The effect of boundary conditions in the numerical solution of 3-D thermoelastic problems

After the extensive research on the capabilities of the Boundary Integral Equation Method produced during the past years the versatility of its applications has been well founded. Maybe the years to come will see the in-depth analysis of several conflictive points, for example, adaptive integration, solution of the system of equations, etc. This line is clear in academic research. In this paper we comment on the incidence of the manner of imposing the boundary conditions in 3-D coupled problems. Here the effects are particularly magnified: in the first place by the simple model used (constant elements) and secondly by the process of solution, i.e. first a potential problem is solved and then the results are used as data for an elasticity problem. The errors add to both processes and small disturbances, unimportant in separated problems, can produce serious errors in the final results. The specific problem we have chosen is especially interesting. Although more general cases (i.e. transient)can be treated, here the domain integrals can be converted into boundary ones and the influence of the manner in which boundary conditions are applied will reflect the whole importance of the problem.

Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter

The onset of X inactivation coincides with accumulation of Xist RNA along the future inactive X chromosome. A recent hypothesis proposed that accumulation is initiated by a promoter switch within Xist. In this hypothesis, an upstream promoter (P0) produces an unstable transcript, while the known downstream promoter (P1) produces a stable RNA. To test this hypothesis, we examined expression and half-life of Xist RNA produced from an Xist transgene lacking P0 but retaining P1. We confirm the previous finding that P0 is dispensable for Xist expression in undifferentiated cells and that P1 can be used in both undifferentiated and differentiated cells. Herein, we show that Xist RNA initiated at P1 is unstable and does not accumulate. Further analysis indicates that the transcriptional boundary at P0 does not represent the 5′ end of a distinct Xist isoform. Instead, P0 is an artifact of cross-amplification caused by a pseudogene of the highly expressed ribosomal protein S12 gene Rps12. Using strand-specific techniques, we find that transcription upstream of P1 originates from the DNA strand opposite Xist and represents the 3′ end of the antisense Tsix RNA. Thus, these data do not support the existence of a P0 promoter and suggest that mechanisms other than switching of functionally distinct promoters control the up-regulation of Xist.

Surface geochemistry of the clay minerals

Clay minerals are layer type aluminosilicates that figure in terrestrial biogeochemical cycles, in the buffering capacity of the oceans, and in the containment of toxic waste materials. They are also used as lubricants in petroleum extraction and as industrial catalysts for the synthesis of many organic compounds. These applications derive fundamentally from the colloidal size and permanent structural charge of clay mineral particles, which endow them with significant surface reactivity. Unraveling the surface geochemistry of hydrated clay minerals is an abiding, if difficult, topic in earth sciences research. Recent experimental and computational studies that take advantage of new methodologies and basic insights derived from the study of concentrated ionic solutions have begun to clarify the structure of electrical double layers formed on hydrated clay mineral surfaces, particularly those in the interlayer region of swelling 2:1 layer type clay minerals. One emerging trend is that the coordination of interlayer cations with water molecules and clay mineral surface oxygens is governed largely by cation size and charge, similarly to a concentrated ionic solution, but the location of structural charge within a clay layer and the existence of hydrophobic patches on its surface provide important modulations. The larger the interlayer cation, the greater the influence of clay mineral structure and hydrophobicity on the configurations of adsorbed water molecules. This picture extends readily to hydrophobic molecules adsorbed within an interlayer region, with important implications for clay–hydrocarbon interactions and the design of catalysts for organic synthesis.

Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye.

Isolated guanine quadruplex structures have been described at high resolution both in solution and in the solid state. The existence of this unusual DNA structure in vivo and its biological significance remain to be determined. We describe the binding of 3,3'-diethyloxadicarbocyanine to dimeric hairpin guanine quadruplexes. This interaction results in a set of unique spectrophotometric signatures, none of which arises from binding to single strands or Watson-Crick duplexes. These unique signatures include a new absorbance peak (lambda max = 534 nm), an induced circular dichroism (lambda = 534-626 nm), a quenching of the dye fluorescence upon excitation with visible light, and strong energy transfer from DNA. This last effect provides the basis for detecting hairpin quadruplex structures in the presence of excess amounts of nonquadruplex DNA structures, such as single strands and Watson-Crick duplexes. The mechanism of quadruplex recognition by this dye is discussed, along with the possibility of using this dye as a probe for hairpin quadruplex structures in vitro and in vivo.

Sequence specificity of triplex DNA formation: Analysis by a combinatorial approach, restriction endonuclease protection selection and amplification.

We have devised a combinatorial method, restriction endonuclease protection selection and amplification (REPSA), to identify consensus ligand binding sequences in DNA. In this technique, cleavage by a type IIS restriction endonuclease (an enzyme that cleaves DNA at a site distal from its recognition sequence) is prevented by a bound ligand while unbound DNA is cleaved. Since the selection step of REPSA is performed in solution under mild conditions, this approach is amenable to the investigation of ligand-DNA complexes that are either insufficiently stable or not readily separable by other methods. Here we report the use of REPSA to identify the consensus duplex DNA sequence recognized by a G/T-rich oligodeoxyribonucleotide under conditions favoring purine-motif triple-helix formation. Analysis of 47 sequences indicated that recognition between 13 bases on the oligonucleotide 3' end and the duplex DNA was sufficient for triplex formation and indicated the possible existence of a new base triplet, G.AT. This information should help identify appropriate target sequences for purine-motif triplex formation and demonstrates the power of REPSA for investigating ligand-DNA interactions.

On the existence and implications of an inverse folding code in proteins.

The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures that encode specific sequence distributions include the classical "secondary" structures, with the notable exception of planar (beta) bends. It is suggested that this has implications as to the mechanism of folding in proteins with extensive sheet/barrel structure. The possible role of structures that do not encode specific sequences as mutation hot spots is noted.

The Judicial Dimension of the European Neighbourhood Policy. EU Diplomacy Paper 08/2013, November 2013

In this paper, the expression “neighbourhood policy” of the European Union (EU) is understood in a broad way which includes the members of the European Free Trade Association (EFTA) contracting parties to the European Economic Area (EEA), the EFTA State Switzerland, candidate states, the countries of the European Neighbour-hood Policy (ENP), and Russia. The European Court of Justice (ECJ) is the centre of gravity in the judicial dimension of this policy. The innermost circle of integration after the EU itself comprises the EFTA States who are party to the European Economic Area. With the EFTA Court, they have their own common court. The existence of two courts – the ECJ and the EFTA Court – raises the question of homogeneity of the case law. The EEA homogeneity rules resemble the ones of the Lugano Convention. The EFTA Court is basically obliged to follow or take into account relevant ECJ case law. But even if the ECJ has gone first, there may be constellations where the EFTA Court comes to the conclusion that it must go its own way. Such constellations may be given if there is new scientific evidence, if the ECJ has left certain questions open, where there is relevant case law of the European Court of Human Rights or where, in light of the specific circumstances of the case, there is room for “creative homogeneity”. However, in the majority of its cases the EFTA Court is faced with novel legal questions. In such cases, the ECJ, its Advocates General and the Court of First Instance make reference to the EFTA Court’s case law. The question may be posed whether the EEA could serve as a model for other regional associations. For the ENP states, candidate States and Russia this is hard to imagine. Their courts will to varying degrees look to the ECJ when giving interpretation to the relevant agreements. The Swiss Government is – at least for the time being – unwilling to make a second attempt to join the EEA. The European Commission has therefore proposed to the Swiss to dock their sectoral agreements with the EU to the institutions of the EFTA pillar, the EFTA Surveillance Authority (ESA) and the EFTA Court. Switzerland would then negotiate the right to nominate a member of the ESA College and of the EFTA Court. The Swiss Government has, however, opted for another model. Swiss courts would continue to look to the ECJ, as they did in the past, and conflicts should also in the future be resolved by diplomatic means. But the ECJ would play a decisive role in dispute settlement. It would, upon unilateral request of one side, give an “authoritative” interpretation of EU law as incorporated into the relevant bilateral agreement. In a “Non-Paper” which was drafted by the chief negotiators, the interpretations of the ECJ are even characterised as binding. The decision-making power would, however, remain with the Joint Committees where Switzerland could say no. The Swiss Government assumes that after a negative decision by the ECJ it would be able to negotiate a compromise solution with the Commission without the ECJ being able to express itself on the outcome. The Government has therefore not tried to emphasise that the ECJ would not be a foreign court. Whether the ECJ would accept its intended role, is an open question. And if it would, the Swiss Government would have to explain to its voters that Switzerland retains the freedom to disregard such a binding decision and that for this reason the ECJ is not only no foreign court, but no adjudicating court at all.

A refined solution to the first terrestrial Pb-isotope paradox

The first terrestrial Pb-isotope paradox refers to the fact that on average, rocks from the Earth's surface (i.e. the accessible Earth) plot significantly to the right of the meteorite isochron in a common Pb-isotope diagram. The Earth as a whole, however, should plot close to the meteorite isochron, implying the existence of at least one terrestrial reservoir that plots to the left of the meteorite isochron. The core and the lower continental crust are the two candidates that have been widely discussed in the past. Here we propose that subducted oceanic crust and associated continental sediment stored as garnetite slabs in the mantle Transition Zone or mid-lower mantle are an additional potential reservoir that requires consideration. We present evidence from the literature that indicates that neither the core nor the lower crust contains sufficient unradiogenic Pb to balance the accessible Earth. Of all mantle magmas, only rare alkaline melts plot significantly to the left of the meteorite isochron. We interpret these melts to be derived from the missing mantle reservoir that plots to the left of the meteorite isochron but, significantly, above the mid-ocean ridge basalt (MORB)-source mantle evolution line. Our solution to the paradox predicts the bulk silicate Earth to be more radiogenic in Pb-207/Pb-204 than present-day MORB-source mantle, which opens the possibility that undegassed primitive mantle might be the source of certain ocean island basalts (OIB). Further implications for mantle dynamics and oceanic magmatism are discussed based on a previously justified proposal that lamproites and associated rocks could derive from the Transition Zone.

Existence and embeddings of partial Steiner triple systems of order ten with cubic leaves

Denote the set of 21 non-isomorphic cubic graphs of order 10 by L. We first determine precisely which L is an element of L occur as the leave of a partial Steiner triple system, thus settling the existence problem for partial Steiner triple systems of order 10 with cubic leaves. Then we settle the embedding problem for partial Steiner triple systems with leaves L is an element of L. This second result is obtained as a corollary of a more general result which gives, for each integer v greater than or equal to 10 and each L is an element of L, necessary and sufficient conditions for the existence of a partial Steiner triple system of order v with leave consisting of the complement of L and v - 10 isolated vertices. (C) 2004 Elsevier B.V. All rights reserved.

Partial regularity of weak solutions of the liquid crystal equilibrium system

For a parameter, we consider the modified relaxed energy of the liquid crystal system. Each minimizer of the modified relaxed energy is a weak solution to the liquid crystal equilibrium system. We prove the partial regularity of minimizers of the modified relaxed energy. We also prove the existence of infinitely many weak solutions for the special boundary value x.

Improved germination of the Australian natives: Hibbertia commutata, Hibbertia amplexicaulis (Dilleniaceae), Chameascilla corymbosa (Liliaceae) and Leucopogon nutans (Epacridaceae)

Hibbertia commutata (Steudel), H. amplexicaulis (Steudel), Chameascilla corymbosa [(R.Br.) F.Muell. Ex Benth.] and Leucopogon nutans (E. Pritzel) are four Australian species that are difficult to germinate during mine-site rehabilitation. Laboratory germination trails were conducted to identify dormancy mechanisms and to improve germination response. Treatments applied to all species included scarification and scarification followed by soaking seeds in smoke water (1, 5 or 10%) or gibberellic-acid solution (50, 200 or 1000 muM). Additional treatments with kinetin solution (50, 200 or 1000 muM) and smoke water (50 or 100%) were applied to scarified or unscarified seeds of C. corymbosa. Thermal-shock treatment was applied to L. nutans fruit, some of which were subsequently scarified and subjected to both smoke water (10%) and gibberellic-acid solution (1000 muM). Significant germination increases were obtained by using dormancy-breaking treatments on H. commutata ( from 12.8 to 76.0%), H. amplexicaulis (from 6.8 to 55.1%) and C. corymbosa (from 48.5 to 86.4%). Scarification alone increased germination of both Hibbertia species, suggesting that these species display a physical seed coat-imposed dormancy mechanism. Germination of H. amplexicaulis was further increased by the application of gibberellic-acid solution, indicating a possible embryo-imposed dormancy mechanism. Scarification followed by the application of smoke water produced the highest germination response for C. corymbosa seeds. Scarification alone did not significantly increase germination, inferring the existence of a smoke-responsive embryo dormancy mechanism. Seeds of L. nutans, although viable, failed to germinate and are thought to display complex seed coat- and embryo-imposed dormancy mechanisms.

Global behavior of positive solutions of nonlinear three-point boundary value problems

We investigate the structure of the positive solution set for nonlinear three-point boundary value problems of the form u('') + h(t) f(u) = 0, u(0) = 0, u(1) = lambdau(eta), where eta epsilon (0, 1) is given lambda epsilon (0, 1/n) is a parameter, f epsilon C ([0, infinity), [0, infinity)) satisfies f (s) > 0 for s > 0, and h epsilon C([0, 1], [0, infinity)) is not identically zero on any subinterval of [0, 1]. Our main results demonstrate the existence of continua of positive solutions of the above problem. (C) 2004 Elsevier Ltd. All rights reserved.

Statistical mechanics of low-density parity check error-correcting codes over Galois fields

A variation of low-density parity check (LDPC) error-correcting codes defined over Galois fields (GF(q)) is investigated using statistical physics. A code of this type is characterised by a sparse random parity check matrix composed of C non-zero elements per column. We examine the dependence of the code performance on the value of q, for finite and infinite C values, both in terms of the thermodynamical transition point and the practical decoding phase characterised by the existence of a unique (ferromagnetic) solution. We find different q-dependence in the cases of C = 2 and C ≥ 3; the analytical solutions are in agreement with simulation results, providing a quantitative measure to the improvement in performance obtained using non-binary alphabets.

Canonical solution groups of a homomorphism : manipulator kinematics, nonparametric regression and distributed object systems

The kinematic mapping of a rigid open-link manipulator is a homomorphism between Lie groups. The homomorphisrn has solution groups that act on an inverse kinematic solution element. A canonical representation of solution group operators that act on a solution element of three and seven degree-of-freedom (do!) dextrous manipulators is determined by geometric analysis. Seven canonical solution groups are determined for the seven do! Robotics Research K-1207 and Hollerbach arms. The solution element of a dextrous manipulator is a collection of trivial fibre bundles with solution fibres homotopic to the Torus. If fibre solutions are parameterised by a scalar, a direct inverse funct.ion that maps the scalar and Cartesian base space coordinates to solution element fibre coordinates may be defined. A direct inverse pararneterisation of a solution element may be approximated by a local linear map generated by an inverse augmented Jacobian correction of a linear interpolation. The action of canonical solution group operators on a local linear approximation of the solution element of inverse kinematics of dextrous manipulators generates cyclical solutions. The solution representation is proposed as a model of inverse kinematic transformations in primate nervous systems. Simultaneous calibration of a composition of stereo-camera and manipulator kinematic models is under-determined by equi-output parameter groups in the composition of stereo-camera and Denavit Hartenberg (DH) rnodels. An error measure for simultaneous calibration of a composition of models is derived and parameter subsets with no equi-output groups are determined by numerical experiments to simultaneously calibrate the composition of homogeneous or pan-tilt stereo-camera with DH models. For acceleration of exact Newton second-order re-calibration of DH parameters after a sequential calibration of stereo-camera and DH parameters, an optimal numerical evaluation of DH matrix first order and second order error derivatives with respect to a re-calibration error function is derived, implemented and tested. A distributed object environment for point and click image-based tele-command of manipulators and stereo-cameras is specified and implemented that supports rapid prototyping of numerical experiments in distributed system control. The environment is validated by a hierarchical k-fold cross validated calibration to Cartesian space of a radial basis function regression correction of an affine stereo model. Basic design and performance requirements are defined for scalable virtual micro-kernels that broker inter-Java-virtual-machine remote method invocations between components of secure manageable fault-tolerant open distributed agile Total Quality Managed ISO 9000+ conformant Just in Time manufacturing systems.

The geochemistry of radioactive waste disposal

The present study attempted to identify the significant parameters which affect radionuclide migration from a low level radioactive waste disposal site located in a clay deposit. From initial sorption studies on smectite minerals, increased Kd with decreasing initial cation concentration was observed, and three sorption mechanisms were identified. The observation of anion dependent sorption was related to the existence of a mechanism in which an anion-cation pair are bound to the clay surface through the anion. The influence of competing cations, typical of inorganic groundwater constituents, depended on: (1) Ni/Co:Mn+(Mn+ = competing cation) ratio, (2) nature of M^n+, (3) total solution ionic strength. The presence of organic material in groundwater is well documented, but its effect on cation sorption has not been established. An initial qualitative investigation involving addition of simple organic ligands to Ni(Co)-hectorite samples demonstrated the formation of metal complexes in the clay interlayers, although some modified behaviour was observed. Further quantitative examination involving likely groundwater organic constituents and more comprehensive physical investigation confirmed this behaviour and enabled separation of the organic compounds used into two classes, according to their effect on cation sorption; (i) acids, (ii) amine compounds. X-ray photoelectron spectroscopy, scanning electron microscopy and Mossbauer spectroscopy were used to investigate the nature of transition metal ions sorbed onto montmorillonite and hectorite. Evidence strongly favoured the sorption of the hexaaquo cation, although a series of sorption sites of slightly different chemical characteristics were responsible for broadened peak widths observed in XPS and Mossbauer investigations. The surface sensitivity of XPS enabled recognition of the two surface sorption sites proposed in earlier sorption studies. Although thermal treatment of Fe^3+/Fe^2+-hectorite samples left iron atoms bonded to the silicate sheet structure, Mossbauer evidence indicated the presence of both ferric and ferrous iron in all samples.