Parameterization of quasigeostrophic eddies in primitive equation ocean models

A parameterization of mesoscale eddy fluxes in the ocean should be consistent with the fact that the ocean interior is nearly adiabatic. Gent and McWilliams have described a framework in which this can be approximated in L-coordinate primitive equation models by incorporating the effects of eddies on the buoyancy field through an eddy-induced velocity. It is also natural to base a parameterization on the simple picture of the mixing of potential vorticity in the interior and the mixing of buoyancy at the surface. The authors discuss the various constraints imposed by these two requirements and attempt to clarify the appropriate boundary conditions on the eddy-induced velocities at the surface. Quasigeostrophic theory is used as a guide to the simplest way of satisfying these constraints.

Triangular mesh parameterization with trimmed surfaces

Given a 2manifold triangular mesh \(M \subset {\mathbb {R}}^3\), with border, a parameterization of \(M\) is a FACE or trimmed surface \(F=\{S,L_0,\ldots, L_m\}\) -- \(F\) is a connected subset or region of a parametric surface \(S\), bounded by a set of LOOPs \(L_0,\ldots ,L_m\) such that each \(L_i \subset S\) is a closed 1manifold having no intersection with the other \(L_j\) LOOPs -- The parametric surface \(S\) is a statistical fit of the mesh \(M\) -- \(L_0\) is the outermost LOOP bounding \(F\) and \(L_i\) is the LOOP of the ith hole in \(F\) (if any) -- The problem of parameterizing triangular meshes is relevant for reverse engineering, tool path planning, feature detection, redesign, etc -- Stateofart mesh procedures parameterize a rectangular mesh \(M\) -- To improve such procedures, we report here the implementation of an algorithm which parameterizes meshes \(M\) presenting holes and concavities -- We synthesize a parametric surface \(S \subset {\mathbb {R}}^3\) which approximates a superset of the mesh \(M\) -- Then, we compute a set of LOOPs trimming \(S\), and therefore completing the FACE \(F=\ {S,L_0,\ldots ,L_m\}\) -- Our algorithm gives satisfactory results for \(M\) having low Gaussian curvature (i.e., \(M\) being quasi-developable or developable) -- This assumption is a reasonable one, since \(M\) is the product of manifold segmentation preprocessing -- Our algorithm computes: (1) a manifold learning mapping \(\phi : M \rightarrow U \subset {\mathbb {R}}^2\), (2) an inverse mapping \(S: W \subset {\mathbb {R}}^2 \rightarrow {\mathbb {R}}^3\), with \ (W\) being a rectangular grid containing and surpassing \(U\) -- To compute \(\phi\) we test IsoMap, Laplacian Eigenmaps and Hessian local linear embedding (best results with HLLE) -- For the back mapping (NURBS) \(S\) the crucial step is to find a control polyhedron \(P\), which is an extrapolation of \(M\) -- We calculate \(P\) by extrapolating radial basis functions that interpolate points inside \(\phi (M)\) -- We successfully test our implementation with several datasets presenting concavities, holes, and are extremely nondevelopable -- Ongoing work is being devoted to manifold segmentation which facilitates mesh parameterization

The Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS) - Part 1: Model description and evaluation

We introduce the Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS). CATT-BRAMS is an on-line transport model fully consistent with the simulated atmospheric dynamics. Emission sources from biomass burning and urban-industrial-vehicular activities for trace gases and from biomass burning aerosol particles are obtained from several published datasets and remote sensing information. The tracer and aerosol mass concentration prognostics include the effects of sub-grid scale turbulence in the planetary boundary layer, convective transport by shallow and deep moist convection, wet and dry deposition, and plume rise associated with vegetation fires in addition to the grid scale transport. The radiation parameterization takes into account the interaction between the simulated biomass burning aerosol particles and short and long wave radiation. The atmospheric model BRAMS is based on the Regional Atmospheric Modeling System (RAMS), with several improvements associated with cumulus convection representation, soil moisture initialization and surface scheme tuned for the tropics, among others. In this paper the CATT-BRAMS model is used to simulate carbon monoxide and particulate material (PM(2.5)) surface fluxes and atmospheric transport during the 2002 LBA field campaigns, conducted during the transition from the dry to wet season in the southwest Amazon Basin. Model evaluation is addressed with comparisons between model results and near surface, radiosondes and airborne measurements performed during the field campaign, as well as remote sensing derived products. We show the matching of emissions strengths to observed carbon monoxide in the LBA campaign. A relatively good comparison to the MOPITT data, in spite of the fact that MOPITT a priori assumptions imply several difficulties, is also obtained.

TESTING THE DISTANCE-DUALITY RELATION WITH GALAXY CLUSTERS AND TYPE Ia SUPERNOVAE

In this Letter, we propose a new and model-independent cosmological test for the distance-duality (DD) relation, eta = D(L)(z)(1 + z)(-2)/D(A)(z) = 1, where D(L) and D(A) are, respectively, the luminosity and angular diameter distances. For D(L) we consider two sub-samples of Type Ia supernovae (SNe Ia) taken from Constitution data whereas D(A) distances are provided by two samples of galaxy clusters compiled by De Filippis et al. and Bonamente et al. by combining Sunyaev-Zeldovich effect and X-ray surface brightness. The SNe Ia redshifts of each sub-sample were carefully chosen to coincide with the ones of the associated galaxy cluster sample (Delta z < 0.005), thereby allowing a direct test of the DD relation. Since for very low redshifts, D(A)(z) approximate to D(L)(z), we have tested the DD relation by assuming that. is a function of the redshift parameterized by two different expressions: eta(z) = 1 + eta(0)z and eta(z) = 1 +eta(0)z/(1 + z), where eta(0) is a constant parameter quantifying a possible departure from the strict validity of the reciprocity relation (eta(0) = 0). In the best scenario (linear parameterization), we obtain eta(0) = -0.28(-0.44)(+0.44) (2 sigma, statistical + systematic errors) for the De Filippis et al. sample (elliptical geometry), a result only marginally compatible with the DD relation. However, for the Bonamente et al. sample (spherical geometry) the constraint is eta(0) = -0.42(-0.34)(+0.34) (3 sigma, statistical + systematic errors), which is clearly incompatible with the duality-distance relation.

The case of thyroid hormones: how to learn physiology by solving a detective case

Lellis-Santos C, Giannocco G, Nunes MT. The case of thyroid hormones: how to learn physiology by solving a detective case. Adv Physiol Educ 35: 219-226, 2011; doi:10.1152/advan.00135.2010.Thyroid diseases are prevalent among endocrine disorders, and careful evaluation of patients' symptoms is a very important part in their diagnosis. Developing new pedagogical strategies, such as problem-based learning (PBL), is extremely important to stimulate and encourage medical and biomedical students to learn thyroid physiology and identify the signs and symptoms of thyroid dysfunction. The present study aimed to create a new pedagogical approach to build deep knowledge about hypo-/hyperthyroidism by proposing a hands-on activity based on a detective case, using alternative materials in place of laboratory animals. After receiving a description of a criminal story involving changes in thyroid hormone economy, students collected data from clues, such as body weight, mesenteric vascularization, visceral fat, heart and thyroid size, heart rate, and thyroid-stimulating hormone serum concentration to solve the case. Nevertheless, there was one missing clue for each panel of data. Four different materials were proposed to perform the same practical lesson. Animals, pictures, small stuffed toy rats, and illustrations were all effective to promote learning, and the detective case context was considered by students as inviting and stimulating. The activity can be easily performed independently of the institution's purchasing power. The practical lesson stimulated the scientific method of data collection and organization, discussion, and review of thyroid hormone actions to solve the case. Hence, this activity provides a new strategy and alternative materials to teach without animal euthanization.

Event structure and double helicity asymmetry in jet production from polarized p plus p collisions at root s=200 GeV

We report on the event structure and double helicity asymmetry (A(LL)) of jet production in longitudinally polarized p + p collisions at root s = 200 GeV. Photons and charged particles were measured by the PHENIX experiment at midrapidity vertical bar eta vertical bar < 0.35 with the requirement of a high-momentum (> 2 GeV/c) photon in the event. Event structure, such as multiplicity, p(T) density and thrust in the PHENIX acceptance, were measured and compared with the results from the PYTHIA event generator and the GEANT detector simulation. The shape of jets and the underlying event were well reproduced at this collision energy. For the measurement of jet A(LL), photons and charged particles were clustered with a seed-cone algorithm to obtain the cluster pT sum (p(T)(reco)). The effect of detector response and the underlying events on p(T)(reco) was evaluated with the simulation. The production rate of reconstructed jets is satisfactorily reproduced with the next-to-leading-order and perturbative quantum chromodynamics jet production cross section. For 4< p(T)(reco) < 12 GeV/c with an average beam polarization of < P > = 49% we measured Lambda(LL) = -0.0014 +/- 0.0037(stat) at the lowest p(T)(reco) bin (4-5 GeV= c) and -0.0181 +/- 0.0282(stat) at the highest p(T)(reco) bin (10-12 GeV= c) with a beam polarization scale error of 9.4% and a pT scale error of 10%. Jets in the measured p(T)(reco) range arise primarily from hard-scattered gluons with momentum fraction 0: 02 < x < 0: 3 according to PYTHIA. The measured A(LL) is compared with predictions that assume various Delta G(x) distributions based on the Gluck-Reya-Stratmann-Vogelsang parameterization. The present result imposes the limit -a.1 < integral(0.3)(0.02) dx Delta G(x, mu(2) = GeV2) < 0.4 at 95% confidence level or integral(0.3)(0.002) dx Delta G(x, mu(2) = 1 GeV2) < 0.5 at 99% confidence level.

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties. (c) 2008 American Institute of Physics.

An exact conserving algorithm for nonlinear dynamics with rotational DOFs and general hyperelasticity. Part 2: shells

Following the approach developed for rods in Part 1 of this paper (Pimenta et al. in Comput. Mech. 42:715-732, 2008), this work presents a fully conserving algorithm for the integration of the equations of motion in nonlinear shell dynamics. We begin with a re-parameterization of the rotation field in terms of the so-called Rodrigues rotation vector, allowing for an extremely simple update of the rotational variables within the scheme. The weak form is constructed via non-orthogonal projection, the time-collocation of which ensures exact conservation of momentum and total energy in the absence of external forces. Appealing is the fact that general hyperelastic materials (and not only materials with quadratic potentials) are permitted in a totally consistent way. Spatial discretization is performed using the finite element method and the robust performance of the scheme is demonstrated by means of numerical examples.

An exact conserving algorithm for nonlinear dynamics with rotational DOFs and general hyperelasticity. Part 1: Rods

A fully conserving algorithm is developed in this paper for the integration of the equations of motion in nonlinear rod dynamics. The starting point is a re-parameterization of the rotation field in terms of the so-called Rodrigues rotation vector, which results in an extremely simple update of the rotational variables. The weak form is constructed with a non-orthogonal projection corresponding to the application of the virtual power theorem. Together with an appropriate time-collocation, it ensures exact conservation of momentum and total energy in the absence of external forces. Appealing is the fact that nonlinear hyperelastic materials (and not only materials with quadratic potentials) are permitted without any prejudice on the conservation properties. Spatial discretization is performed via the finite element method and the performance of the scheme is assessed by means of several numerical simulations.

An EFG method for the nonlinear analysis of plates undergoing arbitrarily large deformations

The applicability of a meshfree approximation method, namely the EFG method, on fully geometrically exact analysis of plates is investigated. Based on a unified nonlinear theory of plates, which allows for arbitrarily large rotations and displacements, a Galerkin approximation via MLS functions is settled. A hybrid method of analysis is proposed, where the solution is obtained by the independent approximation of the generalized internal displacement fields and the generalized boundary tractions. A consistent linearization procedure is performed, resulting in a semi-definite generalized tangent stiffness matrix which, for hyperelastic materials and conservative loadings, is always symmetric (even for configurations far from the generalized equilibrium trajectory). Besides the total Lagrangian formulation, an updated version is also presented, which enables the treatment of rotations beyond the parameterization limit. An extension of the arc-length method that includes the generalized domain displacement fields, the generalized boundary tractions and the load parameter in the constraint equation of the hyper-ellipsis is proposed to solve the resulting nonlinear problem. Extending the hybrid-displacement formulation, a multi-region decomposition is proposed to handle complex geometries. A criterium for the classification of the equilibrium`s stability, based on the Bordered-Hessian matrix analysis, is suggested. Several numerical examples are presented, illustrating the effectiveness of the method. Differently from the standard finite element methods (FEM), the resulting solutions are (arbitrary) smooth generalized displacement and stress fields. (c) 2007 Elsevier Ltd. All rights reserved.

Protein fold recognition without Boltzmann statistics or explicit physical basis

We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.

A randomized trial of a problem-based learning approach for teaching epidemiology

Purpose. To conduct a controlled trial of traditional and problem-based learning (PBL) methods of teaching epidemiology. Method. All second-year medical students (n = 136) at The University of Western Australia Medical School were offered the chance to participate in a randomized controlled trial of teaching methods fur an epidemiology course. Students who consented to participate (n = 80) were randomly assigned to either a PBL or a traditional course. Students who did not consent or did not return the consent form (n = 56) were assigned to the traditional course, Students in both streams took identical quizzes and exams. These scores, a collection of semi-quantitative feedback from all students, and a qualitative analysis of interviews with a convenience sample of six students from each stream were compared. Results. There was no significant difference in performances on quizzes or exams between PBL and traditional students. Students using PBL reported a stronger grasp of epidemiologic principles, enjoyed working with a group, and, at the end of the course, were more enthusiastic about epidemiology and its professional relevance to them than were students in the traditional course. PBL students worked more steadily during the semester but spent only marginally more time on the epidemiology course overall. Interviews corroborated these findings. Non-consenting students were older (p < 0.02) and more likely to come from non-English-speaking backgrounds (p < 0.005). Conclusions. PBL provides an academically equivalent but personally far richer learning experience. The adoption of PBL approaches to medical education makes it important to study whether PBL presents particular challenges for students whose first language is not the language of instruction.

Construction and validation of a Bovine Innate Immune Microarray

Background: Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategies that exploit these genes to enhance resistance to disease in an individual or animal population. Results: The Bovine Innate Immune Microarray developed in this study consists of 1480 characterised genes identified by literature searches, 31 positive and negative control elements and 5376 cDNAs derived from subtracted and normalised libraries. The cDNA libraries were produced from 'challenged' bovine epithelial and leukocyte cells. The microarray was found to have a limit of detection of 1 pg/mu g of total RNA and a mean slide-to-slide correlation co-efficient of 0.88. The profiles of differentially expressed genes from Concanavalin A ( ConA) stimulated bovine peripheral blood lymphocytes were determined. Three distinct profiles highlighted 19 genes that were rapidly up-regulated within 30 minutes and returned to basal levels by 24 h; 76 genes that were upregulated between 2 - 8 hours and sustained high levels of expression until 24 h and 10 genes that were down-regulated. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray analysis. The results indicate that there is a dynamic process involving gene activation and regulatory mechanisms re-establishing homeostasis in the ConA activated lymphocytes. The Bovine Innate Immune Microarray was also used to determine the cross-species hybridisation capabilities of an ovine PBL sample. Conclusion: The Bovine Innate Immune Microarray has been developed which contains a set of well-characterised genes and anonymous cDNAs from a number of different bovine cell types. The microarray can be used to determine the gene expression profiles underlying innate immune responses in cattle and sheep.