bluuebunny/crossref_metadata_2025_split huggingface dataset:
PNS and statistical experiments simulation in subcritical systems using Monte-Carlo method on example of Yalina-Thermal assembly
Authors: Sadovich Sergey , Talamo A. , Burnos V. , Kiyavitskaya H. , Fokov Yu. 
Published: June 2014

In subcritical systems driven by an external neutron source, the experimental methods based on pulsed neutron source and statistical techniques play an important role for reactivity measurement. Simulation of these methods is very time-consumed procedure. For simulations in Monte-Carlo programs several improvements for neutronic calculations have been made. This paper introduces a new method for simulation PNS and statistical measurements. In this method all events occurred in the detector during simulation are stored in a file using PTRAC feature in the MCNP. After that with a special code (or post-processing) PNS and statistical methods can be simulated. Additionally different shapes of neutron pulses and its lengths as well as dead time of detectors can be included into simulation.
The methods described above were tested on subcritical assembly Yalina-Thermal, located in Joint Institute for Power and Nuclear Research SOSNY, Minsk, Belarus. A good agreement between experimental and simulated results was shown.
Vectorization of a 2D–1D Iterative Algorithm for the 3D Neutron Transport Problem in Prismatic Geometries
Authors: Moustafa Salli , Févotte François , Lathuilière Bruno , Plagne Laurent 
Published: June 2014

The past few years have been marked by a noticeable increase in the interest in 3D whole-core heterogeneous deterministic neutron transport solvers for reference calculations. Due to the extremely large problem sizes tackled by such solvers, they need to use adapted numerical methods and need to be efficiently implemented to take advantage of the full computing power of modern systems.As for numerical methods, one possible approach consists in iterating over resolutions of 2D and 1D MOC problems by taking advantage of prismatic geometries. The MICADO solver, developed at EDF R&D, is a parallel implementation of such a method in distributed and shared memory systems. However it is currently unable to use SIMD vectorization to leverage the full computing power of modern CPUs.In this paper, we describe our first effort to support vectorization in MICADO, typically targeting Intel©SSE CPUs.Both the 2D and 1D algorithms are vectorized, allowing for high expected speedups for the whole spatial solver. We present benchmark computations, which show nearly optimal speedups for our vectorized implementation on the TAKEDA case.
Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION
Authors: Trost Nico , Jiménez Javier , Lukarski Dimitar , Sanchez Victor 
Published: June 2014

COBAYA3 is a multi-physics system of codes which includes two 3D multi-group neutron diffusion codes, ANDES and COBAYA3-PBP, coupled with COBRA-TF, COBRA-IIIc and SUBCHANFLOW sub-channel thermal-hydraulic codes, for the simulation of LWR core transients. The 3D multi-group neutron diffusion equations are expressed in terms of a sparse linear system which can be solved using different iterative Krylov subspace solvers. The mathematical SPARSKIT library has been used for these purposes as it implements among others, external GMRES, PGMRES and BiCGStab solvers.
Multi-core CPUs and graphical processing units (GPUs) provide high performance capabilities which are able to accelerate many scientific computations. To take advantage of these new hardware features in daily use computer codes, the integration of the PARALUTION library to solve sparse systems of linear equations is a good choice. It features several types of iterative solvers and preconditioners which can run on both multi-core CPUs and GPU devices without any modification from the interface point of view. This feature is due to the great portability obtained by the modular and flexible design of the library.
By exploring this technology, namely the implementation of the PARALUTION library in COBAYA3, we are able to decrease the solution time of the sparse linear systems by a factor 5.15x on GPU and 2.56x on multi-core CPU using standard hardware. These obtained speedup factors in addition to the implementation details are discussed in this paper.
Solving the Heterogeneous VHTR Core with Efficient Grid Computing
Authors: John Connolly Kevin , Rahnema Farzad 
Published: June 2014

This paper uses the coarse mesh transport method COMET to solve the eigenvalue and pin fission density distribution of the Very High Temperature Reactor (VHTR). It does this using the Boltzmann transport equation without such low-order approximations as diffusion, and it does not simplify the reactor core problem through homogenization techniques. This method is chosen as it makes highly efficient use of grid computing resources: it conducts a series of calculations at the block level using Monte Carlo to model the explicit geometry within the core without approximation, and compiles a compendium of data with the solution set. From there, it is able to solve the desired core configuration on a single processor in a fraction of the time necessary for whole-core deterministic or stochastic transport calculations. Thus, the method supplies a solution which has the accuracy of a whole-core Monte Carlo solution via the computing power available to the user.
The core solved herein, the VHTR, was chosen due to its complexity. With a high level of detailed heterogeneity present from the core level to the pin level, and with asymmetric blocks and control material present outside of the fueled region of the core, this reactor geometry creates problems for methods which rely on homogenization or diffusion methods. Even transport methods find it challenging to solve. As it is desirable to reduce the number of assumptions necessary for a whole core calculation, this choice of reactor and solution method combination is an appropriate choice for a demonstration on an efficient use of grid computing.
Estimation of Secondary Neutron Dose during Proton Therapy
Authors: Urban Tomas , Klusoň Jaroslav 
Published: June 2014

During proton radiotherapy, secondary neutrons are produced by nuclear interactions in the material along the beam path, in the treatment nozzle (including the fixed scatterer, range modulator, etc.) and, of course, after entering the patient. The dose equivalent deposited by these neutrons is usually not considered in routine treatment planning. In this study, there has been estimated the neutron dose in patient (in as well as around the target volume) during proton radiotherapy using scattering and scanning techniques.
The proton induced neutrons (and photons) have been simulated in the simple geometry of the single scattering and the pencil beam scanning universal nozzles and in geometry of the plastic phantom (made of tissue equivalent material – RW3 – imitate the patient). In simulations of the scattering nozzle, different types of brass collimators have been used as well. Calculated data have been used as an approximation of the radiation field in and around the chosen/potential target volume in the patient (plastic phantom). For the dose equivalent evaluation, fluence-to-dose conversion factors from ICRP report have been employed.
The results of calculated dose from neutrons in various distances from the spot for different treatment technique and for different energies of incident protons have been compared and evaluated in the context of the dose deposited in the target volume.
This work was supported by RVO: 68407700 and Grant Agency of the CTU in Prague, grant No. SGS12/200/OHK4/3T/14.
Octree Ray Tracing Method for Complicated Reactor Geometry
Authors: Poveshchenko Oxana Yu. , Vujic Jasmina L. 
Published: June 2014

This paper presents the new approach to ray tracing for nuclear reactor neutron transport computer simulation analysis. This method is aimed for Monte-Carlo methods as well as for deterministic neutron transport methods. Special attention is attended for reactor core composed of a set of material zones with complicate geometrical boundaries.
The idea of this approach is described. Method works for 3-D space in general case. Algorithms of octree map generation and the tracing phases for typical geometric bodies are given. Simple 2-D numerical benchmark is given to demonstrate the advantage of new approach.
Benchmarking of Proton Transport in Super Monte Carlo Simulation Program
Authors: Wang Yongfeng , Li Gui , Song Jing , Zheng Huaqing , Sun Guangyao , Hao Lijuan , Wu Yican 
Published: June 2014

The Monte Carlo (MC) method has been traditionally applied in nuclear design and analysis due to its capability of dealing with complicated geometries and multi-dimensional physics problems as well as obtaining accurate results. The Super Monte Carlo Simulation Program (SuperMC) is developed by FDS Team in China for fusion, fission, and other nuclear applications. The simulations of radiation transport, isotope burn-up, material activation, radiation dose, and biology damage could be performed using SuperMC. Complicated geometries and the whole physical process of various types of particles in broad energy scale can be well handled. Bi-directional automatic conversion between general CAD models and full-formed input files of SuperMC is supported by MCAM, which is a CAD/image-based automatic modeling program for neutronics and radiation transport simulation. Mixed visualization of dynamical 3D dataset and geometry model is supported by RVIS, which is a nuclear radiation virtual simulation and assessment system. Continuous-energy cross section data from hybrid evaluated nuclear data library HENDL are utilized to support simulation. Neutronic fixed source and critical design parameters calculates for reactors of complex geometry and material distribution based on the transport of neutron and photon have been achieved in our former version of SuperMC.
Recently, the proton transport has also been intergrated in SuperMC in the energy region up to 10 GeV. The physical processes considered for proton transport include electromagnetic processes and hadronic processes. The electromagnetic processes include ionization, multiple scattering, bremsstrahlung, and pair production processes. Public evaluated data from HENDL are used in some electromagnetic processes. In hadronic physics, the Bertini intra-nuclear cascade model with exitons, preequilibrium model, nucleus explosion model, fission model, and evaporation model are incorporated to treat the intermediate energy nuclear reactions for proton. Some other hadronic models are also being developed now.
The benchmarking of proton transport in SuperMC has been performed according to Accelerator Driven subcritical System (ADS) benchmark data and model released by IAEA from IAEA’s Cooperation Research Plan (CRP). The incident proton energy is 1.0 GeV. The neutron flux and energy deposition were calculated. The results simulated using SupeMC and FLUKA are in agreement within the statistical uncertainty inherent in the Monte Carlo method. The proton transport in SuperMC has also been applied in China Lead-Alloy cooled Reactor (CLEAR), which is designed by FDS Team for the calculation of spallation reaction in the target.
Requirements and limits for life in the context of exoplanets
Authors: McKay Christopher P. 
Published: June 2014

Significance
Our understanding of life on exoplanets and exomoons must be based on what we know about life on Earth. Liquid water is the common ecological requirement for Earth life. Temperature on an exoplanet is the first parameter to consider both because of its influence on liquid water and because it can be directly estimated from orbital and climate models of exoplanetary systems. Life needs some water, but deserts show that even a little can be enough. Only a small amount of light from the central star is required to provide for photosynthesis. Some nitrogen must be present for life and the presence of oxygen would be a good indicator of photosynthesis and possibly complex life.
Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer
Authors: Janghorban Mahnaz , Farrell Amy S. , Allen-Petersen Brittany L. , Pelz Carl , Daniel Colin J. , Oddo Jessica , Langer Ellen M. , Christensen Dale J. , Sears Rosalie C. 
Published: June 2014

Significance
Increased kinase activity and suppressed phosphatase activity are hallmarks of oncogenic signaling. The transcription factor c-MYC, a master driver of human cancer, is stabilized and activated by persistent serine 62 phosphorylation. The tumor suppressor protein phosphatase 2A (PP2A) targets this site and negatively regulates c-MYC. Here, we show that two cellular inhibitors of PP2A, the SET oncoprotein and cancerous inhibitor of PP2A (CIP2A), are overexpressed in breast cancer, and depletion or inhibition of SET or CIP2A reduces c-MYC expression and activity and decreases the tumorigenic potential of breast cancer cells. These findings strongly suggest that inhibiting SET or CIP2A to reactivate PP2A may be an effective therapeutic strategy for targeting c-MYC in breast cancer.
Perilipins 2 and 3 lack a carboxy-terminal domain present in perilipin 1 involved in sequestering ABHD5 and suppressing basal lipolysis
Authors: Patel Satish , Yang Wei , Kozusko Kristina , Saudek Vladimir , Savage David B. 
Published: June 2014

Significance
Lipolysis refers to the hydrolysis of triacylglycerol stored within lipid droplets. It is an essential step in the catabolism of triacylglycerol in all cells. Within adipocytes, the regulation is highly dynamic, whereas in other cell types basal lipolytic flux is less effectively suppressed and lipolysis is not as dramatically stimulated. These differences reflect the obviously different functions of adipose tissue, the body’s principle energy store, compared with other sites such as the liver or skeletal muscle, where lipids may be exported within lipoproteins or oxidized. Our data suggest that the molecular differences between perilipins1, 2, and 3 can largely account for these functional differences and thus provide a plausible hypothesis for their preservation in evolution.
Resting GABA and glutamate concentrations do not predict visual gamma frequency or amplitude
Authors: Cousijn Helena , Haegens Saskia , Wallis George , Near Jamie , Stokes Mark G. , Harrison Paul J. , Nobre Anna C. 
Published: June 2014

SignificanceIn vitro and modeling studies have indicated that GABAergic signaling underlies gamma oscillations. It would be valuable to measure this correlation between GABA and gamma oscillations in the human brain, and a recent study [Muthukumaraswamy SD, et al. (2009)Proc Natl Acad Sci USA106(20):8356–8361] indicated that this is possible, using magnetoencephalography and magnetic resonance spectroscopy. If true, such a correlation would make the gamma peak frequency a useful surrogate marker of cortical excitability for studies investigating clinical populations and/or the effects of pharmacological agents. However, magnetic resonance spectroscopy does not measure synaptic GABA specifically, and the results from the current study (n= 50) indicate that GABA, as measured with magnetic resonance spectroscopy, does not correlate with gamma peak frequency.
Proterozoic oxygen rise linked to shifting balance between seafloor and terrestrial weathering
Authors: Mills Benjamin , Lenton Timothy M. , Watson Andrew J. 
Published: June 2014

Significance
We investigate the balance between two mechanisms that remove carbon from the atmosphere and oceans over long timescales—weathering of terrestrial silicates and alteration of the ocean floor. We show that this balance should strongly influence atmospheric oxygen concentration, since it dictates the delivery rate of the ultimate limiting nutrient phosphorus to the ocean. Increasing solar luminosity and declining seafloor spreading rates over Proterozoic time are expected to have shifted the balance of carbon removal toward terrestrial weathering. This leads to the prediction of a gradually increasing oxygen concentration over Proterozoic time, with transient higher oxygen concentration in the late Neoproterozoic.
Primary cilia control hedgehog signaling during muscle differentiation and are deregulated in rhabdomyosarcoma
Authors: Fu Wenxiang , Asp Patrik , Canter Brian , Dynlacht Brian David 
Published: June 2014

Significance
The primary cilium is an organelle emanating from the cell surface, and recent evidence suggests that it regulates various cellular signaling pathways and development and that aberrations in its assembly and function could result in tumorigenesis. Skeletal muscle differentiation proceeds through a temporally defined series of events to form multinucleated myofibers, and in rhabdomyosarcomas (RMS), myoblasts fail to differentiate. However, whether primary cilia are functionally linked to normal muscle differentiation or RMS is not known. In this study we show that in skeletal myoblasts, primary cilia are important for proliferation, hedgehog signaling, and differentiation. Furthermore, the deregulation of cilia and hedgehog in RMS could suggest the utility of therapeutically targeting ciliary components in these tumors.
Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection
Authors: Mallajosyula Vamsee V. A. , Citron Michael , Ferrara Francesca , Lu Xianghan , Callahan Cheryl , Heidecker Gwendolyn J. , Sarma Siddhartha P. , Flynn Jessica A. , Temperton Nigel J. , Liang Xiaoping , Varadarajan Raghavan 
Published: June 2014

Significance
Hemagglutinin (HA), the major influenza virus envelope glycoprotein, is the principal target of neutralizing antibodies. Wide diversity and variation of HA entails annual vaccination, as current vaccines typically fail to elicit/boost cross-reactive, broadly neutralizing antibodies (bnAbs). Although several bnAbs bind at the conserved stem of HA making it an attractive universal vaccine candidate, the metastable conformation of this domain imposes challenges in designing a stable, independently folding HA stem immunogen. We rationally designed a stem-fragment immunogen, mimicking the native HA stem that binds conformation-specific bnAbs with high affinity. The immunogen elicited bnAbs and conferred robust protection against lethal, heterologous virus challenge in vivo. Additionally, soluble bacterial expression of such a thermotolerant, disulfide-free immunogen allows for rapid scale-up during pandemic outbreak.
Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells
Authors: Kaplinsky Joseph , Li Anthony , Sun Amy , Coffre Maryaline , Koralov Sergei B. , Arnaout Ramy 
Published: June 2014

Significance
Antibodies play essential roles in vaccination, infection, autoimmunity, aging, and cancer. A key question is how the antibody repertoire achieves its remarkable diversity. Part of the answer is that B cells, which express antibodies on their surface, are selected for survival based on the specific antigens that their antibodies bind, with antigen specificity determined by the protein sequence of antibodies’ antigen-binding regions. Unexpectedly, we find that B cells are also selected based on whether their antibodies have a loose or tight “elbow joint,” independent of the sequence of their antigen-binding regions. This discovery, enabled by sequencing technology and mathematics, adds a surprising new dimension to our understanding of antibody repertoires, and might one day help us shape them ourselves.
DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin
Authors: Ayrapetov Marina K. , Gursoy-Yuzugullu Ozge , Xu Chang , Xu Ye , Price Brendan D. 
Published: June 2014

Significance
Double-strand break (DSB) repair initiates dynamic changes in histone modifications that are required to maintain genome stability. Methylation of histone H3 lysine-9 (H3K9me3) is critical for activating ataxia telangiectasia-mutated (ATM) kinase, but how H3K9 methylation is regulated at DSBs is unknown. We show that a complex containing the suv39h1 methyltransferase is rapidly recruited to DSBs, where it directs H3K9 methylation on large chromatin domains adjacent to the DSB. This process results in transient formation of repressive chromatin and serves to both stabilize the chromatin structure and promote activation of DSB-signaling proteins, including ATM kinase. Dynamic changes in H3K9 modification in euchromatin by suv39h1 are therefore one of the earliest signaling events required for processing and remodeling of the damaged chromatin template.
Evolution of TNF-induced apoptosis reveals 550 My of functional conservation
Authors: Quistad Steven D. , Stotland Aleksandr , Barott Katie L. , Smurthwaite Cameron A. , Hilton Brett Jameson , Grasis Juris A. , Wolkowicz Roland , Rohwer Forest L. 
Published: June 2014

Significance
The TNF receptor-ligand superfamily is a central mediator of apoptosis or programmed cell death. Here we show that TNF-induced apoptosis has been functionally maintained for more than half a billion years of evolution. In response to human TNFα, coral cells underwent the classical stages of apoptosis including cellular blebbing, caspase activation, and eventual cell death. Next, the reciprocal experiment showed that coral TNF kills human cells through direct interaction with the death receptor pathway. In addition, corals were found to possess more putative TNF receptors than any organism previously described, including humans. This work provides important insight into the general evolution of apoptosis and demonstrates remarkable conservation of the TNF apoptotic response.
Nod/Ripk2 signaling in dendritic cells activates IL-17A–secreting innate lymphoid cells and drives colitis inT-bet−/−.Rag2−/−(TRUC) mice
Authors: Ermann Joerg , Staton Tracy , Glickman Jonathan N. , de Waal Malefyt Rene , Glimcher Laurie H. 
Published: June 2014

SignificanceDisease mechanisms in inflammatory bowel disease (IBD) are incompletely understood. In this study, we analyzed the role of IL-17A–secreting innate lymphoid cells (ILCs) in a mouse model of microbiota-driven innate immune-mediated colitis. We report that the pathogenic IL-17A response in ILCs is controlled indirectly by microbial stimulation of dendritic cells (DCs) via the nucleotide-binding oligomerization domain containing (Nod)/receptor-interacting serine-threonine kinase 2 (Ripk2) signaling pathway and requires the cytokines IL-23 and IL-1. Insight into the complex interactions between various immune cells as demonstrated here for DCs and ILCs is a prerequisite for the development of more efficacious therapies in IBD.
Energy landscape of self-assembled superlattices of PbSe nanocrystals
Authors: Quan Zewei , Wu Di , Zhu Jinlong , Evers Wiel H. , Boncella James M. , Siebbeles Laurens D. A. , Wang Zhongwu , Navrotsky Alexandra , Xu Hongwu 
Published: June 2014

Significance
Different polymorphs with very similar energetics can be made by slight changes in growth conditions. This is, to our knowledge, the first direct experimental validation of a complex energy landscape for superlattice self-assembly. Our results suggest that fundamental thermodynamic driving forces can be harnessed to tailor specific superlattice assemblies of potential technological significance.