Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.

Genetic and migratory evidence for sympatric spawning of tropical Pacific eels from Vanuatu

The spawning areas of tropical anguillid eels in the South Pacific are poorly known, and more information about their life histories is needed to facilitate conservation. We genetically characterized 83 out of 84 eels caught on Gaua Island (Vanuatu) and tagged 8 eels with pop-up satellite transmitters. Based on morphological evidence, 32 eels were identified as Anguilla marmorata, 45 as A. megastoma and 7 as A. obscura. Thirteen of these eels possessed a mitochondrial DNA sequence (control region, 527 bp) or nuclear haplotype (GTH2b, 268 bp) conflicting with their species designation. These individuals also had multi-locus genotypes (6 microsatellite loci) intermediate between the species, and 9 of these eels further possessed heterozygote genotypes at species-diagnostic nuclear single nucleotide polymorphisms (SNPs). We classified these individuals as possibly admixed between A. marmorata and A. megastoma. One A. marmorata and 1 A. megastoma migrated 634 and 874 km, respectively, towards the border between the South Equatorial Current and the South Equatorial Counter Current. Both species descended from around 200 m depth at night to 750 m during the day. Lunar cycle affected the upper limit of migration depths of both species. The tags remained attached for 3 and 5 mo and surfaced <300 km from the pop-up location of a previously tagged A. marmorata pop-up location. A salinity maximum at the pop-up locations corresponding to the upper nighttime eel migration depths may serve as a seamark of the spawning area. The similar pop-up locations of both species and the evidence for admixture suggest that these tropical eels share a sympatric spawning area.

State-selective one-electron capture by slow state-prepared N2+(P-2) ground-state ions in collisions with hydrogen atoms

The technique of double translational energy spectroscopy.(DTES), recently successfully developed in this laboratory for use with targets of atomic hydrogen, has been used to study one-electron capture by ground-state N2+(2s22p)(2)p(0) ions in collisions with hydrogen atoms at energies within the range 0.8-6.0 keV. Cross sections for the formation of the main excited product channels have been determined. The measurements allow a re-evaluation of our previous TES measurements carried out with N2+ primary beams containing an admixture of metastable N2+(2s2p2)(4)p ions. The main findings of these earlier measurements are confirmed and the DTES measurements now remove any ambiguity in interpretation of the experimental data. While recent theoretical studies correctly predict the two main N+ D-3(0) and P-3(0) product channels, the quantitative agreement with experiment is only partially satisfactory.

Filling Ability and Passing Ability of Self-Consolidating Concrete

This paper reviews statistical models obtained from a composite factorial design study, which was carried out to determine the influence of three key parameters of mixture composition on filling ability and passing ability of self-consolidating concrete (SCC). This study was a part of the European project “Testing SCC”- GRD2-2000-30024. The parameters considered in this study were the dosages of water and high-range water-reducing admixture (HRWRA), and the volume of coarse aggregates. The responses of the derived statistical models were slump flow, T50 , T60, V-funnel flow time, Orimet flow time, and blocking ratio (L-box). The retention of these tests was also measured at 30 and 60 minutes after adding the first water. The models are valid for mixtures made with 188 to 208 L/m3 (317 to 350 lb/yd3) of water, 3.8 to 5.8 kg/m3 (570 to 970 mL/100 kg of binder) of HRWRA, and 220 to 360 L/m3 (5.97 to 9.76 ft3/yd3) of coarse aggregates. The utility of such models to optimize concrete mixtures and to achieve a good balance between filling ability and passing ability is discussed. Examples highlighting the usefulness of the models are presented using isoresponse surfaces to demonstrate single and coupled effects of mixture parameters on slump flow, T50 , T60 , V-funnel flow time, Orimet flow time, and blocking ratio. The paper also illustrates the various trade-offs between the mixture parameters on the derived responses that affected the filling and the passing ability.

Diagnostics on an atmospheric pressure plasma jet

The atmospheric pressure plasma jet (APPJ) is a homogeneous non-equilibrium discharge at ambient pressure. It operates with a noble base gas and a percentage-volume admixture of a molecular gas. Applications of the discharge are mainly based on reactive species in the effluent. The effluent region of a discharge operated in helium with an oxygen admixture has been investigated. The optical emission from atomic oxygen decreases with distance from the discharge but can still be observed several centimetres in the effluent. Ground state atomic oxygen, measured using absolutely calibrated two-photon laser induced fluorescence spectroscopy, shows a similar behaviour. Detailed understanding of energy transport mechanisms requires investigations of the discharge volume and the effluent region. An atmospheric pressure plasma jet has been designed providing excellent diagnostics access and a simple geometry ideally suited for modelling and simulation. Laser spectroscopy and optical emission spectroscopy can be applied in the discharge volume and the effluent region.

Absolute Atomic Oxygen Density Distributions in the Effluent of a Micro Scale Atmospheric Pressure Plasma Jet

The coplanar microscale atmospheric pressure plasma jet (µ-APPJ) is a capacitively coupled radio frequency discharge (13.56 MHz, ~15W rf power) designed for optimized optical diagnostic access. It is operated in a homogeneous glow mode with a noble gas flow (1.4 slm He) containing a small admixture of molecular oxygen (~0.5%). Ground state atomic oxygen densities in the effluent up to 2 × 1014 cm-3 are measured by two-photon absorption laser-induced fluorescence spectroscopy (TALIF) providing space resolved density maps. The quantitative calibration of the TALIF setup is performed by comparative measurements with xenon. A maximum of the atomic oxygen density is observed for 0.6% molecular oxygen admixture. Furthermore, an increase in the rf power up to about 15W (depending on gas flow and mixture) leads to an increase in the effluent’s atomic oxygen density, then reaching a constant level for higher powers.

Generation of Atomic Oxygen in the Effluent of an Atmospheric Pressure Plasma Jet

The planar 13.56MHz RF-excited low temperature atmospheric pressure plasma jet (APPJ) investigated in this study is operated with helium feed gas and a small molecular oxygen admixture. The effluent leaving the discharge through the jet’s nozzle contains very few charged particles and a high reactive oxygen species’ density. As its main reactive radical, essential for numerous applications, the ground state atomic oxygen density in the APPJ’s effluent is measured spatially resolved with two-photon absorption laser induced fluorescence spectroscopy. The atomic oxygen density at the nozzle reaches a value of ~1016 cm-3. Even at several centimetres distance still 1% of this initial atomic oxygen density can be detected. Optical emission spectroscopy (OES) reveals the presence of short living excited oxygen atoms up to 10 cm distance from the jet’s nozzle. The measured high ground state atomic oxygen density and the unaccounted for presence of excited atomic oxygen require further investigations on a possible energy transfer from the APPJ’s discharge region into the effluent: energetic vacuum ultraviolet radiation, measured by OES down to 110 nm, reaches far into the effluent where it is presumed to be responsible for the generation of atomic oxygen.

Effect of Mix Proportions on Rheological and Hardened Properties of Composite Cement Pastes

There is an increasing need to identify the effect of mix composition on the rheological properties of composite cement pastes using simple tests to determine the fluidity, the cohesion and other mechanical properties of grouting applications such as compressive strength. This paper reviews statistical models developed using a fractional factorial design which was carried out to model the influence of key parameters on properties affecting the performance of composite cement paste. Such responses of fluidity included mini-slump, flow time using Marsh cone and cohesion measured by Lombardi plate meter and unit weight, and compressive strength at 3 d, 7 d and 28 d. The models are valid for mixes with 0.35 to 0.42 water-to-binder ratio (W/B), 10% to 40% of pulverised fuel ash (PFA) as replacement of cement by mass, 0.02 to 0.06% of viscosity enhancer admixture (VEA), by mass of binder, and 0.3 to 1.2% of superplasticizer (SP), by mass of binder. The derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of composite cement paste are presented. Such parameters can be useful to reduce the test protocol needed for proportioning of composite cement paste. This paper attempts also to demonstrate the usefulness of the models to better understand trade-offs between parameters and compare the responses obtained from the various test methods which are highlighted. The multi parametric optimization is used in order to establish isoresponses for a desirability function of cement composite paste. Results indicate that the replacement of cement by PFA is compromising the early compressive strength and up 26%, the desirability function decreased.

Experimental Design to Optimize High-Volume Ash Grout in the Presence of Welan Gum and Superplasticizer

Applications such as soil, rock and oil-well grouting all require enormous amounts of cement and are good examples of areas where a high volume of fly ash could partially replace cement to produce low-cost, environmentally safe and durable concrete. There is an increasing need to identify the rheological properties of cement grout using a simple test to determine the fluidity, and other properties of underwater grouts such as washout resistance and compressive strength. This paper presents statistical models developed using a fractorial design which was carried out to model the influence of key parameters on properties affecting the performance of underwater grout. Such responses of fluidity included mini-slump and flow time measured by Marsh cone, washout resistance, unit weight and compressive strength. The models are valid for mixes with 0.40 to 0.60 water-to-cementitious materials ratio, 0.02 to 0.08% of anti-washout admixture, by mass of binder, and 0.6 to 1.8% of superplasticizer, by mass of cementitious materials. The grout was made with 50% of pulverized-fuel ash replacement, by mass ofcementitious materials. Also presented are the derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of underwater cement grout. Such parameters can be useful to reduce the test protocol needed for proportioning of underwater cement grout. This paper highlighted the influence of W/CM and dosage of antiwashout admixture and superplasticizer on fluidity, washout resistance and compressive strength and attempted also to demonstrate the usefulness of the models to improve understanding of trade-offs between parameters.

Factorial Design of Modelling Mix Proportion Parameters of Underwater Composite Cement Grouts

There is an increasing need to identify the rheological properties of cement grout using a simple test to determine the fluidity, and other properties of underwater applications such as washout resistance and compressive strength. This paper reviews statistical models developed using a factorial design that was carried out to model the influence of key parameters on properties affecting the performance of underwater cement grout. Such responses of fluidity included minislump and flow time measured by Marsh cone, washout resistance, unit weight, and compressive strength. The models are valid for mixes with 0.35–0.55 water-to-binder ratio (W/B), 0.053–0.141% of antiwashout admixture (AWA), by mass of water, and 0.4–1.8% (dry extract) of superplasticizer (SP), by mass of binder. Two types of underwater grout were tested: the first one made with cement and the second one made with 20% of pulverised fuel ash (PFA) replacement, by mass of binder. Also presented are the derived models that enable the identification of underlying primary factors and their interactions that influence the modelled responses of underwater cement grout. Such parameters can be useful to reduce the test protocol needed for proportioning of underwater cement grout. This paper attempts also to demonstrate the usefulness of the models to better understand trade-offs between parameters and compare the responses obtained from the various test methods that are highlighted.

Effect of Mixture Composition on Washout Resistance of Highly Flowable Underwater Concrete

The underwater casting of relatively thin lifts of concrete in water requires the proportioning of highly flowable concrete that can resist water dilution and segregation and spread readily into place. An investigation was carried out to determine the effects of antiwashout admixture concentration, water-cementitious materials ratio, and binder composition on the washout resistance of highly flowable concrete. Two main types of antiwashout admixtures were used: 1) a powdered welan gum at concentrations of 0.07 and 0.15% (by mass of binder); and 2) a liquid-based cellulosic admixture with dosages up to 1.65 L/100 kg of binder. The water-cementitious materials ratios were set at 0.41 and 0.47, corresponding to high-quality underwater concrete. Four binder compositions were used: a standard Canadian Type 10 cement, the same cement with 10% silica fume replacement, the cement with 50% granulated blast-furnace slag replacement, and a ternary cement containing 6% silica fume and 20% Class F fly ash. The concentrations of anti-washout admixture have direct impact on washout resistance. For a given washout loss, greater slump flow consistency can be achieved with the increases in anti-washout admixture concentration and decreases in water-binder ratio. The washout mass loss can be reduced, for a given consistency

Effect of Mixture Composition on Relative Strength of Highly Flowable Underwater Concrete

Concrete used for underwater repair is often proportioned to spread readily into place and self-consolidate, and to develop high resistance to segregation and water dilution. An investigation was carried out to determine the effect of the dosage of antiwashout admixture, water-cementitious materials ratio (w/cm), and binder composition on the relative residual strength of highly flowable underwater concrete. Two types of antiwashout admixtures were used: a powdered welan gum at 0.07 and 0.15% by mass of binder, and a liquid-based cellulosic admixture employed at a high dosage of 1 to 1.65 L/100 kg of cementitious materials. The w/cms were set at 0.41 and 0.47 to secure adequate performance of underwater concrete for construction and repair. Four binder compositions were used: a Canadian Type 10 cement; a cement with 10% silica fume replacement; a cement with 50% replacement of granulated blast-furnace slag; and a ternary binder containing 6% silica fume and 20% Class F fly ash. Test results indicate that for a given washout mass loss and slump flow consistency, greater relative residual strength can be secured when the dosage of antiwashout admixture is increased, the w/cm is reduced, and a binary binder with 10% silica fume substitution or the ternary binder are employed. Such mixtures can develop relative residual compressive strengths of 85 and 80%, compared to mixtures cast in air, when the value of washout loss is limited to 4 and 6% for mixtures with slump flow values of 450 and 550 mm, respectively.

Non-invasive VHF monitoring of low-temperature atmospheric pressure plasma

A real-time VHF swept frequency (20–300 MHz) reflectometry measurement for radio-frequency capacitive-coupled atmospheric pressure plasmas is described. The measurement is scalar, non-invasive and deployed on the main power line of the plasma chamber. The purpose of this VHF signal injection is to remotely interrogate in real-time the frequency reflection properties of plasma. The information obtained is used for remote monitoring of high-value atmospheric plasma processing. Measurements are performed under varying gas feed (helium mixed with 0–2% oxygen) and power conditions (0–40 W) on two contrasting reactors. The first is a classical parallel-plate chamber driven at 16 MHz with well-defined electrical grounding but limited optical access and the second is a cross-field plasma jet driven at 13.56 MHz with open optical access but with poor electrical shielding of the driven electrode. The electrical measurements are modelled using a lumped element electrical circuit to provide an estimate of power dissipated in the plasma as a function of gas and applied power. The performances of both reactors are evaluated against each other. The scalar measurements reveal that 0.1% oxygen admixture in helium plasma can be detected. The equivalent electrical model indicates that the current density between the parallel-plate reactor is of the order of 8–20 mA cm-2 . This value is in accord with 0.03 A cm-2 values reported by Park et al (2001 J. Appl. Phys. 89 20–8). The current density of the cross-field plasma jet electrodes is found to be 20 times higher. When the cross-field plasma jet unshielded electrode area is factored into the current density estimation, the resultant current density agrees with the parallel-plate reactor. This indicates that the unshielded reactor radiates electromagnetic energy into free space and so acts as a plasma antenna.

Phylogeographic structure of brown trout (Salmo trutta) in Britain and Ireland: glacial refugia, post-glacial colonisation, and origins of sympatric populations

The phylogeographical structure of brown trout Salmo trutta in Britain and Ireland was studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of four mitochondrial DNA segments (16S/ND1, ND5/6, COXIII/ND5 and ND5/12S). Analysis of 3636 individuals from 83 sites-morphotypes revealed a total of 25 haplotypes. These haplotypes were nested in seven two-step clades. Although there was a clear geographical patterning to the occurrence of derived clades, admixture among ancestral clades was extensive throughout the studied area. A relevant feature of the data was that some populations contained mixtures of highly divergent clades. This type II phylogeographic pattern is uncommon in nature. Clade intermixing is likely to have taken place during earlier interglacials as well as since the Last Glacial Maximum. The anadromous life history of many S. trutta populations has probably also contributed to clade mixing. Based on the data presented here and published data, postglacial colonization of Britain and Ireland most likely involved S. trutta from at least five potential glacial refuges. Probable locations for such refugia were: south of England-western France, east of the Baltic Sea, western Ireland, Celtic Sea and North Sea. Ferox S. trutta, as defined by their longevity, late maturation and piscivory, exhibited a strong association with a particular clade indicating that they share a common ancestor. Current evidence indicates that the Lough Melvin gillaroo S. trutta and sonaghen S. trutta sympatric types diverged prior to colonization of Lough Melvin and, although limited gene flow has occurred since secondary contact, they have remained largely reproductively isolated due to inlet and outlet river spawning segregation. Gillaroo S. trutta may reflect descendents of a previously more widespread lineage that has declined due to habitat alterations particularly affecting outlet rivers. The mosaic-like distribution of mtDNA lineages means that conservation prioritization in Britain and Ireland should be based on the biological characteristics of local populations rather than solely on evolutionary lineages.

Neural Network Modeling of Rheological Parameters of Grouts Containing Viscosity-Modifying Agent

The development of artificial neural network (ANN) models to predict the rheological behavior of grouts is described is this paper and the sensitivity of such parameters to the variation in mixture ingredients is also evaluated. The input parameters of the neural network were the mixture ingredients influencing the rheological behavior of grouts, namely the cement content, fly ash, ground-granulated blast-furnace slag, limestone powder, silica fume, water-binder ratio (w/b), high-range water-reducing admixture, and viscosity-modifying agent (welan gum). The six outputs of the ANN models were the mini-slump, the apparent viscosity at low shear, and the yield stress and plastic viscosity values of the Bingham and modified Bingham models, respectively. The model is based on a multi-layer feed-forward neural network. The details of the proposed ANN with its architecture, training, and validation are presented in this paper. A database of 186 mixtures from eight different studies was developed to train and test the ANN model. The effectiveness of the trained ANN model is evaluated by comparing its responses with the experimental data that were used in the training process. The results show that the ANN model can accurately predict the mini-slump, the apparent viscosity at low shear, the yield stress, and the plastic viscosity values of the Bingham and modified Bingham models of the pseudo-plastic grouts used in the training process. The results can also predict these properties of new mixtures within the practical range of the input variables used in the training with an absolute error of 2%, 0.5%, 8%, 4%, 2%, and 1.6%, respectively. The sensitivity of the ANN model showed that the trend data obtained by the models were in good agreement with the actual experimental results, demonstrating the effect of mixture ingredients on fluidity and the rheological parameters with both the Bingham and modified Bingham models.