Modern medical imaging techniques enable the acquisition of in vivo high resolution images of the vascular system. Most common methods for the detection of vessels in these images, such as multiscale Hessian-based operators and matched filters, rely on the assumption that at each voxel there is a single cylinder. Such an assumption is clearly violated at the multitude of branching points that are easily observed in all, but the Most focused vascular image studies. In this paper, we propose a novel method for detecting vessels in medical images that relaxes this single cylinder assumption. We directly exploit local neighborhood intensities and extract characteristics of the local intensity profile (in a spherical polar coordinate system) which we term as the polar neighborhood intensity profile. We present a new method to capture the common properties shared by polar neighborhood intensity profiles for all the types of vascular points belonging to the vascular system. The new method enables us to detect vessels even near complex extreme points, including branching points. Our method demonstrates improved performance over standard methods on both 2D synthetic images and 3D animal and clinical vascular images, particularly close to vessel branching regions. (C) 2008 Elsevier B.V. All rights reserved.; NIH[R01HL065662]; NIH; NIH[R01EB006494]; NIH; American Surgical Association Research Fellowship Award; American Surgical Association Research Fellowship Award

Intravascular ultrasound (IVUS) phantoms are important to calibrate and evaluate many IVUS imaging processing tasks. However, phantom generation is never the primary focus of related works; hence, it cannot be well covered, and is usually based on more than one platform, which may not be accessible to investigators. Therefore, we present a framework for creating representative IVUS phantoms, for different intraluminal pressures, based on the finite element method and Field II. First, a coronary cross-section model is selected. Second, the coronary regions are identified to apply the properties. Third, the corresponding mesh is generated. Fourth, the intraluminal force is applied and the deformation computed. Finally, the speckle noise is incorporated. The framework was tested taking into account IVUS contrast, noise and strains. The outcomes are in line with related studies and expected values. Moreover, the framework toolbox is freely accessible and fully implemented in a single platform. (E-mail: fernando.okara@gmail.com) (c) 2012 World Federation for Ultrasound in Medicine & Biology.; Brazilian National Council of Scientific and Technological Development (CNPq); Brazilian National Council of Technological and Scientific Development (CNPq); Sao Paulo Research Foundation (FAPESP); Sao Paulo Research Foundation (FAPESP); Biomedical Engineering Laboratory of the University of Sao Paulo...

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2...

Microalgae are considered a promising source for various high value products, such as carotenoids, ω-3 and ω-6 polyunsaturated fatty acids (PUFA). The unicellular green alga Lobosphaera (Parietochloris) incisa is an outstanding candidate for the efficient phototrophic production of arachidonic acid (AA), an essential ω-6 PUFA for infant brain development and a widely used ingredient in the baby formula industry. Although phototrophic production of such algal products has not yet been established, estimated costs are considered to be 2–5 times higher than competing heterotrophic production costs. This alga accumulates unprecedented amounts of AA within triacylglycerols and the molecular pathway of AA biosynthesis in L. incisa has been previously elucidated. Thus, progress in transformation and metabolic engineering of this high value alga could be exploited for increasing the efficient production of AA at competitive prices. We describe here the first successful transformation of L. incisa using the ble gene as a selection marker, under the control of the endogenous RBCS promoter. Furthermore, we have succeeded in the functional complementation of the L. incisa mutant strain P127, containing a mutated, inactive version of the delta-5 (Δ5) fatty acid desaturase gene. A copy of the functional Δ5 desaturase gene...

A review of the experimental data for natC(n,gamma) and 12C(n,gamma) was made to identify the origin of the natC capture cross sections included in evaluated data libraries and to clarify differences observed in neutronic calculations for graphite moderated reactors using different libraries. The performance of the JEFF-3.1.2 and ENDF/B-VII.1 libraries was verified by comparing results of criticality calculations with experimental results obtained for the BR1 reactor. This reactor is an air-cooled reactor with graphite as moderator and is located at the Belgian Nuclear Research Centre SCK-CEN in Mol (Belgium). The results of this study confirm conclusions drawn from neutronic calculations of the High Temperature Engineering Test Reactor (HTTR) in Japan. Furthermore, both BR1 and HTTR calculations support the capture cross section of 12C at thermal energy which is recommended by Firestone and Révay. Additional criticality calculations were carried out in order to illustrate that the natC thermal capture cross section is important for systems with a large amount of graphite. The present study shows that only the evaluation carried out for JENDL-4.0 reflects the current status of the experimental data.; JRC.D.4-Standards for Nuclear Safety...

High temperature nuclear reactors are a technology, of which early versions were demonstrated in the 1960s–1980s in Germany (AVR, THTR) and the United States (Peach Bottom, Fort St. Vrain). HTRs were initially designed for high temperature, high efficiency electricity generation but the technology, the market and the targeted applications have evolved since then to address industrial cogeneration and new operational conditions (in particular new safety regulations). This paper intends to analyse the latest status of HTR today, as regards their intrinsic strengths and weaknesses and their external context, whether positive (opportunities) or negative (threats). Different dimensions are covered by the analysis: technology status, results from R&D programmes (especially in Europe), competences and skills, licensing aspects, experience feedback from demonstrator operation (in particular in Germany), economic conditions and other non-technical aspects. Europe has a comprehensive experience in the field of HTR with capabilities in both pebble bed and prismatic designs (R&D, engineering, manufacturing, operation, dismantling, and the full fuel cycle). Europe is also a promising market for HTR as the process heat market is large with good industrial and cogeneration infrastructures. The analysis of the European situation is to a good deal indicative for the global potential of this technology.; JRC.F.4-Nuclear Reactor Integrity Assessment and Knowledge Management

This paper presents assessment analysis of damage domains of the 30 MWth prototype High-Temperature Engineering Test Reactor (HTTR) operated by Japan Atomic Energy Agency (JAEA). For this purpose, an in-house deterministic risk assessment computational tool was developed based on the Theory of Stimulated Dynamics (TSD). To illustrate the methodology and applicability of the developed modelling approach, assessment results of a control rod (CR) withdrawal accident during subcritical condition are presented and compared with those obtained by the JAEA.; JRC.F.5-Nuclear Reactor Safety Assessment

New techniques for obtaining various thermophysical properties, i.e., densities and incremental enthalpies of selected materials at high temperatures have been developed with emphasis on the utilization of levitation technique and drop calorimetry. The density of liquid copper has been evaluated at 1550K. The incremental enthalpies of various Gd$sb2$O$sb3$-doped UO$sb2$ nuclear fuel pellets have been obtained at temperatures between 1700 and 2100K. Determinations of incremental enthalpies, the heat of fusion and specific heats for a liquid Ni-based superalloy have been carried out using levitation drop calorimetry. Contact angle studies between liquid titanium and selected ceramic materials have also been performed.

A critical step towards certifying safety-critical systems is to check their conformance to hard real-time requirements. A promising way to achieve this is by building the systems from pre-verified components and verifying their correctness in a compositional manner. We previously reported a formal approach to verifying function blocks (FBs) using tabular expressions and the PVS proof assistant. By applying our approach to the IEC 61131-3 standard of Programmable Logic Controllers (PLCs), we constructed a repository of precise specification and reusable (proven) theorems of feasibility and correctness for FBs. However, we previously did not apply our approach to verify FBs against timing requirements, since IEC 61131-3 does not define composite FBs built from timers. In this paper, based on our experience in the nuclear domain, we conduct two realistic case studies, consisting of the software requirements and the proposed FB implementations for two subsystems of an industrial control system. The implementations are built from IEC 61131-3 FBs, including the on-delay timer. We find issues during the verification process and suggest solutions.; Comment: In Proceedings ESSS 2015, arXiv:1506.03250

At present, coronary angiography is the well known standard for the diagnosis of coronary artery disease. Conventional coronary angiography is an invasive procedure with a small, yet inherent risk of myocardial infarction, stroke, potential arrhythmias, and death. Other noninvasive diagnostic tools, such as electrocardiography, echocardiography, and nuclear imaging are now widely available but are limited by their inability to directly visualize and quantify coronary artery stenoses and predict the stability of plaques. Coronary magnetic resonance angiography (MRA) is a technique that allows visualization of the coronary arteries by noninvasive means; however, it has not yet reached a stage where it can be used in routine clinical practice. Although coronary MRA is a potentially useful diagnostic tool, it has limitations. Further research should focus on improving the diagnostic resolution and accuracy of coronary MRA. This paper will helps to cardiologists to take the clear look of spatial filtered imaging of coronary arteries.; Comment: 06 Pages, 18 figures

Coupled problems with various combinations of multiple physics, scales, and domains can be found in numerous areas of science and engineering. A key challenge in the formulation and implementation of corresponding coupled models is to facilitate communication of information across physics, scale, and domain interfaces, as well as between iterations of solvers used for response computations. In a probabilistic context, any information that is to be communicated between subproblems or iterations should be characterized by an appropriate probabilistic representation. In this work, we consider stochastic coupled problems whose subproblems involve only uncertainties that are statistically independent of one another; for these problems, we present a characterization of the exchanged information by using a reduced chaos expansion with random coefficients. This expansion provides a reduced-dimensional representation of the exchanged information, while maintaining segregation between sources of uncertainty that stem from different subproblems. Further, we present a measure transformation that allows stochastic expansion methods to exploit this dimension reduction to obtain an efficient solution of subproblems in a reduced-dimensional space. We show that owing to the uncertainty source segregation...

This paper discusses the design and implementation of a Python-based toolset to aid in assessing the response of the UK's Advanced Gas Reactor nuclear power stations to earthquakes. The seismic analyses themselves are carried out with a commercial Finite Element solver, but understanding the raw model output this produces requires customised post-processing and visualisation tools. Extending the existing tools had become increasingly difficult and a decision was made to develop a new, Python-based toolset. This comprises of a post-processing framework (aftershock) which includes an embedded Python interpreter, and a plotting package (afterplot) based on numpy and matplotlib. The new toolset had to be significantly more flexible and easier to maintain than the existing code-base, while allowing the majority of development to be carried out by engineers with little training in software development. The resulting architecture will be described with a focus on exploring how the design drivers were met and the successes and challenges arising from the choices made.; Comment: Part of the Proceedings of the 7th European Conference on Python in Science (EuroSciPy 2014), Pierre de Buyl and Nelle Varoquaux editors, (2014)

We exploit ferromagnetic imprinting to create complex laterally defined regions of nuclear spin polarization in lithographically patterned MnAs/GaAs epilayers grown by molecular beam epitaxy (MBE). A time-resolved Kerr rotation microscope with approximately 1 micron spatial resolution uses electron spin precession to directly image the GaAs nuclear polarization. These measurements indicate that the polarization varies from a maximum under magnetic mesas to zero several microns from the mesa perimeter, resulting in large (10**4 T/m) effective field gradients. The results reveal a flexible scheme for lateral engineering of spin-dependent energy landscapes in the solid state.; Comment: Submitted to Physical Review B Rapid Communications. 18 pages, 4 figures

Recently, there has been a growing interest in developing Computer Aided Diagnostic (CAD) systems for improving the reliability and consistency of pathology test results. This paper describes a novel CAD system for the Anti-Nuclear Antibody (ANA) test via Indirect Immunofluorescence protocol on Human Epithelial Type 2 (HEp-2) cells. While prior works have primarily focused on classifying cell images extracted from ANA specimen images, this work takes a further step by focussing on the specimen image classification problem itself. Our system is able to efficiently classify specimen images as well as producing meaningful descriptions of ANA pattern class which helps physicians to understand the differences between various ANA patterns. We achieve this goal by designing a specimen-level image descriptor that: (1) is highly discriminative; (2) has small descriptor length and (3) is semantically meaningful at the cell level. In our work, a specimen image descriptor is represented by its overall cell attribute descriptors. As such, we propose two max-margin based learning schemes to discover cell attributes whilst still maintaining the discrimination of the specimen image descriptor. Our learning schemes differ from the existing discriminative attribute learning approaches as they primarily focus on discovering image-level attributes. Comparative evaluations were undertaken to contrast the proposed approach to various state-of-the-art approaches on a novel HEp-2 cell dataset which was specifically proposed for the specimen-level classification. Finally...

CEA, ANDRA and EDF are jointly developing the software platform ALLIANCES which aim is to produce a tool for the simulation of nuclear waste storage and disposal repository. This type of simulations deals with highly coupled thermo-hydro-mechanical and chemical (T-H-M-C) processes. A key objective of Alliances is to give the capability for coupling algorithms development between existing codes. The aim of this paper is to present coupling methodology use in the context of this software platform.; Comment: 7 pages

Coupled problems with various combinations of multiple physics, scales, and domains are found in numerous areas of science and engineering. A key challenge in the formulation and implementation of corresponding coupled numerical models is to facilitate the communication of information across physics, scale, and domain interfaces, as well as between the iterations of solvers used for response computations. In a probabilistic context, any information that is to be communicated between subproblems or iterations should be characterized by an appropriate probabilistic representation. Although the number of sources of uncertainty can be expected to be large in most coupled problems, our contention is that exchanged probabilistic information often resides in a considerably lower dimensional space than the sources themselves. This work thus presents an investigation into the characterization of the exchanged information by a reduced-dimensional representation and, in particular, by an adaptation of the Karhunen-Loeve decomposition. The effectiveness of the proposed dimension-reduction methodology is analyzed and demonstrated through a multiphysics problem relevant to nuclear engineering.

A set of physics models for nanodosimetry simulation is being re-engineered for use in Geant4-based simulations. This extension of Geant4 capabilities is part of a larger scale R&D project for multi-scale simulation involving adaptable, co-working condensed and discrete transport schemes. The project in progress reengineers the physics modeling capabilities associated with an existing FORTRAN track-structure code for nanodosimetry into a software design suitable to collaborate with an object oriented simulation kernel. The first experience and results of the ongoing re-engineering process are presented.; Comment: 4 pages, 2 figures and images, to appear in proceedings of the Nuclear Science Symposium and Medical Imaging Conference 2009, Orlando

A new mechanism of LENR in solids is proposed, which is based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). In particular, so called gap DBs, which can arise in diatomic crystals such as metal hydrides, are argued to be the LENR catalyzers. The large mass difference between H or D and the metal atoms provides a gap in phonon spectrum, in which DBs can be excited in the H/D sub-lattice resulting in extreme dynamic closing of adjacent H/D atoms (~ 0.01 {\AA}) required for the tunneling through nuclear Coulomb barrier. DBs have been shown to arise either via thermal activation at elevated temperatures or via knocking atoms out of equilibrium positions under non-equilibrium gas loading conditions, employed under radiolysis or plasma deposition methods. The DB statistics in both cases is analyzed, and an attempt is made to quantify part of the vibrational problem in terms of electrochemical current or ion flux, connecting them with external excitation of DBs that act as nano-colliders of deuterons triggering LENR. Resulting analytical expressions (under selected set of material parameters) describe quantitatively the observed exponential dependence on temperature and linear dependence on the electric (or ion) current. Possible ways of engineering the nuclear active environment based on the present concept are discussed.; Comment: 22 pages...

In solid_state hybrid electron_nuclear spin systems quantum entanglement plays vital role in allowing accessible transfer of information between subatomic particles, regardless of the host lattice coordination spatial geometry, revealing the powerful resource for nuclear quantum states engineering. Here we present study of 2 MeV superfocused channeled proton (SCP) beam induced polarization of atom_photon correlated states, established in isotopically purified silicon nanocrystal. Two level entangling interaction which couples an initial quantum state to two possible light_matter states via silicon nanocrystal interface is presented. The anisotropic hyperfine coupling is demonstrated by strong mixing of quantum states within the control mechanism of the coherent proton pulse sequence. Obtained results reveal the mutual predictable correlation of particles of energy_matter, by using the fully broadcastable and precise hybrid electron_nuclear spin qubit manipulations which can be exploited for the speed_superior communication channels keeping at the same time the maximum degree of data preservation.; Comment: 8 pages, 9 figures

The Gamma Ray Large Area Space Telescope (GLAST) Large Area Telescope (LAT) is a pair-production high-energy (>20 MeV) gamma-ray telescope being built by an international partnership of astrophysicists and particle physicists for a satellite launch in 2006, designed to study a wide variety of high-energy astrophysical phenomena. As part of the development effort, the collaboration has built a Balloon Flight Engineering Model (BFEM) for flight on a high-altitude scientific balloon. The BFEM is approximately the size of one of the 16 GLAST-LAT towers and contains all the components of the full instrument: plastic scintillator anticoincidence system (ACD), high-Z foil/Si strip pair-conversion tracker (TKR), CsI hodoscopic calorimeter (CAL), triggering and data acquisition electronics (DAQ), commanding system, power distribution, telemetry, real-time data display, and ground data processing system. The principal goal of the balloon flight was to demonstrate the performance of this instrument configuration under conditions similar to those expected in orbit. Results from a balloon flight from Palestine, Texas, on August 4, 2001, show that the BFEM successfully obtained gamma-ray data in this high-background environment.; Comment: To be published in IEEE Transactions on Nuclear Science...