Community Detection and Growth Potential Prediction Using the Stochastic Block Model and the Long Short-term Memory from Patent Citation Networks

Scoring patent documents is very useful for technology management. However, conventional methods are based on static models and, thus, do not reflect the growth potential of the technology cluster of the patent. Because even if the cluster of a patent has no hope of growing, we recognize the patent is important if PageRank or other ranking score is high. Therefore, there arises a necessity of developing citation network clustering and prediction of future citations. In our research, clustering of patent citation networks by Stochastic Block Model was done with the aim of enabling corporate managers and investors to evaluate the scale and life cycle of technology. As a result, we confirmed nested SBM is appropriate for graph clustering of patent citation networks. Also, a high MAPE value was obtained and the direction accuracy achieved a value greater than 50% when predicting growth potential for each cluster by using LSTM.Comment: arXiv admin note: substantial text overlap with arXiv:1904.1204

Construction of a novel kinetic model for the production process of a CVA6 VLP vaccine in CHO cells

Bioprocess development benefits from kinetic models in many aspects, including scale-up, optimization, and process understanding. However, current models are unable to simulate the production process of a coxsackievirus A6 (CVA6) virus-like particle (VLP) vaccine using Chinese hamster ovary cell culture. In this study, a novel kinetic model was constructed, correlating (1) cell growth, death, and lysis kinetics, (2) metabolism of major metabolites, and (3) CVA6 VLP production. To construct the model, two batches of a laboratory-scale 2 L bioreactor cell culture were prepared and various pH shift strategies were applied to examine the effect of pH shift. The proposed model described the experimental data under various conditions with high accuracy and quantified the effect of pH shift. Next, cell culture performance with various pH shift timings was predicted by the calibrated model. A trade-off relationship was found between product yield and quality. Consequently, multiple objective optimization was performed by integrating desirability methodology with model simulation. Finally, the optimal operating conditions that balanced product yield and quality were predicted. In general, the proposed model improved the process understanding and enabled in silico process development of a CVA6 VLP vaccine.The version of record of this article, first published in Cytotechnology, is available online at Publisher’s website: https://doi.org/10.1007/s10616-023-00598-

Unraveling the Nature of Unidentified High Galactic Latitude Fermi/LAT Gamma-ray Sources with Suzaku

We report on the results of deep X-ray follow-up observations of four unidentified Fermi/LAT gamma-ray sources at high Galactic latitudes using Suzaku. The studied objects were detected with high significance during the first 3 months of Fermi/LAT operation, and subsequently better localized in the Fermi/LAT 1 year catalog (1FGL). Possible associations with pulsars and active galaxies have subsequently been discussed, and our observations provide an important contribution to this debate. In particular, an X-ray point source was found within the 95% confidence error circle of 1FGL J1231.1-1410. X-ray spectrum is well-fitted by a blackbody with an additional power-law. This supports the recently claimed identification of this source with a millisecond pulsar (MSP) PSR J1231-1411. Concerning 1FGL J1311.7-3429, two X-ray sources were found within the LAT error circle. Even though the X-ray spectral and variability properties were accessed, their nature and relationship with the gamma-ray source remain uncertain. We found several weak X-ray sources in the field of 1FGL J1333.2+5056, one coinciding with CLASS J1333+5057. We argue the available data are consistent with the association between these two objects. Finally, we have detected an X-ray source in the vicinity of 1FGL J2017.3+0603. This object was recently suggested to be associated with a newly discovered MSP PSR J2017+0603, because of the spatial-coincidence and the gamma-ray pulse detection. We have only detected the X-ray counterpart of the CLASS J2017+0603, while we determined an X-ray flux upper limit at the pulsar position. All in all, our studies indicate while a significant fraction of unidentified high Galactic latitude gamma-ray sources is related to the pulsar and blazar phenomena, associations with other classes of astrophysical objects are still valid options.Comment: Accepted for publication in the Ap

Defect in Synaptic Vesicle Precursor Transport and Neuronal Cell Death in KIF1A Motor Protein–deficient Mice

The nerve axon is a good model system for studying the molecular mechanism of organelle transport in cells. Recently, the new kinesin superfamily proteins (KIFs) have been identified as candidate motor proteins involved in organelle transport. Among them KIF1A, a murine homologue of unc-104 gene of Caenorhabditis elegans, is a unique monomeric neuron– specific microtubule plus end–directed motor and has been proposed as a transporter of synaptic vesicle precursors (Okada, Y., H. Yamazaki, Y. Sekine-Aizawa, and N. Hirokawa. 1995. Cell. 81:769–780). To elucidate the function of KIF1A in vivo, we disrupted the KIF1A gene in mice. KIF1A mutants died mostly within a day after birth showing motor and sensory disturbances. In the nervous systems of these mutants, the transport of synaptic vesicle precursors showed a specific and significant decrease. Consequently, synaptic vesicle density decreased dramatically, and clusters of clear small vesicles accumulated in the cell bodies. Furthermore, marked neuronal degeneration and death occurred both in KIF1A mutant mice and in cultures of mutant neurons. The neuronal death in cultures was blocked by coculture with wild-type neurons or exposure to a low concentration of glutamate. These results in cultures suggested that the mutant neurons might not sufficiently receive afferent stimulation, such as neuronal contacts or neurotransmission, resulting in cell death. Thus, our results demonstrate that KIF1A transports a synaptic vesicle precursor and that KIF1A-mediated axonal transport plays a critical role in viability, maintenance, and function of neurons, particularly mature neurons

Observation of optical emission from high refractive index waveguide excited by traveling electron beam

金沢大学理工研究域電子情報学系A new scheme for optical emission using a high refractive index waveguide and the traveling electron beam in vacuum was demonstrated. Optical emission around wavelength of 1.5 pm was observed for electron acceleration voltage of 40KV. © 2008 Optical Society of America

Optical emission from a high-refractive-index waveguide excited by a traveling electron beam

金沢大学理工研究域電子情報学系An optical emission scheme was demonstrated, in which a high-refractive-index waveguide is excited by a traveling electron beam in a vacuum environment. The waveguide was made of Si- SiO2 layers. The velocity of light propagating in the waveguide was slowed down to 1/3 of that in free space due to the high refractive index of Si. The light penetrated partly into the vacuum in the form of a surface wave. The electron beam was emitted from an electron gun and propagated along the surface of the waveguide. When the velocity of the electron coincided with that of the light, optical emission was observed. This emission is a type of Cherenkov radiation and is not conventional cathode luminescence from the waveguide materials because Si and SiO2 are transparent to light at the emitted wavelength. This type of emission was observed in an optical wavelength range from 1.2 to 1.6 μm with an electron acceleration voltage of 32-42 kV. The characteristics of the emitted light, such as the polarization direction and the relation between the acceleration voltage of the electron beam and the optical wavelength, coincided well with the theoretical results. The coherent length of an electron wave in the vacuum was confirmed to be equal to the electron spacing, as found by measuring the spectral profile of the emitted light. © 2008 American Institute of Physics

HBO1-MLL interaction promotes AF4/ENL/P-TEFb-mediated leukemogenesis

白血病を引き起こすタンパク質間相互作用の発見. 京都大学プレスリリース. 2021-08-31.Leukemic oncoproteins cause uncontrolled self-renewal of hematopoietic progenitors by aberrant gene activation, eventually causing leukemia. However, the molecular mechanism underlying aberrant gene activation remains elusive. Here, we showed that leukemic MLL fusion proteins associate with the HBO1 histone acetyltransferase (HAT) complex through their trithorax homology domain 2 (THD2) in various human cell lines. MLL proteins associated with the HBO1 complex through multiple contacts mediated mainly by the ING4/5 and PHF16 subunits in a chromatin-bound context where histone H3 lysine 4 tri-methylation marks were present. Of the many MLL fusions, MLL-ELL particularly depended on the THD2-mediated association with the HBO1 complex for leukemic transformation. The C-terminal portion of ELL provided a binding platform for multiple factors including AF4, EAF1, and p53. MLL-ELL activated gene expression in murine hematopoietic progenitors by loading an AF4/ENL/P-TEFb (AEP) complex onto the target promoters wherein the HBO1 complex promoted the association with AEP complex over EAF1 and p53. Moreover, the NUP98-HBO1 fusion protein exerted its oncogenic properties via interaction with MLL but not its intrinsic HAT activity. Thus, the interaction between the HBO1 complex and MLL is an important nexus in leukemic transformation, which may serve as a therapeutic target for drug development

Photo-excitation band-structure engineering of 2H-NbSe2_2 probed by time- and angle-resolved photoemission spectroscopy

We investigated the nonequilibrium electronic structure of 2H-NbSe$_2$ by time- and angle-resolved photoemission spectroscopy. We find that the band structure is distinctively modulated by strong photo-excitation, as indicated by the unusual increase in the photoelectron intensities around E$_F$. In order to gain insight into the observed photo-induced electronic state, we performed DFT calculations with modulated lattice structures, and found that the variation of the Se height from the Nb layer results in a significant change in the effective mass and band gap energy. We further study the momentum-dependent carrier dynamics. The results suggest that the relaxation is faster at the K-centered Fermi surface than at the $\Gamma$-centered Fermi surface, which can be attributed to the stronger electron-lattice coupling at the K-centered Fermi surface. Our demonstration of band structure engineering suggests a new role for light as a tool for controlling the functionalities of solid-state materials.Comment: 7 pages, 5 figure