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1. Neoantigen-specific cytotoxic Tr1 CD4 T cells suppress cancer immunotherapy

Author

Sultan, Hussein, Takeuchi, Yoshiko, Ward, Jeffrey P., Sharma, Naveen, Liu, Tian-Tian, Sukhov, Vladimir, Firulyova, Maria, Song, Yuang, Ameh, Samuel, Brioschi, Simone, Khantakova, Darya, Arthur, Cora D., White, J. Michael, Kohlmiller, Heather, Salazar, Andres M., Burns, Robert, Costa, Helio A., Moynihan, Kelly D., Yeung, Yik Andy, Djuretic, Ivana, Schumacher, Ton N., Sheehan, Kathleen C. F., Colonna, Marco, Allison, James P., Murphy, Kenneth M., Artyomov, Maxim N., and Schreiber, Robert D.

Published
2024
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3. Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial

Author

Verschoor, Yara L., van de Haar, Joris, van den Berg, José G., van Sandick, Johanna W., Kodach, Liudmila L., van Dieren, Jolanda M., Balduzzi, Sara, Grootscholten, Cecile, IJsselsteijn, Marieke E., Veenhof, Alexander A. F. A., Hartemink, Koen J., Vollebergh, Marieke A., Jurdi, Adham, Sharma, Shruti, Spickard, Erik, Owers, Emilia C., Bartels-Rutten, Annemarieke, den Hartog, Peggy, de Miranda, Noel F. C. C., van Leerdam, Monique E., Haanen, John B. A. G., Schumacher, Ton N., Voest, Emile E., and Chalabi, Myriam

Published
2024
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4. Determination of the titanium spectral function from (e,e'p) data

Author

Jiang, L., Ankowski, A. M., Abrams, D., Gu, L., Aljawrneh, B., Alsalmi, S., Bane, J., Batz, A., Barcus, S., Barroso, M., Bellini, V., Benhar, O., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Dai, H., Day, D., Dirican, A., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T. J., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Jerzyk, Z., Johnson, A. M., Keppel, C., Lanham, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Murphy, M., Nguyen, D., Nycz, M., Ou, L., Pandey, B., Pandey, V., Park, K., Perera, G., Puckett, A. J. R., Santiesteban, S. N., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
Nuclear Experiment, High Energy Physics - Experiment, Nuclear Theory
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has measured the (e,e'p) cross section in parallel kinematics using a natural titanium target. Here, we report the full results of the analysis of the data set corresponding to beam energy 2.2 GeV, and spanning the missing momentum and missing energy range 15 <= pm <= 250 MeV/c and 12 <= Em <= 80 MeV. The reduced cross section has been measured with ~7% accuracy as function of both missing momentum and missing energy. We compared our data to the results of a Monte Carlo simulations performed using a model spectral function and including the effects of final state interactions. The overall agreement between data and simulations is quite good (chi2/d.o.f. = 0.9)., Comment: 6 pages, 4 figures, published in Phys. Rev. D. arXiv admin note: substantial text overlap with arXiv:2203.01748

Published
2022
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5. Determination of the titanium spectral function from (e, e′p) data

Author

Jiang, L, Ankowski, AM, Abrams, D, Gu, L, Aljawrneh, B, Alsalmi, S, Bane, J, Batz, A, Barcus, S, Barroso, M, Bellini, V, Benhar, O, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Dai, H, Day, D, Dirican, A, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, TJ, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Jerzyk, Z, Johnson, AM, Keppel, C, Lanham, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Murphy, M, Nguyen, D, Nycz, M, Ou, L, Pandey, B, Pandey, V, Park, K, Perera, G, Puckett, AJR, Santiesteban, SN, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has measured the (e,e′p) cross section in parallel kinematics using a natural titanium target. In this paper, we report the analysis of the dataset obtained in different kinematics for our solid natural titanium target. Data were obtained in a range of missing momentum and missing energy between 15?pm?250 MeV/c and 12?Em?80 MeV, respectively, and using an electron beam energy of 2.2 GeV. We measured the reduced cross section with ∼7% accuracy as a function of both missing momentum and missing energy. Our Monte Carlo simulation, including both a model spectral function and the effects of final-state interactions, satisfactorily reproduces the data.

Published
2023

7. Determination of the argon spectral function from (e,e'p) data

Author

Jiang, L., Ankowski, A. M., Abrams, D., Gu, L., Aljawrneh, B., Alsalmi, S., Bane, J., Batz, A., Barcus, S., Barroso, M., Bellini, V., Benhar, O., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Dai, H., Day, D., Dirican, A., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T. J., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Jerzyk, Z., Keppel, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Murphy, M., Nguyen, D., Nycz, M., Ou, L., Pandey, B., Pandey, V., Park, K., Perera, G., Puckett, A. J. R., Santiesteban, S. N., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
Nuclear Experiment, High Energy Physics - Experiment
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has measured the $(e, e'p)$ cross section in parallel kinematics using a natural argon target. Here, we report the full results of the analysis of the data set corresponding to beam energy 2.222 GeV, and spanning the missing momentum and missing energy range $15 \lesssim p_m \lesssim 300$ MeV/c and $12 \lesssim E_m \lesssim 80$ MeV. The reduced cross section, determined as a function of $p_m$ and $E_m$ with $\approx$4\% accuracy, has been fitted using the results of Monte Carlo simulations involving a model spectral function and including the effects of final state interactions. The overall agreement between data and simulations turns out to be quite satisfactory ($\chi^2$/n.d.o.f.=1.9). The resulting spectral function will provide valuable new information, needed for the interpretation of neutrino interactions in liquid argon detectors., Comment: Published version

Published
2022
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8. Author Correction: Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial

Author

Verschoor, Yara L., van de Haar, Joris, van den Berg, José G., van Sandick, Johanna W., Kodach, Liudmila L., van Dieren, Jolanda M., Balduzzi, Sara, Grootscholten, Cecile, IJsselsteijn, Marieke E., Veenhof, Alexander A. F. A., Hartemink, Koen J., Vollebergh, Marieke A., Jurdi, Adham, Sharma, Shruti, Spickard, Erik, Owers, Emilia C., Bartels-Rutten, Annemarieke, den Hartog, Peggy, de Miranda, Noel F. C. C., van Leerdam, Monique E., Haanen, John B. A. G., Schumacher, Ton N., Voest, Emile E., and Chalabi, Myriam

Published
2024
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9. Deeply virtual Compton scattering cross section at high Bjorken $x_B$

Author

Georges, F., Rashad, M. N. H., Stefanko, A., Dlamini, M., Karki, B., Ali, S. F., Lin, P-J., Ko, H-S, Israel, N., Adikaram, D., Ahmed, Z., Albataineh, H., Aljawrneh, B., Allada, K., Allison, S., Alsalmi, S., Androic, D., Aniol, K., Annand, J., Atac, H., Averett, T., Gayoso, C. Ayerbe, Bai, X., Bane, J., Barcus, S., Bartlett, K., Bellini, V., Beminiwattha, R., Bericic, J., Biswas, D., Brash, E., Bulumulla, D., Campbell, J., Camsonne, A., Carmignotto, M., Castellano, J., Chen, C., Chen, J-P., Chetry, T., Christy, M. E., Cisbani, E., Clary, B., Cohen, E., Compton, N., Cornejo, J. C., Dusa, S. Covrig, Crowe, B., Danagoulian, S., Danley, T., De Persio, F., Deconinck, W., Defurne, M., Desnault, C., Di, D., Duer, M., Duran, B., Ent, R., Fanelli, C., Franklin, G., Fuchey, E., Gal, C., Gaskell, D., Gautam, T., Glamazdin, O., Gnanvo, K., Gray, V. M., Gu, C., Hague, T., Hamad, G., Hamilton, D., Hamilton, K., Hansen, O., Hauenstein, F., Henry, W., Higinbotham, D. W., Holmstrom, T., Horn, T., Huang, Y., Huber, G. M., Hyde, C., Ibrahim, H., Jen, C-M., Jin, K., Jones, M., Kabir, A., Keppel, C., Khachatryan, V., King, P. M., Li, S., Li, W. B., Liu, J., Liu, H., Liyanage, A., Magee, J., Malace, S., Mammei, J., Markowitz, P., McClellan, E., Mazouz, M., Meddi, F., Meekins, D., Mesik, K., Michaels, R., Mkrtchyan, A., Montgomery, R., Camacho, C. Muñoz, Myers, L. S., Nadel-Turonski, P., Nazeer, S. J., Nelyubin, V., Nguyen, D., Nuruzzaman, N., Nycz, M., Obretch, O. F., Ou, L., Palatchi, C., Pandey, B., Park, S., Park, K., Peng, C., Pomatsalyuk, R., Pooser, E., Puckett, A. J. R., Punjabi, V., Quinn, B., Rahman, S., Reimer, P. E., Roche, J., Sapkota, I., Sarty, A., Sawatzky, B., Saylor, N. H., Schmookler, B., Shabestari, M. H., Shahinyan, A., Sirca, S., Smith, G. R., Sooriyaarachchilage, S., Sparveris, N., Spies, R., Su, T., Subedi, A., Sulkosky, V., Sun, A., Thorne, L., Tian, Y., Ton, N., Tortorici, F., Trotta, R., Urciuoli, G. M., Voutier, E., Waidyawansa, B., Wang, Y., Wojtsekhowski, B., Wood, S., Yan, X., Ye, L., Ye, Z., Yero, C., Zhang, J., Zhao, Y., and Zhu, P.

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment, Nuclear Experiment
Abstract

We report high-precision measurements of the Deeply Virtual Compton Scattering (DVCS) cross section at high values of the Bjorken variable $x_B$. DVCS is sensitive to the Generalized Parton Distributions of the nucleon, which provide a three-dimensional description of its internal constituents. Using the exact analytic expression of the DVCS cross section for all possible polarization states of the initial and final electron and nucleon, and final state photon, we present the first experimental extraction of all four helicity-conserving Compton Form Factors (CFFs) of the nucleon as a function of $x_B$, while systematically including helicity flip amplitudes. In particular, the high accuracy of the present data demonstrates sensitivity to some very poorly known CFFs.

Published
2022
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10. Determination of the argon spectral function from (e,e′p) data

Author

Jiang, L, Ankowski, AM, Abrams, D, Gu, L, Aljawrneh, B, Alsalmi, S, Bane, J, Batz, A, Barcus, S, Barroso, M, Bellini, V, Benhar, O, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Dai, H, Day, D, Dirican, A, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, TJ, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Jerzyk, Z, Keppel, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Murphy, M, Nguyen, D, Nycz, M, Ou, L, Pandey, B, Pandey, V, Park, K, Perera, G, Puckett, AJR, Santiesteban, SN, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has measured the (e,e′p) cross section in parallel kinematics using a natural argon target. Here, we report the full results of the analysis of the data set corresponding to beam energy 2.222 GeV, and spanning the missing momentum and missing energy range 1 pm 300 MeV/c and 12 Em 80 MeV. The reduced cross section, determined as a function of pm and Em with ≈4% accuracy, has been fitted using the results of Monte Carlo simulations involving a model spectral function and including the effects of final state interactions. The overall agreement between data and simulations turns out to be quite satisfactory (χ2/d.o.f.=1.9). The resulting spectral function will provide valuable new information, needed for the interpretation of neutrino interactions in liquid argon detectors.

Published
2022

11. Investigation of the ground-state spin inversion in the neutron-rich 47,49Cl isotopes

Author

Linh, B. D., Corsi, A., Gillibert, A., Obertelli, A., Doornenbal, P., Barbieri, C., Chen, S., Chung, L. X., Duguet, T., Gómez-Ramos, M., Holt, J. D., Moro, A., Navrátil, P., Ogata, K., Phuc, N. T. T., Shimizu, N., Somà, V., Utsuno, Y., Achouri, N. L., Baba, H., Browne, F., Calvet, D., Château, F., Chiga, N., Cortés, M. L., Delbart, A., Gheller, J. -M., Giganon, A., Hilaire, C., Isobe, T., Kobayashi, T., Kubota, Y., Lapoux, V., Liu, H. N., Motobayashi, T., Murray, I., Otsu, H., Panin, V., Paul, N., Rodriguez, W., Sakurai, H., Sasano, M., Steppenbeck, D., Stuhl, L., Sun, Y. L., Togano, Y., Uesaka, T., Wimmer, K., Yoneda, K., Aktas, O., Aumann, T., Flavigny, F., Franchoo, S., Gašparić, I., Gerst, R. -B., Gibelin, J., Hahn, K. I., Khai, N. T., Kim, D., Koiwai, T., Kondo, Y., Koseoglou, P., Lee, J., Lehr, C., Lokotko, T., MacCormick, M., Moschner, K., Nakamura, T., Park, S. Y., Rossi, D., Sahin, E., Sohler, D., Söderström, P. -A., Takeuchi, S., Ton, N. D., Törnqvist, H., Vaquero, V., Wagner, V., Wang, H., Werner, V., Xu, X., Yamada, Y., Yan, D., Yang, Z., Yasuda, M., and Zanetti, L.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

A first gamma-ray study of 47,49Cl spectroscopy was performed at the Radioactive Isotope Beam Factory with 50Ar projectiles at 217 MeV/nucleon, impinging on the liquid hydrogen target of the MINOS device. Prompt de-excitation gamma-rays were measured with the NaI(Tl) array DALI2+. Through the one-proton knockout reaction 50Ar(p,2p), a spin assignment could be determined for the low-lying states of 49Cl from the momentum distribution obtained with the SAMURAI spectrometer. A spin-parity J = 3/2+ is deduced for the ground state of 49Cl, similar to the recently studied N = 32 isotope 51K.

Published
2021
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16. Measurement of the generalized spin polarizabilities of the neutron in the low $Q^2$ region

Author

Sulkosky, V., Peng, C., Chen, J. -P., Deur, A., Abrahamyan, S., Aniol, K. A., Armstrong, D. S., Averett, T., Bailey, S. L., Beck, A., Bertin, P., Butaru, F., Boeglin, W., Camsonne, A., Cates, G. D., Chang, C. C., Choi, Seonho, Chudakov, E., Coman, L., Cornejo, J. C, Craver, B., Cusanno, F., De Leo, R., de Jager, C. W., Denton, J. D., Dhamija, S., Feuerbach, R., Finn, J. M., Frullani, S., Fuoti, K., Gao, H., Garibaldi, F., Gayou, O., Gilman, R., Glamazdin, A., Glashausser, C., Gomez, J., Hansen, J. -O., Hayes, D., Hersman, B., Higinbotham, D. W., Holmstrom, T., Humensky, T. B., Hyde, C. E., Ibrahim, H., Iodice, M., Jiang, X., Kaufman, L. J., Kelleher, A., Keister, K. E., Kim, W., Kolarkar, A., Kolb, N., Korsch, W., Kramer, K., Kumbartzki, G., Lagamba, L., Laine, V., Laveissiere, G., Lerose, J. J., Lhuillier, D., Lindgren, R., Liyanage, N., Lu, H. -J., Ma, B., Margaziotis, D. J., Markowitz, P., McCormick, K., Meziane, M., Meziani, Z. -E., Michaels, R., Moffit, B., Monaghan, P., Nanda, S., Niedziela, J., Niskin, M., Pandolfi, R., Paschke, K. D., Potokar, M., Puckett, A., Punjabi, V. A., Qiang, Y., Ransome, R., Reitz, B., Roche, R., Saha, A., Shabetai, A., Sirca, S., Singh, J. T., Slifer, K., Snyder, R., Solvignon, P., Stringer, R., Subedi, R., Tobias, W. A., Ton, N., Ulmer, P. E., Urciuoli, G. M., Vacheret, A., Voutier, E., Wang, K., Wan, L., Wojtsekhowski, B., Woo, S., Yao, H., Yuan, J., Zhan, X., Zheng, X., and Zhu, L.

Subjects
Nuclear Experiment
Abstract

Understanding the nucleon spin structure in the regime where the strong interaction becomes truly strong poses a challenge to both experiment and theory. At energy scales below the nucleon mass of about 1 GeV, the intense interaction among the quarks and gluons inside the nucleon makes them highly correlated. Their coherent behaviour causes the emergence of effective degrees of freedom, requiring the application of non-perturbative techniques, such as chiral effective field theory. Here, we present measurements of the neutron's generalized spin-polarizabilities that quantify the neutron's spin precession under electromagnetic fields at very low energy-momentum transfer squared down to 0.035 GeV$^2$. In this regime, chiral effective field theory calculations are expected to be applicable. Our data, however, show a strong discrepancy with these predictions, presenting a challenge to the current description of the neutron's spin properties., Comment: V1: initial version submitted to Nature Physics. V2: Published version. 16 pages, 7 figures. Additional material: 4 data tables (18 pages) V3: Typo corrected in author list. Paper content unchanged

Published
2021
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17. Form Factors and Two-Photon Exchange in High-Energy Elastic Electron-Proton Scattering

Author

Christy, M. E., Gautam, T., Ou, L., Schmookler, B., Wang, Y., Adikaram, D., Ahmed, Z., Albataineh, H., Ali, S. F., Aljawrneh, B., Allada, K., Allison, S. L., Alsalmi, S., Androic, D., Aniol, K., Annand, J., Arrington, J., Atac, H., Averett, T., Gayoso, C. Ayerbe, Bai, X., Bane, J., Barcus, S., Bartlett, K., Bellini, V., Beminiwattha, R., Bericic, J., Bhatt, H., Bhetuwal, D., Biswas, D., Brash, E., Bulumulla, D., Camacho, C. M., Campbell, J., Camsonne, A., Carmignotto, M., Castellanos, J., Chen, C., Chen, J-P., Chetry, T., Cisbani, E., Clary, B., Cohen, E., Compton, N., Cornejo, J. C., Dusa, S. Covrig, Crowe, B., Danagoulian, S., Danley, T., Deconinck, W., Defurne, M., Desnault, C., Di, D., Dlamini, M., Duer, M., Duran, B., Ent, R., Fanelli, C., Fuchey, E., Gal, C., Gaskell, D., Georges, F., Gilad, S., Glamazdin, O., Gnanvo, K., Gramolin, A. V., Gray, V. M., Gu, C., Habarakada, A., Hague, T., Hamad, G., Hamilton, D., Hamilton, K., Hansen, O., Hauenstein, F., Hernandez, A. V., Henry, W., Higinbotham, D. W., Holmstrom, T., Horn, T., Huang, Y., Huber, G. M., Hyde, C., Ibrahim, H., Israel, N., Jen, C-M., Jin, K., Jones, M., Kabir, A., Karki, B., Keppel, C., Khachatryan, V., King, P. M., Li, S., Li, W., Liu, H., Liu, J., Liyanage, A. H., Mack, D., Magee, J., Malace, S., Mammei, J., Markowitz, P., Mayilyan, S., McClellan, E., Meddi, F., Meekins, D., Mesick, K., Michaels, R., Mkrtchyan, A., Moffit, B., Montgomery, R., Myers, L. S., Nadel-Turonski, P., Nazeer, S. J., Nelyubin, V., Nguyen, D., Nuruzzaman, N., Nycz, M., Obrecht, R. F., Ohanyan, K., Palatchi, C., Pandey, B., Park, K., Park, S., Peng, C., Persio, F. D., Pomatsalyuk, R., Pooser, E., Puckett, A. J. R., Punjabi, V., Quinn, B., Rahman, S., Rashad, M. N. H., Riordan, S., Roche, J., Sapkota, I., Sarty, A., Sawatzky, B., Saylor, N. H., Shabestari, M. H., Shahinyan, A., Sirca, S., Smith, G. R., Sooriyaarachchilage, S., Sparveris, N., Spies, R., Stefanko, A., Su, T., Subedi, A., Sulkosky, V., Sun, A., Tan, Y., Thorne, L., Ton, N., Tortorici, F., Trotta, R., Uniyal, R., Urciuoli, G. M., Voutier, E., Waidyawansa, B., Wojtsekhowski, B., Wood, S., Yan, X., Ye, L., Ye, Z. H., Yero, C., Zhang, J., Zhao, Y. X., and Zhu, P.

Subjects
Nuclear Experiment, High Energy Physics - Experiment
Abstract

We present new precision measurements of the elastic electron-proton scattering cross section for momentum transfer (Q$^2$) up to 15.75~\gevsq. Combined with existing data, these provide an improved extraction of the proton magnetic form factor at high Q$^2$ and double the range over which a longitudinal/transverse separation of the cross section can be performed. The difference between our results and polarization data agrees with that observed at lower Q$^2$ and attributed to hard two-photon exchange (TPE) effects, extending to 8~(GeV/c)$^2$ the range of Q$^2$ for which a discrepancy is established at $>$95\% confidence. We use the discrepancy to quantify the size of TPE contributions needed to explain the cross section at high Q$^2$., Comment: 7 pages, 2 figures

Published
2021
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18. Measurement of the Ar(e,e$^\prime$ p) and Ti(e,e$^\prime$ p) cross sections in Jefferson Lab Hall A

Author

Gu, L., Abrams, D., Ankowski, A. M., Jiang, L., Aljawrneh, B., Alsalmi, S., Bane, J., Batz, A., Barcus, S., Barroso, M., Benhar, O., Bellini, V., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Dai, H., Day, D., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Keppel, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Murphy, M., Nguyen, D., Nycz, M., Ou, L., Pandey, B., Pandey, V., Park, K., Perera, G., Puckett, A. J. R., Santiesteban, S. N., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has collected exclusive electron-scattering data (e,e$^\prime$p) in parallel kinematics using natural argon and natural titanium targets. Here, we report the first results of the analysis of the data set corresponding to beam energy of 2,222 MeV, electron scattering angle 21.5 deg, and proton emission angle -50 deg. The differential cross sections, measured with $\sim$4% uncertainty, have been studied as a function of missing energy and missing momentum, and compared to the results of Monte Carlo simulations, obtained from a model based on the Distorted Wave Impulse Approximation., Comment: 14 pages, 8 figures (submitted to PRC)

Published
2020
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19. Deep exclusive electroproduction of $\pi^0$ at high $Q^2$ in the quark valence regime

Author

The Jefferson Lab Hall A Collaboration, Dlamini, M., Karki, B., Ali, S. F., Lin, P-J., Georges, F., Ko, H-S, Israel, N., Rashad, M. N. H., Stefanko, A., Adikaram, D., Ahmed, Z., Albataineh, H., Aljawrneh, B., Allada, K., Allison, S., Alsalmi, S., Androic, D., Aniol, K., Annand, J., Atac, H., Averett, T., Gayoso, C. Ayerbe, Bai, X., Bane, J., Barcus, S., Bartlett, K., Bellini, V., Beminiwattha, R., Bericic, J., Biswas, D., Brash, E., Bulumulla, D., Campbell, J., Camsonne, A., Carmignotto, M., Castellano, J., Chen, C., Chen, J-P., Chetry, T., Christy, M. E., Cisbani, E., Clary, B., Cohen, E., Compton, N., Cornejo, J. C., Dusa, S. Covrig, Crowe, B., Danagoulian, S., Danley, T., De Persio, F., Deconinck, W., Defurne, M., Desnault, C., Di, D., Duer, M., Duran, B., Ent, R., Fanelli, C., Franklin, G., Fuchey, E., Gal, C., Gaskell, D., Gautam, T., Glamazdin, O., Gnanvo, K., Gray, V. M., Gu, C., Hague, T., Hamad, G., Hamilton, D., Hamilton, K., Hansen, O., Hauenstein, F., Henry, W., Higinbotham, D. W., Holmstrom, T., Horn, T., Huang, Y., Huber, G. M., Hyde, C., Ibrahim, H., Jen, C-M., Jin, K., Jones, M., Kabir, A., Keppel, C., Khachatryan, V., King, P. M., Li, S., Li, W., Liu, J., Liu, H., Liyanage, A., Magee, J., Malace, S., Mammei, J., Markowitz, P., McClellan, E., Meddi, F., Meekins, D., Mesik, K., Michaels, R., Mkrtchyan, A., Montgomery, R., Camacho, C. Munoz, Myers, L. S., Nadel-Turonski, P., Nazeer, S. J., Nelyubin, V., Nguyen, D., Nuruzzaman, N., Nycz, M., Obretch, O. F., Ou, L., Palatchi, C., Pandey, B., Park, S., Park, K., Peng, C., Pomatsalyuk, R., Pooser, E., Puckett, A. J. R., Punjabi, V., Quinn, B., Rahman, S., Reimer, P. E., Roche, J., Sapkota, I., Sarty, A., Sawatzky, B., Saylor, N. H., Schmookler, B., Shabestari, M. H., Shahinyan, A., Sirca, S., Smith, G. R., Sooriyaarachchilage, S., Sparveris, N., Spies, R., Su, T., Subedi, A., Sulkosky, V., Sun, A., Thorne, L., Tian, Y., Ton, N., Tortorici, F., Trotta, R., Urciuoli, G. M., Voutier, E., Waidyawansa, B., Wang, Y., Wojtsekhowski, B., Wood, S., Yan, X., Ye, L., Ye, Z., Yero, C., Zhang, J., Zhao, Y., and Zhu, P.

Subjects
High Energy Physics - Experiment, Nuclear Experiment
Abstract

We report measurements of the exclusive neutral pion electroproduction cross section off protons at large values of $x_B$ (0.36, 0.48 and 0.60) and $Q^2$ (3.1 to 8.4 GeV$^2$) obtained from Jefferson Lab Hall A experiment E12-06-014. The corresponding structure functions $d\sigma_L/dt+\epsilon d\sigma_T/dt$, $d\sigma_{TT}/dt$, $d\sigma_{LT}/dt$ and $d\sigma_{LT'}/dt$ are extracted as a function of the proton momentum transfer $t-t_{min}$. The results suggest the amplitude for transversely polarized virtual photons continues to dominate the cross-section throughout this kinematic range. The data are well described by calculations based on transversity Generalized Parton Distributions coupled to a helicity flip Distribution Amplitude of the pion, thus providing a unique way to probe the structure of the nucleon.

Published
2020
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20. Differential effects of PD-1 and CTLA-4 blockade on the melanoma-reactive CD8 T cell response

Author

Gangaev, Anastasia, Rozeman, Elisa A, Rohaan, Maartje W, Isaeva, Olga I, Philips, Daisy, Patiwael, Sanne, van den Berg, Joost H, Ribas, Antoni, Schadendorf, Dirk, Schilling, Bastian, Schumacher, Ton N, Blank, Christian U, Haanen, John BAG, and Kvistborg, Pia

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer, Clinical Research, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Adult, Aged, Aged, 80 and over, CD8-Positive T-Lymphocytes, CTLA-4 Antigen, Cohort Studies, Epitopes, T-Lymphocyte, Female, Hepatitis A Virus Cellular Receptor 2, Humans, Immune Checkpoint Inhibitors, In Vitro Techniques, Kinetics, Lymphocyte Activation, Male, Melanoma, Melanoma-Specific Antigens, Middle Aged, Programmed Cell Death 1 Receptor, Receptors, Antigen, T-Cell, alpha-beta, Receptors, CXCR5, PD-1, CTLA-4, melanoma-reactive CD8 T cells
Abstract

Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) have revolutionized the treatment of melanoma patients. Based on early studies addressing the mechanism of action, it was assumed that PD-1 blockade mostly influences T cell responses at the tumor site. However, recent work has demonstrated that PD-1 blockade can influence the T cell compartment in peripheral blood. If the activation of circulating, tumor-reactive T cells would form an important mechanism of action of PD-1 blockade, it may be predicted that such blockade would alter either the frequency and/or the breadth of the tumor-reactive CD8 T cell response. To address this question, we analyzed CD8 T cell responses toward 71 melanoma-associated epitopes in peripheral blood of 24 melanoma patients. We show that both the frequency and the breadth of the circulating melanoma-reactive CD8 T cell response was unaltered upon PD-1 blockade. In contrast, a broadening of the circulating melanoma-reactive CD8 T cell response was observed upon CTLA-4 blockade, in concordance with our prior data. Based on these results, we conclude that PD-1 and CTLA-4 blockade have distinct mechanisms of action. In addition, the data provide an argument in favor of the hypothesis that anti-PD-1 therapy may primarily act at the tumor site.

Published
2021

21. PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial

Author

Voorwerk, Leonie, Isaeva, Olga I., Horlings, Hugo M., Balduzzi, Sara, Chelushkin, Maksim, Bakker, Noor A. M., Champanhet, Elisa, Garner, Hannah, Sikorska, Karolina, Loo, Claudette E., Kemper, Inge, Mandjes, Ingrid A. M., de Maaker, Michiel, van Geel, Jasper J. L., Boers, Jorianne, de Boer, Maaike, Salgado, Roberto, van Dongen, Marloes G. J., Sonke, Gabe S., de Visser, Karin E., Schumacher, Ton N., Blank, Christian U., Wessels, Lodewyk F. A., Jager, Agnes, Tjan-Heijnen, Vivianne C. G., Schröder, Carolien P., Linn, Sabine C., and Kok, Marleen

Published
2023
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22. Measurement of the Ar(e,e′p) and Ti(e,e′p) cross sections in Jefferson Lab Hall A

Author

Gu, L, Abrams, D, Ankowski, AM, Jiang, L, Aljawrneh, B, Alsalmi, S, Bane, J, Batz, A, Barcus, S, Barroso, M, Benhar, O, Bellini, V, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Dai, H, Day, D, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, T, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Keppel, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Murphy, M, Nguyen, D, Nycz, M, Ou, L, Pandey, B, Pandey, V, Park, K, Perera, G, Puckett, AJR, Santiesteban, SN, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
Nuclear and Plasma Physics, Synchrotrons and Accelerators, Physical Sciences, nucl-ex, nucl-th, Nuclear and plasma physics
Abstract

The E12-14-012 experiment, performed in Jefferson Lab Hall A, has collected exclusive electron-scattering data (e,e′p) in parallel kinematics using natural argon and natural titanium targets. Here we report the first results of the analysis of the data set corresponding to beam energy 2222 GeV, electron scattering angle 21.5∘, and proton emission angle -50∘. The differential cross sections, measured with ≈4% uncertainty, have been studied as a function of missing energy and missing momentum, and compared to the results of Monte Carlo simulations, obtained from a model based on the distorted-wave impulse approximation.

Published
2021

23. DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age

Author

Jos Urbanus, Jason Cosgrove, Joost B. Beltman, Yuval Elhanati, Rafael A. Moral, Cecile Conrad, Jeroen W. van Heijst, Emilie Tubeuf, Arno Velds, Lianne Kok, Candice Merle, Jens P. Magnusson, Léa Guyonnet, Jonas Frisén, Silvia Fre, Aleksandra M. Walczak, Thierry Mora, Heinz Jacobs, Ton N. Schumacher, and Leïla Perié

Subjects
Science
Abstract

Abstract Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.

Published
2023
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24. γδ T cells are effectors of immunotherapy in cancers with HLA class I defects

Author

de Vries, Natasja L., van de Haar, Joris, Veninga, Vivien, Chalabi, Myriam, Ijsselsteijn, Marieke E., van der Ploeg, Manon, van den Bulk, Jitske, Ruano, Dina, van den Berg, Jose G., Haanen, John B., Zeverijn, Laurien J., Geurts, Birgit S., de Wit, Gijs F., Battaglia, Thomas W., Gelderblom, Hans, Verheul, Henk M. W., Schumacher, Ton N., Wessels, Lodewyk F. A., Koning, Frits, de Miranda, Noel F. C. C., and Voest, Emile E.

Published
2023
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25. Measurement of the 3He Spin-Structure Functions and of Neutron (3He) Spin-Dependent Sum Rules at 0.035<Q^2<0.24 GeV^2

Author

Sulkosky, V., Singh, J. T., Peng, C., Chen, J. -P., Deur, A., Abrahamyan, S., Aniol, K. A., Armstrong, D. S., Averett, T., Bailey, S. L., Beck, A., Bertin, P., Butaru, F., Boeglin, W., Camsonne, A., Cates, G. D., Chang, C. C., Choi, Seonho, Chudakov, E., Coman, L., Cornejo, J. C, Craver, B., Cusanno, F., De Leo, R., de Jager, C. W., Denton, J. D., Dhamija, S., Feuerbach, R., Finn, J. M., Frullani, S., Fuoti, K., Gao, H., Garibaldi, F., Gayou, O., Gilman, R., Glamazdin, A., Glashausser, C., Gomez, J., Hansen, J. -O., Hayes, D., Hersman, B., Higinbotham, D. W., Holmstrom, T., Humensky, T. B., Hyde, C. E., Ibrahim, H., Iodice, M., Jiang, X., Kaufman, L. J., Kelleher, A., Keister, K. E., Kim, W., Kolarkar, A., Kolb, N., Korsch, W., Kramer, K., Kumbartzki, G., Lagamba, L., Laine, V., Laveissiere, G., Lerose, J. J., Lhuillier, D., Lindgren, R., Liyanage, N., Lu, H. -J., Ma, B., Margaziotis, D. J., Markowitz, P., McCormick, K., Meziane, M., Meziani, Z. -E., Michaels, R., Moffit, B., Monaghan, P., Nanda, S., Niedziela, J., Niskin, M., Pandolfi, R., Paschke, K. D., Potokar, M., Puckett, A., Punjabi, V. A., Qiang, Y., Ransome, R., Reitz, B., Roche, R., Saha, A., Shabetai, A., Sirca, S., Slifer, K., Snyder, R., Solvignon, P., Stringer, R., Subedi, R., Tobias, W. A., Ton, N., Ulmer, P. E., Urciuoli, G. M., Vacheret, A., Voutier, E., Wang, K., Wan, L., Wojtsekhowski, B., Woo, S., Yao, H., Yuan, J., Zhan, X., Zheng, X., and Zhu, L.

Subjects
Nuclear Experiment, High Energy Physics - Experiment
Abstract

The spin-structure functions $g_1$ and $g_2$, and the spin-dependent partial cross-section $\sigma_\mathrm{TT}$ have been extracted from the polarized cross-sections differences, $\Delta \sigma_{\parallel}\hspace{-0.06cm}\left(\nu,Q^{2}\right)$ and $\Delta \sigma_{\perp}\hspace{-0.06cm}\left(\nu,Q^{2}\right)$ measured for the $\vec{^\textrm{3}\textrm{He}}(\vec{\textrm{e}},\textrm{e}')\textrm{X}$ reaction, in the E97-110 experiment at Jefferson Lab. Polarized electrons with energies from 1.147 to 4.404 GeV were scattered at angles of 6$^{\circ}$ and 9$^{\circ}$ from a longitudinally or transversely polarized $^{3}$He target. The data cover the kinematic regions of the quasi-elastic, resonance production and beyond. From the extracted spin-structure functions, the first moments $\overline{\Gamma_1}\hspace{-0.06cm}\left(Q^{2}\right)$, $\Gamma_2\hspace{-0.06cm}\left(Q^{2}\right)$ and $I_{\mathrm{TT}}\hspace{-0.06cm}\left(Q^{2}\right)$ are evaluated with high precision for the neutron in the $Q^2$ range from 0.035 to 0.24~GeV$^{2}$. The comparison of the data and the chiral effective field theory predictions reveals the importance of proper treatment of the $\Delta$ degree of freedom for spin observables., Comment: 7 pages, 5 figures, 3 tables. Version published in Phys. Lett. B

Published
2019
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26. Measurement of the cross sections for inclusive electron scattering in the E12-14-012 experiment at Jefferson Lab

Author

Murphy, M., Dai, H., Gu, L., Abrams, D., Ankowski, A. M., Aljawrneh, B., Alsalmi, S., Bane, J., Barcus, S., Benhar, O., Bellini, V., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Day, D., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Jen, C. M., Keppel, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Nguyen, D., Nycz, M., Ou, L., Pandey, B., Pandey, V., Park, K., Perera, G., Puckett, A. J. R., Santiesteban, S. N., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology, Nuclear Experiment
Abstract

The E12-14-012 experiment performed at Jefferson Lab Hall A has collected inclusive electron-scattering data for different targets at the kinematics corresponding to beam energy 2.222 GeV and scattering angle 15.54 deg. Here we present a comprehensive analysis of the collected data and compare the double-differential cross sections for inclusive scattering of electrons, extracted using solid targets (aluminum, carbon, and titanium) and a closed argon-gas cell. The data extend over broad range of energy transfer, where quasielastic interaction, Delta-resonance excitation, and inelastic scattering yield contributions to the cross section. The double-differential cross sections are reported with high precision (~3%) for all targets over the covered kinematic range., Comment: 11 pages, 10 figures

Published
2019
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27. B cells and tertiary lymphoid structures promote immunotherapy response

Author

Helmink, Beth A, Reddy, Sangeetha M, Gao, Jianjun, Zhang, Shaojun, Basar, Rafet, Thakur, Rohit, Yizhak, Keren, Sade-Feldman, Moshe, Blando, Jorge, Han, Guangchun, Gopalakrishnan, Vancheswaran, Xi, Yuanxin, Zhao, Hao, Amaria, Rodabe N, Tawbi, Hussein A, Cogdill, Alex P, Liu, Wenbin, LeBleu, Valerie S, Kugeratski, Fernanda G, Patel, Sapna, Davies, Michael A, Hwu, Patrick, Lee, Jeffrey E, Gershenwald, Jeffrey E, Lucci, Anthony, Arora, Reetakshi, Woodman, Scott, Keung, Emily Z, Gaudreau, Pierre-Olivier, Reuben, Alexandre, Spencer, Christine N, Burton, Elizabeth M, Haydu, Lauren E, Lazar, Alexander J, Zapassodi, Roberta, Hudgens, Courtney W, Ledesma, Deborah A, Ong, SuFey, Bailey, Michael, Warren, Sarah, Rao, Disha, Krijgsman, Oscar, Rozeman, Elisa A, Peeper, Daniel, Blank, Christian U, Schumacher, Ton N, Butterfield, Lisa H, Zelazowska, Monika A, McBride, Kevin M, Kalluri, Raghu, Allison, James, Petitprez, Florent, Fridman, Wolf Herman, Sautès-Fridman, Catherine, Hacohen, Nir, Rezvani, Katayoun, Sharma, Padmanee, Tetzlaff, Michael T, Wang, Linghua, and Wargo, Jennifer A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Immunization, Cancer, Vaccine Related, Genetics, B-Lymphocytes, Biomarkers, Tumor, Carcinoma, Renal Cell, Cell Cycle Checkpoints, Clone Cells, Dendritic Cells, Follicular, Gene Expression Regulation, Neoplastic, Humans, Immunologic Memory, Immunotherapy, Mass Spectrometry, Melanoma, Neoplasm Metastasis, Phenotype, Prognosis, RNA-Seq, Receptors, Immunologic, Single-Cell Analysis, T-Lymphocytes, Tertiary Lymphoid Structures, Transcriptome, General Science & Technology
Abstract

Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers1-10 and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity11-15, although these have been less well-studied in ICB treatment16. A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling17 that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter18) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.

Published
2020

28. Measurement of the cross sections for inclusive electron scattering in the E12-14-012 experiment at Jefferson Lab

Author

Murphy, M, Dai, H, Gu, L, Abrams, D, Ankowski, AM, Aljawrneh, B, Alsalmi, S, Bane, J, Barcus, S, Benhar, O, Bellini, V, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Day, D, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, T, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Jen, CM, Keppel, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Nguyen, D, Nycz, M, Ou, L, Pandey, B, Pandey, V, Park, K, Perera, G, Puckett, AJR, Santiesteban, SN, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
hep-ex, hep-ph, nucl-ex, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics
Abstract

The E12-14-012 experiment performed at Jefferson Lab Hall A has collected inclusive electron-scattering data for different targets at the kinematics corresponding to beam energy 2.222 GeV and scattering angle 15.54. Here we present a comprehensive analysis of the collected data and compare the double-differential cross sections for inclusive scattering of electrons, extracted using solid targets (aluminum, carbon, and titanium) and a closed argon-gas cell. The data extend over broad range of energy transfer, where quasielastic interaction, Δ-resonance excitation, and inelastic scattering yield contributions to the cross section. The double-differential cross sections are reported with high precision (∼3%) for all targets over the covered kinematic range.

Published
2019

29. An adverse tumor-protective effect of IDO1 inhibition

Author

Kenski, Juliana C.N., Huang, Xinyao, Vredevoogd, David W., de Bruijn, Beaunelle, Traets, Joleen J.H., Ibáñez-Molero, Sofía, Schieven, Sebastiaan M., van Vliet, Alex, Krijgsman, Oscar, Kuilman, Thomas, Pozniak, Joanna, Loayza-Puch, Fabricio, Terry, Alexandra M., Müller, Judith, Logtenberg, Meike E.W., de Bruijn, Marjolein, Levy, Pierre, Körner, Pierre-René, Goding, Colin R., Schumacher, Ton N., Marine, Jean-Christophe, Agami, Reuven, and Peeper, Daniel S.

Published
2023
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30. Protocol for ex vivo culture of patient-derived tumor fragments

Author

Lisanne M. Roelofsen, Paula Voabil, Marjolein de Bruijn, Petra Herzig, Alfred Zippelius, Ton N. Schumacher, and Daniela S. Thommen

Subjects
Cell Biology, Cell Culture, Single Cell, Cancer, Immunology, Biotechnology and Bioengineering, Science (General), Q1-390
Abstract

Summary: The lack of suitable models currently hampers our understanding of how the tumor microenvironment responds to immunotherapy treatment. Here, we present a protocol for ex vivo culture of patient-derived tumor fragments (PDTFs). We describe the steps for tumor collection, generation and cryopreservation of PDTFs, and their subsequent thawing. We detail culture of PDTFs and their preparation for analysis. This protocol preserves the tumor microenvironment’s composition, architecture, and cellular interactions, which can be perturbed by ex vivo treatment.For complete details on the use and execution of this protocol, please refer to Voabil et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published
2023
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31. Neoadjuvant Immunotherapy in Locally Advanced Mismatch Repair–Deficient Colon Cancer

Author

Chalabi, Myriam, primary, Verschoor, Yara L., additional, Tan, Pedro Batista, additional, Balduzzi, Sara, additional, Van Lent, Anja U., additional, Grootscholten, Cecile, additional, Dokter, Simone, additional, Büller, Nikè V., additional, Grotenhuis, Brechtje A., additional, Kuhlmann, Koert, additional, Burger, Jacobus W., additional, Huibregtse, Inge L., additional, Aukema, Tjeerd S., additional, Hendriks, Eduard R., additional, Oosterling, Steven J., additional, Snaebjornsson, Petur, additional, Voest, Emile E., additional, Wessels, Lodewyk F., additional, Beets-Tan, Regina G., additional, Van Leerdam, Monique E., additional, Schumacher, Ton N., additional, van den Berg, José G., additional, Beets, Geerard L., additional, and Haanen, John B., additional

Published
2024
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34. First Measurement of the Ar$(e,e^\prime)X$ Cross Section at Jefferson Lab

Author

Dai, H., Murphy, M., Pandey, V., Abrams, D., Nguyen, D., Aljawrneh, B., Alsalmi, S., Ankowski, A. M., Bane, J., Barcus, S., Benhar, O., Bellini, V., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Day, D., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Jen, C. M., Keppel, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Nycz, M., Ou, L., Pandey, B., Park, K., Perera, G., Puckett, A. J. R., Santiesteban, S. N., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
Nuclear Experiment, High Energy Physics - Experiment, Nuclear Theory
Abstract

The success of the ambitious programs of both long- and short-baseline neutrino-oscillation experiments employing liquid-argon time-projection chambers will greatly rely on the precision with which the weak response of the argon nucleus can be estimated. In the E12-14-012 experiment at Jefferson Lab Hall A, we have studied the properties of the argon nucleus by scattering a high-quality electron beam off a high-pressure gaseous argon target. Here, we present the measured $^{40}$Ar$(e,e^{\prime})$ double differential cross section at incident electron energy $E=2.222$~GeV and scattering angle $\theta = 15.541^\circ$. The data cover a broad range of energy transfers, where quasielastic scattering and delta production are the dominant reaction mechanisms. The result for argon is compared to our previously reported cross sections for titanium and carbon, obtained in the same kinematical setup., Comment: 6 pages, 4 figures

Published
2018
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35. First Measurement of the Ti$(e,e^\prime){\rm X}$ Cross Section at Jefferson Lab

Author

Dai, H., Murphy, M., Pandey, V., Abrams, D., Nguyen, D., Aljawrneh, B., Alsalmi, S., Ankowski, A. M., Bane, J., Barcus, S., Benhar, O., Bellini, V., Bericic, J., Biswas, D., Camsonne, A., Castellanos, J., Chen, J. -P., Christy, M. E., Craycraft, K., Cruz-Torres, R., Day, D., Dusa, S. -C., Fuchey, E., Gautam, T., Giusti, C., Gomez, J., Gu, C., Hague, T., Hansen, J. -O., Hauenstein, F., Higinbotham, D. W., Hyde, C., Jen, C. M., Keppel, C., Li, S., Lindgren, R., Liu, H., Mariani, C., McClellan, R. E., Meekins, D., Michaels, R., Mihovilovic, M., Nycz, M., Ou, L., Pandey, B., Park, K., Perera, G., Puckett, A. J. R., Širca, S., Su, T., Tang, L., Tian, Y., Ton, N., Wojtsekhowski, B., Wood, S., Ye, Z., and Zhang, J.

Subjects
Nuclear Experiment, High Energy Physics - Experiment, Nuclear Theory
Abstract

To probe CP violation in the leptonic sector using GeV energy neutrino beams in current and future experiments using argon detectors, precise models of the complex underlying neutrino and antineutrino interactions are needed. The E12-14-012 experiment at Jefferson Lab Hall A was designed to perform a combined analysis of inclusive and exclusive electron scatterings on both argon ($N = 22$) and titanium ($Z = 22$) nuclei using GeV energy electron beams. The measurement on titanium nucleus provides essential information to understand the neutrino scattering on argon, large contribution to which comes from scattering off neutrons. Here we report the first experimental study of electron-titanium scattering as double differential cross section at beam energy $E=2.222$ GeV and electron scattering angle $\theta = 15.541$ deg, measured over a broad range of energy transfer, spanning the kinematical regions in which quasielastic scattering and delta production are the dominant reaction mechanisms. The data provide valuable new information needed to develop accurate theoretical models of the electromagnetic and weak cross sections of these complex nuclei in the kinematic regime of interest to neutrino experiments., Comment: 6 pages, 5 figures. Version published in Physical Review C

Published
2018
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36. First measurement of the Ar(e,e′)X cross section at Jefferson Laboratory

Author

Dai, H, Murphy, M, Pandey, V, Abrams, D, Nguyen, D, Aljawrneh, B, Alsalmi, S, Ankowski, AM, Bane, J, Barcus, S, Benhar, O, Bellini, V, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Day, D, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, T, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Jen, CM, Keppel, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Nycz, M, Ou, L, Pandey, B, Park, K, Perera, G, Puckett, AJR, Santiesteban, SN, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
nucl-ex, hep-ex, nucl-th, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics
Abstract

The success of the ambitious programs of both long- and short-baseline neutrino-oscillation experiments employing liquid-argon time-projection chambers will greatly rely on the precision with which the weak response of the argon nucleus can be estimated. In the E12-14-012 experiment at Jefferson Lab Hall A, we studied the properties of the argon nucleus by scattering a high-quality electron beam off a high-pressure gaseous argon target. Here, we present the measured Ar40(e,e′) double differential cross section at incident electron energy E=2.222 GeV and scattering angle θ=15.54â. The data cover a broad range of energy transfers, where quasielastic scattering and delta production are the dominant reaction mechanisms. The result for argon is compared to our previously reported cross sections for titanium and carbon, obtained in the same kinematical setup.

Published
2019

37. T cells targeted to TdT kill leukemic lymphoblasts while sparing normal lymphocytes

Author

Ali, Muhammad, Giannakopoulou, Eirini, Li, Yingqian, Lehander, Madeleine, Virding Culleton, Stina, Yang, Weiwen, Knetter, Cathrine, Odabasi, Mete Can, Bollineni, Ravi Chand, Yang, Xinbo, Foldvari, Zsofia, Böschen, Maxi-Lu, Taraldsrud, Eli, Strønen, Erlend, Toebes, Mireille, Hillen, Amy, Mazzi, Stefania, de Ru, Arnoud H., Janssen, George M. C., Kolstad, Arne, Tjønnfjord, Geir Erland, Lie, Benedicte A., Griffioen, Marieke, Lehmann, Sören, Osnes, Liv Toril, Buechner, Jochen, Garcia, K. Christopher, Schumacher, Ton N., van Veelen, Peter A., Leisegang, Matthias, Jacobsen, Sten Eirik W., Woll, Petter, and Olweus, Johanna

Published
2022
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39. First measurement of the Ti(e,e′)X cross section at Jefferson Lab

Author

Dai, H, Murphy, M, Pandey, V, Abrams, D, Nguyen, D, Aljawrneh, B, Alsalmi, S, Ankowski, AM, Bane, J, Barcus, S, Benhar, O, Bellini, V, Bericic, J, Biswas, D, Camsonne, A, Castellanos, J, Chen, J-P, Christy, ME, Craycraft, K, Cruz-Torres, R, Day, D, Dusa, S-C, Fuchey, E, Gautam, T, Giusti, C, Gomez, J, Gu, C, Hague, T, Hansen, J-O, Hauenstein, F, Higinbotham, DW, Hyde, C, Jen, CM, Keppel, C, Li, S, Lindgren, R, Liu, H, Mariani, C, McClellan, RE, Meekins, D, Michaels, R, Mihovilovic, M, Nycz, M, Ou, L, Pandey, B, Park, K, Perera, G, Puckett, AJR, Širca, S, Su, T, Tang, L, Tian, Y, Ton, N, Wojtsekhowski, B, Wood, S, Ye, Z, and Zhang, J

Subjects
nucl-ex, hep-ex, nucl-th, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics
Abstract

To probe CP violation in the leptonic sector using GeV energy neutrino beams in current and future experiments using argon detectors, precise models of the complex underlying neutrino and antineutrino interactions are needed. The E12-14-012 experiment at Jefferson Lab Hall A was designed to perform a combined analysis of inclusive and exclusive electron scatterings on both argon (N=22) and titanium (Z=22) nuclei using GeV-energy electron beams. The measurement on titanium nucleus provides essential information to understand the neutrino scattering on argon, large contribution to which comes from scattering off neutrons. Here we report the first experimental study of electron-titanium scattering as double-differential cross section at beam energy E=2.222 GeV and electron-scattering angle θ=15.541, measured over a broad range of energy transfer, spanning the kinematical regions in which quasielastic scattering and delta production are the dominant reaction mechanisms. The data provide valuable new information needed to develop accurate theoretical models of the electromagnetic and weak cross sections of these complex nuclei in the kinematic regime of interest to neutrino experiments.

Published
2018

40. Neoadjuvant immunotherapy with nivolumab and ipilimumab induces major pathological responses in patients with head and neck squamous cell carcinoma

Author

Joris L. Vos, Joris B. W. Elbers, Oscar Krijgsman, Joleen J. H. Traets, Xiaohang Qiao, Anne M. van der Leun, Yoni Lubeck, Iris M. Seignette, Laura A. Smit, Stefan M. Willems, Michiel W. M. van den Brekel, Richard Dirven, M. Baris Karakullukcu, Luc Karssemakers, W. Martin C. Klop, Peter J. F. M. Lohuis, Willem H. Schreuder, Ludi E. Smeele, Lilly-Ann van der Velden, I. Bing Tan, Suzanne Onderwater, Bas Jasperse, Wouter V. Vogel, Abrahim Al-Mamgani, Astrid Keijser, Vincent van der Noort, Annegien Broeks, Erik Hooijberg, Daniel S. Peeper, Ton N. Schumacher, Christian U. Blank, Jan Paul de Boer, John B. A. G. Haanen, and Charlotte L. Zuur

Subjects
Science
Abstract

Immune checkpoint blockade has become standard care for patients with recurrent metastatic head and neck squamous cell carcinoma (HNSCC). Here the authors present the results of a non-randomized phase Ib/IIa trial, reporting safety and efficacy of neoadjuvant nivolumab monotherapy and nivolumab plus ipilimumab prior to standard-of-care surgery in patients with HNSCC. .

Published
2021
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41. QPCTL regulates macrophage and monocyte abundance and inflammatory signatures in the tumor microenvironment

Author

Kaspar Bresser, Meike E. W. Logtenberg, Mireille Toebes, Natalie Proost, Justin Sprengers, Bjorn Siteur, Manon Boeije, Lona J. Kroese, and Ton N. Schumacher

Subjects
QPCTL, tumor micro-environment, cancer-associated fibroblasts, genetically modified mouse model, Immunologic diseases. Allergy, RC581-607, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

The enzyme glutaminyl-peptide cyclotransferase-like protein (QPCTL) catalyzes the formation of pyroglutamate residues at the NH2-terminus of proteins, thereby influencing their biological properties. A number of studies have implicated QPCTL in the regulation of chemokine stability. Furthermore, QPCTL activity has recently been shown to be critical for the formation of the high-affinity SIRPα binding site of the CD47 “don’t-eat-me” protein. Based on the latter data, interference with QPCTL activity —and hence CD47 maturation—may be proposed as a means to promote anti-tumor immunity. However, the pleiotropic activity of QPCTL makes it difficult to predict the effects of QPCTL inhibition on the tumor microenvironment (TME). Using a syngeneic mouse melanoma model, we demonstrate that QPCTL deficiency alters the intra-tumoral monocyte-to-macrophage ratio, results in a profound increase in the presence of pro-inflammatory cancer-associated fibroblasts (CAFs) relative to immunosuppressive TGF-β1-driven CAFs, and leads to an increased IFN and decreased TGF-β transcriptional response signature in tumor cells. Importantly, the functional relevance of the observed TME remodeling is demonstrated by the synergy between QPCTL deletion and anti PD-L1 therapy, sensitizing an otherwise refractory melanoma model to anti-checkpoint therapy. Collectively, these data provide support for the development of strategies to interfere with QPCTL activity as a means to promote tumor-specific immunity.

Published
2022
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42. The Human Cell Atlas.

Author

Regev, Aviv, Teichmann, Sarah A, Lander, Eric S, Amit, Ido, Benoist, Christophe, Birney, Ewan, Bodenmiller, Bernd, Campbell, Peter, Carninci, Piero, Clatworthy, Menna, Clevers, Hans, Deplancke, Bart, Dunham, Ian, Eberwine, James, Eils, Roland, Enard, Wolfgang, Farmer, Andrew, Fugger, Lars, Göttgens, Berthold, Hacohen, Nir, Haniffa, Muzlifah, Hemberg, Martin, Kim, Seung, Klenerman, Paul, Kriegstein, Arnold, Lein, Ed, Linnarsson, Sten, Lundberg, Emma, Lundeberg, Joakim, Majumder, Partha, Marioni, John C, Merad, Miriam, Mhlanga, Musa, Nawijn, Martijn, Netea, Mihai, Nolan, Garry, Pe'er, Dana, Phillipakis, Anthony, Ponting, Chris P, Quake, Stephen, Reik, Wolf, Rozenblatt-Rosen, Orit, Sanes, Joshua, Satija, Rahul, Schumacher, Ton N, Shalek, Alex, Shapiro, Ehud, Sharma, Padmanee, Shin, Jay W, Stegle, Oliver, Stratton, Michael, Stubbington, Michael JT, Theis, Fabian J, Uhlen, Matthias, van Oudenaarden, Alexander, Wagner, Allon, Watt, Fiona, Weissman, Jonathan, Wold, Barbara, Xavier, Ramnik, Yosef, Nir, and Human Cell Atlas Meeting Participants

Subjects
Human Cell Atlas Meeting Participants, Eukaryotic Cells, Humans, Human Body, International Cooperation, Atlases as Topic, cell atlas, cell biology, computational biology, human, lineage, mouse, science forum, single-cell genomics, systems biology, Biochemistry and Cell Biology
Abstract

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

Published
2017

43. Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening

Author

Moravec, Ziva, primary, Zhao, Yue, additional, Voogd, Rhianne, additional, Cook, Danielle R., additional, Kinrot, Seon, additional, Capra, Benjamin, additional, Yang, Haiyan, additional, Raud, Brenda, additional, Ou, Jiayu, additional, Xuan, Jiekun, additional, Wei, Teng, additional, Ren, Lili, additional, Hu, Dandan, additional, Wang, Jun, additional, Haanen, John B.A.G., additional, Schumacher, Ton N., additional, Chen, Xi, additional, Porter, Ely, additional, and Scheper, Wouter, additional

Published
2024
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45. Studies of relative gain and timing response of fine-mesh photomultiplier tubes in high magnetic fields

Author

Sulkosky, V., Allison, L., Barber, C., Cao, T., Ilieva, Y., Jin, K., Kalicy, G., Park, K., Ton, N., and Zheng, X.

Subjects
Physics - Instrumentation and Detectors, Nuclear Experiment
Abstract

We investigated the use of Hamamatsu fine-mesh photomultiplier tube assemblies H6152-70 and H6614-70 with regards to their gain and timing resolution in magnetic fields up to 1.9 T. Our results show that the H6614-70 assembly can operate reliably in magnetic fields exceeding 1.5 T, while preserving a reasonable timing resolution even with a gain reduction of a factor of approximately 100. The reduction of the relative gain of the H6152-70 is similar to the H6614-70's near 1.5 T, but its timing resolution worsens considerably at this high field., Comment: 14 pages, 9 figures, to be published in Nuclear Instruments and Methods in physics research section A

Published
2016
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46. An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer

Author

Voabil, Paula, de Bruijn, Marjolein, Roelofsen, Lisanne M., Hendriks, Sanne H., Brokamp, Simone, van den Braber, Marlous, Broeks, Annegien, Sanders, Joyce, Herzig, Petra, Zippelius, Alfred, Blank, Christian, Hartemink, Koen J., Monkhorst, Kim, Haanen, John B.A.G., Schumacher, Ton N., and Thommen, Daniela S.

Subjects
Oncology, Experimental, Tumors -- Models -- Care and treatment -- Patient outcomes, Organs, Culture of -- Usage, Immune response -- Health aspects -- Research, Immunotherapy -- Patient outcomes, Cancer -- Research, Biological sciences, Health
Abstract

Inhibitors of the PD-1-PD-L1 axis have been approved as therapy for many human cancers. In spite of the evidence for their widespread clinical activity, little is known about the immunological alterations that occur in human cancer tissue after PD-1 blockade. We developed and employed a patient-derived tumor fragment platform to dissect the early immunological response of human tumor tissue to ex vivo PD-1 blockade. We observed that the capacity of immune cells to be reactivated ex vivo was predictive of clinical response, and perturbation analyses identified tumor-resident T cells as a key component of this immunological response. In addition, through combined analysis of baseline properties and immune response capacity, we identified a new subgroup of infiltrated tumors that lacks the capacity to respond to PD-1 blockade. Finally, the baseline presence of tertiary lymphoid structures and their components correlated with the capacity of cancers to undergo intratumoral immune cell reactivation. An ex vivo platform of patient-derived tumor fragments enables the assessment of intratumoral immune reactivation after PD-1 blockade that is predictive of clinical outcomes in patients with cancer., Author(s): Paula Voabil [sup.1] , Marjolein de Bruijn [sup.2] , Lisanne M. Roelofsen [sup.2] , Sanne H. Hendriks [sup.2] [sup.7] , Simone Brokamp [sup.2] , Marlous van den Braber [sup.2] [...]

Published
2021
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47. Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features

Author

Anastasia Gangaev, Steven L. C. Ketelaars, Olga I. Isaeva, Sanne Patiwael, Anna Dopler, Kelly Hoefakker, Sara De Biasi, Lara Gibellini, Cristina Mussini, Giovanni Guaraldi, Massimo Girardis, Cami M. P. Talavera Ormeno, Paul J. M. Hekking, Neubury M. Lardy, Mireille Toebes, Robert Balderas, Ton N. Schumacher, Huib Ovaa, Andrea Cossarizza, and Pia Kvistborg

Subjects
Science
Abstract

Many viral antigens have been identified in patients with COVID-19 patients, but which of these result in meaningful immune responses is unclear. Here the authors identify a range of SARS-CoV-2 CD8+ T cell responses across patients including a response targeting an epitope of ORF1ab with immunodominant properties.

Published
2021
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49. DNA damage induces p53-independent apoptosis through ribosome stalling.

Author

Boon, Nicolaas J., Oliveira, Rafaela A., Körner, Pierré-René, Kochavi, Adva, Mertens, Sander, Malka, Yuval, Voogd, Rhianne, van der Horst, Suzanne E. M., Huismans, Maarten A., Smabers, Lidwien P., Draper, Jonne M., Wessels, Lodewyk F. A., Haahr, Peter, Roodhart, Jeanine M. L., Schumacher, Ton N. M., Snippert, Hugo J., Agami, Reuven, and Brummelkamp, Thijn R.

Published
2024

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