SMLSOM: The shrinking maximum likelihood self-organizing map

Determining the number of clusters in a dataset is a fundamental issue in data clustering. Many methods have been proposed to solve the problem of selecting the number of clusters, considering it to be a problem with regard to model selection. This paper proposes an efficient algorithm that automatically selects a suitable number of clusters based on a probability distribution model framework. The algorithm includes the following two components. First, a generalization of Kohonen's self-organizing map (SOM) is introduced. In Kohonen's SOM, clusters are modeled as mean vectors. In the generalized SOM, each cluster is modeled as a probabilistic distribution and constructed by samples classified based on the likelihood. Second, the dynamically updating method of the SOM structure is introduced. In Kohonen's SOM, each cluster is tied to a node of a fixed two-dimensional lattice space and learned using neighborhood relations between nodes based on Euclidean distance. The extended SOM defines a graph with clusters as vertices and neighborhood relations as links and updates the graph structure by cutting weakly-connection and unnecessary vertex deletions. The weakness of a link is measured using the Kullback--Leibler divergence, and the redundancy of a vertex is measured using the minimum description length. Those extensions make it efficient to determine the appropriate number of clusters. Compared with existing methods, the proposed method is computationally efficient and can accurately select the number of clusters

Fault detection system for ICRF transmission line in LHD

The transmission line is one of the most important components of ion cyclotron range of frequencies (ICRF) heating devices. In the case of unexpected trouble on the line, such as a breakdown, immediate power-off is necessary in order to avoid severe damage on the line. Breakdowns are difficult to detect with a reflection monitor, since the reflection may originate from a change in the antenna-plasma coupling. In the Large Helical Device (LHD), a Fault Detection System (FDS) for the transmission line was developed, which detects the breakdown utilizing the unbalance of three signals from the both ends of the line. For the precise balancing in the normal condition, the calibration is iteratively conducted. FDS is insensitive to the change of the antenna impedance, therefore, FDS can detect breakdown clearly. Frequency shift is also detectable with the FDS applied to a long transmission line. Therefore, the self-oscillation accompanying frequency shift could be detected in addition to breakdown

Overview of polar exhibit tanks and List of the creatures in house

The Tenth Symposium on Polar Science/Ordinary sessions : [OB] Polar Biology, Wed. 4 Dec. / Entrance Hall (1st floor) , National Institute of Polar Researc

Study of ion cyclotron range of frequencies heating characteristics in deuterium plasma in the Large Helical Device

The characteristics of ion cyclotron range of frequencies (ICRF) minority ion heating with a hydrogen minority and deuterium majority plasma were studied by ICRF modulation injection experiments in the Large Helical Device (LHD). In recent experiments with deuterium plasma, no significant increase in the neutron emission rate due to ICRF second harmonic deuteron heating was observed. Therefore, in this study, the neutron emission rate was used to refer to the information regarding the thermal ion component. Like the results of the observations of the heating efficiencies at various minority proton ratios, the experimental results showed good agreement with the simple model simulation of ICRF wave absorption. During these experiments, the accelerated minority hydrogen ions were observed by neutral particle analyzers. The counting rates of the energetic particles were higher in the lines of sight passing through the helical ripple than across the magnetic axis, and the counting rate decreased as the minority hydrogen ion ratio increased. The dependence of the minority hydrogen ion ratio on the density of the energetic ions was consistent with the experimentally observed heating efficiencies and simulations. The heating efficiency of ICRF minority ion heating could be well explained by simple model simulation in the LHD deuterium experiment

Magnetohydrodynamic hybrid simulation model with kinetic thermal ions and energetic particles

A new kinetic-magnetohydrodynamic hybrid simulation model where the gyrokinetic particle-in-cell simulation is applied to both thermal ions and energetic particles is presented. Toroidal Alfvén eigenmodes (TAEs) destabilized by energetic ions in tokamak plasmas are simulated with the new simulation model. Energy channeling from energetic ions to thermal ions through Alfvén eigenmodes (AEs) is demonstrated by the simulation. The distribution function fluctuations and the resonance condition are analyzed for both thermal ions and energetic ions. The strong energy transfer between the particles and the AE and the strong particle transport occur when the following conditions are satisfied at the resonance location in phase space: (1) the poloidal resonance number is close to the poloidal mode number of the AE, (2) the AE has a substantial amplitude, (3) the distribution function has a substantial gradient along the $E^{^{\prime}} = \textrm{const.}$ line, where $E^{^{\prime}}$ is a conserved variable for the wave-particle interaction. While the distribution function fluctuations for energetic ions are consistent with the resonance condition with the TAEs, the distribution function fluctuations for thermal ions do not satisfy the resonance condition when the bulk plasma beta is 1%. This indicates that the resonance does not play an important role in the interaction between thermal ions and the TAE for the relatively low bulk plasma temperature. On the other hand, when the bulk plasma beta is 4%, the resonance between thermal ions and the TAEs become important leading to Landau damping

Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions

光エネルギーで新しい化学修飾核酸を合成 --核酸リン原子の第三級アルキル化に成功--. 京都大学プレスリリース. 2023-11-01.Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2’-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study

A Role of Suppressor of Cytokine Signaling 3 (SOCS3/CIS3/SSI3) in CD28-mediated Interleukin 2 Production

Suppressor of cytokine signaling (SOCS)3 has been characterized as a negative feedback regulator in cytokine-mediated Janus kinase signal transducer and activator of transcription signaling. However, this study shows that T cells from transgenic mice expressing SOCS3 exhibit a significant reduction in interleukin (IL)-2 production induced by T cell receptor cross-linking when T cells are costimulated with CD28. Decreased protein expression in SOCS3+/− mice enhanced CD28-mediated IL-2 production, clearly indicating the correlation between expression level of SOCS3 and IL-2 production ability. The SOCS3 protein interacted with phosphorylated CD28 through its SH2 domain but not the kinase inhibitory region. In addition, a point mutation in the SOCS3 SH2 domain attenuated the inhibition of CD28 function in IL-2 promoter activation. Committed T helper (Th)2 cells exclusively expressed SOCS3 and production of Th2 cytokines, such as IL-4 and IL-5, was much less dependent on CD28 costimulation compared with interferon γ and IL-2 production in Th1 cells. Consistent with this notion, the expression level of SOCS3 in early T cell activation influenced the ability of IL-2 production induced by CD28 costimulation. Therefore, the SOCS3 may play an alternative role in prohibiting excessive progression of CD28-mediated IL-2 production

Improved Three-Dimensional CCS Method Analysis for the Reconstruction of the Peripheral Magnetic Field Structure in a Finite Beta Helical Plasma

In the previous 3D Cauchy-condition surface (CCS) method analysis to reconstruct the magnetic field profile in the Large Helical Device (LHD), one assumed an impractically large number of magnetic sensors, i.e., 440 field sensors and 126 flux loops. In the singular value decomposition (SVD) process employed in the CCS method, a gap is found in the magnitude of the singular values. The most accurate field results can be obtained if all the singular values smaller than the gap threshold are eliminated, independent of the number of boundary elements on the CCS and the number of sensors as well. With the reduction in the number of boundary elements, the required numbers of field sensors and flux loops are significantly reduced to 110 and 25, respectively, without losing the solution accuracy. They can be further reduced to 58 and 13 respectively if considering the symmetry of the field profile in the LHD. This result suggests the possibility of actual application to the LHD

Improvement of Automatic Physics Data Analysis Environment for the LHD Experiment

The physical data of the Large Helical Device (LHD) project have been serviced by the Analyzed Data Server system, and approximately 600 kinds of physical data are served. In order to execute simulation programs for the LHD experiment, one must gather sets of physical data. Because the Automatic Analyzed Server (AutoAna) calculates the physical data automatically, it eases the scientist’s task of collecting these physical data. The AutoAna has provided better computing environments for the scientists. Thus, the scientists, having recognized its benefits, make various requests as issues arise. In this paper, the authors introduce the current status of the AutoAna system