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1. Study of the doubly Cabibbo-suppressed decays $D^+_s\to K^+K^+\pi^-$ and $D^+_s\to K^+K^+\pi^-\pi^0$

Author

BESIII Collaboration, Ablikim, M., Achasov, M. N., Adlarson, P., Afedulidis, O., Ai, X. C., Aliberti, R., Amoroso, A., An, M. R., An, Q., Bai, Y., Bakina, O., Balossino, I., Ban, Y., Bao, H. -R., Batozskaya, V., Begzsuren, K., Berger, N., Berlowski, M., Bertani, M., Bettoni, D., Bianchi, F., Bianco, E., Bortone, A., Boyko, I., Briere, R. A., Brueggemann, A., Cai, H., Cai, X., Calcaterra, A., Cao, G. F., Cao, N., Cetin, S. A., Chang, J. F., Che, G. R., Chelkov, G., Chen, C., Chen, Chao, Chen, G., Chen, H. S., Chen, M. L., Chen, S. J., Chen, S. L., Chen, S. M., Chen, T., Chen, X. R., Chen, X. T., Chen, Y. B., Chen, Y. Q., Chen, Z. J., Chen, Z. Y., Choi, S. K., Cibinetto, G., Coen, S. C., Cossio, F., Cui, J. J., Dai, H. L., Dai, J. P., Dbeyssi, A., de Boer, R. E., Dedovich, D., Deng, Z. Y., Denig, A., Denysenko, I., Destefanis, M., De Mori, F., Ding, B., Ding, X. X., Ding, Y., Dong, J., Dong, L. Y., Dong, M. Y., Dong, X., Du, M. C., Du, S. X., Duan, Z. H., Egorov, P., Fan, Y. H., Fang, J., Fang, S. S., Fang, W. X., Fang, Y., Fang, Y. Q., Farinelli, R., Fava, L., Feldbauer, F., Felici, G., Feng, C. Q., Feng, J. H., Feng, Y. T., Fischer, K., Fritsch, M., Fu, C. D., Fu, J. L., Fu, Y. W., Gao, H., Gao, Y. N., Gao, Yang, Garbolino, S., Garzia, I., Ge, L., Ge, P. T., Ge, Z. W., Geng, C., Gersabeck, E. M., Gilman, A., Goetzen, K., Gong, L., Gong, W. X., Gradl, W., Gramigna, S., Greco, M., Gu, M. H., Gu, Y. T., Guan, C. Y., Guan, Z. L., Guo, A. Q., Guo, L. B., Guo, M. J., Guo, R. P., Guo, Y. P., Guskov, A., Gutierrez, J., Han, T. T., Han, W. Y., Hao, X. Q., Harris, F. A., He, K. K., He, K. L., Heinsius, F. H., Heinz, C. H., Heng, Y. K., Herold, C., Holtmann, T., Hong, P. C., Hou, G. Y., Hou, X. T., Hou, Y. R., Hou, Z. L., Hu, B. Y., Hu, H. M., Hu, J. F., Hu, T., Hu, Y., Huang, G. S., Huang, K. X., Huang, L. Q., Huang, X. T., Huang, Y. P., Hussain, T., Hölzken, F., Hüsken, N, der Wiesche, N. in, Jackson, J., Jaeger, S., Janchiv, S., Jeong, J. H., Ji, Q., Ji, Q. P., Ji, X. B., Ji, X. L., Ji, Y. Y., Jia, X. Q., Jia, Z. K., Jiang, H. B., Jiang, P. C., Jiang, S. S., Jiang, T. J., Jiang, X. S., Jiang, Y., Jiao, J. B., Jiao, Z., Jin, S., Jin, Y., Jing, M. Q., Jing, X. M., Johansson, T., Kabana, S., Kalantar-Nayestanaki, N., Kang, X. L., Kang, X. S., Kavatsyuk, M., Ke, B. C., Khachatryan, V., Khoukaz, A., Kiuchi, R., Kliemt, R., Kolcu, O. B., Kopf, B., Kuessner, M., Kui, X., Kumar, N., Kupsc, A., Kühn, W., Lane, J. J., Larin, P., Lavania, A., Lavezzi, L., Lei, T. T., Lei, Z. H., Lellmann, M., Lenz, T., Li, C., Li, C. H., Li, Cheng, Li, D. M., Li, F., Li, G., Li, H. B., Li, H. J., Li, H. N., Li, Hui, Li, J. R., Li, J. S., Li, J. W., Li, Ke, Li, L. J, Li, L. K., Li, Lei, Li, M. H., Li, P. R., Li, Q. X., Li, S. X., Li, T., Li, W. D., Li, W. G., Li, X. H., Li, X. L., Li, Xiaoyu, Li, Y. G., Li, Z. J., Li, Z. X., Liang, C., Liang, H., Liang, Y. F., Liang, Y. T., Liao, G. R., Liao, L. Z., Libby, J., Limphirat, A., Lin, D. X., Lin, T., Liu, B. J., Liu, B. X., Liu, C., Liu, C. X., Liu, F. H., Liu, Fang, Liu, Feng, Liu, G. M., Liu, H., Liu, H. B., Liu, H. M., Liu, Huanhuan, Liu, Huihui, Liu, J. B., Liu, J. Y., Liu, K., Liu, K. Y., Liu, Ke, Liu, L., Liu, L. C., Liu, Lu, Liu, M. H., Liu, P. L., Liu, Q., Liu, S. B., Liu, T., Liu, W. K., Liu, W. M., Liu, X., Liu, Y., Liu, Y. B., Liu, Z. A., Liu, Z. Q., Lou, X. C., Lu, F. X., Lu, H. J., Lu, J. G., Lu, X. L., Lu, Y., Lu, Y. P., Lu, Z. H., Luo, C. L., Luo, M. X., Luo, T., Luo, X. L., Lyu, X. R., Lyu, Y. F., Ma, F. C., Ma, H., Ma, H. L., Ma, J. L., Ma, L. L., Ma, M. M., Ma, Q. M., Ma, R. Q., Ma, X. Y., Ma, Y., Ma, Y. M., Maas, F. E., Maggiora, M., Malde, S., Mangoni, A., Mao, Y. J., Mao, Z. P., Marcello, S., Meng, Z. X., Messchendorp, J. G., Mezzadri, G., Miao, H., Min, T. J., Mitchell, R. E., Mo, X. H., Moses, B., Muchnoi, N. Yu., Muskalla, J., Nefedov, Y., Nerling, F., Nikolaev, I. B., Ning, Z., Nisar, S., Niu, Q. L., Niu, W. D., Niu, Y., Olsen, S. L., Ouyang, Q., Pacetti, S., Pan, X., Pan, Y., Pathak, A., Patteri, P., Pei, Y. P., Pelizaeus, M., Peng, H. P., Peng, Y. Y., Peters, K., Ping, J. L., Ping, R. G., Plura, S., Prasad, V., Qi, F. Z., Qi, H., Qi, H. R., Qi, M., Qi, T. Y., Qian, S., Qian, W. B., Qiao, C. F., Qiao, X. K., Qin, J. J., Qin, L. Q., Qin, L. Y., Qin, X. S., Qin, Z. H., Qiu, J. F., Qu, S. Q., Redmer, C. F., Ren, K. J., Rivetti, A., Rolo, M., Rong, G., Rosner, Ch., Ruan, S. N., Salone, N., Sarantsev, A., Schelhaas, Y., Schoenning, K., Scodeggio, M., Shan, K. Y., Shan, W., Shan, X. Y., Shangguan, J. F., Shao, L. G., Shao, M., Shen, C. P., Shen, H. F., Shen, W. H., Shen, X. Y., Shi, B. A., Shi, H., Shi, H. C., Shi, J. L., Shi, J. Y., Shi, Q. Q., Shi, X., Song, J. J., Song, T. Z., Song, W. M., Song, Y. J., Song, Y. X., Sosio, S., Spataro, S., Stieler, F., Su, Y. J., Sun, G. B., Sun, G. X., Sun, H., Sun, H. K., Sun, J. F., Sun, K., Sun, L., Sun, S. S., Sun, T., Sun, W. Y., Sun, Y., Sun, Y. J., Sun, Y. Z., Sun, Z. T., Tang, C. J., Tang, G. Y., Tang, J., Tang, Y. A., Tao, L. Y., Tao, Q. T., Tat, M., Teng, J. X., Thoren, V., Tian, W. H., Tian, Y., Tian, Z. F., Uman, I., Wan, Y., Wang, S. J., Wang, B., Wang, B. L., Wang, Bo, Wang, C. W., Wang, D. Y., Wang, F., Wang, H. J., Wang, J. P., Wang, K., Wang, L. L., Wang, M., Wang, Meng, Wang, N. Y., Wang, S., Wang, T., Wang, T. J., Wang, W., Wang, W. P., Wang, X., Wang, X. F., Wang, X. J., Wang, X. L., Wang, Y., Wang, Y. D., Wang, Y. F., Wang, Y. L., Wang, Y. N., Wang, Y. Q., Wang, Yaqian, Wang, Yi, Wang, Z., Wang, Z. L., Wang, Z. Y., Wang, Ziyi, Wei, D. H., Weidner, F., Wen, S. P., Wenzel, C., Wiedner, U., Wilkinson, G., Wolke, M., Wollenberg, L., Wu, C., Wu, J. F., Wu, L. H., Wu, L. J., Wu, X., Wu, X. H., Wu, Y., Wu, Y. H., Wu, Y. J., Wu, Z., Xia, L., Xian, X. M., Xiang, T., Xiao, D., Xiao, G. Y., Xiao, S. Y., Xiao, Y. L., Xiao, Z. J., Xie, C., Xie, X. H., Xie, Y., Xie, Y. G., Xie, Y. H., Xie, Z. P., Xing, T. Y., Xu, C. F., Xu, C. J., Xu, G. F., Xu, H. Y., Xu, M., Xu, Q. J., Xu, Q. N., Xu, W., Xu, W. L., Xu, X. P., Xu, Y. C., Xu, Z. P., Xu, Z. S., Yan, F., Yan, L., Yan, W. B., Yan, W. C., Yan, X. Q., Yang, H. J., Yang, H. L., Yang, H. X., Yang, Tao, Yang, Y., Yang, Y. F., Yang, Y. X., Yang, Yifan, Yang, Z. W., Yao, Z. P., Ye, M., Ye, M. H., Yin, J. H., You, Z. Y., Yu, B. X., Yu, C. X., Yu, G., Yu, J. S., Yu, T., Yu, X. D., Yu, Y. C., Yuan, C. Z., Yuan, L., Yuan, S. C., Yuan, Y., Yuan, Z. Y., Yue, C. X., Zafar, A. A., Zeng, F. R., Zeng, S. H., Zeng, X., Zeng, Y., Zhai, X. Y., Zhai, Y. C., Zhan, Y. H., Zhang, A. Q., Zhang, B. L., Zhang, B. X., Zhang, D. H., Zhang, G. Y., Zhang, H., Zhang, H. C., Zhang, H. H., Zhang, H. Q., Zhang, H. Y., Zhang, J., Zhang, J. J., Zhang, J. L., Zhang, J. Q., Zhang, J. W., Zhang, J. X., Zhang, J. Y., Zhang, J. Z., Zhang, Jianyu, Zhang, L. M., Zhang, Lei, Zhang, P., Zhang, Q. Y., Zhang, Shuihan, Zhang, Shulei, Zhang, X. D., Zhang, X. M., Zhang, X. Y., Zhang, Y., Zhang, Y. T., Zhang, Y. H., Zhang, Yan, Zhang, Yao, Zhang, Z. D., Zhang, Z. H., Zhang, Z. L., Zhang, Z. Y., Zhao, G., Zhao, J. Y., Zhao, J. Z., Zhao, Lei, Zhao, Ling, Zhao, M. G., Zhao, R. P., Zhao, S. J., Zhao, Y. B., Zhao, Y. X., Zhao, Z. G., Zhemchugov, A., Zheng, B., Zheng, J. P., Zheng, W. J., Zheng, Y. H., Zhong, B., Zhong, X., Zhou, H., Zhou, L. P., Zhou, S., Zhou, X., Zhou, X. K., Zhou, X. R., Zhou, X. Y., Zhou, Y. Z., Zhu, J., Zhu, K., Zhu, K. J., Zhu, L., Zhu, L. X., Zhu, S. H., Zhu, S. Q., Zhu, T. J., Zhu, Y. C., Zhu, Z. A., Zou, J. H., and Top, J. Zu

Subjects
High Energy Physics - Experiment
Abstract

Based on 7.33 fb$^{-1}$ of $e^+e^-$ collision data collected at center-of-mass energies between 4.128 and 4.226 GeV with the BESIII detector, the experimental studies of the doubly Cabibbo-suppressed decays $D^+_s\to K^+K^+\pi^-$ and $D^+_s\to K^+K^+\pi^-\pi^0$ are reported. We determine the absolute branching fraction of $D^+_s\to K^+K^+\pi^-$ to be (${1.23^{+0.28}_{-0.25}}({\rm stat})\pm0.06({\rm syst})$) $\times 10^{-4}$. No significant signal of $D^+_s\to K^+K^+\pi^-\pi^0$ is observed and the upper limit on its decay branching fraction at 90\% confidence level is set to be $1.7\times10^{-4}$., Comment: 10 pages, 4 figures, 4 tables

Published
2023
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2. Measurements of $e^+e^-\rightarrow \eta_{\rm c}\pi^+ \pi^-\pi^0$, $\eta_{\rm c}\pi^+ \pi^-$ and $\eta_{\rm c}\pi^0\gamma$ at $\sqrt{s}$ from 4.18 to 4.60\,GeV, and search for a $Z_{\rm c}$ state close to the $D\bar{D}$ threshold decaying to $\eta_{\rm c}\pi$ at $\sqrt{s}$ = 4.23 GeV

Author

BESIII Collaboration, Ablikim, M., Achasov, M. N., Adlarson, P., Ahmed, S., Albrecht, M., Aliberti, R., Amoroso, A., An, M. R., An, Q., Bai, X. H., Bai, Y., Bakina, O., Ferroli, R. Baldini, Balossino, I., Ban, Y., Begzsuren, K., Berger, N., Bertani, M., Bettoni, D., Bianchi, F., Biernat, J, Bloms, J., Bortone, A., Boyko, I., Briere, R. A., Cai, H., Cai, X., Calcaterra, A., Cao, G. F., Cao, N., Cetin, S. A., Chang, J. F., Chang, W. L., Chelkov, G., Chen, D. Y., Chen, G., Chen, H. S., Chen, M. L., Chen, S. J., Chen, X. R., Chen, Y. B., Chen, Z. J, Cheng, W. S., Cibinetto, G., Cossio, F., Cui, X. F., Dai, H. L., Dai, X. C., Dbeyssi, A., de Boer, R. E., Dedovich, D., Deng, Z. Y., Denig, A., Denysenko, I., Destefanis, M., De Mori, F., Ding, Y., Dong, C., Dong, J., Dong, L. Y., Dong, M. Y., Dong, X., Du, S. X., Fan, Y. L., Fang, J., Fang, S. S., Fang, Y., Farinelli, R., Fava, L., Feldbauer, F., Felici, G., Feng, C. Q., Fritsch, M., Fu, C. D., Gao, Y., Gao, Y. G., Garzia, I., Ge, P. T., Geng, C., Gersabeck, E. M., Gilman, A., Goetzen, K., Gong, L., Gong, W. X., Gradl, W., Greco, M., Gu, L. M., Gu, M. H., Gu, S., Gu, Y. T., Guan, C. Y, Guo, A. Q., Guo, L. B., Guo, R. P., Guo, Y. P., Guskov, A., Han, T. T., Han, W. Y., Hao, X. Q., Harris, F. A., He, K. L., Heinsius, F. H., Heinz, C. H., Held, T., Heng, Y. K., Herold, C., Himmelreich, M., Holtmann, T., Hou, Y. R., Hou, Z. L., Hu, H. M., Hu, J. F., Hu, T., Hu, Y., Huang, G. S., Huang, L. Q., Huang, X. T., Huang, Y. P., Huang, Z., Huesken, N., Hussain, T., Andersson, W. Ikegami, Imoehl, W., Irshad, M., Jaeger, S., Janchiv, S., Ji, Q., Ji, Q. P., Ji, X. B., Ji, X. L., Jiang, H. B., Jiang, X. S., Jiao, J. B., Jiao, Z., Jin, S., Jin, Y., Johansson, T., Kalantar-Nayestanaki, N., Kang, X. S., Kappert, R., Kavatsyuk, M., Ke, B. C., Keshk, I. K., Khoukaz, A., Kiese, P., Kiuchi, R., Kliemt, R., Koch, L., Kolcu, O. B., Kopf, B., Kuemmel, M., Kuessner, M., Kupsc, A., Kurth, M. G., Kühn, W., Lane, J. J., Lange, J. S., Larin, P., Lavania, A., Lavezzi, L., Lei, Z. H., Leithoff, H., Lellmann, M., Lenz, T., Li, C., Li, C. H., Li, Cheng, Li, D. M., Li, F., Li, G., Li, H., Li, H. B., Li, H. J., Li, J. L., Li, J. Q., Li, Ke, Li, L. K., Li, Lei, Li, P. R., Li, S. Y., Li, W. D., Li, W. G., Li, X. H., Li, X. L., Li, Z. Y., Liang, H., Liang, Y. F., Liang, Y. T., Liao, L. Z., Libby, J., Lin, C. X., Liu, B. J., Liu, C. X., Liu, D., Liu, F. H., Liu, Fang, Liu, Feng, Liu, H. B., Liu, H. M., Liu, Huanhuan, Liu, Huihui, Liu, J. B., Liu, J. L., Liu, J. Y., Liu, K., Liu, K. Y., Liu, Ke, Liu, L., Liu, M. H., Liu, P. L., Liu, Q., Liu, S. B., Liu, Shuai, Liu, T., Liu, W. M., Liu, X., Liu, Y., Liu, Y. B., Liu, Z. A., Liu, Z. Q., Lou, X. C., Lu, F. X., Lu, H. J., Lu, J. D., Lu, J. G., Lu, X. L., Lu, Y., Lu, Y. P., Luo, C. L., Luo, M. X., Luo, P. W., Luo, T., Luo, X. L., Lusso, S., Lyu, X. R., Ma, F. C., Ma, H. L., Ma, L. L., Ma, M. M., Ma, Q. M., Ma, R. Q., Ma, R. T., Ma, X. X., Ma, X. Y., Maas, F. E., Maggiora, M., Maldaner, S., Malde, S., Malik, Q. A., Mangoni, A., Mao, Y. J., Mao, Z. P., Marcello, S., Meng, Z. X., Messchendorp, J. G., Mezzadri, G., Min, T. J., Mitchell, R. E., Mo, X. H., Mo, Y. J., Muchnoi, N. Yu., Muramatsu, H., Nakhoul, S., Nefedov, Y., Nerling, F., Nikolaev, I. B., Ning, Z., Nisar, S., Olsen, S. L., Ouyang, Q., Pacetti, S., Pan, X., Pan, Y., Pathak, A., Patteri, P., Pelizaeus, M., Peng, H. P., Peters, K., Pettersson, J., Ping, J. L., Ping, R. G., Poling, R., Prasad, V., Qi, H., Qi, H. R., Qi, K. H., Qi, M., Qi, T. Y., Qian, S., Qian, W. -B., Qian, Z., Qiao, C. F., Qin, L. Q., Qin, X. S., Qin, Z. H., Qiu, J. F., Qu, S. Q., Rashid, K. H., Ravindran, K., Redmer, C. F., Rivetti, A., Rodin, V., Rolo, M., Rong, G., Rosner, Ch., Rump, M., Sang, H. S., Sarantsev, A., Schelhaas, Y., Schnier, C., Schoenning, K., Scodeggio, M., Shan, D. C., Shan, W., Shan, X. Y., Shangguan, J. F., Shao, M., Shen, C. P., Shen, P. X., Shen, X. Y., Shi, H. C., Shi, R. S., Shi, X., Shi, X. D, Song, W. M., Song, Y. X., Sosio, S., Spataro, S., Su, K. X., Su, P. P., Sui, F. F., Sun, G. X., Sun, H. K., Sun, J. F., Sun, L., Sun, S. S., Sun, T., Sun, W. Y., Sun, X, Sun, Y. J., Sun, Y. K., Sun, Y. Z., Sun, Z. T., Tan, Y. H., Tan, Y. X., Tang, C. J., Tang, G. Y., Tang, J., Teng, J. X., Thoren, V., Uman, I., Wang, B., Wang, C. W., Wang, D. Y., Wang, H. J., Wang, H. P., Wang, K., Wang, L. L., Wang, M., Wang, M. Z., Wang, Meng, Wang, W. H., Wang, W. P., Wang, X., Wang, X. F., Wang, X. L., Wang, Y., Wang, Y. D., Wang, Y. F., Wang, Y. Q., Wang, Y. Y., Wang, Z., Wang, Z. Y., Wang, Ziyi, Wang, Zongyuan, Wei, D. H., Weidenkaff, P., Weidner, F., Wen, S. P., White, D. J., Wiedner, U., Wilkinson, G., Wolke, M., Wollenberg, L., Wu, J. F., Wu, L. H., Wu, L. J., Wu, X., Wu, Z., Xia, L., Xiao, H., Xiao, S. Y., Xiao, Z. J., Xie, X. H., Xie, Y. G., Xie, Y. H., Xing, T. Y., Xu, G. F., Xu, Q. J., Xu, W., Xu, X. P., Yan, F., Yan, L., Yan, W. B., Yan, W. C., Yan, Xu, Yang, H. J., Yang, H. X., Yang, L., Yang, S. L., Yang, Y. X., Yang, Yifan, Yang, Zhi, Ye, M., Ye, M. H., Yin, J. H., You, Z. Y., Yu, B. X., Yu, C. X., Yu, G., Yu, J. S., Yu, T., Yuan, C. Z., Yuan, L., Yuan, X. Q., Yuan, Y., Yuan, Z. Y., Yue, C. X., Yuncu, A., Zafar, A. A., Zeng, Y., Zhang, B. X., Zhang, Guangyi, Zhang, H., Zhang, H. H., Zhang, H. Y., Zhang, J. J., Zhang, J. L., Zhang, J. Q., Zhang, J. W., Zhang, J. Y., Zhang, J. Z., Zhang, Jianyu, Zhang, Jiawei, Zhang, Lei, Zhang, S., Zhang, S. F., Zhang, Shulei, Zhang, X. D., Zhang, X. Y., Zhang, Y., Zhang, Y. H., Zhang, Y. T., Zhang, Yan, Zhang, Yao, Zhang, Yi, Zhang, Z. H., Zhang, Z. Y., Zhao, G., Zhao, J., Zhao, J. Y., Zhao, J. Z., Zhao, Lei, Zhao, Ling, Zhao, M. G., Zhao, Q., Zhao, S. J., Zhao, Y. B., Zhao, Y. X., Zhao, Z. G., Zhemchugov, A., Zheng, B., Zheng, J. P., Zheng, Y., Zheng, Y. H., Zhong, B., Zhong, C., Zhou, L. P., Zhou, Q., Zhou, X., Zhou, X. K., Zhou, X. R., Zhu, A. N., Zhu, J., Zhu, K., Zhu, K. J., Zhu, S. H., Zhu, T. J., Zhu, W. J., Zhu, X. L., Zhu, Y. C., Zhu, Z. A., Zou, B. S., and Top, J. H. Zou

Subjects
High Energy Physics - Experiment
Abstract

We study $\eta_{\rm c}$ production at center-of-mass energies $\sqrt{s}$ from 4.18 to 4.60 GeV in $e^+e^-$ annihilation data collected with the BESIII detector operating at the BEPCII storage ring, corresponding to 7.3 fb$^{-1}$ of integrated luminosity. We measure the cross sections of the three different exclusive reactions $e^+e^-\rightarrow \eta_{\rm c}\pi^+ \pi^-\pi^0$, $e^+e^- \rightarrow \eta_{\rm c}\pi^+ \pi^-$, and $e^+e^- \rightarrow \eta_{\rm c}\pi^0\gamma$. We find significant $\eta_{\rm c}$ production in $e^+e^-\rightarrow \eta_{\rm c}\pi^+ \pi^-\pi^0$ at $\sqrt{s}$ of 4.23 GeV and 4.26 GeV and observe a significant energy-dependent Born cross section that we measure to be consistent with the production via the intermediate $Y(4260)$ resonance. In addition, we perform a search for a charmonium-like $Z_{\rm c}$ state close to the $D\bar{D}$ threshold that decays to $\eta_{\rm c}\pi$, involving ground state charmonium, and observe no signal. Corresponding upper limits on the cross section of $\eta_{\rm c}$ and $Z_{\rm c}$ production are provided, where the yields are not found to be significant., Comment: 19 pages, 9 figures, accepted for publication in PRD

Published
2020
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3. Linear differential equations with finite differential Galois group

Author

van der Put, M., Malagón, C. Sanabria, and Top, J.

Subjects
Mathematics - Classical Analysis and ODEs, Mathematics - Algebraic Geometry, 34M15, 34M50
Abstract

For a differential operator $L$ of order $n$ over $C(z)$ with a finite (differential) Galois group $G\subset {\rm GL}(C^n)$, there is an algorithm, by M. van Hoeij and J.-A.~Weil, which computes the associated evaluation of the invariants $ev:C[X_1,\dots ,X_n]^G\rightarrow C(z)$. The procedure proposed here does the opposite: it uses a theorem of E.~Compoint and computes the operator $L$ from a given evaluation $h$. Moreover it solves a part of the inverse problem of producing $L$ for a given representation of a finite group $G$. Another part considered here, is finding irreducible $G$-invariant curves $Z\subset \mathbb{P}(C^n)$ with $Z/G$ of genus zero and constructing evaluations from this. The theory developed here is illustrated by various examples, and relates to and continues classical work of H.A.~Schwarz, G.~Fano, F.~Klein and A.~Hurwitz., Comment: 29 pages

Published
2018

5. Equivalence of differential equations of order one

Author

Ngo, L. X. Chau, Nguyen, K. A., van der Put, M., and Top, J.

Subjects
Mathematics - Algebraic Geometry, 34M15, 34M35, 34M55
Abstract

The notions of equivalence and strict equivalence for order one differential equations are introduced. The more explicit notion of strict equivalence is applied to examples and questions concerning autonomous equations and equations having the Painleve property. The order one equation determines an algebraic curve. If this curve has genus zero or one, then it is difficult to verify strict equivalence. However, for higher genus strict equivalence can be tested by an algorithm sketched in the text. For autonomous equations, testing strict equivalence and the existence of algebraic solutions are shown to be algorithmic., Comment: 19 pages

Published
2013

8. Comparison of Metagenomic Tools in Gut Microbiome Analysis of COVID-19 Patients

Author

Muhamad Rifki Ramadhan, Ramadhan, Top, J (Thesis Advisor), Muhamad Rifki Ramadhan, Ramadhan, and Top, J (Thesis Advisor)

Abstract

Coronavirus disease 2019 or COVID-19 is originated in Hubei province of China in late 2019. Since then, it spread worldwide and caused a worldwide pandemic through most of 2020 and 2021. Gut microbiota has a key role in human health through its protective, trophic, and metabolic actions. Alteration of gut microbiota or gut dysbiosis is found in other virus infection (e.g., hepatitis B, HIV, and influenza). This raises a possibility that COVID-19 might also influence the gut microbiota. Metagenomic analysis is a powerful method to analyze microbiome composition in an environment. In this review, five studies that used metagenomic sequencing to analyze gut microbiome composition in COVID-19 patients were compared. The methods compared include taxonomic profiling, functional annotation, and differential abundance analysis. Based on the approach and tools used, one study differs substantially from the other four studies. This study used protein to protein BLAST for taxonomic profiling, manual alignment to various databases for functional annotation, and non-parametric test of Kruskal-Wallis H and Wilcoxon rank-sum test for differential abundance. In contrast, all four other studies used the biobakery pipeline (MetaPhlAn for taxonomic profiling and HUMAnN for functional annotation) and MaAsLin for the differential abundance analysis of the microbial taxa and pathway. The dissimilarity of the methods between these studies is reflected in the results. The results from each of the four other studies share more agreements with each other even though they are quite different as well. Besides the methods and tools used, the results of these studies are affected by their experimental design (e.g., sample size, sample collections, patients’ comorbidities), and the gut microbiota itself is influenced by a lot of other factors (e.g., diet, lifestyle, and medication). It is very difficult to point out whether the differences in the results are caused by the different tools used.

Published
2022

14. Two-Descent on Some Genus Two Curves

Author

Evink, T., Heiden, G.J. van der, Top, J., Evink, T., Heiden, G.J. van der, and Top, J.

Abstract

Contains fulltext : 246711.pdf (Publisher’s version ) (Closed access)

Published
2021

15. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17)

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Research line 2, MMB Zorg, MMB Medische Staf, MS Verloskunde, Epi Infectieziekten, MMB, Verschuuren, T D, van Hout, D, Arredondo-Alonso, S, Fluit, A C, Reuland, E A, Top, J, Schürch, A C, Bosch, T, Bonten, M J M, Kluytmans, J A J W, Willems, R J L, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Research line 2, MMB Zorg, MMB Medische Staf, MS Verloskunde, Epi Infectieziekten, MMB, Verschuuren, T D, van Hout, D, Arredondo-Alonso, S, Fluit, A C, Reuland, E A, Top, J, Schürch, A C, Bosch, T, Bonten, M J M, Kluytmans, J A J W, and Willems, R J L

Published
2021

19. Mutational signature in colorectal cancer caused by genotoxic pks⁺ E. coli

Author

Pleguezuelos-Manzano, C, Puschhof, J, Rosendahl Huber, A, van Hoeck, A, Wood, HM, Nomburg, J, Gurjao, C, Manders, F, Dalmasso, G, Stege, PB, Paganelli, FL, Geurts, MH, Beumer, J, Mizutani, T, Miao, Y, van der Linden, R, van Elst, S, Genomics England Research Consortium, Garcia, KC, Top, J, Willems, RJL, Giannakis, M, Bonnet, R, Quirke, P, Meyerson, M, Cuppen, E, van Boxtel, R, and Clevers, H

Abstract

Various species of the intestinal microbiota have been associated with the development of colorectal cancer (CRC) but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin. This compound is believed to alkylate DNA on adenine residues and induces double-strand breaks in cultured cells. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in CRC. Our study describes a distinct mutational signature in CRC and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.

Published
2020

20. Measurements of $e^+e^-\rightarrow ��_{\rm c}��^+ ��^-��^0$, $��_{\rm c}��^+ ��^-$ and $��_{\rm c}��^0��$ at $\sqrt{s}$ from 4.18 to 4.60\,GeV, and search for a $Z_{\rm c}$ state close to the $D\bar{D}$ threshold decaying to $��_{\rm c}��$ at $\sqrt{s}$ = 4.23 GeV

Author

BESIII Collaboration, Ablikim, M., Achasov, M. N., Adlarson, P., Ahmed, S., Albrecht, M., Aliberti, R., Amoroso, A., An, M. R., An, Q., Bai, X. H., Bai, Y., Bakina, O., Ferroli, R. Baldini, Balossino, I., Ban, Y., Begzsuren, K., Berger, N., Bertani, M., Bettoni, D., Bianchi, F., Biernat, J, Bloms, J., Bortone, A., Boyko, I., Briere, R. A., Cai, H., Cai, X., Calcaterra, A., Cao, G. F., Cao, N., Cetin, S. A., Chang, J. F., Chang, W. L., Chelkov, G., Chen, D. Y., Chen, G., Chen, H. S., Chen, M. L., Chen, S. J., Chen, X. R., Chen, Y. B., Chen, Z. J, Cheng, W. S., Cibinetto, G., Cossio, F., Cui, X. F., Dai, H. L., Dai, X. C., Dbeyssi, A., de Boer, R. E., Dedovich, D., Deng, Z. Y., Denig, A., Denysenko, I., Destefanis, M., De Mori, F., Ding, Y., Dong, C., Dong, J., Dong, L. Y., Dong, M. Y., Dong, X., Du, S. X., Fan, Y. L., Fang, J., Fang, S. S., Fang, Y., Farinelli, R., Fava, L., Feldbauer, F., Felici, G., Feng, C. Q., Fritsch, M., Fu, C. D., Gao, Y., Gao, Y. G., Garzia, I., Ge, P. T., Geng, C., Gersabeck, E. M., Gilman, A., Goetzen, K., Gong, L., Gong, W. X., Gradl, W., Greco, M., Gu, L. M., Gu, M. H., Gu, S., Gu, Y. T., Guan, C. Y, Guo, A. Q., Guo, L. B., Guo, R. P., Guo, Y. P., Guskov, A., Han, T. T., Han, W. Y., Hao, X. Q., Harris, F. A., He, K. L., Heinsius, F. H., Heinz, C. H., Held, T., Heng, Y. K., Herold, C., Himmelreich, M., Holtmann, T., Hou, Y. R., Hou, Z. L., Hu, H. M., Hu, J. F., Hu, T., Hu, Y., Huang, G. S., Huang, L. Q., Huang, X. T., Huang, Y. P., Huang, Z., Huesken, N., Hussain, T., Andersson, W. Ikegami, Imoehl, W., Irshad, M., Jaeger, S., Janchiv, S., Ji, Q., Ji, Q. P., Ji, X. B., Ji, X. L., Jiang, H. B., Jiang, X. S., Jiao, J. B., Jiao, Z., Jin, S., Jin, Y., Johansson, T., Kalantar-Nayestanaki, N., Kang, X. S., Kappert, R., Kavatsyuk, M., Ke, B. C., Keshk, I. K., Khoukaz, A., Kiese, P., Kiuchi, R., Kliemt, R., Koch, L., Kolcu, O. B., Kopf, B., Kuemmel, M., Kuessner, M., Kupsc, A., Kurth, M. G., K��hn, W., Lane, J. J., Lange, J. S., Larin, P., Lavania, A., Lavezzi, L., Lei, Z. H., Leithoff, H., Lellmann, M., Lenz, T., Li, C., Li, C. H., Li, Cheng, Li, D. M., Li, F., Li, G., Li, H., Li, H. B., Li, H. J., Li, J. L., Li, J. Q., Li, Ke, Li, L. K., Li, Lei, Li, P. R., Li, S. Y., Li, W. D., Li, W. G., Li, X. H., Li, X. L., Li, Z. Y., Liang, H., Liang, Y. F., Liang, Y. T., Liao, L. Z., Libby, J., Lin, C. X., Liu, B. J., Liu, C. X., Liu, D., Liu, F. H., Liu, Fang, Liu, Feng, Liu, H. B., Liu, H. M., Liu, Huanhuan, Liu, Huihui, Liu, J. B., Liu, J. L., Liu, J. Y., Liu, K., Liu, K. Y., Liu, Ke, Liu, L., Liu, M. H., Liu, P. L., Liu, Q., Liu, S. B., Liu, Shuai, Liu, T., Liu, W. M., Liu, X., Liu, Y., Liu, Y. B., Liu, Z. A., Liu, Z. Q., Lou, X. C., Lu, F. X., Lu, H. J., Lu, J. D., Lu, J. G., Lu, X. L., Lu, Y., Lu, Y. P., Luo, C. L., Luo, M. X., Luo, P. W., Luo, T., Luo, X. L., Lusso, S., Lyu, X. R., Ma, F. C., Ma, H. L., Ma, L. L., Ma, M. M., Ma, Q. M., Ma, R. Q., Ma, R. T., Ma, X. X., Ma, X. Y., Maas, F. E., Maggiora, M., Maldaner, S., Malde, S., Malik, Q. A., Mangoni, A., Mao, Y. J., Mao, Z. P., Marcello, S., Meng, Z. X., Messchendorp, J. G., Mezzadri, G., Min, T. J., Mitchell, R. E., Mo, X. H., Mo, Y. J., Muchnoi, N. Yu., Muramatsu, H., Nakhoul, S., Nefedov, Y., Nerling, F., Nikolaev, I. B., Ning, Z., Nisar, S., Olsen, S. L., Ouyang, Q., Pacetti, S., Pan, X., Pan, Y., Pathak, A., Patteri, P., Pelizaeus, M., Peng, H. P., Peters, K., Pettersson, J., Ping, J. L., Ping, R. G., Poling, R., Prasad, V., Qi, H., Qi, H. R., Qi, K. H., Qi, M., Qi, T. Y., Qian, S., Qian, W. -B., Qian, Z., Qiao, C. F., Qin, L. Q., Qin, X. S., Qin, Z. H., Qiu, J. F., Qu, S. Q., Rashid, K. H., Ravindran, K., Redmer, C. F., Rivetti, A., Rodin, V., Rolo, M., Rong, G., Rosner, Ch., Rump, M., Sang, H. S., Sarantsev, A., Schelhaas, Y., Schnier, C., Schoenning, K., Scodeggio, M., Shan, D. C., Shan, W., Shan, X. Y., Shangguan, J. F., Shao, M., Shen, C. P., Shen, P. X., Shen, X. Y., Shi, H. C., Shi, R. S., Shi, X., Shi, X. D, Song, W. M., Song, Y. X., Sosio, S., Spataro, S., Su, K. X., Su, P. P., Sui, F. F., Sun, G. X., Sun, H. K., Sun, J. F., Sun, L., Sun, S. S., Sun, T., Sun, W. Y., Sun, X, Sun, Y. J., Sun, Y. K., Sun, Y. Z., Sun, Z. T., Tan, Y. H., Tan, Y. X., Tang, C. J., Tang, G. Y., Tang, J., Teng, J. X., Thoren, V., Uman, I., Wang, B., Wang, C. W., Wang, D. Y., Wang, H. J., Wang, H. P., Wang, K., Wang, L. L., Wang, M., Wang, M. Z., Wang, Meng, Wang, W. H., Wang, W. P., Wang, X., Wang, X. F., Wang, X. L., Wang, Y., Wang, Y. D., Wang, Y. F., Wang, Y. Q., Wang, Y. Y., Wang, Z., Wang, Z. Y., Wang, Ziyi, Wang, Zongyuan, Wei, D. H., Weidenkaff, P., Weidner, F., Wen, S. P., White, D. J., Wiedner, U., Wilkinson, G., Wolke, M., Wollenberg, L., Wu, J. F., Wu, L. H., Wu, L. J., Wu, X., Wu, Z., Xia, L., Xiao, H., Xiao, S. Y., Xiao, Z. J., Xie, X. H., Xie, Y. G., Xie, Y. H., Xing, T. Y., Xu, G. F., Xu, Q. J., Xu, W., Xu, X. P., Yan, F., Yan, L., Yan, W. B., Yan, W. C., Yan, Xu, Yang, H. J., Yang, H. X., Yang, L., Yang, S. L., Yang, Y. X., Yang, Yifan, Yang, Zhi, Ye, M., Ye, M. H., Yin, J. H., You, Z. Y., Yu, B. X., Yu, C. X., Yu, G., Yu, J. S., Yu, T., Yuan, C. Z., Yuan, L., Yuan, X. Q., Yuan, Y., Yuan, Z. Y., Yue, C. X., Yuncu, A., Zafar, A. A., Zeng, Y., Zhang, B. X., Zhang, Guangyi, Zhang, H., Zhang, H. H., Zhang, H. Y., Zhang, J. J., Zhang, J. L., Zhang, J. Q., Zhang, J. W., Zhang, J. Y., Zhang, J. Z., Zhang, Jianyu, Zhang, Jiawei, Zhang, Lei, Zhang, S., Zhang, S. F., Zhang, Shulei, Zhang, X. D., Zhang, X. Y., Zhang, Y., Zhang, Y. H., Zhang, Y. T., Zhang, Yan, Zhang, Yao, Zhang, Yi, Zhang, Z. H., Zhang, Z. Y., Zhao, G., Zhao, J., Zhao, J. Y., Zhao, J. Z., Zhao, Lei, Zhao, Ling, Zhao, M. G., Zhao, Q., Zhao, S. J., Zhao, Y. B., Zhao, Y. X., Zhao, Z. G., Zhemchugov, A., Zheng, B., Zheng, J. P., Zheng, Y., Zheng, Y. H., Zhong, B., Zhong, C., Zhou, L. P., Zhou, Q., Zhou, X., Zhou, X. K., Zhou, X. R., Zhu, A. N., Zhu, J., Zhu, K., Zhu, K. J., Zhu, S. H., Zhu, T. J., Zhu, W. J., Zhu, X. L., Zhu, Y. C., Zhu, Z. A., Zou, B. S., and Top, J. H. Zou

Subjects
High Energy Physics - Experiment (hep-ex), FOS: Physical sciences, High Energy Physics::Experiment
Abstract

We study $��_{\rm c}$ production at center-of-mass energies $\sqrt{s}$ from 4.18 to 4.60 GeV in $e^+e^-$ annihilation data collected with the BESIII detector operating at the BEPCII storage ring, corresponding to 7.3 fb$^{-1}$ of integrated luminosity. We measure the cross sections of the three different exclusive reactions $e^+e^-\rightarrow ��_{\rm c}��^+ ��^-��^0$, $e^+e^- \rightarrow ��_{\rm c}��^+ ��^-$, and $e^+e^- \rightarrow ��_{\rm c}��^0��$. We find significant $��_{\rm c}$ production in $e^+e^-\rightarrow ��_{\rm c}��^+ ��^-��^0$ at $\sqrt{s}$ of 4.23 GeV and 4.26 GeV and observe a significant energy-dependent Born cross section that we measure to be consistent with the production via the intermediate $Y(4260)$ resonance. In addition, we perform a search for a charmonium-like $Z_{\rm c}$ state close to the $D\bar{D}$ threshold that decays to $��_{\rm c}��$, involving ground state charmonium, and observe no signal. Corresponding upper limits on the cross section of $��_{\rm c}$ and $Z_{\rm c}$ production are provided, where the yields are not found to be significant., 19 pages, 9 figures, accepted for publication in PRD

Published
2020
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23. Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium

Author

Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R.C., van Schaik, W., Kaski, S., Willems, R. J.L., Corander, J., Schürch, A. C., Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R.C., van Schaik, W., Kaski, S., Willems, R. J.L., Corander, J., and Schürch, A. C.

Published
2020

24. Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium

Author

MMB Research line 2, Infection & Immunity, MMB Kweek en Resistentie A, MMB, Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R.C., van Schaik, W., Kaski, S., Willems, R. J.L., Corander, J., Schürch, A. C., MMB Research line 2, Infection & Immunity, MMB Kweek en Resistentie A, MMB, Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J. C., Rogers, M. R.C., van Schaik, W., Kaski, S., Willems, R. J.L., Corander, J., and Schürch, A. C.

Published
2020

25. KB DDHT project 8: Non-destructive and non-invasive sensor technologies in food supply chains : project deliverables 1.1-1.4

Author

Bouzembrak, Y., Chauhan, A., Daniels, F., Gavai, A., Gonzalez Rojas, J., Kamphuis, C., Marvin, H., Meesters, L., Mishra, P., Mueller-Maatsch, J., Ouweltjes, W., Paillert, M., Petie, R., Petropoulou, A., Plantenga, F., Rijgersberg, H., Top, J., Tsafaras, I., Ummels, M., van Breukelen, A., Weesepoel, Y., Bouzembrak, Y., Chauhan, A., Daniels, F., Gavai, A., Gonzalez Rojas, J., Kamphuis, C., Marvin, H., Meesters, L., Mishra, P., Mueller-Maatsch, J., Ouweltjes, W., Paillert, M., Petie, R., Petropoulou, A., Plantenga, F., Rijgersberg, H., Top, J., Tsafaras, I., Ummels, M., van Breukelen, A., and Weesepoel, Y.

Abstract

This report details the activities carried out in 2019 in the KB DDHT project 8 “Exploring the potential of non-destructive and non-invasive sensor technologies in food supply chains”. It compiles all four deliverables of this project as a single narrative. There are five case studies at the core of this project which address animal welfare, indoor farming, inspection of fresh food products, personalized nutrition advise and food fraud detection. Multiple activities were planned in these case studies with main focus on sensor technologies for non-destructive and non-invasive sensing. One of the key activities was to conduct a survey of sensor technologies applicable and potentially suitable for each case study. In addition, for each case study, one or more experiments were conducted which involved data acquisition using novel sensors as well as building knowledge on data analysis of data from the new sensors. Furthermore, as one of the goal of this project is to explore new sensor technologies, it is expected that this project will generate valuable data. Therefore, focus was also on FAIR data sharing and management. A workshop was organized in collaboration with WDCC on this topic. Most of the case studies also aligned with OnePlanet Research centre, and as a result multiple experiments are in planning for 2020 in cooperation with OnePlanet.

Published
2020

26. Comparative genomics of ESBL-producingEscherichia coli(ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014–17)

Author

Verschuuren, T D, primary, van Hout, D, additional, Arredondo-Alonso, S, additional, Fluit, A C, additional, Reuland, E A, additional, Top, J, additional, Schürch, A C, additional, Bosch, T, additional, Bonten, M J M, additional, Kluytmans, J A J W, additional, and Willems, R J L, additional

Published
2021
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27. Unnoticed spread of integron-carrying enterobacteriaceae in intensive care units

Author

Nijssen, S., Florijn, A., Top, J., Willems, R., Fluit, A., and Bonten, M.

Subjects
Nucleotide sequencing -- Research, Intensive care units -- Management, Enterobacteriaceae -- Genetic aspects, Enterobacteriaceae -- Research, Enterobacter -- Genetic aspects, Enterobacter -- Research, Company business management, Health, Health care industry
Published
2005

31. Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

Author

Arredondo-Alonso, S., primary, Top, J., additional, McNally, A., additional, Puranen, S., additional, Pesonen, M., additional, Pensar, J., additional, Marttinen, P., additional, Braat, J. C., additional, Rogers, M. R. C., additional, van Schaik, W., additional, Kaski, S., additional, Willems, R. J. L., additional, Corander, J., additional, and Schürch, A. C., additional

Published
2020
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39. PBP profiles of ampicillin-resistant Enterococcus raffinosus

Author

Barone, Me, Ayala, J, Leon-Sampedro, Rl, Tedim, A, Novais, C., Freitas, A, Peixe, L, Loens, K, Cattoir, V, Goossens, H, Sadowy, E., Top, J, Willems, Rj, Campanile, F, Stefani, S, Cantón, R, Baquero, F, and Coque, Tm.

Published
2018

41. Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

Author

Arredondo-Alonso, S, primary, Top, J, additional, Schürch, AC, additional, McNally, A, additional, Puranen, S, additional, Pesonen, M, additional, Pensar, J, additional, Marttinen, P, additional, Braat, JC, additional, Rogers, MRC, additional, van Schaik, W, additional, Kaski, S, additional, Corander, J, additional, and Willems, RJL, additional

Published
2019
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43. Intestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Research line 1, Epi Infectieziekten, Van den Bunt, G., Top, J., Hordijk, J., De Greeff, S. C., Mughini-Gras, L., Corander, J., van Pelt, W., Bonten, M. J.M., Fluit, A. C., Willems, R. J.L., Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Research line 1, Epi Infectieziekten, Van den Bunt, G., Top, J., Hordijk, J., De Greeff, S. C., Mughini-Gras, L., Corander, J., van Pelt, W., Bonten, M. J.M., Fluit, A. C., and Willems, R. J.L.

Published
2018

44. Isogenies for Point Counting on Genus Two Hyperelliptic Curves with Maximal Real Multiplication

Author

Ballentine, S., Guillevic, A., Lorenzo-Garcia, E., Martindale, C.R., Maisserer, M., Smith, B., Top, J., Howe, E.W., Lauter, K.E., Walker, J.L., Department of Mathematics [College Park], University of Maryland [College Park], University of Maryland System-University of Maryland System, University of Calgary, Pacific Institute for the Mathematical Sciences (PIMS), University of Calgary-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universiteit Leiden, Lithe and fast algorithmic number theory (LFANT), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), University of New South Wales [Sydney] (UNSW), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Geometry, arithmetic, algorithms, codes and encryption (GRACE), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Bernoulli Institute for Mathematics and Computer Science and Artificial Intelligence, University of Groningen [Groningen], Institute for Pure and Applied Mathematics (IPAM), University of California, Los Angeles (UCLA), E. W. Howe, K. E. Lauter, J. L. Walker, ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), Department of Mathematics, University of Maryland, Pacific Institute for the Mathematical Sciences ( PIMS ), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Universiteit Leiden [Leiden], University of New South Wales [Sydney] ( UNSW ), Laboratoire d'informatique de l'École polytechnique [Palaiseau] ( LIX ), Centre National de la Recherche Scientifique ( CNRS ) -École polytechnique ( X ), Geometry, arithmetic, algorithms, codes and encryption ( GRACE ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ), Johann Bernoulli Institute for Mathematics and Computer Science ( JBI ), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Inria Saclay - Ile de France, Discrete Mathematics, Coding Theory and Cryptology, and Algebra

Subjects
FOS: Computer and information sciences, Computer Science - Cryptography and Security, Mathematics::Number Theory, [ INFO.INFO-CR ] Computer Science [cs]/Cryptography and Security [cs.CR], 010103 numerical & computational mathematics, 01 natural sciences, [ MATH.MATH-NT ] Mathematics [math]/Number Theory [math.NT], [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], cs.CR, Mathematics::Algebraic Geometry, FOS: Mathematics, Number Theory (math.NT), 0101 mathematics, Mathematics, Discrete mathematics, Mathematics - Number Theory, [MATH.MATH-NT]Mathematics [math]/Number Theory [math.NT], 010101 applied mathematics, Schoof–Elkies–Atkin algorithm, math.NT, Elliptic curve, Finite field, Discriminant, Counting points on elliptic curves, Multiplication, Schoof's algorithm, Cryptography and Security (cs.CR), Division polynomials
Abstract

Schoof's classic algorithm allows point-counting for elliptic curves over finite fields in polynomial time. This algorithm was subsequently improved by Atkin, using factorizations of modular polynomials, and by Elkies, using a theory of explicit isogenies. Moving to Jacobians of genus-2 curves, the current state of the art for point counting is a generalization of Schoof's algorithm. While we are currently missing the tools we need to generalize Elkies' methods to genus 2, recently Martindale and Milio have computed analogues of modular polynomials for genus-2 curves whose Jacobians have real multiplication by maximal orders of small discriminant. In this article, we prove Atkin-style results for genus-2 Jacobians with real multiplication by maximal orders, with a view to using these new modular polynomials to improve the practicality of point-counting algorithms for these curves., Comment: 31 pages

Published
2017

46. Inspiratiedag Global Food 2017

Author

Top, J., Praasterink, F., Kouwenhoven, G., Jong, J. de, Hedel, P., Top, J., Praasterink, F., Kouwenhoven, G., Jong, J. de, and Hedel, P.

Abstract

Op maandag 15 mei 2017 organiseerde het OnderwijsVernieuwingsProgramma (OVP) Voedsel & Consument, in samenwerking met het Centrum voor Innovatief Vakmanschap Agri & Food (CIV) en het Centre of Expertise Food (CoE), de Inspiratiedag Global Food. Op de inspiratiedag ontmoeten Onderwijs, Onderzoek, Ondernemers, Overheid en hun Omgeving elkaar. Met innovatieve thema's en veel interactie, zijn er weer nieuwe ingrediënten voor inspiratie in het onderwijs geboden. Verandering van het voedselsysteem is noodzakelijk, omdat door toename van de wereldbevolking de vraag naar eten stijgt. De opgave is, om een hoogwaardig efficiënt voedselsysteem te ontwerpen, dat voldoende eten oplevert en in balans is met de draagkracht van de aarde. De overheid heeft met de voedselagenda duidelijk ingezet op duurzaamheid, vertaald in de ambitie dat “Nederland over 5 tot 10 jaar wereldwijd de onbetwiste koploper moet zijn in gezonde en duurzame voeding”. Deze ambitie geeft in belangrijke mate richting aan R&D van onderzoek en bedrijfsleven. De inspiratiedag bood je de mogelijkheid om de impact hiervan, in de vorm van uitdagingen en mogelijkheden, op je onderwijs te verkennen. Dus hoe kan het onderwijs inhaken op het wereldvoedselvraagstuk en de nationale en internationale ontwikkelingen op dit terrein? Hier vind je de presentaties van de Global Food Inspiration day 2017

Published
2017

47. Molecular analysis of human, porcine, and poultry Enterococcus faecium isolates and their erm(B) genes

Author

Leener, E. De, Martel, A., Graef, E.M. De, Top, J., Butaye, P., Decostere, A., Haesebrouck, F., and Willems, R.

Subjects
Genetic code -- Observations, Enterococcal infections -- Research, Conformational analysis, Biological sciences
Abstract

Fifty-nine erm(B)-positive Enterococcus faecium strains isolated from pigs, broilers, and humans were typed using multilocus sequence typing (MLST). The coding sequence of the erm(B) gene is determined and identical erm(B) gene sequences are detected in genetically unrelated isolates.

Published
2005

48. Conceptual Quantum Chemistry Analysis of bonding and noncovalent interactions in the formation of frustrated Lewis Pairs

Author

Gabriella Skara, Balasz Pintér, Top, J., Paul Geerlings, Frank De Proft, Freija De Vleeschouwer, General Chemistry, and Chemistry

Subjects
Conceptual Quantum Chemistry
Abstract

The contributions of covalent and noncovalent interactions to the formation of classical adducts of bulky Lewis acids and bases and frustrated Lewis pairs (FLPs) were scrutinized by using various conceptual quantum chemical techniques. Significantly negative complexation energies were calculated for fourteen investigated Lewis pairs containing bases and acids with substituents of various sizes. A Ziegler–Rauk-type energy decomposition analysis confirmed that two types of Lewis pairs can be distinguished on the basis of the nature of the primary interactions between reactants; dative-bond formation and concomitant charge transfer from the Lewis base to the acid is the dominant and most stabilizing factor in the formation of Lewis acid–base adducts, whereas weak interactions are the main thermodynamic driving force (>50 %) for FLPs. Moreover, the ease and extent of structural deformation of the monomers appears to be a key component in the formation of the former type of Lewis pairs. A Natural Orbital for Chemical Valence (NOCV) analysis, which was used to visualize and quantify the charge transfer between the base and the acid, clearly showed the importance and lack of this type of interaction for adducts and FLPs, respectively. The Noncovalent Interaction (NCI) method revealed several kinds of weak interactions between the acid and base components, such as dispersion, π–π stacking, C[BOND]H⋅⋅⋅π interaction, weak hydrogen bonding, halogen bonding, and weak acid–base interactions, whereas the Quantum Theory of Atoms in Molecules (QTAIM) provided further conceptual insight into strong acid–base interactions.

Published
2015

49. Expression of p53, Ki67, EcPV2- and EcPV3 DNA, and viral genes in relation to metastasis and outcome in equine penile and preputial squamous cell carcinoma

Author

van den Top, J G B, Harkema, L, Lange, C, Ensink, J M, van de Lest, C H A, Barneveld, A, van Weeren, P R, Gröne, A, Martens, A, ES AVM, ES TR, LS Pathobiologie, LS Heelkunde, LS Equine Muscoskeletal Biology, LS Veterinaire biochemie, Dep Gezondheidszorg Paard, LS Pathologie, dPB CR, dPB I&I, dES AVR, dES RMSC, and dB&C FR-RMSC FR

Subjects
squamous cell carcinoma, p53, penis, immunohistochemistry, grading, Ki67, EcPV2, EcPV3, horse
Abstract

REASONS FOR PERFORMING STUDY: Equine penile and preputial squamous cell carcinoma (SCC) is a potentially lethal disease of which little is known regarding the relationship between tumour characteristics and prognosis. OBJECTIVES: To assess the relationship between tumour differentiation grade (tumour subtype), presence of papillomaviruses, expression of viral genes (E2, E6, L1), nuclear proteins p53 and Ki67 and metastasis in equine penile and preputial SCC and to assess the relationship of tumour subtype, presence of papillomavirus type 2, p53 and Ki67 with survival. STUDY DESIGN: Retrospective case-control study using archived material. METHODS: Samples (n = 103) from 87 horses with penile and/or preputial intraepithelial neoplasia (PIN), papilloma or SCC and corresponding case files were evaluated. Tumours were graded microscopically and p53 and Ki67 expression evaluated immunohistochemically. Equine papillomavirus (EcPV) types 2 and 3 DNA was detected by conventional PCR. Real-time PCR was used for quantification of E2, E6 and L1 mRNA. RESULTS: Equine papillomavirus type 2 DNA was detected in 89.4% and EcPV3 in 1.5% of horses. No differences in quantitative expression of E2, E6 and L1 oncogenes between subtypes were found. Expression of p53 and occurrence of metastasis were positively correlated to a less differentiated subtype (r = 0.429, P

Published
2015

50. Global Spread of Vancomycin-resistant Enterococcus faecium from Distinct Nosocomial Genetic Complex

Author

Rob Willems, Top, J., Santen, M., Robinson, D. A., Coque, T. M., Baquero, F., Grundmann, H., and Bonten, M. J.

Subjects
VRE, vancomycin-resistance, Penicillin Resistance, Enterococcus faecium, lcsh:Medicine, Population structure, lcsh:Infectious and parasitic diseases, Evolution, Molecular, Dogs, Bacterial Proteins, Animals, Humans, lcsh:RC109-216, Gram-Positive Bacterial Infections, Recombination, Genetic, Cross Infection, Research, lcsh:R, Genetic evolution, Australia, Vancomycin Resistance, biochemical phenomena, metabolism, and nutrition, South America, Europe, Africa, North America, Cats, Cattle, Keywords: molecular epidemiology, Multilocus Sequence Typing
Abstract

Vancomycin-resistant enterococci (VRE) have caused hospital outbreaks worldwide, and the vancomycin-resistance gene (vanA) has crossed genus boundaries to methicillin-resistant Staphylococcus aureus. Spread of VRE, therefore, represents an immediate threat for patient care and creates a reservoir of mobile resistance genes for other, more virulent pathogens. Evolutionary genetics, population structure, and geographic distribution of 411 VRE and vancomycin-susceptible Enterococcus faecium isolates, recovered from human and nonhuman sources and community and hospital reservoirs in 5 continents, identified a genetic lineage of E. faecium (complex-17) that has spread globally. This lineage is characterized by 1) ampicillin resistance, 2) a pathogenicity island, and 3) an association with hospital outbreaks. Complex-17 is an example of cumulative evolutionary processes that improved the relative fitness of bacteria in hospital environments. Preventing further spread of this epidemic E. faecium subpopulation is critical, and efforts should focus on the early disclosure of ampicillin-resistant complex-17 strains.

Published
2005

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