1H analysis of urines from diabetic volunteers

USGS Publications Warehouse

Coplen, T.B.; Harper, I.T.

1994-01-01

The H2-H2O ambient-temperature equilibration technique for the determination of 2H/1H ratios in urinary waters from diabetic subjects provides improved accuracy over the conventional Zn reduction technique. The standard deviation, ~ 1-2???, is at least a factor of three better than that of the Zn reduction technique on urinary waters from diabetic volunteers. Experiments with pure water and solutions containing glucose, urea and albumen indicate that there is no measurable bias in the hydrogen equilibration technique.The H2-H2O ambient-temperature equilibration technique for the determination of 2H/1H ratios in urinary waters from diabetic subjects provides improved accuracy over the conventional Zn reduction technique. The standard deviation, approximately 1-2%, is at least a factor of three better than that of the Zn reduction technique on urinary waters from diabetic volunteers. Experiments with pure water and solutions containing glucose, urea and albumen indicate that there is no measurable bias in the hydrogen equilibration technique.

An Evaluation of Total Solar Reflectance and Spectral Band Ratioing Techniques for Estimating Soil Water Content

NASA Technical Reports Server (NTRS)

Reginato, R. J.; Vedder, J. F.; Idso, S. B.; Jackson, R. D.; Blanchard, M. B.; Goettelman, R.

1977-01-01

For several days in March of 1975, reflected solar radiation measurements were obtained from smooth and rough surfaces of wet, drying, and continually dry Avondale loam at Phoenix, Arizona, with pyranometers located 50 cm above the ground surface and a multispectral scanner flown at a 300-m height. The simple summation of the different band radiances measured by the multispectral scanner proved equally as good as the pyranometer data for estimating surface soil water content if the multispectral scanner data were standardized with respect to the intensity of incoming solar radiation or the reflected radiance from a reference surface, such as the continually dry soil. Without this means of standardization, multispectral scanner data are most useful in a spectral band ratioing context. Our results indicated that, for the bands used, no significant information on soil water content could be obtained by band ratioing. Thus the variability in soil water content should insignificantly affect soil-type discrimination based on identification of type-specific spectral signatures. Therefore remote sensing, conducted in the 0.4- to 1.0-micron wavelength region of the solar spectrum, would seem to be much More suited to identifying crop and soil types than to estimating of soil water content.

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption

PubMed Central

2015-01-01

Objective Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. Methods To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Results Our solution supports evaluation of the D′ measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. Conclusions With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical. PMID:26732892

Privacy-preserving genome-wide association studies on cloud environment using fully homomorphic encryption.

PubMed

Lu, Wen-Jie; Yamada, Yoshiji; Sakuma, Jun

2015-01-01

Developed sequencing techniques are yielding large-scale genomic data at low cost. A genome-wide association study (GWAS) targeting genetic variations that are significantly associated with a particular disease offers great potential for medical improvement. However, subjects who volunteer their genomic data expose themselves to the risk of privacy invasion; these privacy concerns prevent efficient genomic data sharing. Our goal is to presents a cryptographic solution to this problem. To maintain the privacy of subjects, we propose encryption of all genotype and phenotype data. To allow the cloud to perform meaningful computation in relation to the encrypted data, we use a fully homomorphic encryption scheme. Noting that we can evaluate typical statistics for GWAS from a frequency table, our solution evaluates frequency tables with encrypted genomic and clinical data as input. We propose to use a packing technique for efficient evaluation of these frequency tables. Our solution supports evaluation of the D' measure of linkage disequilibrium, the Hardy-Weinberg Equilibrium, the χ2 test, etc. In this paper, we take χ2 test and linkage disequilibrium as examples and demonstrate how we can conduct these algorithms securely and efficiently in an outsourcing setting. We demonstrate with experimentation that secure outsourcing computation of one χ2 test with 10, 000 subjects requires about 35 ms and evaluation of one linkage disequilibrium with 10, 000 subjects requires about 80 ms. With appropriate encoding and packing technique, cryptographic solutions based on fully homomorphic encryption for secure computations of GWAS can be practical.

Optimum coding techniques for MST radars

NASA Technical Reports Server (NTRS)

Sulzer, M. P.; Woodman, R. F.

1986-01-01

The optimum coding technique for MST (mesosphere stratosphere troposphere) radars is that which gives the lowest possible sidelobes in practice and can be implemented without too much computing power. Coding techniques are described in Farley (1985). A technique mentioned briefly there but not fully developed and not in general use is discussed here. This is decoding by means of a filter which is not matched to the transmitted waveform, in order to reduce sidelobes below the level obtained with a matched filter. This is the first part of the technique discussed here; the second part consists of measuring the transmitted waveform and using it as the basis for the decoding filter, thus reducing errors due to imperfections in the transmitter. There are two limitations to this technique. The first is a small loss in signal to noise ratio (SNR), which usually is not significant. The second problem is related to incomplete information received at the lowest ranges. An appendix shows a technique for handling this problem. Finally, it is shown that the use of complementary codes on transmission and nonmatched decoding gives the lowest possible sidelobe level and the minimum loss in SNR due to mismatch.

Defect inspection using a time-domain mode decomposition technique

NASA Astrophysics Data System (ADS)

Zhu, Jinlong; Goddard, Lynford L.

2018-03-01

In this paper, we propose a technique called time-varying frequency scanning (TVFS) to meet the challenges in killer defect inspection. The proposed technique enables the dynamic monitoring of defects by checking the hopping in the instantaneous frequency data and the classification of defect types by comparing the difference in frequencies. The TVFS technique utilizes the bidimensional empirical mode decomposition (BEMD) method to separate the defect information from the sea of system errors. This significantly improve the signal-to-noise ratio (SNR) and moreover, it potentially enables reference-free defect inspection.

Damage assessment in reinforced concrete using nonlinear vibration techniques

NASA Astrophysics Data System (ADS)

Van Den Abeele, K.; De Visscher, J.

2000-07-01

Reinforced concrete (RC) structures are subject to microcrack initiation and propagation at load levels far below the actual failure load. In this paper, nonlinear vibration techniques are applied to investigate stages of progressive damage in RC beams induced by static loading tests. At different levels of damage, a modal analysis is carried out, assuming the structure to behave linearly. At the same time, measurement of resonant frequencies and damping ratios as function of vibration amplitude are performed using a frequency domain technique as well as a time domain technique. We compare the results of the linear and nonlinear techniques, and value them against the visual damage evaluation.

Laser ablation inductively coupled plasma mass spectrometry for direct isotope ratio measurements on solid samples

NASA Astrophysics Data System (ADS)

Pickhardt, Carola; Dietze, Hans-Joachim; Becker, J. Sabine

2005-04-01

Isotope ratio measurements have been increasingly used in quite different application fields, e.g., for the investigation of isotope variation in nature, in geoscience (geochemistry and geochronology), in cosmochemistry and planetary science, in environmental science, e.g., in environmental monitoring, or by the application of the isotope dilution technique for quantification purposes using stable or radioactive high-enriched isotope tracers. Due to its high sensitivity, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is today a challenging mass spectrometric technique for the direct determination of precise and accurate isotope ratios in solid samples. In comparison to laser ablation quadrupole ICP-MS (LA-ICP-QMS), laser ablation coupled to a double-focusing sector field ICP-MS (LA-ICP-SFMS) with single ion detection offers a significant improvement of sensitivity at low mass resolution, whereby isotope ratios can be measured with a precision to 0.1% relative standard deviation (R.S.D.). In LA-ICP-SFMS, many disturbing isobaric interferences of analyte and molecular ions can be separated at the required mass resolution (e.g., 40Ar16O+ and 56Fe+ for iron isotope ratio measurements). The precision on isotope ratio measurements was improved by one order of magnitude via the simultaneous detection of mass-separated ion currents of isotopes using multiple ion collectors in LA-ICP-MS (LA-MC-ICP-MS). The paper discusses the state of the art, the challenges and limits in isotope ratio measurements by LA-ICP-MS using different instrumentations at the trace and ultratrace level in different fields of application as in environmental and biological research, geochemistry and geochronology with respect to their precision and accuracy.

Accurate and precise determination of isotopic ratios by MC-ICP-MS: a review.

PubMed

Yang, Lu

2009-01-01

For many decades the accurate and precise determination of isotope ratios has remained a very strong interest to many researchers due to its important applications in earth, environmental, biological, archeological, and medical sciences. Traditionally, thermal ionization mass spectrometry (TIMS) has been the technique of choice for achieving the highest accuracy and precision. However, recent developments in multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) have brought a new dimension to this field. In addition to its simple and robust sample introduction, high sample throughput, and high mass resolution, the flat-topped peaks generated by this technique provide for accurate and precise determination of isotope ratios with precision reaching 0.001%, comparable to that achieved with TIMS. These features, in combination with the ability of the ICP source to ionize nearly all elements in the periodic table, have resulted in an increased use of MC-ICP-MS for such measurements in various sample matrices. To determine accurate and precise isotope ratios with MC-ICP-MS, utmost care must be exercised during sample preparation, optimization of the instrument, and mass bias corrections. Unfortunately, there are inconsistencies and errors evident in many MC-ICP-MS publications, including errors in mass bias correction models. This review examines "state-of-the-art" methodologies presented in the literature for achievement of precise and accurate determinations of isotope ratios by MC-ICP-MS. Some general rules for such accurate and precise measurements are suggested, and calculations of combined uncertainty of the data using a few common mass bias correction models are outlined.

Advantage of the modified Lunn-McNeil technique over Kalbfleisch-Prentice technique in competing risks

NASA Astrophysics Data System (ADS)

Lukman, Iing; Ibrahim, Noor A.; Daud, Isa B.; Maarof, Fauziah; Hassan, Mohd N.

2002-03-01

Survival analysis algorithm is often applied in the data mining process. Cox regression is one of the survival analysis tools that has been used in many areas, and it can be used to analyze the failure times of aircraft crashed. Another survival analysis tool is the competing risks where we have more than one cause of failure acting simultaneously. Lunn-McNeil analyzed the competing risks in the survival model using Cox regression with censored data. The modified Lunn-McNeil technique is a simplify of the Lunn-McNeil technique. The Kalbfleisch-Prentice technique is involving fitting models separately from each type of failure, treating other failure types as censored. To compare the two techniques, (the modified Lunn-McNeil and Kalbfleisch-Prentice) a simulation study was performed. Samples with various sizes and censoring percentages were generated and fitted using both techniques. The study was conducted by comparing the inference of models, using Root Mean Square Error (RMSE), the power tests, and the Schoenfeld residual analysis. The power tests in this study were likelihood ratio test, Rao-score test, and Wald statistics. The Schoenfeld residual analysis was conducted to check the proportionality of the model through its covariates. The estimated parameters were computed for the cause-specific hazard situation. Results showed that the modified Lunn-McNeil technique was better than the Kalbfleisch-Prentice technique based on the RMSE measurement and Schoenfeld residual analysis. However, the Kalbfleisch-Prentice technique was better than the modified Lunn-McNeil technique based on power tests measurement.

Orthopaedic regenerative tissue engineering en route to the holy grail: disequilibrium between the demand and the supply in the operating room.

PubMed

Cengiz, Ibrahim Fatih; Pereira, Hélder; de Girolamo, Laura; Cucchiarini, Magali; Espregueira-Mendes, João; Reis, Rui L; Oliveira, Joaquim Miguel

2018-05-22

Orthopaedic disorders are very frequent, globally found and often partially unresolved despite the substantial advances in science and medicine. Their surgical intervention is multifarious and the most favourable treatment is chosen by the orthopaedic surgeon on a case-by-case basis depending on a number of factors related with the patient and the lesion. Numerous regenerative tissue engineering strategies have been developed and studied extensively in laboratory through in vitro experiments and preclinical in vivo trials with various established animal models, while a small proportion of them reached the operating room. However, based on the available literature, the current strategies have not yet achieved to fully solve the clinical problems. Thus, the gold standards, if existing, remain unchanged in the clinics, notwithstanding the known limitations and drawbacks. Herein, the involvement of regenerative tissue engineering in the clinical orthopaedics is reviewed. The current challenges are indicated and discussed in order to describe the current disequilibrium between the needs and solutions made available in the operating room. Regenerative tissue engineering is a very dynamic field that has a high growth rate and a great openness and ability to incorporate new technologies with passion to edge towards the Holy Grail that is functional tissue regeneration. Thus, the future of clinical solutions making use of regenerative tissue engineering principles for the management of orthopaedic disorders is firmly supported by the clinical need.

A detailed description of the sequential probability ratio test for 2-IMU FDI

NASA Technical Reports Server (NTRS)

Rich, T. M.

1976-01-01

The sequential probability ratio test (SPRT) for 2-IMU FDI (inertial measuring unit failure detection/isolation) is described. The SPRT is a statistical technique for detecting and isolating soft IMU failures originally developed for the strapdown inertial reference unit. The flowchart of a subroutine incorporating the 2-IMU SPRT is included.

Exploiting excess sharing: a more powerful test of linkage for affected sib pairs than the transmission/disequilibrium test.

PubMed Central

Wicks, J

2000-01-01

The transmission/disequilibrium test (TDT) is a popular, simple, and powerful test of linkage, which can be used to analyze data consisting of transmissions to the affected members of families with any kind pedigree structure, including affected sib pairs (ASPs). Although it is based on the preferential transmission of a particular marker allele across families, it is not a valid test of association for ASPs. Martin et al. devised a similar statistic for ASPs, Tsp, which is also based on preferential transmission of a marker allele but which is a valid test of both linkage and association for ASPs. It is, however, less powerful than the TDT as a test of linkage for ASPs. What I show is that the differences between the TDT and Tsp are due to the fact that, although both statistics are based on preferential transmission of a marker allele, the TDT also exploits excess sharing in identity-by-descent transmissions to ASPs. Furthermore, I show that both of these statistics are members of a family of "TDT-like" statistics for ASPs. The statistics in this family are based on preferential transmission but also, to varying extents, exploit excess sharing. From this family of statistics, we see that, although the TDT exploits excess sharing to some extent, it is possible to do so to a greater extent-and thus produce a more powerful test of linkage, for ASPs, than is provided by the TDT. Power simulations conducted under a number of disease models are used to verify that the most powerful member of this family of TDT-like statistics is more powerful than the TDT for ASPs. PMID:10788332

Exploiting excess sharing: a more powerful test of linkage for affected sib pairs than the transmission/disequilibrium test.

PubMed

Wicks, J

2000-06-01

The transmission/disequilibrium test (TDT) is a popular, simple, and powerful test of linkage, which can be used to analyze data consisting of transmissions to the affected members of families with any kind pedigree structure, including affected sib pairs (ASPs). Although it is based on the preferential transmission of a particular marker allele across families, it is not a valid test of association for ASPs. Martin et al. devised a similar statistic for ASPs, Tsp, which is also based on preferential transmission of a marker allele but which is a valid test of both linkage and association for ASPs. It is, however, less powerful than the TDT as a test of linkage for ASPs. What I show is that the differences between the TDT and Tsp are due to the fact that, although both statistics are based on preferential transmission of a marker allele, the TDT also exploits excess sharing in identity-by-descent transmissions to ASPs. Furthermore, I show that both of these statistics are members of a family of "TDT-like" statistics for ASPs. The statistics in this family are based on preferential transmission but also, to varying extents, exploit excess sharing. From this family of statistics, we see that, although the TDT exploits excess sharing to some extent, it is possible to do so to a greater extent-and thus produce a more powerful test of linkage, for ASPs, than is provided by the TDT. Power simulations conducted under a number of disease models are used to verify that the most powerful member of this family of TDT-like statistics is more powerful than the TDT for ASPs.

Chemiluminescence-based multivariate sensing of local equivalence ratios in premixed atmospheric methane-air flames

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

Tripathi, Markandey M.; Krishnan, Sundar R.; Srinivasan, Kalyan K.

Chemiluminescence emissions from OH*, CH*, C2, and CO2 formed within the reaction zone of premixed flames depend upon the fuel-air equivalence ratio in the burning mixture. In the present paper, a new partial least square regression (PLS-R) based multivariate sensing methodology is investigated and compared with an OH*/CH* intensity ratio-based calibration model for sensing equivalence ratio in atmospheric methane-air premixed flames. Five replications of spectral data at nine different equivalence ratios ranging from 0.73 to 1.48 were used in the calibration of both models. During model development, the PLS-R model was initially validated with the calibration data set using themore » leave-one-out cross validation technique. Since the PLS-R model used the entire raw spectral intensities, it did not need the nonlinear background subtraction of CO2 emission that is required for typical OH*/CH* intensity ratio calibrations. An unbiased spectral data set (not used in the PLS-R model development), for 28 different equivalence ratio conditions ranging from 0.71 to 1.67, was used to predict equivalence ratios using the PLS-R and the intensity ratio calibration models. It was found that the equivalence ratios predicted with the PLS-R based multivariate calibration model matched the experimentally measured equivalence ratios within 7%; whereas, the OH*/CH* intensity ratio calibration grossly underpredicted equivalence ratios in comparison to measured equivalence ratios, especially under rich conditions ( > 1.2). The practical implications of the chemiluminescence-based multivariate equivalence ratio sensing methodology are also discussed.« less

Linkage Disequilibrium and Haplotype Diversity in the Genes of the Renin–Angiotensin System: Findings From the Family Blood Pressure Program

PubMed Central

Zhu, Xiaofeng; Yan, Denise; Cooper, Richard S.; Luke, Amy; Ikeda, Morna A.; Chang, Yen-Pei C.; Weder, Alan; Chakravarti, Aravinda

2003-01-01

Association studies of candidate genes with complex traits have generally used one or a few single nucleotide polymorphisms (SNPs), although variation in the extent of linkage disequilibrium (LD) within genes markedly influences the sensitivity and precision of association studies. The extent of LD and the underlying haplotype structure for most candidate genes are still unavailable. We sampled 193 blacks (African-Americans) and 160 whites (European-Americans) and estimated the intragenic LD and the haplotype structure in four genes of the renin–angiotensin system. We genotyped 25 SNPs, with all but one of the pairs spaced between 1 and 20 kb, thus providing resolution at small scale. The pattern of LD within a gene was very heterogeneous. Using a robust method to define haplotype blocks, blocks of limited haplotype diversity were identified at each locus; between these blocks, LD was lost owing to the history of recombination events. As anticipated, there was less LD among blacks, the number of haplotypes was substantially larger, and shorter haplotype segments were found, compared with whites. These findings have implications for candidate-gene association studies and indicate that variation between populations of European and African origin in haplotype diversity is characteristic of most genes. [The sequence data described in this paper are available in GenBank under the following accession nos: AGT, MIM 106150; Renin, MIM 179820; ACE, MIM 106180; Angiotensin receptor I, MIM 106165. Supplementary material is available online at http://www.genome.org.] PMID:12566395

Ratios and effect size.

PubMed

Robinson, Jasper

2017-10-01

Responding to a related pair of measurements is often expressed as a single discrimination ratio. Authors have used various discrimination ratios; yet, little information exists to guide their choice. A second use of ratios is to correct for the influence of a nuisance variable on the measurement of interest. I examine 4 discrimination ratios using simulated data sets. Three ratios, of the form a/(a + b), b/(a + b), and (a - b)/(a + b), introduced distortions to their raw data. The fourth ratio, (b - a)/b largely avoided such distortions and was the most sensitive at detecting statistical differences. Effect size statistics were also often improved with a correction ratio. Gustatory sensory preconditioning experiments involved measurement of rats' sucrose and saline consumption; these flavors served as either a target flavor or a control flavor and were counterbalanced across rats. However, sensory preconditioning was often masked by a bias for sucrose over saline. Sucrose and saline consumption scores were multiplied by the ratio of the overall consumption to the consumption of that flavor alone, which corrected the bias. The general utility of discrimination and correction ratios for data treatment is discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

On the Use of Line Depth Ratios to Measure Starspot Properties on Magnetically Active Stars

NASA Astrophysics Data System (ADS)

O'Neal, Douglas

2006-07-01

Photometric and spectroscopic techniques have proven to be effective ways to measure the properties of dark, cool starspots on magnetically active stars. Recently, a technique was introduced using atomic line depth ratios (LDRs) to measure starspot properties. Carefully reproducing this technique using a new set of spectroscopic observations of active stars, we find that the LDR technique encounters difficulties, specifically by overestimating spot temperatures (because the atomic lines blend with titanium oxide absorption in cooler spots) and by not tightly constraining the filling factor of spots. While the use of LDRs for active star studies has great promise, we believe that these concerns need to be addressed before the technique is more widely applied. This paper includes data taken at McDonald Observatory of the University of Texas at Austin.

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

PubMed

Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

2012-08-01

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Improving the therapeutic ratio of craniospinal irradiation in medulloblastoma

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

Maor, M.H.; Fields, R.S.; Hogstrom, K.R.

1985-04-01

Radiation therapy delivered to the entire cerebrospinal axis is indicated for a number of pediatric brain tumors, especially medulloblastoma. Improved radiotherapy techniques have changed the near fatal prognosis for children with medulloblastoma to a 50%, 5-year survival. Nevertheless, the treatment results in substantial acute toxicity, and many survivors have serious sequelae. Refinements in radiotherapy technique, however, can improve the therapeutic ratio of the treatment by lowering its side effects. In the last year children who required craniospinal irradiation at M.D. Anderson Hospital were treated with 6 MV photons to the brain and primary tumor and with 15-17 MeV electrons tomore » the spinal canal. The elective dose to the whole brain was 30 Gy in 17 fractions and 30 Gy in 20 fractions to the spine. The primary tumor received an additional 20-25 Gy. An electron-beam dose distribution was drawn on a computerized tomography (CT) reconstructed sagittal plane. The treatment was well tolerated in the first five patients. It is projected that the current technique will cause fewer late effects and improve the tolerance to chemotherapy.« less

Detection strategies for extreme mass ratio inspirals

NASA Astrophysics Data System (ADS)

Cornish, Neil J.

2011-05-01

The capture of compact stellar remnants by galactic black holes provides a unique laboratory for exploring the near-horizon geometry of the Kerr spacetime, or possible departures from general relativity if the central cores prove not to be black holes. The gravitational radiation produced by these extreme mass ratio inspirals (EMRIs) encodes a detailed map of the black hole geometry, and the detection and characterization of these signals is a major scientific goal for the LISA mission. The waveforms produced are very complex, and the signals need to be coherently tracked for tens of thousands of cycles to produce a detection, making EMRI signals one of the most challenging data analysis problems in all of gravitational wave astronomy. Estimates for the number of templates required to perform an exhaustive grid-based matched-filter search for these signals are astronomically large, and far out of reach of current computational resources. Here I describe an alternative approach that employs a hybrid between genetic algorithms and Markov chain Monte Carlo techniques, along with several time-saving techniques for computing the likelihood function. This approach has proven effective at the blind extraction of relatively weak EMRI signals from simulated LISA data sets.

Reusable High Aspect Ratio 3-D Nickel Shadow Mask

PubMed Central

Shandhi, M.M.H.; Leber, M.; Hogan, A.; Warren, D.J.; Bhandari, R.; Negi, S.

2017-01-01

Shadow Mask technology has been used over the years for resistless patterning and to pattern on unconventional surfaces, fragile substrate and biomaterial. In this work, we are presenting a novel method to fabricate high aspect ratio (15:1) three-dimensional (3D) Nickel (Ni) shadow mask with vertical pattern length and width of 1.2 mm and 40 μm respectively. The Ni shadow mask is 1.5 mm tall and 100 μm wide at the base. The aspect ratio of the shadow mask is 15. Ni shadow mask is mechanically robust and hence easy to handle. It is also reusable and used to pattern the sidewalls of unconventional and complex 3D geometries such as microneedles or neural electrodes (such as the Utah array). The standard Utah array has 100 active sites at the tip of the shaft. Using the proposed high aspect ratio Ni shadow mask, the Utah array can accommodate 300 active sites, 200 of which will be along and around the shaft. The robust Ni shadow mask is fabricated using laser patterning and electroplating techniques. The use of Ni 3D shadow mask will lower the fabrication cost, complexity and time for patterning out-of-plane structures. PMID:29056835

Autoregressive linear least square single scanning electron microscope image signal-to-noise ratio estimation.

PubMed

Sim, Kok Swee; NorHisham, Syafiq

2016-11-01

A technique based on linear Least Squares Regression (LSR) model is applied to estimate signal-to-noise ratio (SNR) of scanning electron microscope (SEM) images. In order to test the accuracy of this technique on SNR estimation, a number of SEM images are initially corrupted with white noise. The autocorrelation function (ACF) of the original and the corrupted SEM images are formed to serve as the reference point to estimate the SNR value of the corrupted image. The LSR technique is then compared with the previous three existing techniques known as nearest neighbourhood, first-order interpolation, and the combination of both nearest neighborhood and first-order interpolation. The actual and the estimated SNR values of all these techniques are then calculated for comparison purpose. It is shown that the LSR technique is able to attain the highest accuracy compared to the other three existing techniques as the absolute difference between the actual and the estimated SNR value is relatively small. SCANNING 38:771-782, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

High aspect ratio nanoholes in glass generated by femtosecond laser pulses with picosecond intervals

NASA Astrophysics Data System (ADS)

Ahn, Sanghoon; Choi, Jiyeon; Noh, Jiwhan; Cho, Sung-Hak

2018-02-01

Because of its potential uses, high aspect ratio nanostructures have been interested for last few decades. In order to generate nanostructures, various techniques have been attempted. Femtosecond laser ablation is one of techniques for generating nanostructures inside a transparent material. For generating nanostructures by femtosecond laser ablation, previous studies have been attempted beam shaping such as Bessel beam and temporal tailored beam. Both methods suppress electron excitation at near surface and initiate interference of photons at certain depth. Recent researches indicate that shape of nanostructures is related with temporal change of electron density and number of self-trapped excitons. In this study, we try to use the temporal change of electron density induced by femtosecond laser pulse for generating high aspect ratio nanoholes. In order to reveal the effect of temporal change of electron density, secondary pulses are irradiated from 100 to 1000 ps after the irradiation of first pulse. Our result shows that diameter of nanoholes is increasing and depth of nanoholes is decreasing as pulse to pulse interval is getting longer. With manipulating of pulse to pulse interval, we could generate high aspect ratio nanoholes with diameter of 250-350 nm and depth of 4∼6 μm inside a glass.

Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.).

PubMed

Blair, Matthew W; Prieto, Sergio; Díaz, Lucy M; Buendía, Héctor F; Cardona, César

2010-04-29

An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome. Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004. We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for

A TEM study of disequilibrium plagioclase breakdown at high pressure: the role of infiltrating fluid

NASA Astrophysics Data System (ADS)

Wayte, Gavin J.; Worden, Richard H.; Rubie, David C.; Droop, Giles T. R.

1989-04-01

High-pressure metamorphism (˜600° C, ˜20 kbar) of the Allalin Gabbro (Western Alps) resulted in the breakdown of plagioclase (˜An63) to fine-grained zoisite, jadeite, kyanite and quartz. In rare cases this reaction failed to reach completion. The resulting textures of partial reaction have been studied by transmission and analytical electron microscopy. In localised regions of a plagioclase crystal where the extent of reaction is <10%, only zoisite developed and the orientation relationship 1 410_2004_Article_BF00372216_TeX2GIFE1.gif left( {100} right)_{{text{Zo}}} //left( {101} right)_{{text{P1}}} and 1 410_2004_Article_BF00372216_TeX2GIFE2.gif left( {012} right)_{{text{Zo}}} //left( {010} right)_{{text{P1}}} is frequently present. In regions where 10 50% of plagioclase has transformed, the reaction plagioclase+H2O→zoisite+kyanite+quartz +(NaSiCa-1Al-1)pl has occurred. The systematic orientation relationship between plagioclase and zoisite is absent at ≥50% transformation. Complete breakdown of plagioclase occurred in localized micron-scale domains by the reaction plagioclase+H2O→zoisite+jadeite+kyanite+quartz and the reaction products are variably orientated with respect to each other. Incomplete reaction, together with the concentration of reaction products around cracks in original plagioclase grains, suggests that extent of reaction was controlled primarily by the availability of H2O. The textural observations are interpreted in terms of two possible disequilibrium reaction models. (1) Plagioclase persists metastably with its original igneous composition to a pressure > 17 kbar at 600° C. Reaction to the equilibrium assemblage then develops adjacent to cracks in response to the presence of aqueous fluid. At intracrystalline sites, only partial reaction occurs because Jadeite, and sometimes kyanite and quartz, fail to nucleate for kinetic reasons. (2) Localized regions of a plagioclase crystal partially equilibrate at several stages during the

Alar setback technique: a controlled method of nasal tip deprojection.

PubMed

Foda, H M

2001-11-01

To describe an alar cartilage-modifying technique aimed at decreasing nasal tip projection in cases with overdeveloped alar cartilages and to compare it with other deprojection techniques used to correct such deformity. Selected case series. University and private practice settings in Alexandria, Egypt. Twenty patients presenting for rhinoplasty who had overprojected nasal tips primarily due to overdeveloped alar cartilages. All cases were primary cases except for one patient, who had undergone 2 previous rhinoplasties. An external rhinoplasty approach was used to set back the alar cartilages by shortening their medial and lateral crura. The choice of performing a high or low setback depended on the preexisting lobule-to-columella ratio. Following the setback, the alar cartilages were reconstructed in a fashion that increased the strength and stability of the tip complex. Subjective evaluation included clinical examination, analysis of preoperative and postoperative photographs, and patient satisfaction. Objective evaluation of nasal tip projection, using the Goode ratio and the nasofacial angle, was performed preoperatively and repeated at least 6 months postoperatively. A low setback was performed in 16 cases (80%) and a high setback in 4 (20%). The mean follow-up period was 18 months (range, 6-36 months). The technique effectively deprojected the nasal tip as evidenced by the considerable postoperative decrease in values of the Goode ratio and the nasofacial angle. No complications were encountered and no revision surgical procedures were required. The alar setback technique has many advantages; it results in precise predictable amounts of deprojection, controls the degree of tip rotation, preserves the natural contour of the nasal tip, respects the tip support mechanisms, increases the strength and stability of nasal tip complex, preserves or restores the normal lobule-to-columella proportion, and does not lead to alar flaring. However, the technique requires

The elastic ratio: introducing curvature into ratio-based image segmentation.

PubMed

Schoenemann, Thomas; Masnou, Simon; Cremers, Daniel

2011-09-01

We present the first ratio-based image segmentation method that allows imposing curvature regularity of the region boundary. Our approach is a generalization of the ratio framework pioneered by Jermyn and Ishikawa so as to allow penalty functions that take into account the local curvature of the curve. The key idea is to cast the segmentation problem as one of finding cyclic paths of minimal ratio in a graph where each graph node represents a line segment. Among ratios whose discrete counterparts can be globally minimized with our approach, we focus in particular on the elastic ratio [Formula: see text] that depends, given an image I, on the oriented boundary C of the segmented region candidate. Minimizing this ratio amounts to finding a curve, neither small nor too curvy, through which the brightness flux is maximal. We prove the existence of minimizers for this criterion among continuous curves with mild regularity assumptions. We also prove that the discrete minimizers provided by our graph-based algorithm converge, as the resolution increases, to continuous minimizers. In contrast to most existing segmentation methods with computable and meaningful, i.e., nondegenerate, global optima, the proposed approach is fully unsupervised in the sense that it does not require any kind of user input such as seed nodes. Numerical experiments demonstrate that curvature regularity allows substantial improvement of the quality of segmentations. Furthermore, our results allow drawing conclusions about global optima of a parameterization-independent version of the snakes functional: the proposed algorithm allows determining parameter values where the functional has a meaningful solution and simultaneously provides the corresponding global solution.

Certification of the Uranium Isotopic Ratios in Nbl Crm 112-A, Uranium Assay Standard (Invited)

NASA Astrophysics Data System (ADS)

Mathew, K. J.; Mason, P.; Narayanan, U.

2010-12-01

Isotopic reference materials are needed to validate measurement procedures and to calibrate multi-collector ion counting detector systems. New Brunswick Laboratory (NBL) provides a suite of certified isotopic and assay standards for the US and international nuclear safeguards community. NBL Certified Reference Material (CRM) 112-A Uranium Metal Assay Standard with a consensus value of 137.88 for the 238U/235U ratio [National Bureau of Standards -- NBS, currently named National Institute for Standards and Technology, Standard Reference Material (SRM) 960 had been renamed CRM 112-A] is commonly used as a natural uranium isotopic reference material within the earth science community. We have completed the analytical work for characterizing the isotopic composition of NBL CRM 112-A Uranium Assay Standard and NBL CRM 145 (uranyl nitrate solution prepared from CRM 112-A). The 235U/238U isotopic ratios were characterized using the total evaporation (TE) and the modified total evaporation (MTE) methods. The 234U/238U isotope ratios were characterized using a conventional analysis technique and verified using the ratios measured in the MTE analytical technique. The analysis plan for the characterization work was developed such that isotopic ratios that are traceable to NBL CRM U030-A are obtained. NBL is preparing a certificate of Analysis and will issue a certificate for Uranium Assay and Isotopics. The results of the CRM 112-A certification measurements will be discussed. These results will be compared with the average values from Richter et al (2010). A comparison of the precision and accuracy of the measurement methods (TE, MTE and Conventional) employed in the certification will be presented. The uncertainties in the 235U/238U and 234U/238U ratios, calculated according to the Guide to the Expression of Uncertainty in Measurements (GUM) and the dominant contributors to the combined standard uncertainty will be discussed.

Techniques and software tools for estimating ultrasonic signal-to-noise ratios

NASA Astrophysics Data System (ADS)

Chiou, Chien-Ping; Margetan, Frank J.; McKillip, Matthew; Engle, Brady J.; Roberts, Ronald A.

2016-02-01

At Iowa State University's Center for Nondestructive Evaluation (ISU CNDE), the use of models to simulate ultrasonic inspections has played a key role in R&D efforts for over 30 years. To this end a series of wave propagation models, flaw response models, and microstructural backscatter models have been developed to address inspection problems of interest. One use of the combined models is the estimation of signal-to-noise ratios (S/N) in circumstances where backscatter from the microstructure (grain noise) acts to mask sonic echoes from internal defects. Such S/N models have been used in the past to address questions of inspection optimization and reliability. Under the sponsorship of the National Science Foundation's Industry/University Cooperative Research Center at ISU, an effort was recently initiated to improve existing research-grade software by adding graphical user interface (GUI) to become user friendly tools for the rapid estimation of S/N for ultrasonic inspections of metals. The software combines: (1) a Python-based GUI for specifying an inspection scenario and displaying results; and (2) a Fortran-based engine for computing defect signal and backscattered grain noise characteristics. The latter makes use of several models including: the Multi-Gaussian Beam Model for computing sonic fields radiated by commercial transducers; the Thompson-Gray Model for the response from an internal defect; the Independent Scatterer Model for backscattered grain noise; and the Stanke-Kino Unified Model for attenuation. The initial emphasis was on reformulating the research-grade code into a suitable modular form, adding the graphical user interface and performing computations rapidly and robustly. Thus the initial inspection problem being addressed is relatively simple. A normal-incidence pulse/echo immersion inspection is simulated for a curved metal component having a non-uniform microstructure, specifically an equiaxed, untextured microstructure in which the average

Combining tracer flux ratio methodology with low-flying aircraft measurements to estimate dairy farm CH4 emissions

NASA Astrophysics Data System (ADS)

Daube, C.; Conley, S.; Faloona, I. C.; Yacovitch, T. I.; Roscioli, J. R.; Morris, M.; Curry, J.; Arndt, C.; Herndon, S. C.

2017-12-01

Livestock activity, enteric fermentation of feed and anaerobic digestion of waste, contributes significantly to the methane budget of the United States (EPA, 2016). Studies question the reported magnitude of these methane sources (Miller et. al., 2013), calling for more detailed research of agricultural animals (Hristov, 2014). Tracer flux ratio is an attractive experimental method to bring to this problem because it does not rely on estimates of atmospheric dispersion. Collection of data occurred during one week at two dairy farms in central California (June, 2016). Each farm varied in size, layout, head count, and general operation. The tracer flux ratio method involves releasing ethane on-site with a known flow rate to serve as a tracer gas. Downwind mixed enhancements in ethane (from the tracer) and methane (from the dairy) were measured, and their ratio used to infer the unknown methane emission rate from the farm. An instrumented van drove transects downwind of each farm on public roads while tracer gases were released on-site, employing the tracer flux ratio methodology to assess simultaneous methane and tracer gas plumes. Flying circles around each farm, a small instrumented aircraft made measurements to perform a mass balance evaluation of methane gas. In the course of these two different methane quantification techniques, we were able to validate yet a third method: tracer flux ratio measured via aircraft. Ground-based tracer release rates were applied to the aircraft-observed methane-to-ethane ratios, yielding whole-site methane emission rates. Never before has the tracer flux ratio method been executed with aircraft measurements. Estimates from this new application closely resemble results from the standard ground-based technique to within their respective uncertainties. Incorporating this new dimension to the tracer flux ratio methodology provides additional context for local plume dynamics and validation of both ground and flight-based data.

Analysis of high-aspect-ratio jet-flap wings of arbitrary geometry

NASA Technical Reports Server (NTRS)

Lissaman, P. B. S.

1973-01-01

An analytical technique to compute the performance of an arbitrary jet-flapped wing is developed. The solution technique is based on the method of Maskell and Spence in which the well-known lifting-line approach is coupled with an auxiliary equation providing the extra function needed in jet-flap theory. The present method is generalized to handle straight, uncambered wings of arbitrary planform, twist, and blowing (including unsymmetrical cases). An analytical procedure is developed for continuous variations in the above geometric data with special functions to exactly treat discontinuities in any of the geometric and blowing data. A rational theory for the effect of finite wing thickness is introduced as well as simplified concepts of effective aspect ratio for rapid estimation of performance.

X-ray dual energy spectral parameter optimization for bone Calcium/Phosphorus mass ratio estimation

NASA Astrophysics Data System (ADS)

Sotiropoulou, P. I.; Fountos, G. P.; Martini, N. D.; Koukou, V. N.; Michail, C. M.; Valais, I. G.; Kandarakis, I. S.; Nikiforidis, G. C.

2015-09-01

Calcium (Ca) and Phosphorus (P) bone mass ratio has been identified as an important, yet underutilized, risk factor in osteoporosis diagnosis. The purpose of this simulation study is to investigate the use of effective or mean mass attenuation coefficient in Ca/P mass ratio estimation with the use of a dual-energy method. The investigation was based on the minimization of the accuracy of Ca/P ratio, with respect to the Coefficient of Variation of the ratio. Different set-ups were examined, based on the K-edge filtering technique and single X-ray exposure. The modified X-ray output was attenuated by various Ca/P mass ratios resulting in nine calibration points, while keeping constant the total bone thickness. The simulated data were obtained considering a photon counting energy discriminating detector. The standard deviation of the residuals was used to compare and evaluate the accuracy between the different dual energy set-ups. The optimum mass attenuation coefficient for the Ca/P mass ratio estimation was the effective coefficient in all the examined set-ups. The variation of the residuals between the different set-ups was not significant.

Mapping an index of the myelin g-ratio in infants using magnetic resonance imaging

PubMed Central

Dean, Douglas C.; O'Muircheartaigh, Jonathan; Dirks, Holly; Travers, Brittany G.; Adluru, Nagesh; Alexander, Andrew L.; Deoni, Sean C.L.

2016-01-01

Optimal myelination of neuronal axons is essential for effective brain and cognitive function. The ratio of the axon diameter to the outer fiber diameter, known as the g-ratio, is a reliable measure to assess axonal myelination and is an important index reflecting the efficiency and maximal conduction velocity of white matter pathways. Although advanced neuroimaging techniques including multicomponent relaxometry (MCR) and diffusion tensor imaging afford insight into the microstructural characteristics of brain tissue, by themselves they do not allow direct analysis of the myelin g-ratio. Here, we show that by combining myelin content information (obtained with mcDESPOT MCR) with neurite density information (obtained through NODDI diffusion imaging) an index of the myelin g-ratio may be estimated. Using this framework, we present the first quantitative study of myelin g-ratio index changes across childhood, examining 18 typically developing children 3 months to 7.5 years of age. We report a spatio-temporal pattern of maturation that is consistent with histological and developmental MRI studies, as well as theoretical studies of the myelin g-ratio. This work represents the first ever in vivo visualization of the evolution of white matter g-ratio indices throughout early childhood. PMID:26908314

Molecular population genetics of X-linked genes in Drosophila pseudoobscura.

PubMed Central

Kovacevic, M; Schaeffer, S W

2000-01-01

This article presents a nucleotide sequence analysis of 500 bp determined in each of five X-linked genes, runt, sisterlessA, period, esterase 5, and Heat-shock protein 83, in 40 Drosophila pseudoobscura strains collected from two populations. Estimates of the neutral migration parameter for the five loci show that gene flow among D. pseudoobscura populations is sufficient to homogenize inversion frequencies across the range of the species. Nucleotide diversity at each locus fails to reject a neutral model of molecular evolution. The sample of 40 chromosomes included six Sex-ratio inversions, a series of three nonoverlapping inversions that are associated with a strong meiotic drive phenotype. The selection driven by the Sex-ratio meiotic drive element has not fixed variation across the X chromosome of D. pseudoobscura because, while significant linkage disequilibrium was observed within the sisterlessA, period, and esterase 5 genes, we did not find evidence for nonrandom association among loci. The Sex-ratio chromosome was estimated to be 25,000 years old based on the decomposition of linkage disequilibrium between esterase 5 and Heat-shock protein 83 or 1 million years old based on the net divergence of esterase 5 between Standard and Sex-ratio chromosomes. Genetic diversity was depressed within esterase 5 within Sex-ratio chromosomes, while the four other genes failed to show a reduction in heterozygosity in the Sex-ratio background. The reduced heterogeneity in esterase 5 is due either to its location near one of the Sex-ratio inversion breakpoints or that it is closely linked to a gene or genes responsible for the Sex-ratio meiotic drive system. PMID:10978282

Influence of ground level SO2 on the diffuse to direct irradiance ratio in the middle ultraviolet

NASA Technical Reports Server (NTRS)

Klenk, K. F.; Green, A. E. S.

1977-01-01

The dependence of the ratio of the diffuse to direct irradiances at the ground were examined for a wavelength of 315.1 nm. A passive remote sensing method based on ratio measurements for obtaining the optical thickness of SO2 in the vertical column was proposed. If, in addition to the ratio measurements, the SO2 density at the ground is determining using an appropriate point-sampling technique then some inference on the vertical extent of SO2 can be drawn. An analytic representation is presented of the ratio for a wide range of SO2 and aerosol optical thicknesses and solar zenith angles which can be inverted algebraically to give the SO2 optical thickness in terms of the measured ratio, aerosol optical thickness and solar zenith angle.

Changing carbon isotope ratio of atmospheric carbon dioxide: implications for food authentication.

PubMed

Peck, William H; Tubman, Stephanie C

2010-02-24

Carbon isotopes are often used to detect the addition of foreign sugars to foods. This technique takes advantage of the natural difference in carbon isotope ratio between C(3) and C(4) plants. Many foods are derived from C(3) plants, but the low-cost sweeteners corn and sugar cane are C(4) plants. Most adulteration studies do not take into account the secular shift of the carbon isotope ratio of atmospheric carbon dioxide caused by fossil fuel burning, a shift also seen in plant tissues. As a result statistical tests and threshold values that evaluate authenticity of foods based on carbon isotope ratios may need to be corrected for changing atmospheric isotope values. Literature and new data show that the atmospheric trend in carbon isotopes is seen in a 36-year data set of maple syrup analyses (n = 246), demonstrating that published thresholds for cane or corn sugar adulteration in maple syrup (and other foods) have become progressively more lenient over time.

Electric-field-ratio profiling at the Silsilah tin-bearing greisen deposit, Kingdom of Saudi Arabia

USGS Publications Warehouse

Kamilli, R.J.; Zablocki, C.J.

1993-01-01

Buried, possibly mineralized granite cupolas at the Silsilah tin deposit in Saudi Arabia have been successfully located using a closely spaced electric-field-ratio profiling technique. In this study electrical fields at 27 and 270 Hz across grounded electrodes spaced 50m apart were measured along six traverses. The technique allowed the authors to identify and distinguish among unroofed granite cupolas, cupolas with their aplite-pegmatite apical contact zones intact, strong and weak greisens, dikes, faults, and pervasively argillized rocks. -from Authors

A certain ratio? The policy implications of minimum staffing ratios in nursing.

PubMed

Buchan, James

2005-10-01

The debate about how best to determine nurse staffing levels continues. The conventional wisdom is that determining staffing levels is something best left to local management, taking account of local workload and resources. This 'bottom up' philosophy has now been challenged by the use of a different approach--the use of 'top down'standardized, and mandatory, nurse:patient or nurse:bed ratios. This paper examines the characteristics and early results of the use of staffing ratios in the two health systems where nurse staffing ratios are now mandatory--the states of Victoria (Australia) and California (USA). It then discusses the policy implications of using ratios. The paper identifies the main weaknesses of the use of nurse:patient ratios as being their relative inflexibility and their potential inefficiency, if they are wrongly calibrated. Their strength is their simplicity and their transparency. Their impact will be most pronounced when ratios are mandatory and where they offer a mechanism to improve and then to maintain staffing levels at some pre-determined level. The biggest challenges in their use are calibration (what is 'safe'? or 'minimum'?) and achieving the support of all stake-holders. The paper concludes that nurse:patient ratios are a blunt instrument for achieving employer compliance, where reliance on alternative, voluntary (and often more sophisticated) methods of determining nurse staffing have not been effective.

Evaluation of a rule-based compositing technique for Landsat-5 TM and Landsat-7 ETM+ images

NASA Astrophysics Data System (ADS)

Lück, W.; van Niekerk, A.

2016-05-01

Image compositing is a multi-objective optimization process. Its goal is to produce a seamless cloud and artefact-free artificial image. This is achieved by aggregating image observations and by replacing poor and cloudy data with good observations from imagery acquired within the timeframe of interest. This compositing process aims to minimise the visual artefacts which could result from different radiometric properties, caused by atmospheric conditions, phenologic patterns and land cover changes. It has the following requirements: (1) image compositing must be cloud free, which requires the detection of clouds and shadows, and (2) the image composite must be seamless, minimizing artefacts and visible across inter image seams. This study proposes a new rule-based compositing technique (RBC) that combines the strengths of several existing methods. A quantitative and qualitative evaluation is made of the RBC technique by comparing it to the maximum NDVI (MaxNDVI), minimum red (MinRed) and maximum ratio (MaxRatio) compositing techniques. A total of 174 Landsat TM and ETM+ images, covering three study sites and three different timeframes for each site, are used in the evaluation. A new set of quantitative/qualitative evaluation techniques for compositing quality measurement was developed and showed that the RBC technique outperformed all other techniques, with MaxRatio, MaxNDVI, and MinRed techniques in order of performance from best to worst.

Comparison of two target classification techniques

NASA Astrophysics Data System (ADS)

Chen, J. S.; Walton, E. K.

1986-01-01

Radar target classification techniques based on backscatter measurements in the resonance region (1.0-20.0 MHz) are discussed. Attention is given to two novel methods currently being tested at the radar range of Ohio State University. The methods include: (1) the nearest neighbor (NN) algorithm for determining the radar cross section (RCS) magnitude and range corrected phase at various operating frequencies; and (2) an inverse Fourier transformation of the complex multifrequency radar returns of the time domain, followed by cross correlation analysis. Comparisons are made of the performance of the two techniques as a function of signal-to-error noise ratio for different types of processing. The results of the comparison are discussed in detail.

The sensitivity of gas-phase models of dense interstellar clouds to changes in dissociative recombination branching ratios

NASA Technical Reports Server (NTRS)

Millar, T. J.; Defrees, D. J.; Mclean, A. D.; Herbst, E.

1988-01-01

The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilized in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called 'early time' when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios.

Effects of a Signaled Delay to Reinforcement in the Previous and Upcoming Ratios on Between-Ratio Pausing in Fixed-Ratio Schedules

ERIC Educational Resources Information Center

Harris, Aimee; Foster, T. Mary; Levine, Joshua; Temple, William

2012-01-01

Domestic hens responded under multiple fixed-ratio fixed-ratio schedules with equal fixed ratios. One component provided immediate reinforcement and the other provided reinforcement after a delay, signaled by the offset of the key light. The components were presented quasi-randomly so that all four possible transitions occurred in each session.…

DSPI technique for nanometer vibration mode measurement

NASA Astrophysics Data System (ADS)

Yue, Kaiduan; Jia, Shuhai; Tan, Yushan

2000-05-01

A time-average DSPI method for nanometer vibration mode measurement is presented in this paper. The phase continuous scan technique is combined with the Bessel fringe-shifting technique to quantitatively analyze the vibration mode by time-average DSPI is used in measurement system. Through the phase continuous scan, the background and speckle items are completely eliminated, which improves the fringe quality and enhances the signal-to-noise ratio of interferogram. There is no need to calibrate the optical phase-shifter exactly in this method. The anti-disturbance capability of this method is higher than that of the phase-stepping technique, so it is robust and easy to be used. In the vibration measurement system, the speckle average technology is used, so the high quality measuring results are obtained.

The aspect ratio effects on the performances of GaN-based light-emitting diodes with nanopatterned sapphire substrates

NASA Astrophysics Data System (ADS)

Kao, Chien-Chih; Su, Yan-Kuin; Lin, Chuing-Liang; Chen, Jian-Jhong

2010-07-01

The nanopatterned sapphire substrates (NPSSs) with aspect ratio that varied from 2.00 to 2.50 were fabricated by nanoimprint lithography. We could improve the epitaxial film quality and enhance the light extraction efficiency by NPSS technique. In this work, the aspect ratio effects on the performances of GaN-based light-emitting diodes (LEDs) with NPSS were investigated. The light output enhancement of GaN-based LEDs with NPSS was increased from 11% to 27% as the aspect ratio of the NPSS increases from 2.00 to 2.50. Owing to the same improvement of crystalline quality by using various aspect ratios of NPSS, these results indicated that the aspect ratio of the NPSS is strongly related to the light extraction efficiency.

Small feature sizes and high aperture ratio organic light-emitting diodes by using laser-patterned polyimide shadow masks

NASA Astrophysics Data System (ADS)

Kajiyama, Yoshitaka; Joseph, Kevin; Kajiyama, Koichi; Kudo, Shuji; Aziz, Hany

2014-02-01

A shadow mask technique capable of realizing high resolution (>330 pixel-per-inch) and ˜100% aperture ratio Organic Light-Emitting Diode (OLED) full color displays is demonstrated. The technique utilizes polyimide contact shadow masks, patterned by laser ablation. Red, green, and blue OLEDs with very small feature sizes (<25 μm) are fabricated side by side on one substrate. OLEDs fabricated via this technique have the same performance as those made by established technology. This technique has a strong potential to achieve high resolution OLED displays via standard vacuum deposition processes even on flexible substrates.

Real-time holographic deconvolution techniques for one-way image transmission through an aberrating medium: characterization, modeling, and measurements.

PubMed

Haji-Saeed, B; Sengupta, S K; Testorf, M; Goodhue, W; Khoury, J; Woods, C L; Kierstead, J

2006-05-10

We propose and demonstrate a new photorefractive real-time holographic deconvolution technique for adaptive one-way image transmission through aberrating media by means of four-wave mixing. In contrast with earlier methods, which typically required various codings of the exact phase or two-way image transmission for correcting phase distortion, our technique relies on one-way image transmission through the use of exact phase information. Our technique can simultaneously correct both amplitude and phase distortions. We include several forms of image degradation, various test cases, and experimental results. We characterize the performance as a function of the input beam ratios for four metrics: signal-to-noise ratio, normalized root-mean-square error, edge restoration, and peak-to-total energy ratio. In our characterization we use false-color graphic images to display the best beam-intensity ratio two-dimensional region(s) for each of these metrics. Test cases are simulated at the optimal values of the beam-intensity ratios. We demonstrate our results through both experiment and computer simulation.

Effect of one-rescuer compression/ventilation ratios on cardiopulmonary resuscitation in infant, pediatric, and adult manikins.

PubMed

Srikantan, Shoba Krishnan; Berg, Robert A; Cox, Tim; Tice, Lisa; Nadkarni, Vinay M

2005-05-01

effective compressions and ventilations delivered during ideal, metronome-paced, one-rescuer CPR. Low ratios of 3:1, 5:1, and 10:2 favor ventilation, and high ratios of 15:2 favor compression, especially in adult manikins. Rescuers subjectively preferred C:V ratios of 10:2 and 15:2 over 3:1 or 5:1. Infant CPR caused less exertion and subjective fatigue than pediatric or adult CPR technique, without significant difference by C:V ratio. We speculate that a universal 10:2 C:V ratio for one-rescuer layperson CPR is physiologically reasonable but warrants further study with particular attention to educational value and technique retention.

Stable estimate of primary OC/EC ratios in the EC tracer method

NASA Astrophysics Data System (ADS)

Chu, Shao-Hang

In fine particulate matter studies, the primary OC/EC ratio plays an important role in estimating the secondary organic aerosol contribution to PM2.5 concentrations using the EC tracer method. In this study, numerical experiments are carried out to test and compare various statistical techniques in the estimation of primary OC/EC ratios. The influence of random measurement errors in both primary OC and EC measurements on the estimation of the expected primary OC/EC ratios is examined. It is found that random measurement errors in EC generally create an underestimation of the slope and an overestimation of the intercept of the ordinary least-squares regression line. The Deming regression analysis performs much better than the ordinary regression, but it tends to overcorrect the problem by slightly overestimating the slope and underestimating the intercept. Averaging the ratios directly is usually undesirable because the average is strongly influenced by unrealistically high values of OC/EC ratios resulting from random measurement errors at low EC concentrations. The errors generally result in a skewed distribution of the OC/EC ratios even if the parent distributions of OC and EC are close to normal. When measured OC contains a significant amount of non-combustion OC Deming regression is a much better tool and should be used to estimate both the primary OC/EC ratio and the non-combustion OC. However, if the non-combustion OC is negligibly small the best and most robust estimator of the OC/EC ratio turns out to be the simple ratio of the OC and EC averages. It not only reduces random errors by averaging individual variables separately but also acts as a weighted average of ratios to minimize the influence of unrealistically high OC/EC ratios created by measurement errors at low EC concentrations. The median of OC/EC ratios ranks a close second, and the geometric mean of ratios ranks third. This is because their estimations are insensitive to questionable extreme

Origin discrimination of defatted pork via trace elements profiling, stable isotope ratios analysis, and multivariate statistical techniques.

PubMed

Park, Yu Min; Lee, Cheong Mi; Hong, Joon Ho; Jamila, Nargis; Khan, Naeem; Jung, Jong-Hyun; Jung, Young-Chul; Kim, Kyong Su

2018-09-01

This study verified the origin of 346 defatted Korean and non-Korean pork samples via trace elements profiling, and C and N stable isotope ratios analysis. The analyzed elements were 6 Li, 7 Li, 10 B, 11 B, 51 V , 50 Cr, 52 Cr, 53 Cr, 55 Mn, 58 Ni, 60 Ni, 59 Co, 63 Cu, 65 Cu, 64 Zn, 66 Zn, 69 Ga, 71 Ga, 75 As, 82 Se, 84 Sr, 86 Sr, 87 Sr, 88 Sr, 85 Rb, 94 Mo, 95 Mo, 97 Mo, 107 Ag, 109 Ag, 110 Cd, 111 Cd, 113 Cd, 112 Cd, 114 Cd, 116 Cd, 133 Cs, 206 Pb, 207 Pb, and 208 Pb. Content (mg/kg) of 51 V (0.012), 50 Cr (0.882), 75 As (0.017), 85 Rb (57.7), and 87 Sr (46.3) were high in Korean pork samples whereas 6 Li, 7 Li, 59 Co, 55 Mn, 58 Ni, 84 Sr, 86 Sr, 88 Sr, 111 Cd, and 133 Cs were found higher in non-Korean samples. The results of discriminant analysis showed that the trace elements content and stable isotope ratios were significant for the discrimination of geographical origins with a perfect discrimination rate of 100%. Copyright © 2018 Elsevier Ltd. All rights reserved.

A comparative study of progressive versus successive spectrophotometric resolution techniques applied for pharmaceutical ternary mixtures

NASA Astrophysics Data System (ADS)

Saleh, Sarah S.; Lotfy, Hayam M.; Hassan, Nagiba Y.; Salem, Hesham

2014-11-01

This work represents a comparative study of a novel progressive spectrophotometric resolution technique namely, amplitude center method (ACM), versus the well-established successive spectrophotometric resolution techniques namely; successive derivative subtraction (SDS); successive derivative of ratio spectra (SDR) and mean centering of ratio spectra (MCR). All the proposed spectrophotometric techniques consist of several consecutive steps utilizing ratio and/or derivative spectra. The novel amplitude center method (ACM) can be used for the determination of ternary mixtures using single divisor where the concentrations of the components are determined through progressive manipulation performed on the same ratio spectrum. Those methods were applied for the analysis of the ternary mixture of chloramphenicol (CHL), dexamethasone sodium phosphate (DXM) and tetryzoline hydrochloride (TZH) in eye drops in the presence of benzalkonium chloride as a preservative. The proposed methods were checked using laboratory-prepared mixtures and were successfully applied for the analysis of pharmaceutical formulation containing the cited drugs. The proposed methods were validated according to the ICH guidelines. A comparative study was conducted between those methods regarding simplicity, limitation and sensitivity. The obtained results were statistically compared with those obtained from the official BP methods, showing no significant difference with respect to accuracy and precision.

Increased depth-diameter ratios in the Medusae Fossae Formation deposits of Mars

NASA Technical Reports Server (NTRS)

Barlow, N. G.

1993-01-01

Depth to diameter ratios for fresh impact craters on Mars are commonly cited as approximately 0.2 for simple craters and 0.1 for complex craters. Recent computation of depth-diameter ratios in the Amazonis-Memnonia region of Mars indicates that craters within the Medusae Fossae Formation deposits found in this region display greater depth-diameter ratios than expected for both simple and complex craters. Photoclinometric and shadow length techniques have been used to obtain depths of craters within the Amazonis-Memnonia region. The 37 craters in the 2 to 29 km diameter range and displaying fresh impact morphologies were identified in the area of study. This region includes the Amazonian aged upper and middle members of the Medusae Fossae Formation and Noachian aged cratered and hilly units. The Medusae Fossae Formation is characterized by extensive, flat to gently undulating deposits of controversial origin. These deposits appear to vary from friable to indurated. Early analysis of crater degradation in the Medusae Fossae region suggested that simple craters excavated to greater depths than expected based on the general depth-diameter relationships derived for Mars. However, too few craters were available in the initial analysis to estimate the actual depth-diameter ratios within this region. Although the analysis is continuing, we are now beginning to see a convergence towards specific values for the depth-diameter ratio depending on geologic unit.

SU-E-I-49: Influence of Scanner Output Measurement Technique on KERMA Ratios in CT.

PubMed

Ogden, K; Roskopf, M; Scalzetti, E

2012-06-01

KERMA ratios (RK) are defined as the ratio of KERMA measured at a specific phantom location (K) to in-air isocenter CT scanner output (KCT). In this work we investigate the impact of measurement methodology on KCT values. OSL dosimeter chips were used to measure KCT for a GE VCT scanner (GE Medical Systems, Waukesha WI), using the 40 mm nominal beam width. Methods included a single point measurement at the center of the beam (1 tube rotation), and extended z-axis measurements using multiple adjacent OSL's (7.5 cm extent), with single tube rotation, multiple contiguous axial scans, and helical scans (pitch of 1.375). Measurements were made in air and on the scan table at 80 and 120 kV. Averaged single point measurements were consistent, with a mean coefficient of variation of 2.5%. For extended measurements with a single tube rotation, the mean value was equivalent to the single point measurements. For multiple contiguous axial scans, the in-air KCT values were higher than the single rotation mean value and single point measurements by 13% and 10.3% at 120 and 80 kV, respectively, and for the on-table measurements the values were 14.9% and 8.1% higher at 120 and 80 kV, respectively. The increase is due to beam overlap caused by z- axis over-beaming. Extended measurements using helical scanning were equivalent to the multiple rotation axial measurements when corrected for the helical pitch. For all methodologies, the in-air values exceeded the on- table measurements by an average of 23% and 19.4% at 80 and 120 kV, respectively. Scanner KCT values must be measured to allow organ dose estimation using published RK values. It is imperative that the KCT measurement methodology is the same as for the published values, or large errors may be introduced into the resulting organ dose estimates. © 2012 American Association of Physicists in Medicine.

Extinction-to-Backscatter Ratios of Lofted Aerosol Layers Observed During the First Three Months of CALIPSO Measurements

NASA Technical Reports Server (NTRS)

Omar, Ali H.; Vaughan, Mark A.; Liu, Zhaoyan; Hu, Yongxiang; Reagan, John A.; Winker, David M.

2007-01-01

Case studies from the first three months of the Cloud and Aerosol Lidar and Infrared Pathfinder Spaceborne Observations (CALIPSO) measurements of lofted aerosol layers are analyzed using transmittance [Young, 1995] and two-wavelength algorithms [Vaughan et al., 2004] to determine the aerosol extinction-to-backscatter ratios at 532 and 1064 nm. The transmittance method requires clear air below the layer so that the transmittance through the layer can be determined. Suitable scenes are selected from the browse images and clear air below features is identified by low 532 nm backscatter signal and confirmed by low depolarization and color ratios. The transmittance and two-wavelength techniques are applied to a number of lofted layers and the extinction-to-backscatter ratios are compared with values obtained from the CALIPSO aerosol models [Omar et al., 2004]. The results obtained from these studies are used to adjust the aerosol models and develop observations based extinction-to-backscatter ratio look-up tables and phase functions. Values obtained by these techniques are compared to Sa determinations using other independent methods with a goal of developing probability distribution functions of aerosol type-specific extinction to backscatter ratios. In particular, the results are compared to values determined directly by the High Spectral Resolution Lidar (HSRL) during the CALIPSO CloudSat Validation Experiments (CCVEX) and Sa determined by the application of the two-wavelength lidar Constrained Ratio Aerosol Model-fit (CRAM) retrieval approach [Cattrall et al., 2005; Reagan et al., 2004] to the HSRL data. The results are also compared to values derived using the empirical relationship between the multiple-scattering fraction and the linear depolarization ratio by using Monte Carlo simulations of water clouds [Hu et al., 2006].

Sex versus asex: An analysis of the role of variance conversion.

PubMed

Lewis-Pye, Andrew E M; Montalbán, Antonio

2017-04-01

The question as to why most complex organisms reproduce sexually remains a very active research area in evolutionary biology. Theories dating back to Weismann have suggested that the key may lie in the creation of increased variability in offspring, causing enhanced response to selection. Under appropriate conditions, selection is known to result in the generation of negative linkage disequilibrium, with the effect of recombination then being to increase genetic variance by reducing these negative associations between alleles. It has therefore been a matter of significant interest to understand precisely those conditions resulting in negative linkage disequilibrium, and to recognise also the conditions in which the corresponding increase in genetic variation will be advantageous. Here, we prove rigorous results for the multi-locus case, detailing the build up of negative linkage disequilibrium, and describing the long term effect on population fitness for models with and without bounds on fitness contributions from individual alleles. Under the assumption of large but finite bounds on fitness contributions from alleles, the non-linear nature of the effect of recombination on a population presents serious obstacles in finding the genetic composition of populations at equilibrium, and in establishing convergence to those equilibria. We describe techniques for analysing the long term behaviour of sexual and asexual populations for such models, and use these techniques to establish conditions resulting in higher fitnesses for sexually reproducing populations. Copyright © 2017 Elsevier Inc. All rights reserved.

Assay for uranium and determination of disequilibrium by means of in situ high resolution gamma-ray spectrometry

USGS Publications Warehouse

Tanner, Allan B.; Moxham, Robert M.; Senftle, F.E.

1977-01-01

Two sealed sondes, using germanium gamma-ray detectors cooled by melting propane, have been field tested to depths of 79 m in water-filled boreholes at the Pawnee Uranium Mine in Bee Co., Texas. When, used as total-count devices, the sondes are comparable in logging speed and counting rate with conventional scintillation detectors for locating zones of high radioactivity. When used with a multichannel analyzer, the sondes are detectors with such high resolution that individual lines from the complex spectra of the uranium and thorium series can be distinguished. Gamma rays from each group of the uranium series can be measured in ore zones permitting determination of the state of equilibrium at each measurement point. Series of 10-minute spectra taken at 0.3- to 0.5-m intervals in several holes showed zones where maxima from the uranium group and from the 222Rn group were displaced relative to each other. Apparent excesses of 230Th at some locations suggest that uranium-group concentrations at those locations were severalfold greater some tens of kiloyears, ago. At the current state of development a 10-minute count yields a sensitivity of about 80 ppm U308. Data reduction could in practice be accomplished in about 5 minutes. The result is practically unaffected by disequilibrium or radon contamination. In comparison with core assay, high-resolution spectrometry samples a larger volume; avoids problems due to incomplete core recovery, loss of friable material to drilling fluids, and errors in depth and marking; and permits use of less expensive drilling methods. Because gamma rays from the radionuclides are accumulated simultaneously, it also avoids the problems inherent in trying to correlate logs made in separate runs with different equipment. Continuous-motion delayed-gamma activation by a 163-?g 252Cf neutron source attached to the sonde yielded poor sensitivity. A better neutron-activation method, in which the sonde is moved in steps so as to place the detector

High-throughput measurements of the optical redox ratio using a commercial microplate reader.

PubMed

Cannon, Taylor M; Shah, Amy T; Walsh, Alex J; Skala, Melissa C

2015-01-01

There is a need for accurate, high-throughput, functional measures to gauge the efficacy of potential drugs in living cells. As an early marker of drug response in cells, cellular metabolism provides an attractive platform for high-throughput drug testing. Optical techniques can noninvasively monitor NADH and FAD, two autofluorescent metabolic coenzymes. The autofluorescent redox ratio, defined as the autofluorescence intensity of NADH divided by that of FAD, quantifies relative rates of cellular glycolysis and oxidative phosphorylation. However, current microscopy methods for redox ratio quantification are time-intensive and low-throughput, limiting their practicality in drug screening. Alternatively, high-throughput commercial microplate readers quickly measure fluorescence intensities for hundreds of wells. This study found that a commercial microplate reader can differentiate the receptor status of breast cancer cell lines (p < 0.05) based on redox ratio measurements without extrinsic contrast agents. Furthermore, microplate reader redox ratio measurements resolve response (p < 0.05) and lack of response (p > 0.05) in cell lines that are responsive and nonresponsive, respectively, to the breast cancer drug trastuzumab. These studies indicate that the microplate readers can be used to measure the redox ratio in a high-throughput manner and are sensitive enough to detect differences in cellular metabolism that are consistent with microscopy results.

High-Precision Isotope Ratio Measurements of Sub-Picogram Actinide Samples

NASA Astrophysics Data System (ADS)

Pollington, A. D.; Kinman, W.

2016-12-01

One of the most exciting trends in analytical geochemistry over the past decade is the push towards smaller and smaller sample sizes while simultaneously achieving high precision isotope ratio measurements. This trend has been driven by advances in clean chemistry protocols, and by significant breakthroughs in mass spectrometer ionization efficiency and detector quality (stability and noise for low signals). In this presentation I will focus on new techniques currently being developed at Los Alamos National Laboratory for the characterization of ultra-small samples (pg, fg, ag), with particular focus on actinide measurements by MC-ICP-MS. Analyses of U, Pu, Th and Am are routinely carried out in our facility using multi-ion counting techniques. I will describe some of the challenges associated with using exclusively ion counting methods (e.g., stability, detector cross calibration, etc.), and how we work to mitigate them. While the focus of much of the work currently being carried out is in the broad field of nuclear forensics and safeguards, the techniques that are being developed are directly applicable to many geologic questions that require analyses of small samples of U and Th, for example. In addition to the description of the technique development, I will present case studies demonstrating the precision and accuracy of the method as applied to real-world samples.

The ZH ratio Analysis of Global Seismic Data

NASA Astrophysics Data System (ADS)

Yano, T.; Shikato, S.; Rivera, L.; Tanimoto, T.

2007-12-01

The ZH ratio, the ratio of vertical to horizontal component of the fundamental Rayleigh wave as a function of frequency, is an alternative approach to phase/group velocity analysis for constructing the S-wave velocity structure. In this study, teleseismic Rayleigh wave data for the frequency range between 0.004Hz to 0.04Hz is used to investigate the interior structure. We have analyzed most of the GEOSCOPE network data and some IRIS GSN stations using a technique developed by Tanimoto and Rivera (2007). Stable estimates of the ZH ratios were obtained for the frequency range for most stations. We have performed the inversion of the measured ZH ratios for the structure in the crust and mantle by using nonlinear iterative scheme. The depth sensitivity kernels for inversion are numerically calculated. Depth sensitivity of the lowest frequency extends to depths beyond 500 km but the sensitivity of the overall data for the frequency band extends down to about 300km. We found that an appropriate selection of an initial model, particularly the depth of Mohorovicic discontinuity, is important for this inversion. The inversion result depends on the initial model and turned out to be non-unique. We have constructed the initial model from the CRUST 2.0. Inversion with equal weighting to each data point tends to reduce variance of certain frequency range only. Therefore, we have developed a scheme to increase weighting to data points that do not fit well after the fifth iteration. This occurs more often for low frequency range, 0.004-0.007Hz. After fitting the lower frequency region, the low velocity zone around a depth of 100km is observed under some stations such as KIP (Kipapa, Hawaii) and ATD (Arta Cave, Djibouti). We have also carried out an analysis on the resolving power of data by examining the eigenvalues-eigenvectors of the least-squares problem. Unfortunately, the normal matrix usually has 1-2 very large eigenvalues, followed by much smaller eigenvalues. The third

Compression Ratio Adjuster

NASA Technical Reports Server (NTRS)

Akkerman, J. W.

1982-01-01

New mechanism alters compression ratio of internal-combustion engine according to load so that engine operates at top fuel efficiency. Ordinary gasoline, diesel and gas engines with their fixed compression ratios are inefficient at partial load and at low-speed full load. Mechanism ensures engines operate as efficiently under these conditions as they do at highload and high speed.

Changes in stimulus and response AC/A ratio with vision therapy in Convergence Insufficiency.

PubMed

Singh, Neeraj Kumar; Mani, Revathy; Hussaindeen, Jameel Rizwana

To evaluate the changes in the stimulus and response Accommodative Convergence to Accommodation (AC/A) ratio following vision therapy (VT) in Convergence Insufficiency (CI). Stimulus and response AC/A ratio were measured on twenty five CI participants, pre and post 10 sessions of VT. Stimulus AC/A ratio was measured using the gradient method and response AC/A ratio was calculated using modified Thorington technique with accommodative responses measured using WAM-5500 open-field autorefractor. The gradient stimulus and response AC/A cross-link ratios were compared with thirty age matched controls. Mean age of the CI and control participants were 23.3±5.2 years and 22.7±4.2 years, respectively. The mean stimulus and response AC/A ratio for CI pre therapy was 2.2±0.72 and 6.3±2.0 PD/D that changed to 4.2±0.9 and 8.28±3.31 PD/D respectively post vision therapy and these changes were statistically significant (paired t-test; p<0.001). The mean stimulus and response AC/A ratio for controls was 3.1±0.81 and 8.95±2.5 PD/D respectively. Stimulus and response AC/A ratio increased following VT, accompanied by clinically significant changes in vergence and accommodation parameters in subjects with convergence insufficiency. This represents the plasticity of the AC/A crosslink ratios that could be achieved with vision therapy in CI. Copyright © 2016 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

Prevalence Odds Ratio versus Prevalence Ratio: Choice Comes with Consequences

PubMed Central

Tamhane, Ashutosh R; Westfall, Andrew O; Burkholder, Greer A; Cutter, Gary R

2016-01-01

Odds ratio (OR), risk ratio (RR), and prevalence ratio (PR) are some of the measures of association which are often reported in research studies quantifying the relationship between an independent variable and the outcome of interest. There has been much debate on the issue of which measure is appropriate to report depending on the study design. However, the literature on selecting a particular category of the outcome to be modeled and/or change in reference group for categorical independent variables and the effect on statistical significance, although known, is scantly discussed nor published with examples. In this article, we provide an example of a cross-sectional study wherein PR was chosen over (Prevalence) OR and demonstrate the analytic implications of the choice of category to be modeled and choice of reference level for independent variables. PMID:27460748

Feasibility of line-ratio spectroscopy on helium and neon as edge diagnostic tool for Wendelstein 7-X

DOE PAGES

Barbui, T.; Krychowiak, M.; König, R.; ...

2016-09-27

A beam emission spectroscopy system on thermal helium (He) and neon (Ne) has been set up at Wendelstein 7-X to measure edge electron temperature and density profiles utilizing the line-ratio technique or its extension by the analysis of absolutely calibrated line emissions. The setup for a first systematic test of these techniques of quantitative atomic spectroscopy in the limiter startup phase (OP1.1) is reported together with first measured profiles. Lastly, this setup and the first results are an important test for developing the technique for the upcoming high density, low temperature island divertor regime.

Airborne intercomparison of nitric oxide measurement techniques

NASA Technical Reports Server (NTRS)

Hoell, James M., Jr.; Gregory, Gerald L.; Mcdougal, David S.; Torres, Arnold L.; Davis, Douglas D.

1987-01-01

Results from an airborne intercomparison of techniques to measure tropospheric levels of nitric oxide (NO) are discussed. The intercomparison was part of the National Aeronautics and Space Administration's Global Tropospheric Experiment and was conducted during missions flown in the fall of 1983 and spring of 1984. Instruments intercompared included a laser-induced fluorescence (LIF) system and two chemiluminescence instruments (CL). NO mixing ratios from below 5 pptv (parts per trillion by volume) to greater than 100 pptv were reported, with the majority less than 20 pptv. Good correlation was observed between the measurements reported by the CL and LIF techniques. The general level of agreement observed for the ensemble of measurements obtained during the two missions provides the basis from which one can conclude that equally 'valid' measurements of background levels of NO can be expected from either CL or LIF instruments. At the same time the periods of disagreement that were observed between the CL and LIF instruments as well as between the two CL instruments highlight the difficulty of obtaining reliable measurements with NO mixing ratios in the 5-20 pptv range and emphasize the vigilance that should be maintained in future NO measurements.

Selenium isotope ratios as indicators of selenium sources and oxyanion reduction

USGS Publications Warehouse

Johnson, T.M.; Herbel, M.J.; Bullen, T.D.; Zawislanski, P.T.

1999-01-01

Selenium stable isotope ratio measurements should serve as indicators of sources and biogeochemical transformations of Se. We report measurements of Se isotope fractionation during selenate reduction, selenite sorption, oxidation of reduced Se in soils, and Se volatilization by algae and soil samples. These results, combined with previous work with Se isotopes, indicate that reduction of soluble oxyanions is the dominant cause of Se isotope fractionation. Accordingly, Se isotope ratios should be useful as indicators of oxyanion reduction, which can transform mobile species to forms that are less mobile and less bioavailable. Additional investigations of Se isotope fractionation are needed to confirm this preliminary assessment. We have developed a new method for measurement of natural Se isotope ratio variation which requires less than 500 ng Se per analysis and yields ??0.2??? precision on 80Se/76Se. A double isotope spike technique corrects for isotopic fractionation during sample preparation and mass spectrometry. The small minimum sample size is important, as Se concentrations are often below 1 ppm in solids and 1 ??g/L in fluids. The Se purification process is rapid and compatible with various sample matrices, including acidic rock or sediment digests.

A preliminary evaluation of the generalized likelihood ratio for detecting and identifying control element failures in a transport aircraft

NASA Technical Reports Server (NTRS)

Bundick, W. T.

1985-01-01

The application of the Generalized Likelihood Ratio technique to the detection and identification of aircraft control element failures has been evaluated in a linear digital simulation of the longitudinal dynamics of a B-737 aircraft. Simulation results show that the technique has potential but that the effects of wind turbulence and Kalman filter model errors are problems which must be overcome.

Do Hf isotopes in magmatic zircons represent those of their host rocks?

NASA Astrophysics Data System (ADS)

Wang, Di; Wang, Xiao-Lei; Cai, Yue; Goldstein, Steven L.; Yang, Tao

2018-04-01

Lu-Hf isotopic system in zircon is a powerful and widely used geochemical tracer in studying petrogenesis of magmatic rocks and crustal evolution, assuming that zircon Hf isotopes can represent initial Hf isotopes of their parental whole rock. However, this assumption may not always be valid. Disequilibrium partial melting of continental crust would preferentially melt out non-zircon minerals with high time-integrated Lu/Hf ratios and generate partial melts with Hf isotope compositions that are more radiogenic than those of its magma source. Dissolution experiments (with hotplate, bomb and sintering procedures) of zircon-bearing samples demonstrate this disequilibrium effect where partial dissolution yielded variable and more radiogenic Hf isotope compositions than fully dissolved samples. A case study from the Neoproterozoic Jiuling batholith in southern China shows that about half of the investigated samples show decoupled Hf isotopes between zircons and the bulk rocks. This decoupling could reflect complex and prolonged magmatic processes, such as crustal assimilation, magma mixing, and disequilibrium melting, which are consistent with the wide temperature spectrum from ∼630 °C to ∼900 °C by Ti-in-zircon thermometer. We suggest that magmatic zircons may only record the Hf isotopic composition of their surrounding melt during crystallization and it is uncertain whether their Hf isotopic compositions can represent the primary Hf isotopic compositions of the bulk magmas. In this regard, using zircon Hf isotopic compositions to trace crustal evolution may be biased since most of these could be originally from disequilibrium partial melts.

A Comparison of seismic instrument noise coherence analysis techniques

USGS Publications Warehouse

Ringler, A.T.; Hutt, C.R.; Evans, J.R.; Sandoval, L.D.

2011-01-01

The self-noise of a seismic instrument is a fundamental characteristic used to evaluate the quality of the instrument. It is important to be able to measure this self-noise robustly, to understand how differences among test configurations affect the tests, and to understand how different processing techniques and isolation methods (from nonseismic sources) can contribute to differences in results. We compare two popular coherence methods used for calculating incoherent noise, which is widely used as an estimate of instrument self-noise (incoherent noise and self-noise are not strictly identical but in observatory practice are approximately equivalent; Holcomb, 1989; Sleeman et al., 2006). Beyond directly comparing these two coherence methods on similar models of seismometers, we compare how small changes in test conditions can contribute to incoherent-noise estimates. These conditions include timing errors, signal-to-noise ratio changes (ratios between background noise and instrument incoherent noise), relative sensor locations, misalignment errors, processing techniques, and different configurations of sensor types.

Bowen ratio/energy balance technique for estimating crop net CO2 assimilation, and comparison with a canopy chamber

NASA Astrophysics Data System (ADS)

Held, A. A.; Steduto, P.; Orgaz, F.; Matista, A.; Hsiao, T. C.

1990-12-01

This paper describes a Bowen ratio/energy balance (BREB) system which, in conjunction with an infra-red gas analyzer (IRGA), is referred to as BREB+ and is used to estimate evapotranspiration ( ET) and net CO2 flux ( NCF) over crop canopies. The system is composed of a net radiometer, soil heat flux plates, two psychrometers based on platinum resistance thermometers (PRT), bridge circuits to measure resistances, an IRGA, air pumps and switching valves, and a data logger. The psychrometers are triple shielded and aspirated, and with aspiration also between the two inner shields. High resistance (1 000 ohm) PRT's are used for dry and wet bulbs to minimize errors due to wiring and connector resistances. A high (55 K ohm) fixed resistance serves as one arm of the resistance bridge to ensure linearity in output signals. To minimize gaps in data, to allow measurements at short (e.g., 5 min) intervals, and to simplify operation, the psychrometers were fixed at their upper and lower position over the crop and not alternated. Instead, the PRT's, connected to the bridge circuit and the data logger, were carefully calibrated together. Field tests using a common air source showed appartent effects of the local environment around each psychrometer on the temperatures measured. ET rates estimated with the BREB system were compared to those measured with large lysimeters. Daily totals agreed within 5%. There was a tendency, however, for the lysimeter measurements to lag behind the BREB measurements. Daily patterns of NCF estimated with the BREB+ system are consistent with expectations from theories and data in the literature. Side-by-side comparisons with a stirred Mylar canopy chamber showed similar NCF patterns. On the other hand, discrepancies between the results of the two methods were quite marked in the morning or afternoon on certain dates. Part of the discrepancies may be attributed to inaccuracies in the psychrometric temperature measurements. Other possible causes

Mixing Characteristics of Coaxial Injectors at High Gas to Liquid Momentum Ratios

NASA Technical Reports Server (NTRS)

Strakey, P. A.; Talley, D. G.; Hutt, J. J.

1999-01-01

A study of the spray of a swirl coaxial gas-liquid injector operating at high gas to liquid momentum ratios is reported. Mixing and droplet size characteristics of the swirl injector are also compared to a shear coaxial injector, currently being used in the Space Shuttle Main Engine fuel preburner. The injectors were tested at elevated chamber pressures using water as a LOX simulant and nitrogen and helium as gaseous hydrogen simulants. The elevated chamber pressure allowed for matching of several of the preburner injector conditions including; gas to liquid momentum ratio, density ratio and Mach number. Diagnostic techniques used to characterize the spray included; strobe back-light imaging, laser sheet spray imaging, mechanical patternation, and a phase Doppler interferometry. Results thus far indicate that the radial spreading of the swirl coaxial spray is much less than was reported in previous studies of swirl injectors operating at atmospheric back-pressure. The swirl coaxial spray does, however, exhibit a smaller overall droplet size which may be interpreted as an increase in local mixing.

Determining the Spatial and Seasonal Variability in OM/OC Ratios across the U.S. Using Multiple Regression

EPA Science Inventory

Data from the Interagency Monitoring of Protected Visual Environments (IMPROVE) network are used to estimate organic mass to organic carbon (OM/OC) ratios across the United States by extending previously published multiple regression techniques. Our new methodology addresses com...

Aesthetic judgment of triangular shape: compactness and not the golden ratio determines perceived attractiveness

PubMed Central

Friedenberg, Jay

2012-01-01

Many studies over a period of more than a century have investigated the influence of the golden ratio on perceived geometric beauty. Surprisingly, very few of these studies used triangular shapes. In Experiment 1, we presented right triangles that differed in regard to their elongation determined by increasing the length of one side relative to another. Attractiveness ratings did not peak at the golden ratio, but there was a very strong influence of axis ratio overall. Participant ratings were a negative decreasing function of ratio. Triangles that pointed upward were judged as significantly more attractive than those that pointed down. We interpret these results according to a compactness hypothesis: triangles that are more compact are less likely to move or break and are thus considered more pleasing. Orientation also affects aesthetics. Upward-pointing triangles with a base parallel to the ground, regardless of their compactness, are also considered more perceptually stable and attractive. These findings were replicated across stimulus type in a second experiment with isosceles triangles and across testing procedure in a third experiment using a paired comparison technique. PMID:23145277

An efficient coordinate transformation technique for unsteady, transonic aerodynamic analysis of low aspect-ratio wings

NASA Technical Reports Server (NTRS)

Guruswamy, G. P.; Goorjian, P. M.

1984-01-01

An efficient coordinate transformation technique is presented for constructing grids for unsteady, transonic aerodynamic computations for delta-type wings. The original shearing transformation yielded computations that were numerically unstable and this paper discusses the sources of those instabilities. The new shearing transformation yields computations that are stable, fast, and accurate. Comparisons of those two methods are shown for the flow over the F5 wing that demonstrate the new stability. Also, comparisons are made with experimental data that demonstrate the accuracy of the new method. The computations were made by using a time-accurate, finite-difference, alternating-direction-implicit (ADI) algorithm for the transonic small-disturbance potential equation.

Scaling images using their background ratio. An application in statistical comparisons of images.

PubMed

Kalemis, A; Binnie, D; Bailey, D L; Flower, M A; Ott, R J

2003-06-07

Comparison of two medical images often requires image scaling as a pre-processing step. This is usually done with the scaling-to-the-mean or scaling-to-the-maximum techniques which, under certain circumstances, in quantitative applications may contribute a significant amount of bias. In this paper, we present a simple scaling method which assumes only that the most predominant values in the corresponding images belong to their background structure. The ratio of the two images to be compared is calculated and its frequency histogram is plotted. The scaling factor is given by the position of the peak in this histogram which belongs to the background structure. The method was tested against the traditional scaling-to-the-mean technique on simulated planar gamma-camera images which were compared using pixelwise statistical parametric tests. Both sensitivity and specificity for each condition were measured over a range of different contrasts and sizes of inhomogeneity for the two scaling techniques. The new method was found to preserve sensitivity in all cases while the traditional technique resulted in significant degradation of sensitivity in certain cases.

Mechanical property changes induced in structural alloys by neutron irradiations with different helium to displacement ratios*1

NASA Astrophysics Data System (ADS)

Mansur, L. K.; Grossbeck, M. L.

1988-07-01

Effects of helium on mechanical properties of irradiated structural materials are reviewed. In particular, variations in response to the ratio of helium to displacement damage serve as the focus. Ductility in creep and tensile tests is emphasized. A variety of early work has led to the current concentration on helium effects for fusion reactor materials applications. A battery of techniques has been developed by which the helium to displacement ratio can be varied. Our main discussion is devoted to the techniques of spectral tailoring and isotopic alloying currently of interest for mixed-spectrum reactors. Theoretical models of physical mechanisms by which helium interacts with displacement damage have been developed in terms of hardening to dislocation motion and grain boundary cavitation. Austenitic stainless steels, ferritic/martensitic steels and vanadium alloys are considered. In each case, work at low strain rates, where the main problems may lie, at the helium to displacement ratios appropriate to fusion reactor materials is lacking. Recent experimental evidence suggests that both in-reactor and high helium results may differ substantially from post-irradiation or low helium results. It is suggested that work in these areas is especially needed.