A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence

An apple rootstock progeny raised from the cross between the very dwarfing ‘M.27’ and the more vigorous ‘M.116’ (‘M.M.106’ × ‘M.27’) was used for the construction of a linkage map comprising a total of 324 loci: 252 previously mapped SSRs, 71 newly characterised or previously unmapped SSR loci (including 36 amplified by 33 out of the 35 novel markers reported here), and the self-incompatibility locus. The map spanned the 17 linkage groups (LG) expected for apple covering a genetic distance of 1,229.5 cM, an estimated 91% of the Malus genome. Linkage groups were well populated and, although marker density ranged from 2.3 to 6.2 cM/SSR, just 15 gaps of more than 15 cM were observed. Moreover, only 17.5% of markers displayed segregation distortion and, unsurprisingly in a semi-compatible backcross, distortion was particularly pronounced surrounding the self-incompatibility locus (S) at the bottom of LG17. DNA sequences of 273 SSR markers and the S locus, representing a total of 314 loci in this investigation, were used to anchor to the ‘Golden Delicious’ genome sequence. More than 260 of these loci were located on the expected pseudo-chromosome on the ‘Golden Delicious’ genome or on its homeologous pseudo-chromosome. In total, 282.4 Mbp of sequence from 142 genome sequence scaffolds of the Malus genome were anchored to the ‘M.27’ × ‘M.116’ map, providing an interface between the marker data and the underlying genome sequence. This will be exploited for the identification of genes responsible for traits of agronomic importance such as dwarfing and water use efficiency.

Viscous coupling of shear-free turbulence across nearly flat fluid interfaces

The interactions between shear-free turbulence in two regions (denoted as + and − on either side of a nearly flat horizontal interface are shown here to be controlled by several mechanisms, which depend on the magnitudes of the ratios of the densities, ρ+/ρ−, and kinematic viscosities of the fluids, μ+/μ−, and the root mean square (r.m.s.) velocities of the turbulence, u0+/u0−, above and below the interface. This study focuses on gas–liquid interfaces so that ρ+/ρ− ≪ 1 and also on where turbulence is generated either above or below the interface so that u0+/u0− is either very large or very small. It is assumed that vertical buoyancy forces across the interface are much larger than internal forces so that the interface is nearly flat, and coupling between turbulence on either side of the interface is determined by viscous stresses. A formal linearized rapid-distortion analysis with viscous effects is developed by extending the previous study by Hunt & Graham (J. Fluid Mech., vol. 84, 1978, pp. 209–235) of shear-free turbulence near rigid plane boundaries. The physical processes accounted for in our model include both the blocking effect of the interface on normal components of the turbulence and the viscous coupling of the horizontal field across thin interfacial viscous boundary layers. The horizontal divergence in the perturbation velocity field in the viscous layer drives weak inviscid irrotational velocity fluctuations outside the viscous boundary layers in a mechanism analogous to Ekman pumping. The analysis shows the following. (i) The blocking effects are similar to those near rigid boundaries on each side of the interface, but through the action of the thin viscous layers above and below the interface, the horizontal and vertical velocity components differ from those near a rigid surface and are correlated or anti-correlated respectively. (ii) Because of the growth of the viscous layers on either side of the interface, the ratio uI/u0, where uI is the r.m.s. of the interfacial velocity fluctuations and u0 the r.m.s. of the homogeneous turbulence far from the interface, does not vary with time. If the turbulence is driven in the lower layer with ρ+/ρ− ≪ 1 and u0+/u0− ≪ 1, then uI/u0− ~ 1 when Re (=u0−L−/ν−) ≫ 1 and R = (ρ−/ρ+)(v−/v+)1/2 ≫ 1. If the turbulence is driven in the upper layer with ρ+/ρ− ≪ 1 and u0+/u0− ≫ 1, then uI/u0+ ~ 1/(1 + R). (iii) Nonlinear effects become significant over periods greater than Lagrangian time scales. When turbulence is generated in the lower layer, and the Reynolds number is high enough, motions in the upper viscous layer are turbulent. The horizontal vorticity tends to decrease, and the vertical vorticity of the eddies dominates their asymptotic structure. When turbulence is generated in the upper layer, and the Reynolds number is less than about 106–107, the fluctuations in the viscous layer do not become turbulent. Nonlinear processes at the interface increase the ratio uI/u0+ for sheared or shear-free turbulence in the gas above its linear value of uI/u0+ ~ 1/(1 + R) to (ρ+/ρ−)1/2 ~ 1/30 for air–water interfaces. This estimate agrees with the direct numerical simulation results from Lombardi, De Angelis & Bannerjee (Phys. Fluids, vol. 8, no. 6, 1996, pp. 1643–1665). Because the linear viscous–inertial coupling mechanism is still significant, the eddy motions on either side of the interface have a similar horizontal structure, although their vertical structure differs.

Advances in sequential data assimilation and numerical weather forecasting: an Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic Ensemble Square Root Filters, and a test of a new time stepping scheme in an atmospheric model

This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn’t represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion in the mean value of the function. Using statistical significance tests both at the local and field level, it is shown that the climatology of the SPEEDY model is not modified by the changed time stepping scheme; hence, no retuning of the parameterizations is required. It is found the accuracy of the medium-term forecasts is increased by using the RAW filter.

The influence of Langmuir turbulence on the scaling for the dissipation rate in the oceanic boundary layer

A model for estimating the turbulent kinetic energy dissipation rate in the oceanic boundary layer, based on insights from rapid-distortion theory, is presented and tested. This model provides a possible explanation for the very high dissipation levels found by numerous authors near the surface. It is conceived that turbulence, injected into the water by breaking waves, is subsequently amplified due to its distortion by the mean shear of the wind-induced current and straining by the Stokes drift of surface waves. The partition of the turbulent shear stress into a shear-induced part and a wave-induced part is taken into account. In this picture, dissipation enhancement results from the same mechanism responsible for Langmuir circulations. Apart from a dimensionless depth and an eddy turn-over time, the dimensionless dissipation rate depends on the wave slope and wave age, which may be encapsulated in the turbulent Langmuir number La_t. For large La_t, or any Lat but large depth, the dissipation rate tends to the usual surface layer scaling, whereas when Lat is small, it is strongly enhanced near the surface, growing asymptotically as ɛ ∝ La_t^{-2} when La_t → 0. Results from this model are compared with observations from the WAVES and SWADE data sets, assuming that this is the dominant dissipation mechanism acting in the ocean surface layer and statistical measures of the corresponding fit indicate a substantial improvement over previous theoretical models. Comparisons are also carried out against more recent measurements, showing good order-of-magnitude agreement, even when shallow-water effects are important.

Turbulence dynamics near a turbulent/non-turbulent interface

The characteristics of the boundary layer separating a turbulence region from an irrotational (or non-turbulent) flow region are investigated using rapid distortion theory (RDT). The turbulence region is approximated as homogeneous and isotropic far away from the bounding turbulent/non-turbulent (T/NT) interface, which is assumed to remain approximately flat. Inviscid effects resulting from the continuity of the normal velocity and pressure at the interface, in addition to viscous effects resulting from the continuity of the tangential velocity and shear stress, are taken into account by considering a sudden insertion of the T/NT interface, in the absence of mean shear. Profiles of the velocity variances, turbulent kinetic energy (TKE), viscous dissipation rate (epsilon), turbulence length scales, and pressure statistics are derived, showing an excellent agreement with results from direct numerical simulations (DNS). Interestingly, the normalized inviscid flow statistics at the T/NT interface do not depend on the form of the assumed TKE spectrum. Outside the turbulent region, where the flow is irrotational (except inside a thin viscous boundary layer), epsilon decays as z^{-6}, where z is the distance from the T/NT interface. The mean pressure distribution is calculated using RDT, and exhibits a decrease towards the turbulence region due to the associated velocity fluctuations, consistent with the generation of a mean entrainment velocity. The vorticity variance and epsilon display large maxima at the T/NT interface due to the inviscid discontinuities of the tangential velocity variances existing there, and these maxima are quantitatively related to the thickness delta of the viscous boundary layer (VBL). For an equilibrium VBL, the RDT analysis suggests that delta ~ eta (where eta is the Kolmogorov microscale), which is consistent with the scaling law identified in a very recent DNS study for shear-free T/NT interfaces.

On the connection between dissipation enhancement in the ocean surface layer and Langmuir circulations

A mechanism for the enhancement of the viscous dissipation rate of turbulent kinetic energy (TKE) in the oceanic boundary layer (OBL) is proposed, based on insights gained from rapid-distortion theory (RDT). In this mechanism, which complements mechanisms purely based on wave breaking, preexisting TKE is amplified and subsequently dissipated by the joint action of a mean Eulerian wind-induced shear current and the Stokes drift of surface waves, the same elements thought to be responsible for the generation of Langmuir circulations. Assuming that the TKE dissipation rate epsilon saturates to its equilibrium value over a time of the order one eddy turnover time of the turbulence, a new scaling expression, dependent on the turbulent Langmuir number, is derived for epsilon. For reasonable values of the input parameters, the new expression predicts an increase of the dissipation rate near the surface by orders of magnitude compared with usual surface-layer scaling estimates, consistent with available OBL data. These results establish on firmer grounds a suspected connection between two central OBL phenomena: dissipation enhancement and Langmuir circulations.

A linear model for the structure of turbulence beneath surface water waves

The structure of turbulence in the ocean surface layer is investigated using a simplified semi-analytical model based on rapid-distortion theory. In this model, which is linear with respect to the turbulence, the flow comprises a mean Eulerian shear current, the Stokes drift of an irrotational surface wave, which accounts for the irreversible effect of the waves on the turbulence, and the turbulence itself, whose time evolution is calculated. By analysing the equations of motion used in the model, which are linearised versions of the Craik–Leibovich equations containing a ‘vortex force’, it is found that a flow including mean shear and a Stokes drift is formally equivalent to a flow including mean shear and rotation. In particular, Craik and Leibovich’s condition for the linear instability of the first kind of flow is equivalent to Bradshaw’s condition for the linear instability of the second. However, the present study goes beyond linear stability analyses by considering flow disturbances of finite amplitude, which allows calculating turbulence statistics and addressing cases where the linear stability is neutral. Results from the model show that the turbulence displays a structure with a continuous variation of the anisotropy and elongation, ranging from streaky structures, for distortion by shear only, to streamwise vortices resembling Langmuir circulations, for distortion by Stokes drift only. The TKE grows faster for distortion by a shear and a Stokes drift gradient with the same sign (a situation relevant to wind waves), but the turbulence is more isotropic in that case (which is linearly unstable to Langmuir circulations).

Dissipation of shear-free turbulence near boundaries

The rapid-distortion model of Hunt & Graham (1978) for the initial distortion of turbulence by a flat boundary is extended to account fully for viscous processes. Two types of boundary are considered: a solid wall and a free surface. The model is shown to be formally valid provided two conditions are satisfied. The first condition is that time is short compared with the decorrelation time of the energy-containing eddies, so that nonlinear processes can be neglected. The second condition is that the viscous layer near the boundary, where tangential motions adjust to the boundary condition, is thin compared with the scales of the smallest eddies. The viscous layer can then be treated using thin-boundary-layer methods. Given these conditions, the distorted turbulence near the boundary is related to the undistorted turbulence, and thence profiles of turbulence dissipation rate near the two types of boundary are calculated and shown to agree extremely well with profiles obtained by Perot & Moin (1993) by direct numerical simulation. The dissipation rates are higher near a solid wall than in the bulk of the flow because the no-slip boundary condition leads to large velocity gradients across the viscous layer. In contrast, the weaker constraint of no stress at a free surface leads to the dissipation rate close to a free surface actually being smaller than in the bulk of the flow. This explains why tangential velocity fluctuations parallel to a free surface are so large. In addition we show that it is the adjustment of the large energy-containing eddies across the viscous layer that controls the dissipation rate, which explains why rapid-distortion theory can give quantitatively accurate values for the dissipation rate. We also find that the dissipation rate obtained from the model evaluated at the time when the model is expected to fail actually yields useful estimates of the dissipation obtained from the direct numerical simulation at times when the nonlinear processes are significant. We conclude that the main role of nonlinear processes is to arrest growth by linear processes of the viscous layer after about one large-eddy turnover time.

The effects of information presentation on real estate market perceptions

The study seeks to identify systematic differences in perception of the real estate market caused by the frames through which people obtain market information. We operationalise the frames through manipulation of data presentation in a commercial real estate market report, selectively controlling time scale, proportionality distortion and negative value presentation. Our findings suggest that such differences are real and their effects should be taken into account in the design and interpretation of market reports.

Digital predistorter design using B-Spline neural network and inverse of De Boor algorithm

This contribution introduces a new digital predistorter to compensate serious distortions caused by memory high power amplifiers (HPAs) which exhibit output saturation characteristics. The proposed design is based on direct learning using a data-driven B-spline Wiener system modeling approach. The nonlinear HPA with memory is first identified based on the B-spline neural network model using the Gauss-Newton algorithm, which incorporates the efficient De Boor algorithm with both B-spline curve and first derivative recursions. The estimated Wiener HPA model is then used to design the Hammerstein predistorter. In particular, the inverse of the amplitude distortion of the HPA's static nonlinearity can be calculated effectively using the Newton-Raphson formula based on the inverse of De Boor algorithm. A major advantage of this approach is that both the Wiener HPA identification and the Hammerstein predistorter inverse can be achieved very efficiently and accurately. Simulation results obtained are presented to demonstrate the effectiveness of this novel digital predistorter design.

Effect of anionic co-ligands on structure and magnetic coupling of bis(μ-phenoxo-bridged dinuclear copper(II) complexes

Two phenoxo bridged dinuclear Cu(II) complexes, [Cu2L2(NO2)(2)] (1) and [Cu2L2(NO3)(2)] (2) have been synthesized using the tridentate reduced Schiff-base ligand 2-[(2-dimethylamino-ethylamino)-methyl]-phenol (HL). The complexes have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. The structures of the two compounds are very similar having the same tridentate chelating ligand (L) and mono-dentate anionic ligand nitrite for 1 and nitrate for 2. In both complexes Cu(II) is penta-coordinated but the square pyramidal geometry of the copper ions is severely distorted (Addison parameter (tau) = 0.33) in 1 while the distortion is quite small (average tau = 0.11) in 2. These differences have marked effect on the magnetic properties of two compounds. Although both are antiferromagnetically coupled, the coupling constants (J = -140.8 and -614.7 cm (1) for 1 and 2, respectively) show that the coupling is much stronger in 2.

When do export subsidies have a redistributional role? Reply

Our differences are three. The first arises from the belief that "... a nonzero value for the optimally chosen policy instrument implies that the instrument is efficient for redistribution" (Alston, Smith, and Vercammen, p. 543, paragraph 3). Consider the two equations: (1) o* = f(P3) and (2) = -f(3) ++r h* (a, P3) representing the solution to the problem of maximizing weighted, Marshallian surplus using, simultaneously, a per-unit border intervention, 9, and a per-unit domestic intervention, wr. In the solution, parameter ot denotes the weight applied to producer surplus; parameter p denotes the weight applied to government revenues; consumer surplus is implicitly weighted one; and the country in question is small in the sense that it is unable to affect world price by any of its domestic adjustments (see the Appendix). Details of the forms of the functions f((P) and h(ot, p) are easily derived, but what matters in the context of Alston, Smith, and Vercammen's Comment is: Redistributivep referencest hatf avorp roducers are consistent with higher values "alpha," and whereas the optimal domestic intervention, 7r*, has both "alpha and beta effects," the optimal border intervention, r*, has only a "beta effect,"-it does not have a redistributional role. Garth Holloway is reader in agricultural economics and statistics, Department of Agricultural and Food Economics, School of Agriculture, Policy, and Development, University of Reading. The author is very grateful to Xavier Irz, Bhavani Shankar, Chittur Srinivasan, Colin Thirtle, and Richard Tiffin for their comments and their wisdom; and to Mario Mazzochi, Marinos Tsigas, and Cal Turvey for their scholarship, including help in tracking down a fairly complete collection of the papers that cite Alston and Hurd. They are not responsible for any errors or omissions. Note, in equation (1), that the border intervention is positive whenever a distortion exists because 8 > 0 implies 3 - 1 + 8 > 1 and, thus, f((P) > 0 (see Appendix). Using Alston, Smith, and Vercammen's definition, the instrument is now "efficient," and therefore has a redistributive role. But now, suppose that the distortion is removed so that 3 - 1 + 8 = 1, 8 = 0, and consequently the border intervention is zero. According to Alston, Smith, and Vercammen, the instrument is now "inefficient" and has no redistributive role. The reader will note that this thought experiment has said nothing about supporting farm incomes, and so has nothing whatsoever to do with efficient redistribution. Of course, the definition is false. It follows that a domestic distortion arising from the "excess-burden argument" 3 = 1 + 8, 8 > 0 does not make an export subsidy "efficient." The export subsidy, having only a "beta effect," does not have a redistributional role. The second disagreement emerges from the comment that Holloway "... uses an idiosyncratic definition of the relevant objective function of the government (Alston, Smith, and Vercammen, p. 543, paragraph 2)." The objective function that generates equations (1) and (2) (see the Appendix) is the same as the objective function used by Gardner (1995) when he first questioned Alston, Carter, and Smith's claim that a "domestic distortion can make a border intervention efficient in transferring surplus from consumers and taxpayers to farmers." The objective function used by Gardner (1995) is the same objective function used in the contributions that precede it and thus defines the literature on the debate about borderversus- domestic intervention (Streeten; Yeh; Paarlberg 1984, 1985; Orden; Gardner 1985). The objective function in the latter literature is the same as the one implied in another literature that originates from Wallace and includes most notably Gardner (1983), but also Alston and Hurd. Amer. J. Agr. Econ. 86(2) (May 2004): 549-552 Copyright 2004 American Agricultural Economics Association This content downloaded on Tue, 15 Jan 2013 07:58:41 AM All use subject to JSTOR Terms and Conditions 550 May 2004 Amer. J. Agr. Econ. The objective function in Holloway is this same objective function-it is, of course, Marshallian surplus.1 The third disagreement concerns scholarship. The Comment does not seem to be cognizant of several important papers, especially Bhagwati and Ramaswami, and Bhagwati, both of which precede Corden (1974, 1997); but also Lipsey and Lancaster, and Moschini and Sckokai; one important aspect of Alston and Hurd; and one extremely important result in Holloway. This oversight has some unfortunate repercussions. First, it misdirects to the wrong origins of intellectual property. Second, it misleads about the appropriateness of some welfare calculations. Third, it prevents Alston, Smith, and Vercammen from linking a finding in Holloway (pp. 242-43) with an old theorem (Lipsey and Lancaster) that settles the controversy (Alston, Carter, and Smith 1993, 1995; Gardner 1995; and, presently, Alston, Smith, and Vercammen) about the efficiency of border intervention in the presence of domestic distortions.

Homoleptic copper(II) and copper(I) complexes of 5,6-dihydro-5,6-epoxy-1,10-phenanthroline. Six-coordinate copper(I) in solution

Reaction of 5,6-dihydro-5,6-epoxy-1,10-phenanthroline (L) with Cu(ClO(4))(2)center dot 6H(2)O in methanol in 3:1 M ratio at room temperature yields light green [CuL(3)](ClO(4))(2)center dot H(2)O (1). The X-ray crystal structure of the hemi acetonitrile solvate [CuL(3)](ClO(4))(2)center dot 0.5CH(3)CN has been determined which shows Jahn-Teller distortion in the CuN(6) core present in the cation [CuL(3)](2+). Complex 1 gives an axial EPR spectrum in acetonitrile-toluene glass with g(parallel to) = 2.262 (A(parallel to) = 169 x 10 (4) cm (1)) and g(perpendicular to) = 2.069. The Cu(II/I) potential in 1 in CH(2)Cl(2) at a glassy carbon electrode is 0.32 V versus NHE. This potential does not change with the addition of extra L in the medium implicating generation of a six-coordinate copper(I) species [CuL(3)](+) in solution. B3LYP/LanL2DZ calculations show that the six Cu-N bond distances in [CuL(3)](+) are 2.33, 2.25, 2.32, 2.25, 2.28 and 2.25 angstrom while the ideal Cu(I)-N bond length in a symmetric Cu(I)N(6) moiety is estimated as 2.25 angstrom. Reaction of L with Cu(CH(3)CN)(4)ClO(4) in dehydrated methanol at room temperature even in 4:1 M proportion yields [CuL(2)]ClO(4) (2). Its (1)H NMR spectrum indicates that the metal in [CuL(2)](+) is tetrahedral. The Cu(II/I) potential in 2 is found to be 0.68 V versus NHE in CH(2)Cl(2) at a glassy carbon electrode. In presence of excess L, 2 yields the cyclic voltammogram of 1. From (1)H NMR titration, the free energy of binding of L to [CuL(2)](+) to produce [CuL(3)](+) in CD(2)Cl(2) at 298 K is estimated as -11.7 (+/-0.2) kJ mol (1).

Assessment of thought–shape fusion: initial validation of a short version of the trait thought–shape fusion scale

Objective: Thought–shape fusion (TSF) is a cognitive distortion that has been linked to eating pathology. Two studies were conducted to further explore this phenomenon and to establish the psychometric properties of a French short version of the TSF scale. Method: In Study 1, students (n 5 284) completed questionnaires assessing TSF and related psychopathology. In Study 2, the responses of women with eating disorders (n 5 22) and women with no history of an eating disorder (n 5 23) were compared. Results: The French short version of the TSF scale has a unifactorial structure, with convergent validity with measures of eating pathology, and good internal consistency. Depression, eating pathology, body dissatisfaction, and thought-action fusion emerged as predictors of TSF. Individuals with eating disorders have higher TSF, and more clinically relevant food-related thoughts than do women with no history of an eating disorder. Discussion: This research suggests that the shortened TSF scale can suitably measure this construct, and provides support for the notion that TSF is associated with eating pathology.

Lord Kelvin’s atmospheric electricity measurements

Lord Kelvin (William Thomson) made important contributions to the study of atmospheric elec- tricity during a brief but productive period from 1859–1861. By 1859 Kelvin had recognised the need for “incessant recording” of atmospheric electrical parameters, and responded by inventing both the water dropper equaliser for measuring the atmospheric potential gradient (PG), and photographic data logging. The water dropper equaliser was widely adopted internationally and is still in use today. Following theoretical consid- erations of electric field distortion by local topography, Kelvin developed a portable electrometer, using it to investigate the PG on the Scottish island of Arran. During these environmental measurements, Kelvin may have unwittingly detected atmospheric PG changes during solar activity in August / September 1859 associated with the “Carrington event”, which is interesting in the context of his later statements that solar magnetic influ- ence on the Earth was impossible. Kelvin’s atmospheric electricity work presents an early representative study in quantitative environmental physics, through the application of mathematical principles to an environmental problem, the design and construction of bespoke instrumentation for real world measurements and recognising the limitations of the original theoretical view revealed by experimental work