bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapamycin attenuates mitochondrial injury and renal tubular cell apoptosis in experimental contrast-induced acute kidney injury in rats
Authors: Yang Xueyan , Yan Xiaojie , Yang Dingping , Zhou Junke , Song Jie , Yang Dingwei
Published: October 2018

Reactive oxygen species (ROS) overproduction and renal tubular epithelial cell (TEC) apoptosis are key mechanisms of contrast-induced acute kidney injury (CI-AKI). Mitochondria are the main source of intracellular ROS. In the present study, the characteristics of mitophagy and the effects of rapamycin on contrast-induced abnormalities in oxidative stress, mitochondrial injury and mitophagy, TEC apoptosis and renal function were investigated in a CI-AKI rat model. Rats were divided into control group, CI-AKI group, and pretreatment groups (with rapamycin dose of 2 or 5 mg/kg). CI-AKI was induced by intraperitoneal injection of iohexol (12.25 g iodine/kg). Renal malondialdehyde (MDA) and catalase (CAT) were measured as oxidative markers. Light-chain 3 (LC3), P62, Beclin-1, PTEN-induced putative kinase (Pink1), and cytochrome c (Cyt c) expression were measured by Western blot. Mitochondrial membrane potential (ΔΨm) was determined by JC-1, colocalization of LC3-labeled autophagosomes with TOMM20-labeled mitochondria or LAMP2-labeled lysosomes was observed by fluorescence microscopy. Significantly increased serum creatinine (Scr), MDA and CAT, obvious mitochondrial injury including increase in cytosolic/mitochondrial Cyt c and decrease in ΔΨm, TEC apoptosis were induced by contrast administration. Contrast administration induced an increased expression of LC3II/I, Beclin-1, and Pink1 and decreased expression of P62. Rapamycin pretreatment induced overexpression of LC3II/I and Beclin-1. Moreover, LC3-labeled autophagosomes increasingly overlapped with TOMM20-labeled mitochondria and LAMP2-labeled lysosomes in CI-AKI, which was further enhanced by rapamycin administration. Contrast-induced Scr increase, oxidative stress, mitochondrial injury, TEC apoptosis, and necrosis were dose-dependently attenuated by rapamycin pretreatment. Rapamycin exerts renoprotective effects against CI-AKI by attenuating mitochondrial injury and oxidative stress, which might be associated with increasing mitophagy.
Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing
Authors: Xue Xiaochun , Wu Jianhua , Li Junhui , Xu Jianguo , Dai Haiying , Tao Congshan , Li Chao , Hu Jinhong
Published: October 2018

It was previously reported that the expression of CD274 was down-regulated in psoriatic epidermis, leading to immune disorders of psoriasis. However, the regulatory mechanisms of CD274 were rarely elucidated. We aimed to explore the regulatory mechanisms of CD274. Skin samples were collected from 18 patients with psoriasis vulgaris and 9 healthy participants for RNA sequencing. Candidate genes were chosen based on degree and k-core difference of genes in the co-expression network. The relations between candidate genes and CD274 were validated by flow cytometry and real-time PCR in primary human epidermal keratinocytes. The therapeutic effect of indirubin was assessed in an imiquimod-treated mouse model. Interferon-γ (IFN-γ), cyclin-dependent kinase (CDK) 1, Toll-like receptor 3 (TLR3), TLR4 and interleukin (IL)-17A were considered as candidate genes. In primary human epidermal keratinocytes, the level of CD274 was obviously increased under the stimulation of IFN-γ and CDK1 inhibitor (indirubin), independent of TLR4, TLR3 or IL-17A. Indirubin alleviated the severity of psoriatic mice in a CD274-dependent manner. Co-expression network analysis served as an effective method for the exploration of molecular mechanisms. We demonstrated for the first time that CD274 was the regulator of indirubin-mediated effect on mouse psoriasis-like skin lesion based on co-expression network analysis, contributing to the alleviation of mouse psoriasis-like skin lesion.
LINC00210 as a miR-328-5p sponge promotes nasopharyngeal carcinoma tumorigenesis by activating NOTCH3 pathway
Authors: Zhang Shu , Li Ping , Zhao Lei , Xu Ling
Published: October 2018

As a kind of essential regulators, long noncoding RNAs (lncRNAs) have attracted a lot of attention in recent years. Nevertheless, the function of lncRNA in nasopharyngeal carcinoma (NPC) remains poorly understood. In the present study, we explained the role and mechanism of LINC00210 in NPC progression. We found that LINC00210 expression was up-regulated in NPC samples. Besides, its overexpression was positively correlated with NPC metastasis while predicting poor prognosis. Based on functional experiments, we revealed that LINC00210 contributed to NPC cell proliferation and invasion in vitro, and promotes tumor growth in vivo. Mechanistically, we identified that LINC00210 was located in the cytoplasm of NPC cells and served as the miR-328-5p sponge. Furthermore, we showed that miR-328-5p targets the 3′ untranslated region (3′-UTR) of NOTCH3. Through inhibiting miR-328-5p activity, LINC00210 promoted NOTCH3 expression in NPC, leading to activation of NOTCH3 signaling pathway. In conclusion, our study indicates LINC00210 promotes NPC progression through modulating proliferation and invasion.
Application of droplet digital PCR to detect the pathogens of infectious diseases
Authors: Li Haiyi , Bai Ruolan , Zhao Zhenyu , Tao Lvyan , Ma Mingbiao , Ji Zhenhua , Jian Miaomiao , Ding Zhe , Dai Xiting , Bao Fukai , Liu Aihua
Published: October 2018

Polymerase chain reaction (PCR) is a molecular biology technique used to multiply certain deoxyribonucleic acid (DNA) fragments. It is a common and indispensable technique that has been applied in many areas, especially in clinical laboratories. The third generation of polymerase chain reaction, droplet digital polymerase chain reaction (ddPCR), is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify DNA. Droplet digital polymerase chain reaction is now widely used in low-abundance nucleic acid detection and is useful in diagnosis of infectious diseases. Here, we summarized the potential advantages of droplet digital polymerase chain reaction in clinical diagnosis of infectious diseases, including viral diseases, bacterial diseases and parasite infections, concluded that ddPCR provides a more sensitive, accurate, and reproducible detection of low-abundance pathogens and may be a better choice than quantitative polymerase chain reaction for clinical applications in the future.
Bioinformatics identification of crucial genes and pathways associated with hepatocellular carcinoma
Authors: Gao Xueren , Wang Xixi , Zhang Shulong
Published: October 2018

Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. Up to date, HCC pathogenesis has not been fully understood. The aim of the present study was to identify crucial genes and pathways associated with HCC by bioinformatics methods. The differentially expressed genes (DEGs) between 14 HCC tissues and corresponding non-cancerous tissues were identified using limma package. Gene Ontology (GO) and KEGG pathway enrichment analysis of DEGs were performed by clusterProfiler package. The protein–protein interaction (PPI) network of DEGs was constructed and visualized by STRING database and Cytoscape software, respectively. The crucial genes in PPI network were identified using a Cytoscape plugin, CytoNCA. Furthermore, the effect of the expression level of the crucial genes on HCC patient survival was analyzed by an interactive web-portal, UALCAN. A total of 870 DEGs including 237 up-regulated and 633 down-regulated genes were identified in HCC tissues. KEGG pathway analysis revealed that DEGs were mainly enriched in complement and coagulation cascades pathway, chemical carcinogenesis pathway, retinol metabolism pathway, fatty acid degradation pathway, and valine, leucine and isoleucine degradation pathway. PPI network analysis showed that CDK1, CCNB1, CCNB2, MAD2L1, ACACB, IGF1, TOP2A, and EHHADH were crucial genes. Survival analysis suggested that the high expression of CDK1, CCNB1, CCNB2, MAD2L1, and TOP2A significantly decreased the survival probability of HCC patients. In conclusion, the identification of the above crucial genes and pathways will not only contribute to elucidating the pathogenesis of HCC, but also provide prognostic markers and therapeutic targets for HCC.
Automatic classification of cervical cancer from cytological images by using convolutional neural network
Authors: Wu Miao , Yan Chuanbo , Liu Huiqiang , Liu Qian , Yin Yi
Published: October 2018

Cervical cancer (CC) is one of the most common gynecologic malignancies in the world. The incidence and mortality keep high in some remote and poor medical condition regions in China. In order to improve the current situation and promote the pathologists’ diagnostic accuracy of CC in such regions, we tried to propose an intelligent and efficient classification model for CC based on convolutional neural network (CNN) with relatively simple architecture compared with others. The model was trained and tested by two groups of image datasets, respectively, which were original image group with a volume of 3012 datasets and augmented image group with a volume of 108432 datasets. Each group has a number of fixed-size RGB images (227*227) of keratinizing squamous, non-keratinizing squamous, and basaloid squamous. The method of three-folder cross-validation was applied to the model. And the classification accuracy of the models, overall, 93.33% for original image group and 89.48% for augmented image group. The improvement of 3.85% has been achieved by using augmented images as input data for the model. The results got from paired-samples ttest indicated that two models’ classification accuracy has a significant difference (P<0.05). The developed scheme we proposed was useful for classifying CCs from cytological images and the model can be served as a pathologist assistance to improve the doctor’s diagnostic level of CC, which has a great meaning and huge potential application in poor medical condition areas in China.
Potential clinical treatment of colitis with cardiotrophin-1
Authors: Escoté Xavier
Published: October 2018

In a recent issue of Clinical Science, Prieto-Vicente et al. [Clin. Sci. (2018) 132, 985–1001] have smartly demonstrated a potential new use of cardiotrophin-1 (CT-1) to treat and palliate an inflammatory bowel disease such as ulcerative colitis. In that work, authors report that in ulcerative colitic mice, administration of exogenous recombinant CT-1 (rCT-1) promotes lower colon damage and lower disease activity index, reducing systemic levels of tumor necrosis factor α (TNF-α) and also diminishing TNF-α expression in colon together with the reduction in other common inflammation markers. Besides, in vivo rCT-1 administration induces activation of several molecular pathways, including nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) and signal transducer and activator of transcription (STAT)-3, and abolishes bacterial translocation from intestine to other organs, including mesenteric ganglia, lungs, and spleen. Additionally, these results were nicely corroborated in CT-1 depleted mice; in which colon damage and ulcerative colitis severity were greater compared with the wild-type counterparts. All together, these results suggested that CT-1 could be a promising new therapeutic approach for treating inflammatory bowel disease, particularly ulcerative colitis. However, further studies are required to determine its major mechanisms of action and the potential efficacy of CT-1 in human inflammatory bowel diseases.
Inhibition of mitochondrial fission as a novel therapeutic strategy to reduce mortality upon myocardial infarction
Authors: Cooper Hannah A. , Eguchi Satoru
Published: October 2018

Ischemia reperfusion (I/R) injury is a common event following myocardial infarction (MI) resulting in excessive oxidative stress, calcium overload, inflammation, and cardiomyocyte death. Mitochondrial homeostasis including their dynamics are imbalanced in cardiac I/R injury in favor of increased mitochondrial fission. Inhibition of mitochondrial fission prior to I/R injury is protective and improves cardiac function following MI. Clinically, patients with MI often receive treatment following initiation of the ischemic event. Thus, treatments with more realistic timing would have better translational value and are important to research. In a recent study published in Clinical Science, Maneechote et al. [Clin. Sci. (2018) 132, 1669–1683] examined the effect of inhibiting mitochondrial fission using the mitochondrial division inhibitor (Mdivi-1) at different time points, pre-ischemia, during-ischemia, and upon onset of reperfusion, in a rat cardiac I/R model. The findings showed the greatest cardiac function improvement with pre-ischemia treatment along with decreased mitochondrial fragmentation and increased mitochondrial function. Mdivi-1 given during ischemia and at onset of reperfusion also improved cardiac function, but to a lesser extent than pre-ischemia intervention. Maneechote et al. postulated that the LV protection by Mdivi-1 in cardiac I/R could be due to an improvement in mitochondrial dysfunction through attenuating excessive mitochondrial fission which then reduces apoptotic myocytes. Their findings provide new insights into future treatment of patients suffering acute MI which could consider targetting the excessive mitochondrial fission during cardiac ischemia or at onset of reperfusion. Here, we will further discuss the background of the study, potential molecular mechanisms of mitochondrial fission, consequences of the fission, and future research directions.
Efficient base driver circuit for silicon carbide bipolar junction transistors
Authors: McNeill N. , Stark B.H. , Finney S.J. , Holliday D. , Dymond H.
Published: October 2018

The silicon carbide bipolar junction transistor needs large transient currents supplied into and out of its base terminal for rapid switching. To realise this, it is normally desirable to have a base driver circuit supply rail at a high voltage. However, the device also needs a steady base current to hold it in the on‐state. Supplying this current from a high‐voltage source is inefficient. A circuit is presented that applies high transient base–emitter voltages, but with low driver circuit power consumption.
Market framework for local energy trading: a review of potential designs and market clearing approaches
Authors: Khorasany Mohsen , Mishra Yateendra , Ledwich Gerard
Published: October 2018

Massive deployment of distributed energy resources (DERs) along with innovations in information and communication technologies have changed the power system from a hierarchical structure to a more deregulated model by introducing new generations at lower levels. This change raises operational and market challenges. Local energy trading provides opportunities to manage these DERs by encouraging localised trading. The concept of local energy trading at the distribution level is widely broadcasted for implementation in the power system. In the design of electricity markets for local energy trading, a clear definition of market participants, their objective, and purpose of market clearing should be established. This design depends on the changing needs of the power system and can be performed from different viewpoints. Classification and organisation of the literature on potential designs for local energy trading can help researchers to develop their future steps properly. This study presents a comprehensive review on this topic and provides a systematic classification of the market players, market clearing objectives, and approaches. Several research works are analysed against different criteria, including scalability, overheads requirements, and network constraints management.
Coordinated control of distributed generation system with improved generalised enhanced phase locked loop control algorithm
Authors: Kewat Seema , Singh Bhim
Published: October 2018

Here, a distributed generation system (DGS) is proposed that allows the different distributed energy resources to operate in coordination with others to provide the electricity in rural areas. Two individual controls are used in the DGS: (i) solar maximum power point tracking (MPPT) and the battery protection control, and (ii) voltage source converter (VSC) control. The proposed VSC control algorithm is based on an improved generalised filter algorithm for power quality improvement of the DGS. This control strategy effectively regulates the active power flow and provides the harmonics mitigation, reactive power compensation, and load balancing in the DGS with low steady‐state error and fast dynamic response under high impulsive noise with DC‐offset component. The solar MPPT control is designed on the basis of battery state of charge (SOC). In this control, the solar PV array operates in limited power point tracking (LPPT) after the storage battery surpasses the maximum SOC limit. In LPPT control, the solar PV MPPT operates in the voltage source operating region of PV array characteristic, thereby, reducing the power generation and avoids the overcharging of the storage battery. The proposed DGS performance is validated through test results under dynamics and steady‐state conditions.
New multi‐stage restoration method for distribution networks with DGs
Authors: Ghasemi Sasan , Khodabakhshian Amin , Hooshmand Rahmat‐allah
Published: October 2018

These main goals of the restoration in distribution networks are to reenergise loads in the area where the power outage occurs. In this study, a new multi‐stage restoration process by the aid of the decision‐making tree algorithm is proposed to maximise the restored loads and also to minimise switching operations in the distribution networks with distributed generations (DGs). This method includes three stages of initial restoration, reconfiguration and optimal load shedding. In order to reduce the search space, the network switches are categorised into different sets which avoid moving to any inappropriate result space. The simulations are carried out on the 69‐bus distribution system and the results show the high capability and accuracy of the proposed method in the restoration of distribution networks.
Harmonic pricing in power systems based on identifying the appropriate contribution of customers
Authors: Saadat Amin , Hooshmand Rahmat‐Allah , Kiyoumarsi Arash , Tadayon Mahdi
Published: October 2018

Today, with the restructuring of the power systems, it is possible to implement a program, such as the demand response for the harmonic issues, and use customers to reduce the harmonic level of the network. In this study, a new method is presented based on harmonic pricing to control the harmonic level of the network. Given the fact that the power system is usually infected by the background harmonics, the basis for pricing is the harmonic contribution determination in order to impose a fine fair on the customers. Usually, the determination of the harmonic contribution at each harmonic order is done separately; therefore, a new index is presented, to sum up, the dominant orders in determining the harmonic contribution. This can provide an appropriate impression of the harmonic emission level at the point of common coupling. Simulation results on the standard IEEE 14‐bus network show that customers are encouraged to control their harmonic level with a fair harmonic pricing, otherwise, the independent system operator can install harmonic filters at appropriate buses, using the fines received from the customers.
Exploring the properties of low-frequency radio emission and magnetic fields in a sample of compact galaxy groups using the LOFAR Two-Metre Sky Survey (LoTSS)
Authors: Nikiel-Wroczyński B. , Berger A. , Herrera Ruiz N. , Bomans D. J. , Blex S. , Horellou C. , Paladino R. , Becker A. , Miskolczi A. , Beck R. , Chyży K. , Dettmar R.-J. , Heald G. , Heesen V. , Jamrozy M. , Shimwell T. W. , Tasse C.
Published: October 2018

We use the LOFAR Two-metre Sky Survey (LoTSS) Data Release I to identify the groups of galaxies (and individual galaxies) from the Hickson compact groups (HCG) and magnitude-limited compact groups (MLCG) samples that emit at the frequency of 150 MHz, characterise their radio emission (extended or limited to the galaxies), and compare new results to earlier observations and theoretical predictions. The detection of 73 systems (and 7 more – probably) out of 120, of which as many as 17 show the presence of extended radio structures, confirms the previous hypothesis of the common character of the magnetic field inside galaxy groups and its detectability. In order to investigate the future potential of low-frequency radio studies of galaxy groups, we also present a more detailed insight into four radio-emitting systems, for which the strength of the magnetic field inside their intergalactic medium (IGM) is calculated. The estimated values are comparable to that found inside star-forming galaxies, suggesting a dynamical and evolutionary importance of the magnetic field in galaxy groups.
A chemistry and cooling module for the NIRVANA code
Authors: Ziegler U.
Published: October 2018

Context. Gas cooling and other thermal processes in the interstellar medium are intimately related to its chemical evolution. To accurately model chemical processes in large-scale gas-dynamical simulations the usage of existing sophisticated astrochemical networks is presently impossible due to prohibitive computational costs. A viable way to deal with the problem is by the design of reduced chemical networks that satisfactorily reproduce the most important features of the more elaborate networks.

Aims. A chemistry and cooling module for the interstellar medium is developed that is realistic for temperatures T ≳ 50 K and for densities up to n ≈ 1010 m−3 at the limit of non-ionizing and non-dissociating background radiation. The module is incorporated into the multiphysics, adaptive-grid code NIRVANA and aims at improving gas-dynamical simulations by explicitly following non-equilibrium chemistry and gas cooling.

Methods. The presented chemical network covers 121 species and 426 reactions. It includes a fully-fledged ionization subnetwork for the ten elements H, D, He, C, N, O, Mg, Ne, Si, and Fe, chemical schemes for the formation and destruction of the important molecular coolants H2, H2O, CO, and OH, a model for dust-catalytic reactions and cosmic ray effects. Metal line cooling was computed from first principles by solving for the energy level population for each ion. Atomic data was adopted from the latest version of the Chianti database. The treatment of rotovibrational line cooling from molecules was based on various up-to-date literature sources.

Results. The implementation has been validated by performing both equilibrium and non-equilibrium (time-dependent) computations. The equilibrium results overall confirm the temperature dependence of chemical abundances and the gas cooling rate that has been found in similar studies. In particular, the ionization structure in the high-temperature regime, at T ≳ 2 × 104 K, excellently agrees with literature results. In the non-equilibrium calculations, the occurrence of ionization lags are prominent and distinguishes the resulting non-equilibrium cooling from equilibrium cooling. In the low-temperature regime, at T ≲ 2 × 104 K, the non-equilibrium cooling rate can be enhanced by up to two orders of magnitude compared to the equilibrium value.

Conclusions. The NIRVANA chemistry and cooling module has been successfully tested against literature results. The underlying chemical network is best compared to recently developed networks in the limit of no radiation with differences appearing in the treatment of dust, cosmic ray heating, and in the choice of reaction coefficients. The gas cooling experiments indicate that a reduction of the present network size seems possible under certain conditions by skipping the elements N and Mg, which turn out to be less important coolants compared to the conglomerate of C, O, Si, and Fe coolants.
Determining the accuracy of VLBI radio source catalogs
Authors: Liu N. , Lambert S. B. , Zhu Z.
Published: October 2018

Aims. We propose to estimate the accuracy of current very long baseline interferometry (VLBI) catalogs.

Methods. The difference of source position estimated from two decimation solutions was analyzed to estimate the scale factor and noise floor for the formal error of radio source positions by two different methods. In one method, we investigated the weighted root-square-mean (wrms) scatter of source positional differences versus the number of observed sessions; for the other one, we compared the wrms difference versus the formal error. Based on the estimated noise floor and scale factor, we determined the realistic error of radio source positions in the standard solution and compared it with that of Gaia DR2 and ICRF2 catalogs.

Results. The estimated scale factors from two methods are rather consistent, which is of ∼1.3 in both coordinates. As for the noise floor, it is estimated to be 20–25 μas for sources observed in at least ten sessions, and it could reduce down to ∼10 μas for sources which have been observed more than 1000 times. The inflated median formal error of our solution is of the same order as the Gaia DR2 catalog in declination and the direction of major axis of the error ellipse, but smaller by a factor of two in right ascension. With respect to the ICRF2 catalog, our solution yields an improved accuracy by a factor of about three.

Conclusions. Currently, the VLBI radio source catalog still provides source positions with the best accuracy which is about 20–25 μas. Moreover, the noise floor of VLBI catalogs could potentially reach 10 μas with more observations in the future.
Radical scavenging activity of lipids from seaweeds isolated by solid-liquid extraction and supercritical fluids
Authors: Terme Nolwenn , Boulho Romain , Kucma Jean-Philippe , Bourgougnon Nathalie , Bedoux Gilles
Published: October 2018

In vitro antioxidant activities of the lipid fractions from two selected seaweeds, Solieria chordalis and Sargassum muticum were investigated according to the extraction methods. The activity of neutral lipids, glycolipids and phospholipids, thanks to extraction by chloroform/methanol (1/1 v/v; CM) mixture, pure supercritical carbon dioxide (sc-CO2), supercritical carbon dioxide with 2% of ethanol (sc-CO2 + EtOH 2%) and supercritical carbon dioxide with 8% of ethanol as co-solvent (sc-CO2 + EtOH 8%), were studied using DPPH radical scavenging assays. All the lipid classes demonstrated a free radical scavenging activity at the concentration of 1 mg/ml. The best scavenging activity (86.6 ± 5.7%) was obtained when the neutral lipid fraction was extracted from S. chordalis with a CM mixture. The neutral lipid fraction extracted with sc-CO2 showed a lower activity than those obtained with solvents. However, the addition of ethanol in sc-CO2 did not affect the antioxidant activity of neutral lipids fixed at around 16% of radical scavenging. For S. muticum, the activity of glycolipids (50.9 ± 0.8%) and phospholipids (48.4 ± 1.6%) obtained with sc-CO2 were twice as large as that of fractions obtained with CM, 29.6 ± 3.4% and 28.0 ± 4.2%, respectively. The activity of neutral lipids did not change with the extraction method with around 25% of radical scavenging. This is the first report of free radical scavenging activity of lipid classes obtained by supercritical carbon dioxide extraction from seaweeds.
Krylov Subspace Solvers and Preconditioners
Authors: Vuik C.
Published: October 2018

In these lecture notes an introduction to Krylov subspace solvers and preconditioners is presented. After a discretization of partial differential equations large, sparse systems of linear equations have to be solved. Fast solution of these systems is very urgent nowadays. The size of the problems can be 1013 unknowns and 1013 equations. Iterative solution methods are the methods of choice for these large linear systems. We start with a short introduction of Basic Iterative Methods. Thereafter preconditioned Krylov subspace methods, which are state of the art, are describeed. A distinction is made between various classes of matrices.

At the end of the lecture notes many references are given to state of the art Scientific Computing methods. Here, we will discuss a number of books which are nice to use for an overview of background material. First of all the books of Golub and Van Loan [19] and Horn and Johnson [26] are classical works on all aspects of numerical linear algebra. These books also contain most of the material, which is used for direct solvers. Varga [50] is a good starting point to study the theory of basic iterative methods. Krylov subspace methods and multigrid are discussed in Saad [38] and Trottenberg, Oosterlee and Schüller [42]. Other books on Krylov subspace methods are [1, 6, 21, 34, 39].
Task-Based Parallelization of an Implicit Kinetic Scheme
Authors: Badwaik Jayesh , Boileau Matthieu , Coulette David , Franck Emmanuel , Helluy Philippe , Klingenberg Christian , Mendoza Laura , Oberlin Herbert
Published: October 2018

In this paper we present and implement the Palindromic Discontinuous Galerkin (PDG) method in dimensions higher than one. The method has already been exposed and tested in [4] in the one-dimensional context. The PDG method is a general implicit high order method for approximating systems of conservation laws. It relies on a kinetic interpretation of the conservation laws containing stiff relaxation terms. The kinetic system is approximated with an asymptotic-preserving high order DG method. We describe the parallel implementation of the method, based on the StarPU runtime library. Then we apply it on preliminary test cases.
Building and Auto-Tuning Computing Kernels: Experimenting with Boast and Starpu in the Gysela Code
Authors: Bigot Julien , Grandgirard Virginie , Latu Guillaume , Mehaut Jean-Francois , Millani Luís Felipe , Passeron Chantal , Masnada Steven Quinito , Richard Jérôme , Videau Brice
Published: October 2018

Modeling turbulent transport is a major goal in order to predict confinement performance in a tokamak plasma. The gyrokinetic framework considers a computational domain in five dimensions to look at kinetic issues in a plasma; this leads to huge computational needs. Therefore, optimization of the code is an especially important aspect, especially since coprocessors and complex manycore architectures are foreseen as building blocks for Exascale systems. This project aims to evaluate the applicability of two auto-tuning approaches with the BOAST and StarPU tools on the GYSELA code in order to circumvent performance portability issues. A specific computation intensive kernel is considered in order to evaluate the benefit of these methods. StarPU enables to match the performance and even sometimes outperform the hand-optimized version of the code while leaving scheduling choices to an automated process. BOAST on the other hand reveals to be well suited to get a gain in terms of execution time on four architectures. Speedups in-between 1.9 and 5.7 are obtained on a cornerstone computation intensive kernel.
Component Mapping Automation for Parametric Component Reduced Basis Techniques (RB-COMPONENT)
Authors: Chakir Rachida , Dapogny Charles , Japhet Caroline , Maday Yvon , Montavon Jean-Baptiste , Pantz Olivier , Patera Anthony
Published: October 2018

The aim of this paper is to develop some techniques for automation of the mappings (between working and reference domains) required by reduced basis methods: the development of geometry mappings is indeed often a substantial impediment to the implementation of reduced basis techniques, especially in the context of the reduced basis element method (RBEM) and the reduced basis component method (RBCM). In the RBCM context, the geometry mappings are applied at the level of components. The methods have been tested on various cases to understand the limits of the approach and try to foresee and overcome the possible failures.
Front Shape Similarity Measure for Shape-Oriented Sensitivity Analysis and Data Assimilation for Eikonal Equation
Authors: Rochoux M.C. , Collin A. , Zhang C. , Trouvé A. , Lucor D. , Moireau P.
Published: October 2018

We present a shape-oriented data assimilation strategy suitable for front-tracking problems through the example of wildfire. The concept of “front” is used to model, at regional scales, the burning area delimitation that moves, undergoes shape and topological changes under heterogeneous orography, biomass fuel and micrometeorology. The simulation-observation discrepancies are represented using a front shape similarity measure deriving from image processing and based on the Chan-Vese contour fitting functional. We show that consistent corrections of the front location and uncertain physical parameters can be obtained using this measure applied on a level-set fire growth model solving for an eikonal equation. This study involves a Luenberger observer for state estimation, including a topological gradient term to track multiple fronts, and of a reduced-order Kalman filter for joint parameter estimation. We also highlight the need – prior to parameter estimation – for sensitivity analysis based on the same discrepancy measure, and for instance using polynomial chaos metamodels, to ensure a meaningful inverse solution is achieved. The performance of the shape-oriented data assimilation strategy is assessed on a synthetic configuration subject to uncertainties in front initial position, near-surface wind magnitude and direction. The use of a robust front shape similarity measure paves the way toward the direct assimilation of infrared images and is a valuable asset in the perspective of data-driven wildfire modeling.
Wenn die Aufbereitung auswandert
Authors: Zaiss Elke
Published: October 2018

Wie leistungsfähig eine OP-Abteilung ist, hängt in hohem Maß von der Versorgung mit Sterilgütern ab. Hier spielt insbesondere die schnelle, zeitgerechte und
sichere Aufbereitung von Instrumenten eine entscheidende Rolle. Denn der chirurgische Eingriff an einem Patienten in Narkose muss ohne Verzögerung durch
fehlende oder unvollständige Instrumente möglich sein. Dies zu gewährleisten, ist in den letzten Jahren eine der größten Herausforderungen für das OP-Management
und die dezentralen Aufbereiter. Unsere Autorin erläutert, wie diese Herausforderung entstanden ist, welche Faktoren diesen Prozess beeinflussen und welche
Lösungen es für die Praxis gibt.
HOT im OP
Authors: Schwab Gisela
Published: October 2018

In lockerer Folge möchten wir Ihnen mit kurzen Steckbriefen Berufsbilder im OP vorstellen. Den Anfang macht die 31-jährige Hybrid-OP-Technologin Alexandra
Sabautzki.
The Activity of Urolithin A and M4 Valerolactone, Colonic Microbiota Metabolites of Polyphenols, in a Prostate Cancer In Vitro Model
Authors: Stanisławska Iwona , Granica Sebastian , Piwowarski Jakub , Szawkało Joanna , Wiązecki Krzysztof , Czarnocki Zbigniew , Kiss Anna
Published: October 2018

The gut microbiota-derived metabolites of ellagitannins and green tea catechins, urolithin A (uroA) and 5-(3′,4′,5′-trihydroxyphenyl)-γ-valerolactone (M4), respectively, are among the main compounds absorbed into human system after ingestion of these polyphenols. The aim of this study was to establish the effects of M4, uroA, and their combinations on LNCaP cells, an androgen dependent prostate cancer in vitro model.. The LNCaP cells were incubated with increasing concentrations of tested metabolites. The cell proliferation was determined by measurement of DNA-bisbenzimide H 33 258 complexes fluorescence. The isobolographic analysis was used to establish the type of interaction between metabolites. The apoptosis, androgen receptor (AR) localization, and phosphorylation of Akt kinase were measured by flow cytometry. Prostate-specific antigen (PSA) secretion was determined by ELISA. M4 showed modest antiproliferative activity in LNCaP cells (IC50 = 117 µM; CI: 81 – 154). UroA decreased proliferation (IC50 = 32.7 µM; CI: 24.3 – 41.1) and induced apoptosis of LNCaP cells. The mixture of M4 with uroA had synergistic antiproliferative effect. Moreover, M4 potentiated inhibition of PSA secretion and enhanced retention of AR in cytoplasm caused by uroA. Interestingly, uroA increased levels of pSer473 Akt in LNCaP cells. These results show that colonic metabolites may contribute to chemoprevention of prostate cancer by varied polyphenol-rich diet or composite polyphenol preparations.
Epónimos en la anatomía y radiología de cabeza y cuello
Authors: Ferraro Fernando Martín , Chaves Hernán , Olivera Plata Federico Martín , Miquelini Luis Ariel , Mukherji Suresh K.
Published: October 2018

En el lenguaje médico, el uso de epónimos es frecuente. Si bien comúnmente se piensa que los epónimos están en vías de extinción, eso no es totalmente cierto. Existe disenso entre quienes creen que su uso debería abandonarse y quienes abogan que los epónimos convierten términos inmemorables en memorizables, transmiten conceptos complejos y promueven el interés en la historia de la Medicina. Nos sentimos parte de ese segundo grupo y nuestra intención es hacer una revisión de ocho epónimos vinculados a la Anatomía y Radiología de cabeza y cuello. Creemos que ese abordaje puede ser útil para la educación de estudiantes de Medicina, residentes y especialistas en diagnóstico por imágenes.
Simplified high-current measurement probe based on a single-mode optical fiber
Authors: Dey Premananda , Shukla Rohit , Sharma Archana
Published: October 2018

A “fiber optic cable tester” of 658 nm wavelength has been used to launch a linearly polarized light to the twisted single mode optical fiber of the designed mega-ampere current measurement probe. Modulated intensity variation of light has been converted to the corresponding electrical signal using a fast photodetector assembly having 100 nS rise-time. The effect of undesired linear birefringence has been overcome by manually twisting the fiber at a twist rate of 40 twists per meter. The sensitivity of the designed probe is 0.247° polarization rotation/kA current-turn product, for a single optical fiber loop.
Comment on “Soliton solutions and chaotic motion of the extended Zakharov-Kuznetsov equations in a magnetized two-ion-temperature dusty plasma” [Phys. Plasmas 21, 073709 (2014)]
Authors: El-Tantawy S. A. , Wazwaz Abdul-Majid
Published: October 2018

The published paper by Zhen et al. [Phys. Plasmas 21, 073709 (2014)] contains some errors which have been pointed out in this comment.
Research on the normal spectral band emissivity of tungsten between 150 and 500 °C
Authors: Zhang Yan , Ji Feng , Zhang Yuzhong , Shu Shuangbao , Lu Rongsheng
Published: October 2018

Tungsten is the baseline divertor material for a tokamak. Due to the effect of the interaction of plasma and the first wall, the first wall accumulates a large amount of heat flux and suffers irreversible damages. Therefore, the diagnosis of the first wall temperature of the tokamak by using a radiation thermometer is the premise to ensure the safe and stable operation of the whole facility. However, in order to achieve high precision of temperature measurement, the emissivity of tungsten must be measured accurately. In this paper, we built a set of emissivity measurement system and a method for accurate calculation of emissivity is proposed. This method effectively eliminated the interference of background radiation and improves the accuracy of emissivity measurement. By using this method, the author measured the emissivity of tungsten under the conditions of different surface roughness in the range of 150 °C–500 °C and discussed the uncertainty of the measurement at the end.
Design of a shattered pellet injection system on J-TEXT tokamak
Authors: Li Y. , Chen Z. Y. , Wei Y. N. , Tong R. H. , Yan W. , Lin Z. F. , Yang Z. J. , Jiang Z. H.
Published: October 2018

Disruptions have the possibility of causing severe wall damage to large tokamaks like ITER. The mitigation of disruption damage is essential to the safe operation of a large-scale tokamak. The shattered pellet injection (SPI) technique, which is regarded as the primary injection method for ITER, presents several advantages relative to massive gas injection, including more rapid particle delivery, higher total particle assimilation, and more centrally peaked particle deposition. A dedicated argon SPI system that focuses on disruption mitigation and runaway current dissipation has been designed for the Joint Texas Experimental Tokamak (J-TEXT). A refrigerator is used to form a single argon pellet at around 64 K. The pellet will be shaped with a 5 mm diameter and a 1.5-10 mm length. Helium gas at room temperature will be used as a propellant gas for pellet acceleration. The pellet can be injected with a speed of 150-300 m/s. The time interval between injection cycles is about 8 min. The pellet will be shattered at the edge of the plasma and then injected into the core of plasma. The first experiments of SPI fast shutdown and runaway current dissipation have been performed.
Velocity-space sensitivity of time-of-flight neutron spectrometer at EAST in deuterium plasma
Authors: Ge L. J. , Hu Z. M. , Zhang Y. M. , Sun J. Q. , Yuan X. , Peng X. Y. , Chen Z. J. , Du T. F. , Nocente M. , Gorini G. , Tardocchi M. , Hu L. Q. , Zhong G. Q. , Wan B. N. , Li X. Q. , Fan T. S.
Published: October 2018

The Time-Of-Flight Enhanced Diagnostics (TOFED) neutron spectrometer with a double-ring structure has been installed at the Experimental Advanced Superconducting Tokamak (EAST) to perform advanced neutron emission spectroscopy diagnosis for deuterium plasma. In order to reduce the random coincidence from the background neutrons and gamma-rays, TOFED was moved outside the experimental hall and placed in the newly-built nuclear diagnostics laboratory in 2017. In this paper, the instrument-specific weight functions of TOFED are derived by taking the instrument response matrix and the radial line of sight in this new layout into consideration. The results show that the instrument is predominantly sensitive to counter-passing particles in the region where time-of-flights < 69.4 ns, while events at higher time-of-flights (corresponding lower neutron energies) are mostly representative of co-passing ions. The instrument-specific weight functions express the relationship between data in a given channel of the spectrum and the velocity space region that contributes to that. The results can be applied for energetic particle physics studies at EAST, in particular to compare data from different diagnostic techniques.
Design of a 3D printed compact interferometric system and required phone application for small angular measurements
Authors: Hussain I. , Nath P.
Published: October 2018

A 3D printed smartphone based interferometric system is proposed, and its usability has been demonstrated by measuring small angular rotations. All necessary fringe processing and data analysis have been performed within the phone itself using custom designed application developed in an android platform. The main objective of the proposed work is to demonstrate the usability of modern smartphone and 3D printing technology for optical interferometric applications. The smartphone camera has been used to record the interference fringes which has been formed due to the change in the optical path difference (OPD) between light rays reflected from the top and bottom surface of a microscopic glass slide. The angular variation of the slide causes a detectable change in the OPD between the interfering beams which subsequently would cause a variation in the fringe pattern. By evaluating necessary interferometric parameters, small angular rotation can be computed within the smartphone application. With the designed smartphone based interferometric system, angular rotation as small as 0.02° can be measured accurately and reliably having a dynamic range of −3.68° to 3.68°. Due to the involvement of the smartphone as a platform for recording as well as onboard fringe processing, the designed interferometric system can be visualized as a truly field portable tool for different optical metrological applications.
Simple and accurate method of diamagnetic flux measurement in Versatile Experimental Spherical Torus (VEST)
Authors: Yang J. , Kim Y. , Jeong W. I. , Hwang Y. S.
Published: October 2018

Diamagnetic flux is measured accurately in the Versatile Experiment Spherical Torus by simply measuring the change in the toroidal field (TF) coil current without additional poloidal loops. Stray couplings mainly with the plasma current (since poloidal field coils are aligned well to the TF coils) are compensated for, resulting in the minimum measurable flux of ±0.2 mWb determined mainly by the finite sensitivity of the TF coil current sensor, implying that the accuracy of this simple method can be improved by measuring the TF coil current change with a higher sensitivity. The poloidal beta is derived from the measured diamagnetic flux with the consideration of the low aspect ratio geometry. The poloidal beta and the plasma stored energy derived from the measurement are in good agreement with those from the equilibrium reconstruction, and the energy confinement time derived from the measurement is consistent with the L mode scaling.
The influence of Hall physics on power-flow along a coaxial transmission line
Authors: Hamlin N. D. , Seyler C. E.
Published: October 2018

Extended-MHD simulations of a coaxial transmission line are performed in axisymmetric cylindrical geometry, in particular, in examining the influence of Hall physics on a plasma layer initialized against the anode versus the cathode, for which an MHD model is insensitive. The results indicate that Hall physics is required in order to model an electron E × B drift current in the electrode plasma, which is parallel to the anode current and opposite the cathode current. This results in confinement of the electrode plasma when initialized against the cathode and expansion of the plasma layer when initialized against the anode. The expansion in the anode-initialized case results in filaments of plasma bridging the gap, causing substantial power-flow losses. These results represent the first fluid simulations of power-flow, to our knowledge, that, by including Hall physics, recover fundamental aspects of anode and cathode dynamics predicted by kinetic theory while simulating over a dynamic range (nine orders of magnitude density variation from solid-density electrodes down to low-density electrode plasma) which is prohibitive for Particle-In-Cell (PIC) codes. This work demonstrates the need for further development of extended-MHD and two-fluid modeling of power-flow dynamics, which, possibly through hybridization with a PIC code, will eventually culminate in a code with reliable predictive capability for power-flow coupling and energy losses in pulsed-power systems.
Experimental densities of subcooled deuterium oxide at pressures up to 160 MPa
Authors: Romeo Raffaella , Lago Simona , Giuliano Albo P. Alberto
Published: October 2018

In this work, the experimental results of deuterium oxide density at high pressure and in a wide range of temperatures, by means of the pseudo-isochoric method, are presented. A specific stainless steel cell was devised to be used as a pycnometer and filled with variable mass of heavy water. The latter was measured by weighing with an analytical balance and using the substitution method. The volume of the pycnometric cell was measured by the gravimetric method and corrected for the effect of temperature and pressure. Each measurement cycle was performed at constant mass, measuring pressure as a function of temperature at equilibrium. From the mass and volume values, density was calculated according to its definition. Heavy water density was measured for temperatures down to 253 K and for pressures up to 163 MPa, thus both in stable and supercooled metastable states. All terms contributing to the uncertainty in determining the volume and the mass were considered, obtaining an expanded relative uncertainty of deuterium oxide density of 0.04%.