A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain

Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools

Internal transport barriers in the National Spherical Torus Experiment

In the National Spherical Torus Experiment [M. Ono , Nucl. Fusion 41, 1435 (2001)], internal transport barriers (ITBs) are observed in reversed (negative) shear discharges where diffusivities for electron and ion thermal channels and momentum are reduced. While neutral beam heating can produce ITBs in both electron and ion channels, high harmonic fast wave heating can also produce electron ITBs (e-ITBs) under reversed magnetic shear conditions without momentum input. Interestingly, the location of the e-ITB does not necessarily match that of the ion ITB (i-ITB). The e-ITB location correlates best with the magnetic shear minima location determined by motional Stark effect constrained equilibria, whereas the i-ITB location better correlates with the location of maximum ExB shearing rate. Measured electron temperature gradients in the e-ITB can exceed critical gradients for the onset of electron thermal gradient microinstabilities calculated by linear gyrokinetic codes. A high-k microwave scattering diagnostic shows locally reduced density fluctuations at wave numbers characteristic of electron turbulence for discharges with strongly negative magnetic shear versus weakly negative or positive magnetic shear. Reductions in fluctuation amplitude are found to be correlated with the local value of magnetic shear. These results are consistent with nonlinear gyrokinetic simulations predicting a reduction in electron turbulence under negative magnetic shear conditions despite exceeding critical gradients.X1128sciescopu

The androgen receptor and signal-transduction pathways in hormone-refractory prostate cancer. Part 2: androgen-receptor cofactors and bypass pathways

Prostate cancer is the second leading cause of cancer related deaths in men from the western world. Treatment of prostate cancer has relied on androgen deprivation therapy for the past 50 years. Response rates are initially high (70-80%), however almost all patients develop androgen escape and subsequently die within 1-2 years. Unlike breast cancer, alternative approaches (chemotherapy and radiotherapy) do not increase survival time. The high rate of prostate cancer mortality is therefore strongly linked to both development of androgen escape and the lack of alternate therapies. AR mutations and amplifications can not explain all cases of androgen escape and post-translational modification of the AR has become an alternative theory. However recently it has been suggested that AR co-activators e.g. SRC-1 or pathways the bypass the AR (Ras/MAP kinase or PI3K/Akt) may stimulated prostate cancer progression independent of the AR. This review will focus on how AR coactivators may act to increase AR transactivation during sub-optimal DHT concentrations and also how signal transduction pathways may promote androgen escape via activation of transcription factors, e.g. AP-1, c-Myc and Myb, that induce cell proliferation or inhibit apoptosis

Electron gyroscale fluctuation measurements in National Spherical Torus Experiment H-mode plasmas

A collective scattering system has measured electron gyroscale fluctuations in National Spherical Torus Experiment [M. Ono et al., Nucl. Fusion 40, 557 (2000)] H-mode plasmas to investigate electron temperature gradient (ETG) turbulence. Observations and results pertaining to fluctuation measurements in ETG-stable regimes, the toroidal field scaling of fluctuation amplitudes, the relation between fluctuation amplitudes and transport quantities, and fluctuation magnitudes and k-spectra are presented. Collectively, the measurements provide insight and guidance for understanding ETG turbulence and anomalous electron thermal transport. (C) 2009 American Institute of Physics. [doi:10.1063/1.3262530]X116sciescopu

Structural Synthesis for GXW Specifications

We define the GXW fragment of linear temporal logic (LTL) as the basis for synthesizing embedded control software for safety-critical applications. Since GXW includes the use of a weak-until operator we are able to specify a number of diverse programmable logic control (PLC) problems, which we have compiled from industrial training sets. For GXW controller specifications, we develop a novel approach for synthesizing a set of synchronously communicating actor-based controllers. This synthesis algorithm proceeds by means of recursing over the structure of GXW specifications, and generates a set of dedicated and synchronously communicating sub-controllers according to the formula structure. In a subsequent step, 2QBF constraint solving identifies and tries to resolve potential conflicts between individual GXW specifications. This structural approach to GXW synthesis supports traceability between requirements and the generated control code as mandated by certification regimes for safety-critical software. Synthesis for GXW specifications is in PSPACE compared to 2EXPTIME-completeness of full-fledged LTL synthesis. Indeed our experimental results suggest that GXW synthesis scales well to industrial-sized control synthesis problems with 20 input and output ports and beyond.Comment: The long (including appendix) version being reviewed by CAV'16 program committee. Compared to the submitted version, one author (out of her wish) is moved to the Acknowledgement. (v2) Corrected typos. (v3) Add an additional remark over environment assumption and easy corner case

Structure and optical properties of Lu <inf>2</inf>SiO <inf>5</inf>:Ce phosphor thin films

Luminescent, cerium doped Lu 2SiO 5 thin films with C2/c symmetry have been prepared by pulsed laser deposition (PLD) at temperatures much lower than the crystallization temperature (2150°C) of the corresponding bulk crystals. The PLD grown films show the typical luminescence resulting from the Ce 3+ 5d-4f transition. Maximum luminescence efficiency was observed for films prepared at an oxygen partial pressure of 200 mTorr at 600°C. These conditions reflect a balance between Ce 4+/Ce 3+ interconversion and the crystalline quality of the films. The results indicate that PLD offers a low temperature deposition technique for complex oxide phosphor materials. © 2006 American Institute of Physics

Short-scale turbulent fluctuations driven by the electron-temperature gradient in the national spherical torus experiment

Measurements with coherent scattering of electromagnetic waves in plasmas of the National Spherical Torus Experiment indicate the existence of turbulent fluctuations in the range of wave numbers k(perpendicular to)rho(e)=0.1-0.4, corresponding to a turbulence scale length nearly equal to the collisionless skin depth. Experimental observations and agreement with numerical results from a linear gyrokinetic stability code support the conjecture that the observed turbulence is driven by the electron-temperature gradient.X1155sciescopu

Observations of Reduced Electron Gyroscale Fluctuations in National Spherical Torus Experiment H-Mode Plasmas with Large E X B Flow Shear

Electron gyroscale fluctuation measurements in National Spherical Torus Experiment H-mode plasmas with large toroidal rotation reveal fluctuations consistent with electron temperature gradient (ETG) turbulence. Large toroidal rotation in National Spherical Torus Experiment plasmas with neutral beam injection generates ExB flow shear rates comparable to ETG linear growth rates. Enhanced fluctuations occur when the electron temperature gradient is marginally stable with respect to the ETG linear critical gradient. Fluctuation amplitudes decrease when the ExB flow shear rate exceeds ETG linear growth rates. The observations indicate that ExB flow shear can be an effective suppression mechanism for ETG turbulence.X1129sciescopu

Controllability and controller-observer design for a class of linear time-varying systems

“The final publication is available at Springer via http://dx.doi.org/10.1007/s10852-012-9212-6"In this paper a class of linear time-varying control systems is considered. The time variation consists of a scalar time-varying coefficient multiplying the state matrix of an otherwise time-invariant system. Under very weak assumptions of this coefficient, we show that the controllability can be assessed by an algebraic rank condition, Kalman canonical decomposition is possible, and we give a method for designing a linear state-feedback controller and Luenberger observer