bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of ion outflow in coupled geospace simulations: 1. Physics‐based ion outflow model development and sensitivity study
Authors: Varney R. H. , Wiltberger M. , Zhang B. , Lotko W. , Lyon J. 
Published: September 2016

AbstractWe describe a coupled geospace model that includes causally regulated ion outflow from a physics‐based ionosphere/polar wind model. The model two‐way couples the multifluid Lyon‐Fedder‐Mobarry magnetohydrodynamics (MHD) model to the ionosphere/polar wind model (IPWM). IPWM includes the H+ and O+ polar wind as well as a phenomenological treatment of energetic O+ accelerated by wave‐particle interactions (WPI). Alfvénic Poynting flux from the MHD simulation causally regulates the ion acceleration. The wave‐particle interactions (WPI) model has been tuned and validated with comparisons to particle‐in‐cell simulations and empirical relationships derived from Fast Auroral Snapshot satellite data. IPWM captures many aspects of the ion outflow that empirical relationships miss. First, the entire coupled model conserves mass between the ionospheric and magnetospheric portions, meaning the amount of outflow produced is limited by realistic photochemistry in the ionosphere. Second, under intense driving conditions, the outflow becomes flux limited by what the ionosphere is capable of providing. Furthermore, the outflows produced exhibit realistic temporal and spatial delays relative to the magnetospheric energy inputs. The coupled model provides a flexible way to explore the impacts of dynamic heavy ion outflow on the coupled geospace system. Some of the example simulations presented exhibit internally driven sawtooth oscillations associated with the outflow, and the properties of these oscillations are analyzed further in a companion paper.
Seismic and infrasonic eruption tremors and their relation to magma discharge rate: A case study for sub‐Plinian events in the 2011 eruption of Shinmoe‐dake, Japan
Authors: Ichihara Mie 
Published: September 2016

AbstractMagma discharge rate is one of the most important parameters in quantifying volcanic activity. Many previous works have attempted to connect observations of seismic and infrasonic eruption tremors with magma discharge rate. Power law scaling relations with different power indices have been proposed based on various data sets and models. The 2011 eruption of Shinmoe‐dake, Japan, provides an excellent data set with which to investigate these relationships for a sustained explosive eruption sequence. Magma discharge rates are well constrained by geodetic, geologic, and remote sensing methods. Seismic and infrasonic data were recorded close to the vent. Moreover, contributions to ground shaking from infrasound can be distinguished from seismic signals in the seismometer records. As a result, linear power law relationships are found to fit all pairs of variables (seismic eruption tremor power, infrasonic eruption tremor power, and magma discharge rate) in the quasi‐stable or slowly growing stages of the sub‐Plinian events. Similar relations have been reported for other eruptions but only between seismic eruption tremors and magma discharge rate or between seismic and infrasonic eruption tremors. Existing models do not fully explain the observed relationships. The possibility is proposed that Plinian‐type eruptions generate both seismic and infrasonic eruption tremors by successive explosions at the fragmentation surface in the conduit; these linear relationships can therefore be observed only under conditions where flow and fragmentation in the conduit are stable.
Convectively coupled Kelvin waves in aquachannel simulations: 1. Propagation speeds, composite structures, and comparison with aquaplanets
Authors: Blanco Joaquín E. , Nolan David S. , Tulich Stefan N. 
Published: September 2016

AbstractConvectively coupled Kelvin waves (CCKWs) represent a significant contribution to the total variability of the Intertropical Convergence Zone (ITCZ). This study analyzes the structure and propagation of CCKWs simulated by the Weather Research and Forecasting (WRF) model using two types of idealized domains. These are the “aquachannel,” a flat rectangle on a beta plane with zonally periodic boundary conditions and length equal to the Earth's circumference at the equator, and the “aquapatch,” a square domain with zonal extent equal to one third of the aquachannel's length. A series of simulations are performed, including a doubly nested aquapatch, in which convection is solved explicitly along the equator. The model intercomparison is carried out throughout the use of several techniques such as power spectra, filtering, wave tracking, and compositing, and it is extended to some simulations from the Aquaplanet Experiment (APE). Results show that despite the equatorial superrotation bias produced by the WRF simulations, the CCKWs simulated with this model propagate with similar phase speeds (relative to the low‐level mean flow) as the corresponding waves from the APE simulations. Horizontal and vertical structures of the CCKWs simulated with aquachannels are also in overall good agreement with those from aquaplanet simulations and observations, although there is a distortion of the zonal extent of anomalies when the shorter aquapatch is used.
Convectively coupled Kelvin waves in aquachannel simulations: 2. Life cycle and dynamical‐convective coupling
Authors: Blanco Joaquín E. , Nolan David S. , Mapes Brian E. 
Published: September 2016

AbstractThis second part of a two‐part study uses Weather Research and Forecasting simulations with aquachannel and aquapatch domains to investigate the time evolution of convectively coupled Kelvin waves (CCKWs). Power spectra, filtering, and compositing are combined with object‐tracking methods to assess the structure and phase speed propagation of CCKWs during their strengthening, mature, and decaying phases. In this regard, we introduce an innovative approach to more closely investigate the wave (Kelvin) versus entity (super cloud cluster or “SCC”) dualism. In general, the composite CCKW structures represent a dynamical response to the organized convective activity. However, pressure and thermodynamic fields in the boundary layer behave differently. Further analysis of the time evolution of pressure and low‐level moist static energy finds that these fields propagate eastward as a “moist” Kelvin wave (MKW), faster than the envelope of organized convection or SCC. When the separation is sufficiently large the SCC dissipates, and a new SCC generates to the east, in the region of strongest negative pressure perturbations. We revisit the concept itself of the “coupling” between convection and dynamics, and we also propose a conceptual model for CCKWs, with a clear distinction between the SCC and the MKW components.
The impact of standard and hard‐coded parameters on the hydrologic fluxes in the Noah‐MP land surface model
Authors: Cuntz Matthias , Mai Juliane , Samaniego Luis , Clark Martyn , Wulfmeyer Volker , Branch Oliver , Attinger Sabine , Thober Stephan 
Published: September 2016

AbstractLand surface models incorporate a large number of process descriptions, containing a multitude of parameters. These parameters are typically read from tabulated input files. Some of these parameters might be fixed numbers in the computer code though, which hinder model agility during calibration. Here we identified 139 hard‐coded parameters in the model code of the Noah land surface model with multiple process options (Noah‐MP). We performed a Sobol' global sensitivity analysis of Noah‐MP for a specific set of process options, which includes 42 out of the 71 standard parameters and 75 out of the 139 hard‐coded parameters. The sensitivities of the hydrologic output fluxes latent heat and total runoff as well as their component fluxes were evaluated at 12 catchments within the United States with very different hydrometeorological regimes. Noah‐MP's hydrologic output fluxes are sensitive to two thirds of its applicable standard parameters (i.e., Sobol' indexes above 1%). The most sensitive parameter is, however, a hard‐coded value in the formulation of soil surface resistance for direct evaporation, which proved to be oversensitive in other land surface models as well. Surface runoff is sensitive to almost all hard‐coded parameters of the snow processes and the meteorological inputs. These parameter sensitivities diminish in total runoff. Assessing these parameters in model calibration would require detailed snow observations or the calculation of hydrologic signatures of the runoff data. Latent heat and total runoff exhibit very similar sensitivities because of their tight coupling via the water balance. A calibration of Noah‐MP against either of these fluxes should therefore give comparable results. Moreover, these fluxes are sensitive to both plant and soil parameters. Calibrating, for example, only soil parameters hence limit the ability to derive realistic model parameters. It is thus recommended to include the most sensitive hard‐coded model parameters that were exposed in this study when calibrating Noah‐MP.
Synthesis of polydopamine‐mediated PP hollow fibrous membranes with good hydrophilicity and antifouling properties
Authors: Jin Jinbo , Zhang Kaizhou , Du Xilan , Yang Jingkui 
Published: September 2016

ABSTRACTMembrane fouling remains a major barrier to membrane separation, particularly obvious in polymer membranes. Dopamine (DA) is of great value as a precursor for conjugation hydrophilic molecules. In this study, PP hollow fibrous membranes were first modified by DA to form a layer of polydopamine (PDA) coating. Then taurine and glycidol were introduced respectively with assisted by PDA reactive layer, the prepared membranes corresponding to PP‐T and PP‐G membranes, respectively. PP and the modified PP membranes were confirmed by a thorough membrane characterization of ATR‐FTIR, XPS, and FESEM measurements. The hydrophilic properties and permeability were measured by water contact angle (WCA) and permeation flux test. BSA was used to as model protein to evaluate the antifouling properties of the membranes. The results showed that taurine and glycidol were successfully introduced onto the membrane surface. The WCA of PP‐T and PP‐G membranes can be reduced to 32° and 26°, and the flux recovery ratio increased around 90.6% and 89.8%, respectively. Based on the experimental results, taurine and glycidol effectively improved the hydrophilic and anti‐fouling performance of PP membrane. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 44430.
p53 in the game of transposons
Authors: Wylie Annika , Jones Amanda E. , Abrams John M. 
Published: September 2016

Throughout the animal kingdom, p53 genes function to restrain mobile elements and recent observations indicate that transposons become derepressed in human cancers. Together, these emerging lines of evidence suggest that cancers driven by p53 mutations could represent “transpospoathies,” i.e. disease states linked to eruptions of mobile elements. The transposopathy hypothesis predicts that p53 acts through conserved mechanisms to contain transposon movement, and in this way, prevents tumor formation. How transposon eruptions provoke neoplasias is not well understood but, from a broader perspective, this hypothesis also provides an attractive framework to explore unrestrained mobile elements as inciters of late‐onset idiopathic disease.Also see the video abstract here.
Genetic engineering of CHO cells for viral resistance to minute virus of mice
Authors: Mascarenhas Joaquina X. , Korokhov Nikolay , Burger Lisa , Kassim Ademola , Tuter Jason , Miller Daniel , Borgschulte Trissa , George Henry J. , Chang Audrey , Pintel David J. , Onions David , Kayser Kevin J. 
Published: September 2016

ABSTRACTContamination by the parvovirus minute virus of mice (MVM) remains a challenge in Chinese hamster ovary (CHO) biopharmaceutical production processes. Although infrequent, infection of a bioreactor can be catastrophic for a manufacturer, can impact patient drug supply and safety, and can have regulatory implications. We evaluated engineering a CHO parental cell line (CHOZN® GS‐/‐) to create a new host cell line that is resistant to MVM infection by modifying the major receptors used by the virus to enter cells. Attachment to a cell surface receptor is a key first step in the infection cycle for many viruses. While the exact functional receptor for MVM binding to CHO cell surface is unknown, sialic acid on the cell surface has been implicated. In this work, we used the zinc finger nuclease gene editing technology to validate the role of sialic acid on the cell surface in the binding and internalization of the MVM virus. Our approach was to systematically mutate genes involved in cell surface sialylation and then challenge each cell line for their ability to resist viral entry and propagation. To test the importance of sialylation, the following genes were knocked out: the CMP‐sialic acid transporter, solute carrier family 35A1 (Slc35a1), the core 1‐β‐1,3‐galactosyltransferase‐1 specific chaperone (Cosmc), and mannosyl (α‐1,3‐)‐glycoprotein β‐1,2‐N‐acetylglucosaminyltransferase (Mgat1) as well as members of the sialyltransferase family. Slc35a1 is responsible for transporting sialic acid into the Golgi. Knocking out function of this gene in a cell results in asialylated glycan structures, thus eliminating the ability of MVM to bind to and enter the cell. The complete absence of sialic acid on the Slc35a1 knockout cell line led to complete resistance to MVM infection. The Cosmc and Mgat1 knockouts also show significant inhibition of infection likely due to their effect on decreasing cell surface sialic acid. Previously in vitro glycan analysis has been used to elucidate the precise sialic acid structures required for MVM binding and internalization. In this work, we performed the sequential knockout of various sialyltransferases that add terminal sialic acid to glycans with different linkage specificities. Cell lines with modifications of the various genes included in this study resulted in varying effects on MVM infection expanding on the knowledge of MVM receptors. MVM resistant host cell lines were also tested for the production of model recombinant proteins. Our data demonstrate that resistance against the MVM virus can be incorporated into CHO production cell lines, adding another level of defense against the devastating financial consequences of MVM infection without compromising recombinant protein yield or quality. Biotechnol. Bioeng. 2017;114: 576–588. © 2016 Wiley Periodicals, Inc.
NMR and DFT Insight into the Synergistic Role of Bovine Serum Albumin–Ionic Liquid for Multicomponent Cascade Aldol/Knoevenagel–thia‐Michael/Michael Reactions in One Pot
Authors: Thopate Yogesh , Singh Richa , Sinha Arun K. , Kumar Vikash , Siddiqi Mohammad Imran 
Published: September 2016

AbstractThe synergistic combination of two catalysts is an emerging strategy towards the formation of unprecedented complex molecules, and herein bovine serum albumin (BSA) and the neutral ionic liquid 1‐butyl‐3‐methylimidazolium bromide ([bmim]Br) are used together for the first time towards multiple C−C and C−S bond‐formation reactions in one pot under metal‐free, acid‐free, and base‐free conditions by merging two classical named reactions, that is, aldol condensation (AC) and thia‐Michael addition (TMA) for the cascade chemoselective generation of β‐aryl‐β‐sulfido carbonyl compounds from aliphatic ketones, aromatic aldehydes, and thiols. NMR spectroscopy and DFT calculations studies provided insight into the synergism, progress, and mechanism of the reaction, and control experiments highlighted that the single catalysts (BSA or IL) alone did not allow even the first AC step to proceed. Moreover this synergistic BSA–[bmim]Br catalytic system offers the step‐economical synthesis of the anticoagulant warfarin through sequential aldol–Michael addition reactions and potent pyridine analogues through a Knoevenagel–Michael route. Besides, the recyclability of the catalytic system (up to 5 times) with the generation of water as a byproduct makes our one‐pot protocol more economically efficient and synthetically attractive than traditional methods.
Accelerating Pre‐stack Kirchhoff Time Migration by Manual Vectorization
Authors: Melo Alves Maicon , da Cruz Pestana Reynam , Alves Prado da Silva Rodrigo , Drummond Lúcia M. A. 
Published: September 2016

SummaryThe Pre‐stack Kirchhoff Time Migration (PKTM) is a central process in petroleum exploration. As PKTM is computationally intensive, many works have proposed the use of accelerators like GPU and FPGA to improve its execution time. On the other hand, although many off‐the‐shelf processors are endowed with a set of SIMD vector instructions, few papers tackle the problem considering vectorization and all of them consider that compilers can successfully vectorize the code. In this paper, we show that programming PKTM by using SIMD vector instructions manually is more efficient than the automatically and semi‐automatically vectorized codes, provided by a hardware specific compiler and library. Experiments considering both real and synthetic datasets showed that our solution is more than four times faster than the traditional code. It also outperformed automatically vectorized codes in all tests. We believe that the proposed strategy can be used together with the other ones to accelerate seismic migration methods in general without new investments in hardware. Copyright © 2016 John Wiley & Sons, Ltd.
Safety‐Critical Java: level 2 in practice
Authors: Luckcuck Matt , Wellings Andy , Cavalcanti Ana 
Published: September 2016

SummarySafety‐Critical Java (SCJ) is a profile of the Real‐Time Specification for Java that brings to the safety‐critical industry the possibility of using Java. SCJ defines three compliance levels: Level 0, Level 1 and Level 2. The SCJ specification is clear on what constitutes a Level 2 application in terms of its use of the defined API but not the occasions on which it should be used. This paper broadly classifies the features that are only available at Level 2 into three groups: nested mission sequencers, managed threads and global scheduling across multiple processors. We explore the first two groups to elicit programming requirements that they support. We identify several areas where the SCJ specification needs modifications to support these requirements fully; these include the following: support for terminating managed threads, the ability to set a deadline on the transition between missions and augmentation of the mission sequencer concept to support composibility of timing constraints. We also propose simplifications to the termination protocol of missions and their mission sequencers. To illustrate the benefit of our changes, we present excerpts from a formal model of SCJ Level 2 written in Circus, a state‐rich process algebra for refinement. Copyright © 2016 John Wiley & Sons, Ltd.
Automatic source‐to‐source error compensation of floating‐point programs: code synthesis to optimize accuracy and time
Authors: Thévenoux Laurent , Langlois Philippe , Martel Matthieu 
Published: September 2016

SummaryNumerical programs with IEEE 754 floating‐point computations may suffer from inaccuracies because finite precision arithmetic is an approximation of real arithmetic. Solutions that reduce the loss of accuracy are available, such as compensated algorithms or double‐double precision floating‐point arithmetic. Our goal is to automatically improve the numerical quality of a numerical program with the smallest impact on its performance. We define and implement source code transformations in order to derive automatically compensated programs. We present several experimental results to compare the transformed programs and existing solutions. The transformed programs are as accurate and efficient as the implementations of compensated algorithms when the latter exist. Furthermore, we propose some transformation strategies allowing us to partially improve the accuracy of programs and to tune the impact on execution time. Trade‐offs between accuracy and performance are assured by code synthesis. Experimental results show that user‐defined trade‐offs are achievable in a reasonable amount of time, with the help of the tools we present in the paper. Copyright © 2016 John Wiley & Sons, Ltd.
Towards a multi‐layers anomaly detection framework for analyzing network traffic
Authors: Li Bo , Zhang Simin , Li Ke 
Published: September 2016

SummaryAnomaly detection plays a crucial part in identifying unforeseen attacks for network and information security. However, the accuracy of existing network anomaly detection approaches is limited because of the lack of sufficient and high‐quality features. Most research works only take information from one network layer into account, which leads to a situation that some key features of other network layers are omitted. To address this issue, we propose a novel approach, named Multi‐Layers Anomaly Detection, which extracts and combines features from different network layers. In order to reduce redundancy and noise derived from the combination of multiple layers, an algorithm called RanPF is designed by applying principal components analysis (PCA) into random forest (RF) algorithm. RanPF uses features selected by PCA to decide the height of every tree in RF and provides a method to select which features for tree nodes to use according to the weights of principal components. To obtain high‐quality features, we adopt an attribute learning mechanism. Naive Bayes is used to characterize the attribute information, which is fast and simple compared with other learning algorithms such as SVM. In addition, a series of experiments conducted on two real‐life datasets demonstrate that our approach outperforms the state‐of‐the‐art methods in terms of detection rate and false alarm rate. MLAD achieves about 99% detection rate and about 0.6% false alarm rate on average when the ratio of the training set is 60%. Copyright © 2016 John Wiley & Sons, Ltd.
Systematic adaptation of stencil‐based 3D MPDATA to GPU architectures
Authors: Rojek Krzysztof , Wyrzykowski Roman , Kuczynski Lukasz 
Published: September 2016

SummaryIn this work, we focus on a systematic adaptation of the stencil‐based multidimensional positive definite advection transport algorithm (MPDATA) to different graphics processing unit (GPU)‐based computing platforms. Another objective of this work is to compare the performance of MPDATA on several platforms, including a multi‐GPU system with two NVIDIA Tesla K80 cards, and single‐card platforms with Tesla K20X, GeForce GTX TITAN, and GeForce GTX 980. The usage of the following optimization methods is proposed to improve the overall performance: (i) reducing the number of operations by the subexpression elimination when implementing 2.5D blocking; (ii) reorganization of boundary conditions for reducing branch instructions; (iii) advanced memory management to increase the coalesced memory access; and (iv) warps rearrangement for optimizing the data access to GPU global memory. The presented methods of the MPDATA adaptation to GPU architectures allow us to efficiently use many graphics processors within a single node by applying peer‐to‐peer data transfers between GPU global memories. We propose an auto‐tuning procedure to compensate architectural differences between the considered platforms. This procedure takes into account algorithm/GPU‐specific parameters. The proposed approach to adaptation of MPDATA to GPU architectures allows us to achieve up to 482.5 Gflop/s for the platform equipped with two NVIDIA K80 GPUs. Copyright © 2016 John Wiley & Sons, Ltd.