Microarray expression profiling in melanoma reveals a BRAF mutation signature

We have used microarray gene expression pro. ling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42 samples (69%) and intragenic mutations of the NRAS gene were detected in seven samples (11%). No cell line carried mutations of both genes. Using support vector machines, we have built a classifier that differentiates between melanoma cell lines based on BRAF mutation status. As few as 83 genes are able to discriminate between BRAF mutant and BRAF wild-type samples with clear separation observed using hierarchical clustering. Multidimensional scaling was used to visualize the relationship between a BRAF mutation signature and that of a generalized mitogen-activated protein kinase ( MAPK) activation ( either BRAF or NRAS mutation) in the context of the discriminating gene list. We observed that samples carrying NRAS mutations lie somewhere between those with or without BRAF mutations. These observations suggest that there are gene-specific mutation signals in addition to a common MAPK activation that result from the pleiotropic effects of either BRAF or NRAS on other signaling pathways, leading to measurably different transcriptional changes.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise F-ST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise F-ST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Quantifying the effects of bycatch reduction devices in Queensland's (Australia) shallow water eastern king prawn (Penaeus plebejus) trawl fishery

This study presents results from an experimental 10-day research charter that was designed to quantify the effects of (a) a turtle excluder device (TED), (b) a radial escape section bycatch reduction device (BRD) and (c) both devices together, on bycatch and prawn catch rates in the Queensland shallow water eastern king prawn (Penaeus plebejus) trawl fishery. The bycatch was comprised of 250 taxa, mainly gurnards, whiting, lizard fish, flathead, dragonets, portunid crabs, turretfish and flounders. The observed mean catch rates of bycatch and marketable eastern king prawns from the standard trawl net (i.e., net with no TED or BRD) used during the charter were 11.06 kg/hectare (ha(-1)) (S.E. 0.90) swept by the trawl gear and 0.94 kg ha(-1), respectively. For the range of depths sampled (20.1-90.7 m), bycatch rates declined significantly at a rate of 0.14 kg ha-1 for every 1 m increase in depth, while prawn catch rates were unaffected. When both the TED and radial escape section BRD were used together, the bycatch rate declined by 24% compared to a standard net, but at a 20% reduction in marketable prawn catch rate. The largest reductions were achieved for stout whiting Sillago robusta (57% reduction) and yellowtail scad Trachurus novaezelandiae (32% reduction). Multidimensional scaling and analysis of similarities revealed that bycatch assemblages differed significantly between depths and latitude, but not between the different combinations of bycatch reduction devices. Despite the lowered prawn catch rates, the reduced bycatch rates are promising, particularly for S. robusta, which is targeted in another fishery. Prawn trawl operators are not permitted to retain S. robusta and the devices examined herein offer the potential to significantly reduce the incidental fishing mortality that this species experiences. (c) 2006 Elsevier B.V. All rights reserved.

Scaling of decoherence effects in quantum computers

The scaling of decoherence rates with qubit number N is studied for a simple model of a quantum computer in the situation where N is large. The two state qubits are localized around well-separated positions via trapping potentials and vibrational centre of mass motion of the qubits occurs. Coherent one and two qubit gating processes are controlled by external classical fields and facilitated by a cavity mode ancilla. Decoherence due to qubit coupling to a bath of spontaneous modes, cavity decay modes and to the vibrational modes is treated. A non-Markovian treatment of the short time behaviour of the fidelity is presented, and expressions for the characteristic decoherence time scales obtained for the case where the qubit/cavity mode ancilla is in a pure state and the baths are in thermal states. Specific results are given for the case where the cavity mode is in the vacuum state and gating processes are absent and the qubits are in (a) the Hadamard state (b) the GHZ state.

Scaling of rectal gland mass in the European lesser-spotted dogfish

In the European lesser-spotted dogfish Scyliorhinus canicula, rectal gland mass in mg (M-Rg) followed the allometric relationship: M-Rg = 1.15 M-0.68, where M is body mass (g). The concept of allometric scaling is an important consideration in studies investigating the function Of osmoregulatory organs. (C) 2003 the Fisheries Society of the British Isles.

A genetic two-factor model of the covariation among a subset of Multidimensional Aptitude Battery and Wechsler Adult Intelligence Scale - Revised subtests

The phenotypic and genetic factor structure of performance on five Multidimensional Aptitude Battery (MAB) subtests and one Wechsler Adult Intelligence Scale-Revised (WAIS-R) subtest was explored in 390 adolescent twin pairs (184 monozygotic [MZ]; 206 dizygotic (DZ)). The temporal stability of these measures was derived from a subsample of 49 twin pairs, with test-retest correlations ranging from .67 to .85. A phenotypic factor model, in which performance and verbal factors were correlated, provided a good fit to the data. Genetic modeling was based on the phenotypic factor structure, but also took into account the additive genetic (A), common environmental (C), and unique environmental (E) parameters derived from a fully saturated ACE model. The best fitting model was characterized by a genetic correlated two-factor structure with specific effects, a general common environmental factor, and overlapping unique environmental effects. Results are compared to multivariate genetic models reported in children and adults, with the most notable difference being the growing importance of common genes influencing diverse abilities in adolescence. (C) 2003 Elsevier Inc. All rights reserved.

Exact solution, scaling behaviour and quantum dynamics of a model of an atom-molecule Bose-Einstein condensate

0We study the exact solution for a two-mode model describing coherent coupling between atomic and molecular Bose-Einstein condensates (BEC), in the context of the Bethe ansatz. By combining an asymptotic and numerical analysis, we identify the scaling behaviour of the model and determine the zero temperature expectation value for the coherence and average atomic occupation. The threshold coupling for production of the molecular BEC is identified as the point at which the energy gap is minimum. Our numerical results indicate a parity effect for the energy gap between ground and first excited state depending on whether the total atomic number is odd or even. The numerical calculations for the quantum dynamics reveals a smooth transition from the atomic to the molecular BEC.

Scaling of multiple postselected quantum gates in optics

We show that interesting multigate circuits can be constructed using a postselected controlled-sign gate that works with a probability (1/3)(n), where n-1 is the number of controlled-sign gates in the circuit, rather than (1/9)(n-1), as would be expected from a sequence of such gates. We suggest some quantum information tasks which could be demonstrated using these circuits, such as parity checking and cluster-state computation.

Cluster cannibalism and scaling relations of galactic stellar nuclei

Recently, very massive compact stellar systems have been discovered in the intracluster regions of galaxy clusters and in the nuclear regions of late-type disk galaxies. It is unclear how these compact stellar systems - known as ultracompact dwarf (UCD) galaxies or nuclear clusters (NCs) - form and evolve. By adopting a formation scenario in which these stellar systems are the product of multiple merging of star clusters in the central regions of galaxies, we investigate, numerically, their physical properties. We find that physical correlations among velocity dispersion, luminosity, effective radius, and average surface brightness in the stellar merger remnants are quite different from those observed in globular clusters. We also find that the remnants have triaxial shapes with or without figure rotation, and these shapes and their kinematics depend strongly on the initial number and distribution of the progenitor clusters. These specific predictions can be compared with the corresponding results of ongoing and future observations of UCDs and NCs, thereby providing a better understanding of the origin of these enigmatic objects.

Investigating social entrepreneurship: A multidimensional model

Social entrepreneurship is an emerging area of investigation within the entrepreneurship and not-for-profit marketing literatures. A review of the literature emerging from a number of domains reveals that it is fragmented and that there is no coherent theoretical framework. In particular, current conceptualizations of social entrepreneurship fail to adequately consider the unique characteristics of social entrepreneurs and the context within which they must operate. Using grounded theory method and drawing on nine in-depth case studies of social entrepreneurial not-for-profit organizations, this paper addresses this research gap and develops a bounded multidimensional model of social entrepreneurship. Implications for social entrepreneurship theory, management practice, and policy directions are discussed.

Use of the Vector (TM) scaling unit in supportive periodontal therapy: a subjective patient evaluation

Background: Patient discomfort is one reason for poor compliance with supportive periodontal therapy (SPT). The aim of this study was to compare the levels of discomfort during SPT, using the Vector (TM) system and treatment with a conventional ultrasonic scaler. Methods: Forty-six patients with an SPT programme were debrided using both the Vector (TM) system and a conventional piezo-electric scaler (Sirona (TM)) in a split mouth design. A visual analogue scale was used to evaluate of pain scores upon completion of treatment. A verbal response scale(VRS) was used to assess discomfort, vibration and noise associated with the scaling system, as well as the volume and taste of the coolant used by these systems. Results: Patients instrumented with the Vector (TM) system experienced approximately half the amount of pain compared with the conventional ultrasonic scaling system. The VRS showed that the Vector (TM) system caused less discomfort than the conventional ultrasonic scaling system when assessed for pain, vibration, noise and volume of coolant. These findings were all statistically significant. There was, however, no statistically significant difference between the two systems when assessed for taste. Conclusion: During SPT the Vector (TM) system caused reduced discomforting sensations compared with conventional methods and may be useful in improving compliance with SPT programmes.

Scaling laws for the critical rupture thickness or common thin films

Despite decades of experimental and theoretical investigation on thin films, considerable uncertainty exists in the prediction of their critical rupture thickness. According to the spontaneous rupture mechanism, common thin films become unstable when capillary waves. at the interfaces begin to grow. In a horizontal film with symmetry at the midplane. unstable waves from adjacent interfaces grow towards the center of the film. As the film drains and becomes thinner, unstable waves osculate and cause the film to rupture, Uncertainty sterns from a number of sources including the theories used to predict film drainage and corrugation growth dynamics. In the early studies, (lie linear stability of small amplitude waves was investigated in the Context of the quasi-static approximation in which the dynamics of wave growth and film thinning are separated. The zeroth order wave growth equation of Vrij predicts faster wave growth rates than the first order equation derived by Sharma and Ruckenstein. It has been demonstrated in an accompanying paper that film drainage rates and times measured by numerous investigations are bounded by the predictions of the Reynolds equation and the more recent theory of Manev, Tsekov, and Radoev. Solutions to combinations of these equations yield simple scaling laws which should bound the critical rupture thickness of foam and emulsion films, In this paper, critical thickness measurements reported in the literature are compared to predictions from the bounding scaling equations and it is shown that the retarded Hamaker constants derived from approximate Lifshitz theory underestimate the critical thickness of foam and emulsion films, The non-retarded Hamaker constant more adequately bounds the critical thickness measurements over the entire range of film radii reported in the literature. This result reinforces observations made by other independent researchers that interfacial interactions in flexible liquid films are not adequately represented by the retarded Hamaker constant obtained from Lifshitz theory and that the interactions become significant at much greater separations than previously thought. (c) 2005 Elsevier B.V. All rights reserved.

Artificial pumping errors in the Kool-Parker scaling model of soil moisture hysteresis

Hysteresis models that eliminate the artificial pumping errors associated with the Kool-Parker (KP) soil moisture hysteresis model, such as the Parker-Lenhard (PL) method, can be computationally demanding in unsaturated transport models since they need to retain the wetting-drying history of the system. The pumping errors in these models need to be eliminated for correct simulation of cyclical systems (e.g. transport above a tidally forced watertable, infiltration and redistribution under periodic irrigation) if the soils exhibit significant hysteresis. A modification is made here to the PL method that allows it to be more readily applied to numerical models by eliminating the need to store a large number of soil moisture reversal points. The modified-PL method largely eliminates any artificial pumping error and so essentially retains the accuracy of the original PL approach. The modified-PL method is implemented in HYDRUS-1D (version 2.0), which is then used to simulate cyclic capillary fringe dynamics to show the influence of removing artificial pumping errors and to demonstrate the ease of implementation. Artificial pumping errors are shown to be significant for the soils and system characteristics used here in numerical experiments of transport above a fluctuating watertable. (c) 2005 Elsevier B.V. All rights reserved.

Mechanisms influencing levitation and the scaling laws in nanopores: Oscillator model theory

We provide here a detailed theoretical explanation of the floating molecule or levitation effect, for molecules diffusing through nanopores, using the oscillator model theory (Phys. Rev. Lett. 2003, 91, 126102) recently developed in this laboratory. It is shown that on reduction of pore size the effect occurs due to decrease in frequency of wall collision of diffusing particles at a critical pore size. This effect is, however, absent at high temperatures where the ratio of kinetic energy to the solid-fluid interaction strength is sufficiently large. It is shown that the transport diffusivities scale with this ratio. Scaling of transport diffusivities with respect to mass is also observed, even in the presence of interactions.