Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Constraints on singlet right-handed neutrinos coming from the Z0 width

We study the constraints on masses and mixing angles imposed by the measured Z0 invisible width, in a model in which a singlet right-handed neutrino mixes with all the standard model neutrinos. © 1993 The American Physical Society.

Constraints on spin-3/2 and excited spin-1/2 fermions coming from the leptonic Z0-partial width

We consider effective interactions among excited spin-1/2 and spin-3/2 leptons with the usual ones. Assuming that these new leptons are lighter than the Z0, we study the constraints on their masses and compositeness scale coming from the leptonic Z0 partial width.

Astrophysical constraints on a light spinless particle coupled to photons

We examine further astrophysical constraints on a light spinless particle coupled only to photons and proposed by Massó and Toldra. We consider constraints coming from measurements of extra galactic background and from ionization of HI clouds.

Constraints on free parameters of the simplest bilepton gauge model from the neutral kaon system mass difference

We consider the contributions of the exotic quarks and gauge bosons to the mass difference between the short- and the long-lived neutral kaon states in the SU(3)C×SU(3)L×U(1)N model. The lower bound MZ′∼14 TeV is obtained for the extra neutral gauge boson Z′0. Ranges for values of one of the exotic quark masses and quark mixing parameters are also presented.

Constraints on electroweak contact interactions from LEP and tevatron data

A complete set of dimension-six effective contact interactions involving Higgs, gauge bosons and quarks is studied. Limits on the coefficients of these new operators are obtained from the experimental values of the Z and W gauge bosons widths.

Indirect constraints on the triple gauge boson couplings from Z → bb partial width: An update

We update the indirect bounds on anomalous triple gauge couplings coming from the non-universal one-loop contributions to the Z → bb width. These bounds, which are independent of the Higgs boson mass, are in agreement with the standard model predictions for the gauge boson self-couplings since the present value of R(b) agrees fairly well with the theoretical estimates. Moreover, these indirect constraints on Δg(Z)/1 and g(Z)/5 are most stringent than the present direct bounds on these quantities, while the indirect limit on λ(Z) is weaker than the available experimental data.

Constraints on space-time manifold in Euclidean supergravity in terms of Dirac eigenvalues

We generalize a previous work on Dirac eigenvalues as dynamical variables of Euclidean supergravity. The most general set of constraints on the curvatures of the tangent bundle and on the spinor bundle of the space-time manifold, under which space-time admits Dirac eigenvalues as observables, are derived.

Remark on the Neves-Wotzasek constraints conversion method

In this work we give an alternative way which generalizes the recently implemented Neves-Wotzasek method of conversion from second to first-class systems. We have proved that this generalization is correct reproducing the results given in the literature using the case of a sphere with an antisymmetric generator as an example. ©2000 The American Physical Society.

Constraints implementation for IQML and mode direction-of-arrival estimators

The iterative quadratic maximum likelihood IQML and the method of direction estimation MODE are well known high resolution direction-of-arrival DOA estimation methods. Their solutions lead to an optimization problem with constraints. The usual linear constraint presents a poor performance for certain DOA values. This work proposes a new linear constraint applicable to both DOA methods and compare their performance with two others: unit norm and usual linear constraint. It is shown that the proposed alternative performs better than others constraints. The resulting computational complexity is also investigated.

Some constraints on the modelling using the uranium isotopes 238U and 234U for dating groundwaters from Guarany aquifer, South America

Groundwaters from the Guarany aquifer located at the South American continent and sampled at four wells with described geological sections in São Paulo State, Brazil, were chemically and isotopically analysed with two aims: to evaluate the quality of this important hydrological resource and to investigate the possibility of using the natural uranium isotopes 234U and 238U as a chronological tool, since the 234U/238U activity ratio and dissolved U content data in groundwater systems have generated models for dating purposes.

On the solution of mathematical programming problems with equilibrium constraints

Mathematical programming problems with equilibrium constraints (MPEC) are nonlinear programming problems where the constraints have a form that is analogous to first-order optimality conditions of constrained optimization. We prove that, under reasonable sufficient conditions, stationary points of the sum of squares of the constraints are feasible points of the MPEC. In usual formulations of MPEC all the feasible points are nonregular in the sense that they do not satisfy the Mangasarian-Fromovitz constraint qualification of nonlinear programming. Therefore, all the feasible points satisfy the classical Fritz-John necessary optimality conditions. In principle, this can cause serious difficulties for nonlinear programming algorithms applied to MPEC. However, we show that most feasible points do not satisfy a recently introduced stronger optimality condition for nonlinear programming. This is the reason why, in general, nonlinear programming algorithms are successful when applied to MPEC.

Steric constraints as folding coadjuvant

Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

Inter and intraspecific variation on reproductive phenology of the Brazilian Atlantic forest Rubiaceae: Ecology and phylogenetic constraints

The reproductive phenology of seven species of Rubiaceae from the Brazilian Atlantic rain forest was compared to evaluate the occurrence of phylogenetic constraints on flowering and fruiting phenologies. Since phenological patterns can be affected by phylogenetic constraints, we expected that reproductive phenology would be similar among plants within a family or genus, occurring during the same time (or season) of the year. Observations on flowering and fruiting phenology were carried out monthly, from December 1996 to January 1998, at Núcleo Picinguaba, Parque Estadual da Serra do Mar, Ubatuba, São Paulo State, Brazil. Nine phenological variables were calculated to characterize, quantify and compare the reproductive phenology of the Rubiaceae species. The flowering patterns were different among the seven species studied, and the Kruskal-Wallis test indicated significant differences in flowering duration, first flowering, peak flowering and flowering synchrony. The peaks and patterns of fruiting intensity were different among the Rubiaceae species studied and they differed significantly from conspecifics in the phenological variables fruiting duration, fruiting peak date, and fruiting synchrony (Kruskal-Wallis test). Therefore, we found no evidence supporting the phylogenetic hypotheses, and climate does not seem to constrain flowering and fruiting patterns of the Rubiaceae species in the understory of the Atlantic forest.

An active/reactive predispatch model incorporating ramp rate constraints solved by dual decomposition/lagrangian relaxation

The Predispatch model (PD) calculates a short-term generation policy for power systems. In this work a PD model is proposed that improves two modeling aspects generally neglected in the literature: voltage/reactive power constraints and ramp rate constraints for generating units. Reactive power constraints turn the PD into a non-linear problem and the ramp rate constraints couple the problem dynamically in time domain. The solution of the PD is turned into a harder task when such constraints are introduced. The dual decomposition/ lagrangian relaxation technique is used in the solution approach for handing dynamic constraints. As a result the PD is decomposed into a series of independent Optimal Power Flow (FPO) sub problems, in which the reactive power is represented in detail. The solution of the independent FPO is coordinated by means of Lagrange multipliers, so that dynamic constraints are iteratively satisfied. Comparisons between dispatch policies calculated with and without the representation of ramp rate constraints are performed, using the IEEE 30 bus test system. The results point-out the importance of representing such constraints in the generation dispatch policy. © 2004 IEEE.