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4,019 results on '"Joshi, J."'

1. The SRG/eROSITA All-Sky Survey. Optical identification and properties of galaxy clusters and groups in the western galactic hemisphere

Author

Kluge, M., Comparat, J., Liu, A., Balzer, F., Bulbul, E., Chitham, J. Ider, Ghirardini, V., Garrel, C., Bahar, Y. E., Artis, E., Bender, R., Clerc, N., Dwelly, T., Fabricius, M. H., Grandis, S., Hernández-Lang, D., Hill, G. J., Joshi, J., Lamer, G., Merloni, A., Nandra, K., Pacaud, F., Predehl, P., Ramos-Ceja, M. E., Reiprich, T. H., Salvato, M., Sanders, J. S., Schrabback, T., Seppi, R., Zelmer, S., Zenteno, A., and Zhang, X.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - High Energy Astrophysical Phenomena
Abstract

The first SRG/eROSITA All-Sky Survey (eRASS1) provides the largest intracluster medium-selected galaxy cluster and group catalog covering the western galactic hemisphere. Compared to samples selected purely on X-ray extent, the sample purity can be enhanced by identifying cluster candidates using optical and near-infrared data from the DESI Legacy Imaging Surveys. Using the red-sequence-based cluster finder eROMaPPer, we measured individual photometric properties (redshift $z_\lambda$, richness $\lambda$, optical center, and BCG position) for 12,000 eRASS1 clusters over a sky area of 13,116 deg$^2$, augmented by 247 cases identified by matching the candidates with known clusters from the literature. The median redshift of the identified eRASS1 sample is $z=0.31$, with 10% of the clusters at $z>0.72$. The photometric redshifts have an accuracy of $\delta z/(1+z)<0.005$ for $0.0595% for $z>0.05$. For these and further quality assessments of the eRASS1 identified catalog, we applied our identification method to a collection of galaxy cluster catalogs in the literature, as well as blindly on the full Legacy Surveys covering 24,069 deg$^2$. Using a combination of these cluster samples, we investigated the velocity dispersion-richness relation, finding $\log(\lambda)=2.401\times\log(\sigma)-5.074$ with an intrinsic scatter of $0.10\pm0.01$ dex. Our main result is the identified eRASS1 cluster catalog with a high purity and a well-defined X-ray selection process, enabling precise cosmological analyses presented in companion papers., Comment: 36 pages, 23 figures, 6 tables. Accepted for publication in A&A

Published
2024
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2. Observations of magnetic reconnection in the deep solar atmosphere in the H-epsilon line

Author

van der Voort, L. Rouppe, Joshi, J., and Krikova, K.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

Magnetic reconnection in the deep solar atmosphere can give rise to enhanced emission in the Balmer hydrogen lines, a phenomenon known as Ellerman bombs (EBs). It is most common to observe EBs in the H-alpha and H-beta lines. High quality shorter wavelength Balmer line observations of EBs are rare but have the potential to provide the most highly resolved view on reconnection. We evaluate the H-epsilon 3970 A line as an EB diagnostic by analyzing high quality observations in different Balmer lines. Observations of different targets and viewing angles were acquired with the Swedish 1-m Solar Telescope. These observations sample EBs in different environments: active regions, quiet Sun, and the penumbra and moat of a sunspot. We employed an automated detection method for quiet Sun EBs based on k-means clustering. Ellerman bombs in the H-epsilon line show similar characteristics as in the longer wavelength Balmer lines: enhanced intensity as compared to the surroundings, rapid variability, and flame-like morphology. In a 24 min quiet Sun time series, we detected 1674 EBs in the H-epsilon line which is 1.7 times more than in H-beta. The quiet Sun EBs measured in H-epsilon are very similar as in H-beta: they have similar lifetimes, area, brightness, and spatial distribution. Most of the EBs detected in H-epsilon are closer to the limb than their H-beta counterparts. This can be explained by the H-epsilon line core EB emission being formed higher in the atmosphere than the H-beta EB wing emission. We conclude that the H-epsilon line is well suited for studying EBs and consequently probes the dynamics of magnetic reconnection in the solar atmosphere at the smallest scales. Our findings suggests that the deep atmosphere in the quiet Sun may host more than 750,000 reconnection events with EB signature at any time. That is significantly more than what was found in earlier H-beta observations., Comment: accepted for publication in A&A. Movies can be found at https://www.mn.uio.no/astro/english/people/aca/rouppe/movies/

Published
2024

3. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

Author

Zhao, Shuang G., Bootsma, Matthew, Zhou, Stanley, Shrestha, Raunak, Moreno-Rodriguez, Thaidy, Lundberg, Arian, Pan, Chu, Arlidge, Christopher, Hawley, James R., Foye, Adam, Weinstein, Alana S., Sjöström, Martin, Zhang, Meng, Li, Haolong, Chesner, Lisa N., Rydzewski, Nicholas R., Helzer, Kyle T., Shi, Yue, Lynch, Molly, Dehm, Scott M., Lang, Joshua M., Alumkal, Joshi J., He, Hansen H., Wyatt, Alexander W., Aggarwal, Rahul, Zwart, Wilbert, Small, Eric J., Quigley, David A., Lupien, Mathieu, and Feng, Felix Y.

Published
2024
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7. The genomic and epigenomic landscape of double-negative metastatic prostate cancer

Author

Lundberg, Arian, Zhang, Meng, Aggarwal, Rahul, Li, Haolong, Zhang, Li, Foye, Adam, Sjöström, Martin, Chou, Jonathan, Chang, Kevin, Moreno-Rodriguez, Thaidy, Shrestha, Raunak, Baskin, Avi, Zhu, Xiaolin, Weinstein, Alana S, Younger, Noah, Alumkal, Joshi J, Beer, Tomasz M, N., Kim, Evans, Christopher P, Gleave, Martin, Lara, Primo N, Reiter, Rob E, Rettig, Matthew B, Witte, Owen N, Wyatt, Alexander W, Feng, Felix Y, Small, Eric J, and Quigley, David A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Genetics, Cancer Genomics, Cancer, Urologic Diseases, Human Genome, Precision Medicine, Biotechnology, Prostate Cancer, Good Health and Well Being, Humans, Male, Prostatic Neoplasms, Castration-Resistant, Receptors, Androgen, Epigenomics, Androgen Antagonists, Androgens, Genomics, Neuroendocrine Tumors, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen signaling. Androgen deprivation therapy and second-generation androgen receptor (AR)-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration-resistant prostate cancer (mCRPC), defined by AR and neuroendocrine (NE) markers. Molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterized treatment-emergent mCRPC by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing from 210 tumors. AR-/NE- tumors were clinically and molecularly distinct from other mCRPC subtypes, with the shortest survival, amplification of the chromatin remodeler CHD7, and PTEN loss. Methylation changes in CHD7 candidate enhancers were linked to elevated CHD7 expression in AR-/NE+ tumors. Genome-wide methylation analysis nominated Krüppel-like factor 5 (KLF5) as a driver of the AR-/NE- phenotype, and KLF5 activity was linked to RB1 loss. These observations reveal the aggressiveness of AR-/NE- mCRPC and could facilitate the identification of therapeutic targets in this highly aggressive disease.SignificanceComprehensive characterization of the five subtypes of metastatic castration-resistant prostate cancer identified transcription factors that drive each subtype and showed that the double-negative subtype has the worst prognosis.

Published
2023

10. Design and Development of 10 MJ Capacitor Bank Pulsed Power Source for Electromagnetic Railgun

Author

Kumar, Gaurav, Swarup, Satyam, Rajput, Shivam, Nomula, Prasanth, Pawar, Anil, Joshi, J. C., Kumar, Pradeep, Nayak, S. K., Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, and Sharma, Archana, editor

Published
2024
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11. Modeling and Simulation of High Energy Capacitor Bank based Electromagnetic Railgun

Author

Rajput, Shivam, Kumar, Gaurav, Swarup, Satyam, Nomula, Prasanth, Pawar, Anil, Joshi, J. C., Kumar, Pradeep, Nayak, S. K., Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, and Sharma, Archana, editor

Published
2024
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13. Survival by first‐line therapy and prognostic group among men with metastatic castration‐resistant prostate cancer

Author

Megan E. V. Caram, Kyle Kumbier, Phoebe A. Tsao, Jennifer Burns, Jordan B. Sparks, Kristian D. Stensland, Zachery R. Reichert, Joshi J. Alumkal, Brent K. Hollenbeck, Vahakn Shahinian, Alexander Tsodikov, and Ted A. Skolarus

Subjects
novel therapies, prognosis, prostate cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Introduction Metastatic castration‐resistant prostate cancer (mCRPC) is a heterogeneous disease with prognoses varying from months to years at time of castration‐resistant diagnosis. Optimal first‐line therapy for those with different prognoses is unknown. Methods We conducted a retrospective cohort study of men in a national healthcare delivery system receiving first‐line therapy for mCRPC (abiraterone, enzalutamide, docetaxel, or ketoconazole) from 2010 to 2017, with follow‐up through 2019. Using commonly drawn prognostic labs at start of mCRPC therapy (hemoglobin, albumin, and alkaline phosphatase), we categorized men into favorable, intermediate, or poor prognostic groups depending on whether they had none, one to two, or all three laboratory values worse than designated laboratory cutoffs. We used Kaplan–Meier methods to examine prostate specific antigen (PSA) progression‐free and overall survival (OS) according to prognostic group and first‐line therapy, and multivariable cox regression to determine variables associated with survival outcomes. Results Among 4135 patients, median PSA progression‐free survival (PFS) was 6.9 months (95% confidence interval [CI] 6.6–7.3), and median OS 18.8 months (95% CI 18.0–19.6), ranging from 5.7 months (95% CI 4.8–7.0) in the poor prognosis group to 31.3 months (95% CI 29.7–32.9) in the favorable group. OS was similar regardless of initial treatment received for favorable and intermediate groups, but worse for those in the poor prognostic group who received ketoconazole (adjusted hazard ratio 2.07, 95% CI 1.2–3.6). PSA PFS was worse for those who received ketoconazole compared to abiraterone across all prognostic groups (favorable HR 1.76, 95% CI 1.34–2.31; intermediate HR 1.78, 95% CI 1.41–2.25; poor HR 8.01, 95% CI 2.93–21.9). Conclusion Commonly drawn labs at mCRPC treatment start may aid in predicting survival and response to therapies, potentially informing discussions with care teams. First‐line treatment selection impacts disease progression for all men with mCRPC regardless of prognostic group, but impacted OS only for men with poor prognosis at treatment start.

Published
2024
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14. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

Author

Sjöström, Martin, Zhao, Shuang G, Levy, Samuel, Zhang, Meng, Ning, Yuhong, Shrestha, Raunak, Lundberg, Arian, Herberts, Cameron, Foye, Adam, Aggarwal, Rahul, Hua, Junjie T, Li, Haolong, Bergamaschi, Anna, Maurice-Dror, Corinne, Maheshwari, Ashutosh, Chen, Sujun, Ng, Sarah WS, Ye, Wenbin, Petricca, Jessica, Fraser, Michael, Chesner, Lisa, Perry, Marc D, Moreno-Rodriguez, Thaidy, Chen, William S, Alumkal, Joshi J, Chou, Jonathan, Morgans, Alicia K, Beer, Tomasz M, Thomas, George V, Gleave, Martin, Lloyd, Paul, Phillips, Tierney, McCarthy, Erin, Haffner, Michael C, Zoubeidi, Amina, Annala, Matti, Reiter, Robert E, Rettig, Matthew B, Witte, Owen N, Fong, Lawrence, Bose, Rohit, Huang, Franklin W, Luo, Jianhua, Bjartell, Anders, Lang, Joshua M, Mahajan, Nupam P, Lara, Primo N, Evans, Christopher P, Tran, Phuoc T, Posadas, Edwin M, He, Chuan, Cui, Xiao-Long, Huang, Jiaoti, Zwart, Wilbert, Gilbert, Luke A, Maher, Christopher A, Boutros, Paul C, N., Kim, Ashworth, Alan, Small, Eric J, He, Housheng H, Wyatt, Alexander W, Quigley, David A, and Feng, Felix Y

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Oncology and Carcinogenesis, Urologic Diseases, Cancer, Prostate Cancer, Human Genome, Aging, Cancer Genomics, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, 4.2 Evaluation of markers and technologies, Good Health and Well Being, Male, Humans, 5-Methylcytosine, Prostatic Neoplasms, Prostate, Biopsy, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease.SignificanceIn prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.

Published
2022

15. Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.

Author

Westbrook, Thomas C, Guan, Xiangnan, Rodansky, Eva, Flores, Diana, Liu, Chia Jen, Udager, Aaron M, Patel, Radhika A, Haffner, Michael C, Hu, Ya-Mei, Sun, Duanchen, Beer, Tomasz M, Foye, Adam, Aggarwal, Rahul, Quigley, David A, Youngren, Jack F, Ryan, Charles J, Gleave, Martin, Wang, Yuzhuo, Huang, Jiaoti, Coleman, Ilsa, Morrissey, Colm, Nelson, Peter S, Evans, Christopher P, Lara, Primo, Reiter, Robert E, Witte, Owen, Rettig, Matthew, Wong, Christopher K, Weinstein, Alana S, Uzunangelov, Vlado, Stuart, Josh M, Thomas, George V, Feng, Felix Y, Small, Eric J, Yates, Joel A, Xia, Zheng, and Alumkal, Joshi J

Subjects
Cell Line, Tumor, Humans, Benzamides, Nitriles, Phenylthiohydantoin, Receptors, Androgen, RNA, Biopsy, Drug Resistance, Neoplasm, Male, E2F1 Transcription Factor, Androgen Receptor Antagonists, Prostatic Neoplasms, Castration-Resistant, Prostate Cancer, Genetics, Urologic Diseases, Cancer, Clinical Research, 2.1 Biological and endogenous factors, Aetiology
Abstract

The androgen receptor (AR) signaling inhibitor enzalutamide (enza) is one of the principal treatments for metastatic castration-resistant prostate cancer (CRPC). Several emergent enza clinical resistance mechanisms have been described, including lineage plasticity in which the tumors manifest reduced dependency on the AR. To improve our understanding of enza resistance, herein we analyze the transcriptomes of matched biopsies from men with metastatic CRPC obtained prior to treatment and at progression (n = 21). RNA-sequencing analysis demonstrates that enza does not induce marked, sustained changes in the tumor transcriptome in most patients. However, three patients' progression biopsies show evidence of lineage plasticity. The transcription factor E2F1 and pathways linked to tumor stemness are highly activated in baseline biopsies from patients whose tumors undergo lineage plasticity. We find a gene signature enriched in these baseline biopsies that is strongly associated with poor survival in independent patient cohorts and with risk of castration-induced lineage plasticity in patient-derived xenograft models, suggesting that tumors harboring this gene expression program may be at particular risk for resistance mediated by lineage plasticity and poor outcomes.

Published
2022

19. Signatures of ubiquitous magnetic reconnection in the deep atmosphere of sunspot penumbrae

Author

van der Voort, L. H. M. Rouppe, Joshi, J., Henriques, V. M. J., and Bose, S.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

Ellerman bombs are regions with enhanced Balmer line wing emission and mark magnetic reconnection in the deep solar atmosphere in active regions and quiet Sun. They are often found in regions where opposite magnetic polarities are in close proximity. Recent high resolution observations suggest that Ellerman bombs are more prevalent than thought before. We aim to determine the occurrence of Ellerman bombs in the penumbra of sunspots. We analyze high spatial resolution observations of sunspots in the Balmer H-alpha and H-beta lines as well as auxiliary continuum channels obtained with the Swedish 1-m Solar Telescope and apply the k-means clustering technique to systematically detect and characterize Ellerman Bombs. Features with all the defining characteristics of Ellerman bombs are found in large numbers over the entire penumbra. The true prevalence of these events is only fully appreciated in the H-beta line due to highest spatial resolution and lower chromospheric opacity. We find that the penumbra hosts some of the highest Ellerman bomb densities, only surpassed by the moat in the immediate surroundings of the sunspot. Some penumbral Ellerman bombs show flame morphology and rapid dynamical evolution. Many penumbral Ellerman bombs are fast moving with typical speed of 3.7 km/s and sometimes more than 10 km/s. Many penumbral Ellerman bombs migrate from the inner to the outer penumbra over hundreds of km and some continue moving beyond the outer penumbral boundary into the moat. Many penumbral Ellerman bombs are found in the vicinity of regions with opposite magnetic polarity. We conclude that reconnection is a near continuous process in the low atmosphere of the penumbra of sunspots as manifest in the form of penumbral Ellerman bombs. These are so prevalent that they may be a major sink of sunspot magnetic energy., Comment: accepted for publication in A&A. Movies can be found at https://www.mn.uio.no/astro/english/people/aca/rouppe/movies/

Published
2021
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20. Measurement of the Atmospheric Muon Rate with the MicroBooNE Liquid Argon TPC

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Basque, V., Bass, M., Bay, F., Berkman, S., Bhanderi, A., Bhat, A., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Foppiani, N., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Gardiner, S., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Green, P., Greenlee, H., Grosso, R., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. C., Itay, R., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Jo, J. H., Johnson, R. A., Joshi, J., Jwa, Y. J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., McConkey, N., Meddage, V., Mettler, T., Miller, K., Mills, J., Mistry, K., Mohayai, T., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Neely, R. K., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Paudel, A., Pavlovic, Z., Piasetzky, E., Porzio, D., Prince, S., Pulliam, G., Qian, X., Raaf, J. L., Radeka, V., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Uchida, M. A., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wospakrik, M., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

MicroBooNE is a near-surface liquid argon (LAr) time projection chamber (TPC) located at Fermilab. We measure the characterisation of muons originating from cosmic interactions in the atmosphere using both the charge collection and light readout detectors. The data is compared with the CORSIKA cosmic-ray simulation. Good agreement is found between the observation, simulation and previous results. Furthermore, the angular resolution of the reconstructed muons inside the TPC is studied in simulation., Comment: 20 pages, 14 figures

Published
2020
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21. Comparison of $pp$ and $p \bar{p}$ differential elastic cross sections and observation of the exchange of a colorless $C$-odd gluonic compound

Author

Abazov, V. M., Abbott, B., Acharya, B. S., Adams, M., Adams, T., Agnew, J. P., Alexeev, G. D., Alkhazov, G., Alton, A., Alves, G. A., Antchev, G., Askew, A., Aspell, P., Jesus, A. C. S. Assis, Atanassov, I., Atkins, S., Augsten, K., Aushev, V., Aushev, Y., Avati, V., Avila, C., Badaud, F., Baechler, J., Bagby, L., Barrera, C. Baldenegro, Baldin, B., Bandurin, D. V., Banerjee, S., Barberis, E., Baringer, P., Barreto, J., Bartlett, J. F., Bassler, U., Bazterra, V., Bean, A., Begalli, M., Bellantoni, L., Berardi, V., Beri, S. B., Bernardi, G., Bernhard, R., Berretti, M., Bertram, I., Besanccon, M., Beuselinck, R., Bhat, P. C., Bhatia, S., Bhatnagar, V., Blazey, G., Blessing, S., Bloom, K., Boehnlein, A., Boline, D., Boos, E. E., Borchsh, V., Borissov, G., Borysova, M., Bossini, E., Bottigli, U., Bozzo, M., Brandt, A., Brandt, O., Brochmann, M., Brock, R., Bross, A., Brown, D., Bu, X. B., Buehler, M., Buescher, V., Bunichev, V., Burdin, S., Burkhardt, H., Buszello, C. P., Cafagna, F. S., Camacho-P'erez, E., Carvahlo, W., Casey, B. C. K., Castilla-Valdez, H., Catanesi, M. G., Caughron, S., Chakrabarti, S., Chan, K. M., Chandra, A., Chapon, E., Chen, G., Cho, S. W., Choi, S., Choudhary, B., Cihangir, S., Claes, D., Clutter, J., Cooke, M., Cooper, W. E., Corcoran, M., Couderc, F., Cousinou, M. -C., Csan'ad, M., Cs"orgHo, T., Cuth, J., Cutts, D., Das, A., Davies, G., Deile, M., de Jong, S. J., De La Cruz-Burelo, E., De Leonardis, F., D'eliot, F., Demina, R., Denisov, D., Denisov, S. P., Desai, S., Deterre, C., DeVaughan, K., Diehl, H. T., Diesburg, M., Ding, P. F., Dominguez, A., Doubek, M., Drutskoy, A., Druzhkin, D., Dubey, A., Dudko, L. V., Duperrin, A., Dutt, S., Eads, M., Edmunds, D., Eggert, K., Ellison, J., Elvira, V. D., Enari, Y., Eremin, V., Evans, H., Evdokimov, A., Evdokimov, V. N., Faur'e, A., Feng, L., Ferbel, T., Ferro, F., Fiedler, F., Fiergolski, A., Filthaut, F., Fisher, W., Fisk, H. E., Forthomme, L., Fortner, M., Fox, H., Franc, J., Fuess, S., Garbincius, P. H., Garcia, F., Garcia-Bellido, A., Garc'ia-Gonz'alez, J. A., Gavrilov, V., Geng, W., Georgiev, V., Gerber, C. E., Gershtein, Y., Giani, S., Ginther, G., Gogota, O., Golovanov, G., Grannis, P. D., Greder, S., Greenlee, H., Grenier, G., Gris, Ph., Grivaz, J. -F., Grohsjean, A., Gr"unendahl, S., Gr"unewald, M. W., Grzanka, L., Guillemin, T., Gutierrez, G., Gutierrez, P., Haley, J., Hammerbauer, J., Han, L., Harder, K., Harel, A., Hauptman, J. M., Hays, J., Head, T., Hebbeker, T., Hedin, D., Hegab, H., Heinson, A. P., Heintz, U., Hensel, C., La Cruz, I. Heredia-De, Herner, K., Hesketh, G., Hildreth, M. D., Hirosky, R., Hoang, T., Hobbs, J. D., Hoeneisen, B., Hogan, J., Hohlfeld, M., Holzbauer, J. L., Howley, I., Hubacek, Z., Hynek, V., Iashvili, I., Ilchenko, Y., Illingworth, R., Isidori, T., Ito, A. S., Ivanchenko, V., Jabeen, S., Jaffr'e, M., Janda, M., Jayasinghe, A., Jeong, M. S., Jesik, R., Jiang, P., Johns, K., Johnson, E., Johnson, M., Jonckheere, A., Jonsson, P., Joshi, J., Jung, A. W., Juste, A., Kajfasz, E., Karev, A., Karmanov, D., Kavspar, J., Katsanos, I., Kaur, M., Kaynak, B., Kehoe, R., Kermiche, S., Khalatyan, N., Khanov, A., Kharchilava, A., Kharzheev, Y. N., Kiselevich, I., Kohli, J. M., Kopal, J., Kozelov, A. V., Kraus, J., Kumar, A., Kundr'at, V., Kupco, A., Kurvca, T., Kuzmin, V. A., Lami, S., Lammers, S., Latino, G., Lebrun, P., Lee, H. S., Lee, S. W., Lee, W. M., Le, X., Lellouch, J., Li, D., Li, H., Li, L., Li, Q. Z., Lim, J. K., Lincoln, D., Lindsey, C., Linhart, R., Linnemann, J., Lipaev, V. V., Lipton, R., Liu, H., Liu, Y., Lobodenko, A., Lokajicek, M., Lokaj'ivcek, M. V., de Sa, R. Lopes, Losurdo, L., Rodr'iguez, F. Lucas, Luna-Garcia, R., Lyon, A. L., Maciel, A. K. A., Macr'i, M., Madar, R., na-Villalba, R. Maga, Malawski, M., Malbouisson, H. B., Malik, S., Malyshev, V. L., Mansour, J., Mart'inez-Ortega, J., McCarthy, R., McGivern, C. L., Meijer, M. M., Melnitchouk, A., Menezes, D., Mercadante, P. G., Merkin, M., Meyer, A., Meyer, J., Miconi, F., Minafra, N., Minutoli, S., Molina, J., Mondal, N. K., Da Motta, H., Mulhearn, M., Mundim, L., Naaranoja, T., Nagy, E., Narain, M., Nayyar, R., Neal, H. A., Negret, J. P., Nemes, F., Neustroev, P., Nguyen, H. T., Niewiadomski, H., Nov'ak, T., Nunnemann, T., Oguri, V., Oliveri, E., Oljemark, F., Orduna, J., Oriunno, M., Osman, N., "Osterberg, K., Pal, A., Palazzi, P., Parashar, N., Parihar, V., Park, S. K., Partridge, R., Parua, N., Pasechnik, R., Passaro, V., Patwa, A., Penning, B., Perfilov, M., Peroutka, Z., Peters, Y., Petridis, K., Petrillo, G., P'etroff, P., Pleier, M. -A., Podstavkov, V. M., Popov, A. V., Da Silva, W. L. Prado, Prewitt, M., Price, D., Proch'azka, J., Prokopenko, N., Qian, J., Quadt, A., Quinn, B., Quinto, M., Raben, T. G., Radermacher, E., Rangel, M., Radicioni, E., Ratoff, P. N., Ravotti, F., Razumov, I., Ripp-Baudot, I., Rizatdinova, F., Robutti, E., Rodrigues, R. F., Rominsky, M., Ross, A., Royon, C., Rubinov, P., Ruchti, R., Ruggiero, G., Saarikko, H., Sajot, G., Samoylenko, V. D., S'anchez-Hern'andez, A., Sanders, M. P., Santoro, A., Santos, A. S., Savage, G., Savitskyi, M., Sawyer, L., Scanlon, T., Schamberger, R. D., Scheglov, Y., Schellman, H., Schott, M., Schwanenberger, C., Schwienhorst, R., Scribano, A., Sekaric, J., Severini, H., Shabalina, E., Shary, V., Shaw, S., Shchukin, A. A., Shkola, O., Simak, V., Siroky, J., Skubic, P., Slattery, P., Smajek, J., Snoeys, W., Snow, G. R., Snow, J., Snyder, S., S"oldner-Rembold, S., Sonnenschein, L., Soustruznik, K., Stark, J., Stefaniuk, N., Stefanovitch, R., Ster, A., Stoyanova, D. A., Strauss, M., Suter, L., Svoisky, P., Szanyi, I., Sziklai, J., Taylor, C., Tcherniaev, E., Titov, M., Tokmenin, V. V., Tsai, Y. -T., Tsybychev, D., Tuchming, B., Tully, C., Turini, N., Urban, O., Uvarov, L., Uvarov, S., Uzunyan, S., Vacek, V., Van Kooten, R., van Leeuwen, W. M., Varelas, N., Varnes, E. W., Vasilyev, I. A., Vavroch, O., Verkheev, A. Y., Vertogradov, L. S., Verzocchi, M., Vesterinen, M., Vilanova, D., Vokac, P., Wahl, H. D., Wang, C., Wang, M. H. L. S., Warchol, J., Watts, G., Wayne, M., Weichert, J., Welti, J., Welty-Rieger, L., Williams, J., Williams, M. R. J., Wilson, G. W., Wobisch, M., Wood, D. R., Wyatt, T. R., Xie, Y., Yamada, R., Yang, S., Yasuda, T., Yatsunenko, Y. A., Ye, W., Ye, Z., Yin, H., Yip, K., Youn, S. W., Yu, J. M., Zennamo, J., Zhao, T. G., Zhou, B., Zhu, J., Zich, J., Zielinski, K., Zielinski, M., Zieminska, D., and Zivkovic, L.

Subjects
High Energy Physics - Experiment
Abstract

We describe an analysis comparing the $p\bar{p}$ elastic cross section as measured by the D0 Collaboration at a center-of-mass energy of 1.96 TeV to that in $pp$ collisions as measured by the TOTEM Collaboration at 2.76, 7, 8, and 13 TeV using a model-independent approach. The TOTEM cross sections extrapolated to a center-of-mass energy of $\sqrt{s} =$ 1.96 TeV are compared with the D0 measurement in the region of the diffractive minimum and the second maximum of the $pp$ cross section. The two data sets disagree at the 3.4$\sigma$ level and thus provide evidence for the $t$-channel exchange of a colorless, $C$-odd gluonic compound, also known as the odderon. We combine these results with a TOTEM analysis of the same $C$-odd exchange based on the total cross section and the ratio of the real to imaginary parts of the forward elastic scattering amplitude in $pp$ scattering. The combined significance of these results is larger than 5$\sigma$ and is interpreted as the first observation of the exchange of a colorless, $C$-odd gluonic compound., Comment: D0 and TOTEM Collaborations

Published
2020
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23. Line formation of He I D3 and He I 10830 {\AA} in a small-scale reconnection event

Author

Libbrecht, T., Bjørgen, J. P., Leenaarts, J., Rodríguez, J. de la Cruz, Hansteen, V., and Joshi, J.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

Aims. We aim to explain line formation of He I D3 and He I 10830 {\AA} in small-scale reconnection events. Methods. We make use of a simulated Ellerman bomb (EB), present in a Bifrost-generated radiative Magnetohydrodynamics (rMHD) snapshot. The resulting He I D3 and He I 10830 \AA\ line intensities are synthesized in 3D using the non-LTE Multi3D code. We compare the synthetic helium spectra with observed SST/TRIPPEL raster scans of EBs in He I 10830 \AA\ and He I D3. Results. Emission in He I D3 and He I 10830 \AA\ is formed in a thin shell around the EB at a height of $\sim 0.8$ Mm while the He I D3 absorption is formed above the EB at $\sim 4$ Mm. The height at which the emission is formed corresponds to the lower boundary of the EB, where the temperature increases rapidly from $6\cdot 10^3$ K to $10^6$ K. The opacity in He I D3 and He I 10830 \AA\ is generated via photoionization-recombination driven by EUV radiation that is locally generated in the EB at temperatures in the range of $2\cdot 10^4 - 2\cdot 10^6$ K and electron densities between $10^{11}$ and $10^{13}$ cm$^{-3}$. The synthetic emission signals are a result of coupling to local conditions in a thin shell around the EB, with temperatures between $7\cdot 10^3$ and $10^4$ K and electron densities ranging from $\sim 10^{12}$ to $10^{13}$ cm$^{-3}$. Hence, both strong non-LTE as well as thermal processes play a role in the formation of He I D3 and He I 10830 \AA\ in the synthetic EB/UV burst that we studied. Conclusions. In conclusion, the synthetic He I D3 and He I 10830 \AA\ emission signatures are an indicator of temperatures of at least $2\cdot 10^4$ K and in this case as high as $\sim 10^6$ K., Comment: 12 pages, 13 figures, submitted to A&A

Published
2020
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24. High-resolution observations of the solar photosphere, chromosphere and transition region. A database of coordinated IRIS and SST observations

Author

van der Voort, L. H. M. Rouppe, De Pontieu, B., Carlsson, M., Rodriguez, J. de la Cruz, Bose, S., Chintzoglou, G., Drews, A., Froment, C., Gosic, M., Graham, D. R., Hansteen, V. H., Henriques, V. M. J., Jafarzadeh, S., Joshi, J., Kleint, L., Kohutova, P., Leifsen, T., Martinez-Sykora, J., Nobrega-Siverio, D., Ortiz, A., Pereira, T. M. D., Popovas, A., Noda, C. Quintero, Dalda, A. Sainz, Scharmer, G. B., Schmit, D., Scullion, E., Skogsrud, H., Szydlarski, M., Timmons, R., Vissers, G. J. M., Woods, M. M., and Zacharias, P.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

NASA's Interface Region Imaging Spectrograph (IRIS) provides high resolution observations of the solar atmosphere through UV spectroscopy and imaging. Since the launch of IRIS in June 2013, we have conducted systematic observation campaigns in coordination with the Swedish 1-m Solar Telescope (SST) on La Palma. The SST provides complementary high-resolution observations of the photosphere and chromosphere. The SST observations include spectro-polarimetric imaging in photospheric Fe I lines and spectrally-resolved imaging in the chromospheric Ca II 8542 A, H-alpha, and Ca II K lines. We present a database of co-aligned IRIS and SST datasets that is open for analysis to the scientific community. The database covers a variety of targets including active regions, sunspots, plage, quiet Sun, and coronal holes., Comment: Accepted for publication in Astronomy & Astrophysics (July 21, 2020)

Published
2020
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25. The ProtoDUNE-SP LArTPC Electronics Production, Commissioning, and Performance

Author

Adams, D., Bass, M., Bishai, M., Bromberg, C., Calcutt, J., Chen, H., Fried, J., Furic, I., Gao, S., Gastler, D., Hugon, J., Joshi, J., Kirby, B., Liu, F., Mahn, K., Mooney, M., Morris, C., Pereyra, C., Pons, X., Radeka, V., Raguzin, E., Shooltz, D., Spanu, M., Timilsina, A., Tufanli, S., Tzanov, M., Viren, B., Gu, W., Williams, Z., Wood, K., Worcester, E., Worcester, M., Yang, G., and Zhang, J.

Subjects
Physics - Instrumentation and Detectors
Abstract

The ProtoDUNE-SP detector is a large-scale prototype of the Single-Phase (SP) Liquid Argon Time Projection Chamber (LArTPC) design proposed for the Deep Underground Neutrino Experiment (DUNE). 15,360 LArTPC wires are instrumented with low electronic noise pre-amplifier and digitization ASICs integrated into Front End Motherboards (FEMBs) operating at cryogenic temperature within the cryostat. The large number of electronics channels and high performance specifications required a large-scale production electronics quality control effort, careful installation into Anode Plane Assemblies (APAs), and rigorous detector commissioning. This successful collaboration-wide effort achieved a working LArTPC electronics channel percentage of 99.7% (15,318 of 15,360 channels in total), whose operating performance exceeded expectations. We summarize the ProtoDUNE-SP cold electronics design and quality control, installation, and commissioning efforts that enabled this excellent electronics performance.

Published
2020
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26. Prostate Radiotherapy With Adjuvant Androgen Deprivation Therapy (ADT) Improves Metastasis-Free Survival Compared to Neoadjuvant ADT: An Individual Patient Meta-Analysis.

Author

Spratt, Daniel E, Malone, Shawn, Roy, Soumyajit, Grimes, Scott, Eapen, Libni, Morgan, Scott C, Malone, Julia, Craig, Julia, Dess, Robert T, Jackson, William C, Hartman, Holly E, Kishan, Amar U, Mehra, Rohit, Kaffenberger, Samuel, Morgan, Todd M, Reichert, Zachery R, Alumkal, Joshi J, Michalski, Jeff, Lee, W Robert, Pisansky, Thomas M, Feng, Felix Y, Shipley, William, Sandler, Howard M, Schipper, Mathew J, Roach, Mack, Sun, Yilun, and Lawton, Colleen AF

Subjects
Clinical Research, Aging, Urologic Diseases, Prostate Cancer, Cancer, Clinical Trials and Supportive Activities, Good Health and Well Being, Androgen Antagonists, Clinical Trials, Phase III as Topic, Humans, Male, Neoadjuvant Therapy, Neoplasm Metastasis, Prostatic Neoplasms, Randomized Controlled Trials as Topic, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeThere remains a lack of clarity regarding the influence of sequencing of androgen deprivation therapy (ADT) and radiotherapy (RT) on outcomes in prostate cancer (PCa). Herein, we evaluate the optimal sequencing of ADT with prostate-directed RT in localized PCa.MethodsMEDLINE (1966-2018), Embase (1982-2018), ClinicalTrials.gov, and conference proceedings (1990-2018) were searched to identify randomized trials evaluating the sequencing, but not duration, of ADT with RT. Two randomized phase III trials were identified, and individual patient data were obtained: Ottawa 0101 and NRG Oncology's Radiation Therapy Oncology Group 9413. Ottawa 0101 randomly assigned patients to neoadjuvant or concurrent versus concurrent or adjuvant short-term ADT. Radiation Therapy Oncology Group 9413, a 2 × 2 factorial trial, included a random assignment of neoadjuvant or concurrent versus adjuvant short-term ADT. The neoadjuvant or concurrent ADT arms of both trials were combined into the neoadjuvant group, and the arms receiving adjuvant ADT were combined into the adjuvant group. The primary end point of this meta-analysis was progression-free survival (PFS).ResultsThe median follow-up was 14.9 years. Overall, 1,065 patients were included (531 neoadjuvant and 534 adjuvant). PFS was significantly improved in the adjuvant group (15-year PFS, 29% v 36%, hazard ratio [HR], 1.25 [95% CI, 1.07 to 1.47], P = .01). Biochemical failure (subdistribution HR [sHR], 1.37 [95% CI, 1.12 to 1.68], P = .002), distant metastasis (sHR, 1.40 [95% CI, 1.00 to 1.95], P = .04), and metastasis-free survival (HR, 1.17 [95% CI, 1.00 to 1.37], P = .050) were all significantly improved in the adjuvant group. There were no differences in late grade ≥ 3 gastrointestinal (2% v 3%, P = .33) or genitourinary toxicity (5% v 5%, P = .76) between groups.ConclusionThe sequencing of ADT with prostate-directed RT has significant association with long-term PFS and MFS in localized PCa. Our findings favor use of an adjuvant over a neoadjuvant approach, without any increase in long-term toxicity.

Published
2021

27. Autoantibody Landscape in Patients with Advanced Prostate Cancer

Author

Chen, William S, Haynes, Winston A, Waitz, Rebecca, Kamath, Kathy, Vega-Crespo, Agustin, Shrestha, Raunak, Zhang, Minlu, Foye, Adam, Carretero, Ignacio Baselga, Garcilazo, Ivan Perez, Zhang, Meng, Zhao, Shuang G, Sjöström, Martin, Quigley, David A, Chou, Jonathan, Beer, Tomasz M, Rettig, Matthew, Gleave, Martin, Evans, Christopher P, Lara, Primo, N., Kim, Reiter, Robert E, Alumkal, Joshi J, Ashworth, Alan, Aggarwal, Rahul, Small, Eric J, Daugherty, Patrick S, Ribas, Antoni, Oh, David Y, Shon, John C, and Feng, Felix Y

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer, Human Genome, Cancer Genomics, Clinical Research, Biotechnology, Prostate Cancer, Vaccine Related, Immunization, Urologic Diseases, Genetics, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Aged, Antigens, Neoplasm, Autoantibodies, Biomarkers, Tumor, Case-Control Studies, Epitopes, Follow-Up Studies, Humans, Male, Mutation, Prognosis, Prospective Studies, Prostatic Neoplasms, Oncology & Carcinogenesis, Clinical sciences, Oncology and carcinogenesis
Abstract

PurposeAutoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC).Experimental designSerum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation-specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes.ResultsSERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1.ConclusionsWe present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest.

Published
2020

28. Search for heavy neutral leptons decaying into muon-pion pairs in the MicroBooNE detector

Author

Abratenko, P., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Basque, V., Berkman, S., Bhanderi, A., Bhat, A., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadón, J. I., Del Tutto, M., Devitt, D., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Foppiani, N., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Gardiner, S., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Green, P., Greenlee, H., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. -C., Itay, R., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Jo, J. H., Johnson, R. A., Joshi, J., Jwa, Y. -J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., LaZur, R., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., McConkey, N., Meddage, V., Mettler, T., Miller, K., Mills, J., Mistry, K., Mogan, A., Mohayai, T., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murrells, R., Naples, D., Neely, R. K., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Paudel, A., Pavlovic, Z., Piasetzky, E., Porzio, D., Prince, S., Pulliam, G., Qian, X., Raaf, J. L., Radeka, V., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Söldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Uchida, M. A., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wospakrik, M., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

We present upper limits on the production of heavy neutral leptons (HNLs) decaying to $\mu \pi$ pairs using data collected with the MicroBooNE liquid-argon time projection chamber (TPC) operating at Fermilab. This search is the first of its kind performed in a liquid-argon TPC. We use data collected in 2017 and 2018 corresponding to an exposure of $2.0 \times 10^{20}$ protons on target from the Fermilab Booster Neutrino Beam, which produces mainly muon neutrinos with an average energy of $\approx 800$ MeV. HNLs with higher mass are expected to have a longer time-of-flight to the liquid-argon TPC than Standard Model neutrinos. The data are therefore recorded with a dedicated trigger configured to detect HNL decays that occur after the neutrino spill reaches the detector. We set upper limits at the $90\%$ confidence level on the element $\lvert U_{\mu4}\rvert^2$ of the extended PMNS mixing matrix in the range $\lvert U_{\mu4}\rvert^2<(6.6$-$0.9)\times 10^{-7}$ for Dirac HNLs and $\lvert U_{\mu4}\rvert^2<(4.7$-$0.7)\times 10^{-7}$ for Majorana HNLs, assuming HNL masses between $260$ and $385$ MeV and $\lvert U_{e 4}\rvert^2 = \lvert U_{\tau 4}\rvert^2 = 0$., Comment: 11 pages, 9 figures. Final accepted version by Phys. Rev. D, minor textual changes

Published
2019
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29. Reconstruction and Measurement of $\mathcal{O}$(100) MeV Energy Electromagnetic Activity from $\pi^0 \rightarrow \gamma\gamma$ Decays in the MicroBooNE LArTPC

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Basque, V., Bass, M., Bay, F., Berkman, S., Bhanderi, A., Bhat, A., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Esquivel, J., Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Foppiani, N., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Gardiner, S., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Green, P., Greenlee, H., Grosso, R., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. C., Itay, R., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Jo, J. H., Johnson, R. A., Joshi, J., Jwa, Y. J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., McConkey, N., Meddage, V., Mettler, T., Miller, K., Mills, J., Mistry, K., Mohayai, T., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Neely, R. K., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Paudel, A., Pavlovic, Z., Piasetzky, E., Porzio, D., Prince, S., Pulliam, G., Qian, X., Raaf, J. L., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wospakrik, M., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

We present results on the reconstruction of electromagnetic (EM) activity from photons produced in charged current $\nu_{\mu}$ interactions with final state $\pi^0$s. We employ a fully-automated reconstruction chain capable of identifying EM showers of $\mathcal{O}$(100) MeV energy, relying on a combination of traditional reconstruction techniques together with novel machine-learning approaches. These studies demonstrate good energy resolution, and good agreement between data and simulation, relying on the reconstructed invariant $\pi^0$ mass and other photon distributions for validation. The reconstruction techniques developed are applied to a selection of $\nu_{\mu} + {\rm Ar} \rightarrow \mu + \pi^0 + X$ candidate events to demonstrate the potential for calorimetric separation of photons from electrons and reconstruction of $\pi^0$ kinematics.

Published
2019
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30. A Method to Determine the Electric Field of Liquid Argon Time Projection Chambers Using a UV Laser System and its Application in MicroBooNE

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Basque, V., Bass, M., Bay, F., Berkman, S., Bhanderi, A., Bhat, A., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Foppiani, N., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Gardiner, S., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Green, P., Greenlee, H., Grosso, R., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. C., Itay, R., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Jo, J. H., Johnson, R. A., Joshi, J., Jwa, Y. J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., McConkey, N., Meddage, V., Mettler, T., Miller, K., Mills, J., Mistry, K., Mohayai, T., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Neely, R. K., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Paudel, A., Pavlovic, Z., Piasetzky, E., Porzio, D., Prince, S., Pulliam, G., Qian, X., Raaf, J. L., Radeka, V., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Uchida, M. A., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wospakrik, M., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
Physics - Instrumentation and Detectors
Abstract

Liquid argon time projection chambers (LArTPCs) are now a standard detector technology for making accelerator neutrino measurements, due to their high material density, precise tracking, and calorimetric capabilities. An electric field (E-field) is required in such detectors to drift ionized electrons to the anode to be collected. The E-field of a TPC is often approximated to be uniform between the anode and the cathode planes. However, significant distortions can appear from effects such as mechanical deformations, electrode failures, or the accumulation of space charge generated by cosmic rays. The latter is particularly relevant for detectors placed near the Earth's surface and with large drift distances and long drift time. To determine the E-field in situ, an ultraviolet (UV) laser system is installed in the MicroBooNE experiment at Fermi National Accelerator Laboratory. The purpose of this system is to provide precise measurements of the E-field, and to make it possible to correct for 3D spatial distortions due to E-field non-uniformities. Here we describe the methodology developed for deriving spatial distortions, the drift velocity and the E-field from UV-laser measurements.

Published
2019
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31. Calibration of the charge and energy loss per unit length of the MicroBooNE liquid argon time projection chamber using muons and protons

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Basque, V., Bass, M., Bay, F., Berkman, S., Bhanderi, A., Bhat, A., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Esquivel, J., Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Foppiani, N., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Gardiner, S., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Green, P., Greenlee, H., Grosso, R., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. C., Itay, R., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Jo, J. H., Johnson, R. A., Joshi, J., Jwa, Y. J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., McConkey, N., Meddage, V., Mettler, T., Miller, K., Mills, J., Mistry, K., Mohayai, T., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Neely, R. K., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Paudel, A., Pavlovic, Z., Piasetzky, E., Porzio, D., Prince, S., Pulliam, G., Qian, X., Raaf, J. L., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wospakrik, M., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

We describe a method used to calibrate the position- and time-dependent response of the MicroBooNE liquid argon time projection chamber anode wires to ionization particle energy loss. The method makes use of crossing cosmic-ray muons to partially correct anode wire signals for multiple effects as a function of time and position, including cross-connected TPC wires, space charge effects, electron attachment to impurities, diffusion, and recombination. The overall energy scale is then determined using fully-contained beam-induced muons originating and stopping in the active region of the detector. Using this method, we obtain an absolute energy scale uncertainty of 2\% in data. We use stopping protons to further refine the relation between the measured charge and the energy loss for highly-ionizing particles. This data-driven detector calibration improves both the measurement of total deposited energy and particle identification based on energy loss per unit length as a function of residual range. As an example, the proton selection efficiency is increased by 2\% after detector calibration., Comment: Accepted version

Published
2019
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32. First Measurement of Inclusive Muon Neutrino Charged Current Differential Cross Sections on Argon at $E_\nu \sim 0.8$ GeV with the MicroBooNE Detector

Author

Abratenko, P., Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Auger, M., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Bass, M., Bay, F., Bhat, A., Bhattacharya, K., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Collin, G. H., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Domine, L., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Esquivel, J., Evans, J. J., Fitzpatrick, R. S., Fleming, B. T., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Greenlee, H., Grosso, R., Gu, L., Gu, W., Guenette, R., Guzowski, P., Hackenburg, A., Hamilton, P., Hen, O., Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. -C., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Johnson, R. A., Joshi, J., Jostlein, H., Jwa, Y. -J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mason, K., Mastbaum, A., Meddage, V., Mettler, T., Mills, J., Mistry, K., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Pavlovic, Z., Piasetzky, E., Porzio, D., Pulliam, G., Qian, X., Raaf, J. L., Rafique, A., Ren, L., Rochester, L., Rogers, H. E., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., Stancari, M., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thomson, M., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Wierman, K., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Wu, W., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
High Energy Physics - Experiment
Abstract

We report the first measurement of the double-differential and total muon neutrino charged current inclusive cross sections on argon at a mean neutrino energy of 0.8 GeV. Data were collected using the MicroBooNE liquid argon time projection chamber located in the Fermilab Booster neutrino beam and correspond to $1.6 \times 10^{20}$ protons on target of exposure. The measured differential cross sections are presented as a function of muon momentum, using multiple Coulomb scattering as a momentum measurement technique, and the muon angle with respect to the beam direction. We compare the measured cross sections to multiple neutrino event generators and find better agreement with those containing more complete treatment of quasielastic scattering processes at low $Q^2$. The total flux integrated cross section is measured to be $0.693 \pm 0.010 \, (\text{stat}) \pm 0.165 \, (\text{syst}) \times 10^{-38} \, \text{cm}^{2}$., Comment: 7 pages, 2 figures

Published
2019
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33. Design and construction of the MicroBooNE Cosmic Ray Tagger system

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Auger, M., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Bass, M., Bay, F., Bhat, A., Bhattacharya, K., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Collin, G. H., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Esquivel, J., Evans, J. J., Fadeeva, A. A., Fitzpatrick, R. S., Fleming, B. T., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Garvey, G. T., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Greenlee, H., Grosso, R., Guenette, R., Guzowski, P., Hackenburg, A., Hamilton, P., Hen, O., Hewes, V, Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. -C., James, C., de Vries, J. Jan, Jiang, L., Johnson, R. A., Joshi, J., Jostlein, H., Jwa, Y. -J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mastbaum, A., Meddage, V., Mettler, T., Mills, G. B., Mistry, K., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Pavlovic, Z., Piasetzky, E., Porzio, D., Pulliam, G., Qian, X., Raaf, J. L., Rafique, A., Rochester, L., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thomson, M., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Wierman, K., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
Physics - Instrumentation and Detectors
Abstract

The MicroBooNE detector utilizes a liquid argon time projection chamber (LArTPC) with an 85 t active mass to study neutrino interactions along the Booster Neutrino Beam (BNB) at Fermilab. With a deployment location near ground level, the detector records many cosmic muon tracks in each beam-related detector trigger that can be misidentified as signals of interest. To reduce these cosmogenic backgrounds, we have designed and constructed a TPC-external Cosmic Ray Tagger (CRT). This sub-system was developed by the Laboratory for High Energy Physics (LHEP), Albert Einstein center for fundamental physics, University of Bern. The system utilizes plastic scintillation modules to provide precise time and position information for TPC-traversing particles. Successful matching of TPC tracks and CRT data will allow us to reduce cosmogenic background and better characterize the light collection system and LArTPC data using cosmic muons. In this paper we describe the design and installation of the MicroBooNE CRT system and provide an overview of a series of tests done to verify the proper operation of the system and its components during installation, commissioning, and physics data-taking.

Published
2019
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34. A Phase Ib/IIa Study of the Pan-BET Inhibitor ZEN-3694 in Combination with Enzalutamide in Patients with Metastatic Castration-resistant Prostate Cancer

Author

Aggarwal, Rahul R, Schweizer, Michael T, Nanus, David M, Pantuck, Allan J, Heath, Elisabeth I, Campeau, Eric, Attwell, Sarah, Norek, Karen, Snyder, Margo, Bauman, Lisa, Lakhotia, Sanjay, Feng, Felix Y, Small, Eric J, Abida, Wassim, and Alumkal, Joshi J

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Urologic Diseases, Cancer, Clinical Research, Prostate Cancer, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Aged, Aged, 80 and over, Androstenes, Antineoplastic Agents, Antineoplastic Combined Chemotherapy Protocols, Benzamides, Disease-Free Survival, Drug Resistance, Neoplasm, Humans, Male, Middle Aged, Neoplasm Metastasis, Nitriles, Phenylthiohydantoin, Progression-Free Survival, Prostatic Neoplasms, Castration-Resistant, Receptors, Androgen, Treatment Outcome, Oncology & Carcinogenesis, Clinical sciences, Oncology and carcinogenesis
Abstract

PurposeZEN-3694 is a bromodomain extraterminal inhibitor (BETi) with activity in androgen-signaling inhibitor (ASI)-resistant models. The safety and efficacy of ZEN-3694 plus enzalutamide was evaluated in a phase Ib/IIa study in metastatic castration-resistant prostate cancer (mCRPC).Patients and methodsPatients had progressive mCRPC with prior resistance to abiraterone and/or enzalutamide. 3+3 dose escalation was followed by dose expansion in parallel cohorts (ZEN-3694 at 48 and 96 mg orally once daily, respectively).ResultsSeventy-five patients were enrolled (N = 26 and 14 in dose expansion at low- and high-dose ZEN-3694, respectively). Thirty (40.0%) patients were resistant to abiraterone, 34 (45.3%) to enzalutamide, and 11 (14.7%) to both. ZEN-3694 dosing ranged from 36 to 144 mg daily without reaching an MTD. Fourteen patients (18.7%) experienced grade ≥3 toxicities, including three patients with grade 3 thrombocytopenia (4%). An exposure-dependent decrease in whole-blood RNA expression of BETi targets was observed (up to fourfold mean difference at 4 hours post-ZEN-3694 dose; P ≤ 0.0001). The median radiographic progression-free survival (rPFS) was 9.0 months [95% confidence interval (CI), 4.6-12.9] and composite median radiographic or clinical progression-free survival (PFS) was 5.5 months (95% CI, 4.0-7.8). Median duration of treatment was 3.5 months (range, 0-34.7+). Lower androgen receptor (AR) transcriptional activity in baseline tumor biopsies was associated with longer rPFS (median rPFS 10.4 vs. 4.3 months).ConclusionsZEN-3694 plus enzalutamide demonstrated acceptable tolerability and potential efficacy in patients with ASI-resistant mCRPC. Further prospective study is warranted including in mCRPC harboring low AR transcriptional activity.

Published
2020

35. Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer

Author

Guan, Xiangnan, Sun, Duanchen, Lu, Eric, Urrutia, Joshua A, Reiter, Robert Evan, Rettig, Matthew, Evans, Christopher P, Lara, Primo, Gleave, Martin, Beer, Tomasz M, Thomas, George V, Huang, Jiaoti, Aggarwal, Rahul R, Quigley, David A, Foye, Adam, Chen, William S, Youngren, Jack, Weinstein, Alana S, Stuart, Joshua M, Feng, Felix Y, Small, Eric J, Xia, Zheng, and Alumkal, Joshi J

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Human Genome, Urologic Diseases, Cancer, Biotechnology, Prostate Cancer, Genetics, Benzamides, Biomarkers, Tumor, Biopsy, Chromosomes, Human, Pair 17, DNA Copy Number Variations, Disease-Free Survival, Drug Resistance, Neoplasm, Humans, Male, Nitriles, Phenylthiohydantoin, Prostate, Prostatic Neoplasms, Castration-Resistant, RNA-Seq, Survival Analysis, Oncology & Carcinogenesis, Clinical sciences, Oncology and carcinogenesis
Abstract

PurposeThe purpose of this study was to measure genomic changes that emerge with enzalutamide treatment using analyses of whole-genome sequencing and RNA sequencing.Experimental designOne hundred and one tumors from men with metastatic castration-resistant prostate cancer (mCRPC) who had not been treated with enzalutamide (n = 64) or who had enzalutamide-resistant mCRPC (n = 37) underwent whole genome sequencing. Ninety-nine of these tumors also underwent RNA sequencing. We analyzed the genomes and transcriptomes of these mCRPC tumors.ResultsCopy number loss was more common than gain in enzalutamide-resistant tumors. Specially, we identified 124 protein-coding genes that were more commonly lost in enzalutamide-resistant samples. These 124 genes included eight putative tumor suppressors located at nine distinct genomic regions. We demonstrated that focal deletion of the 17q22 locus that includes RNF43 and SRSF1 was not present in any patient with enzalutamide-naïve mCRPC but was present in 16% (6/37) of patients with enzalutamide-resistant mCRPC. 17q22 loss was associated with lower RNF43 and SRSF1 expression and poor overall survival from time of biopsy [median overall survival of 19.3 months in 17q22 intact vs. 8.9 months in 17q22 loss, HR, 3.44 95% confidence interval (CI), 1.338-8.867, log-rank P = 0.006]. Finally, 17q22 loss was linked with activation of several targetable factors, including CDK1/2, Akt, and PLK1, demonstrating the potential therapeutic relevance of 17q22 loss in mCRPC.ConclusionsCopy number loss is common in enzalutamide-resistant tumors. Focal deletion of chromosome 17q22 defines a previously unappreciated molecular subset of enzalutamide-resistant mCRPC associated with poor clinical outcome.

Published
2020

36. The DNA methylation landscape of advanced prostate cancer

Author

Zhao, Shuang G, Chen, William S, Li, Haolong, Foye, Adam, Zhang, Meng, Sjöström, Martin, Aggarwal, Rahul, Playdle, Denise, Liao, Arnold, Alumkal, Joshi J, Das, Rajdeep, Chou, Jonathan, Hua, Junjie T, Barnard, Travis J, Bailey, Adina M, Chow, Eric D, Perry, Marc D, Dang, Ha X, Yang, Rendong, Moussavi-Baygi, Ruhollah, Zhang, Li, Alshalalfa, Mohammed, Laura Chang, S, Houlahan, Kathleen E, Shiah, Yu-Jia, Beer, Tomasz M, Thomas, George, Chi, Kim N, Gleave, Martin, Zoubeidi, Amina, Reiter, Robert E, Rettig, Matthew B, Witte, Owen, Yvonne Kim, M, Fong, Lawrence, Spratt, Daniel E, Morgan, Todd M, Bose, Rohit, Huang, Franklin W, Li, Hui, Chesner, Lisa, Shenoy, Tanushree, Goodarzi, Hani, Asangani, Irfan A, Sandhu, Shahneen, Lang, Joshua M, Mahajan, Nupam P, Lara, Primo N, Evans, Christopher P, Febbo, Phillip, Batzoglou, Serafim, Knudsen, Karen E, He, Housheng H, Huang, Jiaoti, Zwart, Wilbert, Costello, Joseph F, Luo, Jianhua, Tomlins, Scott A, Wyatt, Alexander W, Dehm, Scott M, Ashworth, Alan, Gilbert, Luke A, Boutros, Paul C, Farh, Kyle, Chinnaiyan, Arul M, Maher, Christopher A, Small, Eric J, Quigley, David A, and Feng, Felix Y

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer, Prostate Cancer, Human Genome, Urologic Diseases, Cancer Genomics, Biotechnology, 2.1 Biological and endogenous factors, Aged, Aged, 80 and over, Carcinogenesis, DNA Methylation, Epigenomics, Gene Expression Regulation, Neoplastic, Genome, Humans, Male, Middle Aged, Mutation, Prospective Studies, Prostatic Neoplasms, Sequence Analysis, DNA, Exome Sequencing, Whole Genome Sequencing, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.

Published
2020

37. A method to determine the electric field of liquid argon time projection chambers using a UV laser system and its application in MicroBooNE

Author

Adams, C, Alrashed, M, An, R, Anthony, J, Asaadi, J, Ashkenazi, A, Balasubramanian, S, Baller, B, Barnes, C, Barr, G, Basque, V, Bass, M, Bay, F, Berkman, S, Bhanderi, A, Bhat, A, Bishai, M, Blake, A, Bolton, T, Camilleri, L, Caratelli, D, Terrazas, IC, Carr, R, Fernandez, RC, Cavanna, F, Cerati, G, Chen, Y, Church, E, Cianci, D, Cohen, EO, Conrad, JM, Convery, M, Cooper-Troendle, L, Crespo-Anadón, JI, Tutto, MD, Devitt, D, Diaz, A, Domine, L, Duffy, K, Dytman, S, Eberly, B, Ereditato, A, Sanchez, LE, Evans, JJ, Fitzpatrick, RS, Fleming, BT, Foppiani, N, Franco, D, Furmanski, AP, Garcia-Gamez, D, Gardiner, S, Genty, V, Goeldi, D, Gollapinni, S, Goodwin, O, Gramellini, E, Green, P, Greenlee, H, Grosso, R, Gu, L, Gu, W, Guenette, R, Guzowski, P, Hamilton, P, Hen, O, Hill, C, Horton-Smith, GA, Hourlier, A, Huang, EC, Itay, R, James, C, De Vries, JJ, Ji, X, Jiang, L, Jo, JH, Johnson, RA, Joshi, J, Jwa, YJ, Karagiorgi, G, Ketchum, W, Kirby, B, Kirby, M, Kobilarcik, T, Kreslo, I, Lepetic, I, Li, Y, Lister, A, Littlejohn, BR, Lockwitz, S, Lorca, D, Louis, WC, Luethi, M, Lundberg, B, Luo, X, Marchionni, A, Marcocci, S, Mariani, C, Marshall, J, Martin-Albo, J, and Caicedo, DAM

Subjects
Ionization and excitation processes, Neutrino detectors, Noble liquid detectors, Time projection chambers, physics.ins-det, Nuclear & Particles Physics, Physical Sciences, Engineering
Abstract

Liquid argon time projection chambers (LArTPCs) are now a standard detector technology for making accelerator neutrino measurements, due to their high material density, precise tracking, and calorimetric capabilities. An electric field (E-field) is required in such detectors to drift ionization electrons to the anode where they are collected. The E-field of a TPC is often approximated to be uniform between the anode and the cathode planes. However, significant distortions can appear from effects such as mechanical deformations, electrode failures, or the accumulation of space charge generated by cosmic rays. The latter effect is particularly relevant for detectors placed near the Earth's surface and with large drift distances and long drift time. To determine the E-field in situ, an ultraviolet (UV) laser system is installed in the MicroBooNE experiment at Fermi National Accelerator Laboratory. The purpose of this system is to provide precise measurements of the E-field, and to make it possible to correct for 3D spatial distortions due to E-field non-uniformities. Here we describe the methodology developed for deriving spatial distortions, the drift velocity and the E-field from UV-laser measurements.

Published
2020

38. Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance

Author

Alumkal, Joshi J, Sun, Duanchen, Lu, Eric, Beer, Tomasz M, Thomas, George V, Latour, Emile, Aggarwal, Rahul, Cetnar, Jeremy, Ryan, Charles J, Tabatabaei, Shaadi, Bailey, Shawna, Turina, Claire B, Quigley, David A, Guan, Xiangnan, Foye, Adam, Youngren, Jack F, Urrutia, Joshua, Huang, Jiaoti, Weinstein, Alana S, Friedl, Verena, Rettig, Matthew, Reiter, Robert E, Spratt, Daniel E, Gleave, Martin, Evans, Christopher P, Stuart, Joshua M, Chen, Yiyi, Feng, Felix Y, Small, Eric J, Witte, Owen N, and Xia, Zheng

Subjects
Urologic Diseases, Genetics, Prostate Cancer, Aging, Cancer, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Aged, Aged, 80 and over, Antineoplastic Agents, Benzamides, Drug Resistance, Neoplasm, Gene Expression Profiling, Humans, Male, Middle Aged, Nitriles, Phenylthiohydantoin, Prostate-Specific Antigen, Prostatic Neoplasms, Castration-Resistant, Receptors, Androgen, enzalutamide, resistance, androgen receptor, stemness
Abstract

The androgen receptor (AR) antagonist enzalutamide is one of the principal treatments for men with castration-resistant prostate cancer (CRPC). However, not all patients respond, and resistance mechanisms are largely unknown. We hypothesized that genomic and transcriptional features from metastatic CRPC biopsies prior to treatment would be predictive of de novo treatment resistance. To this end, we conducted a phase II trial of enzalutamide treatment (160 mg/d) in 36 men with metastatic CRPC. Thirty-four patients were evaluable for the primary end point of a prostate-specific antigen (PSA)50 response (PSA decline ≥50% at 12 wk vs. baseline). Nine patients were classified as nonresponders (PSA decline

Published
2020

39. Germline polymorphisms associated with impaired survival outcomes and somatic tumor alterations in advanced prostate cancer

Author

Chen, William S, Feng, Eric L, Aggarwal, Rahul, Foye, Adam, Beer, Tomasz M, Alumkal, Joshi J, Gleave, Martin, Chi, Kim N, Reiter, Robert E, Rettig, Matthew B, Evans, Christopher P, Small, Eric J, Sharifi, Nima, and Zhao, Shuang G

Subjects
Biotechnology, Cancer, Clinical Research, Human Genome, Genetic Testing, Prostate Cancer, Genetics, Urologic Diseases, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Aged, Androgen Antagonists, Biomarkers, Tumor, DNA, Neoplasm, Follow-Up Studies, Germ Cells, Humans, Male, Polymorphism, Genetic, Prognosis, Prostatic Neoplasms, Castration-Resistant, Retrospective Studies, Survival Rate, Oncology and Carcinogenesis, Urology & Nephrology
Abstract

IntroductionGermline variants in androgen metabolism genes may influence clinical response to androgen deprivation therapy (ADT) in advanced prostate cancer. We sought to investigate the prognostic significance of germline variants in androgen metabolism genes with respect to overall survival (OS) after ADT, and to associate germline variants with tumor genomic features.MethodsGermline and somatic whole-genome sequencing (WGS) data were evaluated in a cohort of 101 men with metastatic castration-resistant prostate cancer (mCRPC). Survival analyses were performed to identify polymorphisms associated with impaired OS after primary ADT. Germline variants found to be prognostic of OS were associated with tumor somatic DNA-sequence alterations based on WGS performed on paired metastasis biopsies from the same 101 patients. Gene set enrichment analysis was performed based on tumor RNA-sequencing data to identify genomic pathways differentially expressed in patients with germline variants.ResultsA comprehensive literature review identified 17 candidate polymorphisms in nine androgen metabolism genes that have been previously shown to have an association with response to ADT in prostate cancer. Of these, the variant rs1856888 allele located 13 kb upstream of HSD3B1 was found to be significantly associated with impaired OS (P = 0.029). Variant rs1856888 was commonly co-inherited with the well-characterized HSD3B1(1245A>C) polymorphism, and there was a trend toward shorter median OS in patients with HSD3B1(1245A>C) compared with homozygous wild-type patients (P = 0.052). While HSD3B1 germline variants were not associated with common somatic tumor DNA alterations, they were associated with increased tumor expression of cell proliferation and cell cycle genes.ConclusionsThis study presents a comprehensive assessment of germline variants in androgen metabolism genes and highlights HSD3B1 polymorphisms as prognostic of OS after ADT and associated with an aggressive gene expression tumor profile in mCRPC.

Published
2020

40. Calibration of the charge and energy loss per unit length of the MicroBooNE liquid argon time projection chamber using muons and protons

Author

Adams, C, Alrashed, M, An, R, Anthony, J, Asaadi, J, Ashkenazi, A, Balasubramanian, S, Baller, B, Barnes, C, Barr, G, Basque, V, Bass, M, Bay, F, Berkman, S, Bhanderi, A, Bhat, A, Bishai, M, Blake, A, Bolton, T, Camilleri, L, Caratelli, D, Terrazas, I Caro, Carr, R, Fernandez, R Castillo, Cavanna, F, Cerati, G, Chen, Y, Church, E, Cianci, D, Cohen, EO, Conrad, JM, Convery, M, Cooper-Troendle, L, Crespo-Anadón, JI, Del Tutto, M, Devitt, D, Diaz, A, Domine, L, Duffy, K, Dytman, S, Eberly, B, Ereditato, A, Sanchez, L Escudero, Esquivel, J, Evans, JJ, Fitzpatrick, RS, Fleming, BT, Foppiani, N, Franco, D, Furmanski, AP, Garcia-Gamez, D, Gardiner, S, Genty, V, Goeldi, D, Gollapinni, S, Goodwin, O, Gramellini, E, Green, P, Greenlee, H, Grosso, R, Gu, L, Gu, W, Guenette, R, Guzowski, P, Hamilton, P, Hen, O, Hill, C, Horton-Smith, GA, Hourlier, A, Huang, E-C, Itay, R, James, C, de Vries, J Jan, Ji, X, Jiang, L, Jo, JH, Johnson, RA, Joshi, J, Jwa, Y-J, Karagiorgi, G, Ketchum, W, Kirby, B, Kirby, M, Kobilarcik, T, Kreslo, I, Lepetic, I, Li, Y, Lister, A, Littlejohn, BR, Lockwitz, S, Lorca, D, Louis, WC, Luethi, M, Lundberg, B, Luo, X, Marchionni, A, Marcocci, S, Mariani, C, Marshall, J, and Martin-Albo, J

Subjects
Nuclear and Plasma Physics, Synchrotrons and Accelerators, Physical Sciences, Affordable and Clean Energy, Calorimeters, dE/dx detectors, Neutrino detectors, Time projection chambers, physics.ins-det, hep-ex, Engineering, Nuclear & Particles Physics, Physical sciences
Abstract

We describe a method used to calibrate the position- and time-dependent response of the MicroBooNE liquid argon time projection chamber anode wires to ionization particle energy loss. The method makes use of crossing cosmic-ray muons to partially correct anode wire signals for multiple effects as a function of time and position, including cross-connected TPC wires, space charge effects, electron attachment to impurities, diffusion, and recombination. The overall energy scale is then determined using fully-contained beam-induced muons originating and stopping in the active region of the detector. Using this method, we obtain an absolute energy scale uncertainty of 2% in data. We use stopping protons to further refine the relation between the measured charge and the energy loss for highly-ionizing particles. This data-driven detector calibration improves both the measurement of total deposited energy and particle identification based on energy loss per unit length as a function of residual range. As an example, the proton selection efficiency is increased by 2% after detector calibration.

Published
2020

41. Search for heavy neutral leptons decaying into muon-pion pairs in the MicroBooNE detector

Author

Abratenko, P, Alrashed, M, An, R, Anthony, J, Asaadi, J, Ashkenazi, A, Balasubramanian, S, Baller, B, Barnes, C, Barr, G, Basque, V, Berkman, S, Bhanderi, A, Bhat, A, Bishai, M, Blake, A, Bolton, T, Camilleri, L, Caratelli, D, Terrazas, I Caro, Fernandez, R Castillo, Cavanna, F, Cerati, G, Chen, Y, Church, E, Cianci, D, Cohen, EO, Conrad, JM, Convery, M, Cooper-Troendle, L, Crespo-Anadón, JI, Del Tutto, M, Devitt, A, Domine, L, Duffy, K, Dytman, S, Eberly, B, Ereditato, A, Sanchez, L Escudero, Evans, JJ, Fitzpatrick, RS, Fleming, BT, Foppiani, N, Franco, D, Furmanski, AP, Garcia-Gamez, D, Gardiner, S, Genty, V, Goeldi, D, Gollapinni, S, Goodwin, O, Gramellini, E, Green, P, Greenlee, H, Gu, L, Gu, W, Guenette, R, Guzowski, P, Hamilton, P, Hen, O, Hill, C, Horton-Smith, GA, Hourlier, A, Huang, E-C, Itay, R, James, C, de Vries, J Jan, Ji, X, Jiang, L, Jo, JH, Johnson, RA, Joshi, J, Jwa, Y-J, Karagiorgi, G, Ketchum, W, Kirby, B, Kirby, M, Kobilarcik, T, Kreslo, I, LaZur, R, Lepetic, I, Li, Y, Lister, A, Littlejohn, BR, Lockwitz, S, Lorca, D, Louis, WC, Luethi, M, Lundberg, B, Luo, X, Marchionni, A, Marcocci, S, Mariani, C, Marshall, J, Martin-Albo, J, Caicedo, DA Martinez, Mason, K, Mastbaum, A, McConkey, N, and Meddage, V

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, hep-ex, physics.ins-det, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics, Mathematical physics, Astronomical sciences, Particle and high energy physics
Abstract

We present upper limits on the production of heavy neutral leptons (HNLs) decaying to μπ pairs using data collected with the MicroBooNE liquid-argon time projection chamber (TPC) operating at Fermilab. This search is the first of its kind performed in a liquid-argon TPC. We use data collected in 2017 and 2018 corresponding to an exposure of 2.0×1020 protons on target from the Fermilab Booster Neutrino Beam, which produces mainly muon neutrinos with an average energy of ≈800 MeV. HNLs with higher mass are expected to have a longer time of flight to the liquid-argon TPC than Standard Model neutrinos. The data are therefore recorded with a dedicated trigger configured to detect HNL decays that occur after the neutrino spill reaches the detector. We set upper limits at the 90% confidence level on the element |Uμ4|2 of the extended PMNS mixing matrix in the range |Uμ4|2

Published
2020

42. Reconstruction and measurement of (100) MeV energy electromagnetic activity from π0 arrow γγ decays in the MicroBooNE LArTPC

Author

Adams, C, Alrashed, M, An, R, Anthony, J, Asaadi, J, Ashkenazi, A, Balasubramanian, S, Baller, B, Barnes, C, Barr, G, Basque, V, Bass, M, Bay, F, Berkman, S, Bhanderi, A, Bhat, A, Bishai, M, Blake, A, Bolton, T, Camilleri, L, Caratelli, D, Terrazas, IC, Carr, R, Fernandez, RC, Cavanna, F, Cerati, G, Chen, Y, Church, E, Cianci, D, Cohen, EO, Conrad, JM, Convery, M, Cooper-Troendle, L, Crespo-Anadón, JI, Tutto, MD, Devitt, D, Diaz, A, Domine, L, Duffy, K, Dytman, S, Eberly, B, Ereditato, A, Sanchez, LE, Esquivel, J, Evans, JJ, Fitzpatrick, RS, Fleming, BT, Foppiani, N, Franco, D, Furmanski, AP, Garcia-Gamez, D, Gardiner, S, Genty, V, Goeldi, D, Gollapinni, S, Goodwin, O, Gramellini, E, Green, P, Greenlee, H, Grosso, R, Gu, L, Gu, W, Guenette, R, Guzowski, P, Hamilton, P, Hen, O, Hill, C, Horton-Smith, GA, Hourlier, A, Huang, EC, Itay, R, James, C, De Vries, JJ, Ji, X, Jiang, L, Jo, JH, Johnson, RA, Joshi, J, Jwa, YJ, Karagiorgi, G, Ketchum, W, Kirby, B, Kirby, M, Kobilarcik, T, Kreslo, I, Lepetic, I, Li, Y, Lister, A, Littlejohn, BR, Lockwitz, S, Lorca, D, Louis, WC, Luethi, M, Lundberg, B, Luo, X, Marchionni, A, Marcocci, S, Mariani, C, Marshall, J, and Martin-Albo, J

Subjects
Noble liquid detectors, Pattern recognition, cluster finding, calibration and fitting methods, Performance of High Energy Physics Detectors, Time projection chambers, hep-ex, physics.ins-det, Pattern recognition, cluster finding, calibration and fitting methods, Nuclear & Particles Physics, Physical Sciences, Engineering
Abstract

We present results on the reconstruction of electromagnetic (EM) activity from photons produced in charged current νμ interactions with final state π0s. We employ a fully-automated reconstruction chain capable of identifying EM showers of (100) MeV energy, relying on a combination of traditional reconstruction techniques together with novel machine-learning approaches. These studies demonstrate good energy resolution, and good agreement between data and simulation, relying on the reconstructed invariant π0 mass and other photon distributions for validation. The reconstruction techniques developed are applied to a selection of νμ + Ar → μ + π0 + X candidate events to demonstrate the potential for calorimetric separation of photons from electrons and reconstruction of π0 kinematics.

Published
2020

43. Rejecting cosmic background for exclusive neutrino interaction studies with Liquid Argon TPCs; a case study with the MicroBooNE detector

Author

MicroBooNE collaboration, Adams, C., Alrashed, M., An, R., Anthony, J., Asaadi, J., Ashkenazi, A., Auger, M., Balasubramanian, S., Baller, B., Barnes, C., Barr, G., Bass, M., Bay, F., Bhat, A., Bhattacharya, K., Bishai, M., Blake, A., Bolton, T., Camilleri, L., Caratelli, D., Terrazas, I. Caro, Carr, R., Fernandez, R. Castillo, Cavanna, F., Cerati, G., Chen, Y., Church, E., Cianci, D., Cohen, E. O., Collin, G. H., Conrad, J. M., Convery, M., Cooper-Troendle, L., Crespo-Anadon, J. I., Del Tutto, M., Devitt, D., Diaz, A., Duffy, K., Dytman, S., Eberly, B., Ereditato, A., Sanchez, L. Escudero, Esquivel, J., Evans, J. J., Fadeeva, A. A., Fitzpatrick, R. S., Fleming, B. T., Franco, D., Furmanski, A. P., Garcia-Gamez, D., Genty, V., Goeldi, D., Gollapinni, S., Goodwin, O., Gramellini, E., Greenlee, H., Grosso, R., Guenette, R., Guzowski, P., Hackenburg, A., Hamilton, P., Hen, O., Hewes, V, Hill, C., Horton-Smith, G. A., Hourlier, A., Huang, E. -C., James, C., de Vries, J. Jan, Ji, X., Jiang, L., Johnson, R. A., Joshi, J., Jostlein, H., Jwa, Y. -J., Karagiorgi, G., Ketchum, W., Kirby, B., Kirby, M., Kobilarcik, T., Kreslo, I., Lepetic, I., Li, Y., Lister, A., Littlejohn, B. R., Lockwitz, S., Lorca, D., Louis, W. C., Luethi, M., Lundberg, B., Luo, X., Marchionni, A., Marcocci, S., Mariani, C., Marshall, J., Martin-Albo, J., Caicedo, D. A. Martinez, Mastbaum, A., Meddage, V., Mettler, T., Mistry, K., Mogan, A., Moon, J., Mooney, M., Moore, C. D., Mousseau, J., Murphy, M., Murrells, R., Naples, D., Nienaber, P., Nowak, J., Palamara, O., Pandey, V., Paolone, V., Papadopoulou, A., Papavassiliou, V., Pate, S. F., Pavlovic, Z., Piasetzky, E., Porzio, D., Pulliam, G., Qian, X., Raaf, J. L., Rafique, A., Ren, L., Rochester, L., Ross-Lonergan, M., von Rohr, C. Rudolf, Russell, B., Scanavini, G., Schmitz, D. W., Schukraft, A., Seligman, W., Shaevitz, M. H., Sharankova, R., Sinclair, J., Smith, A., Snider, E. L., Soderberg, M., Soldner-Rembold, S., Soleti, S. R., Spentzouris, P., Spitz, J., John, J. St., Strauss, T., Sutton, K., Sword-Fehlberg, S., Szelc, A. M., Tagg, N., Tang, W., Terao, K., Thomson, M., Thornton, R. T., Toups, M., Tsai, Y. -T., Tufanli, S., Usher, T., Van De Pontseele, W., Van de Water, R. G., Viren, B., Weber, M., Wei, H., Wickremasinghe, D. A., Wierman, K., Williams, Z., Wolbers, S., Wongjirad, T., Woodruff, K., Yang, T., Yarbrough, G., Yates, L. E., Zeller, G. P., Zennamo, J., and Zhang, C.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment, Nuclear Experiment, Physics - Data Analysis, Statistics and Probability
Abstract

Cosmic ray (CR) interactions can be a challenging source of background for neutrino oscillation and cross-section measurements in surface detectors. We present methods for CR rejection in measurements of charged-current quasielastic-like (CCQE-like) neutrino interactions, with a muon and a proton in the final state, measured using liquid argon time projection chambers (LArTPCs). Using a sample of cosmic data collected with the MicroBooNE detector, mixed with simulated neutrino scattering events, a set of event selection criteria is developed that produces an event sample with minimal contribution from CR background. Depending on the selection criteria used a purity between 50% and 80% can be achieved with a signal selection efficiency between 50% and 25%, with higher purity coming at the expense of lower efficiency. While using a specific dataset from the MicroBooNE detector and selection criteria values optimized for CCQE-like events, the concepts presented here are generic and can be adapted for various studies of exclusive {\nu}{\mu} interactions in LArTPCs., Comment: 12 pages, 10 figures, 1 table

Published
2018

44. MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer

Author

Nickols, Nicholas G, Nazarian, Ramin, Zhao, Shuang G, Tan, Victor, Uzunangelov, Vladislav, Xia, Zheng, Baertsch, Robert, Neeman, Elad, Gao, Allen C, Thomas, George V, Howard, Lauren, De Hoedt, Amanda M, Stuart, Josh, Goldstein, Theodore, Chi, Kim, Gleave, Martin E, Graff, Julie N, Beer, Tomasz M, Drake, Justin M, Evans, Christopher P, Aggarwal, Rahul, Foye, Adam, Feng, Felix Y, Small, Eric J, Aronson, William J, Freedland, Stephen J, Witte, Owen N, Huang, Jiaoti, Alumkal, Joshi J, Reiter, Robert E, and Rettig, Matthew B

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Prostate Cancer, Cancer, Urologic Diseases, Genetics, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Aged, Antineoplastic Agents, Biopsy, Disease-Free Survival, Gene Amplification, Gene Expression Regulation, Neoplastic, Humans, MAP Kinase Signaling System, Male, Middle Aged, Mitogen-Activated Protein Kinase 3, Molecular Targeted Therapy, Phosphorylation, Prospective Studies, Prostate, Prostatic Neoplasms, Castration-Resistant, Protein Kinase Inhibitors, Pyridones, Pyrimidinones, RNA-Seq, Urology & Nephrology, Clinical sciences, Oncology and carcinogenesis
Abstract

BackgroundMetastatic castration resistant prostate cancer (mCRPC) is incurable and progression after drugs that target the androgen receptor-signaling axis is inevitable. Thus, there is an urgent need to develop more effective treatments beyond hormonal manipulation. We sought to identify activated kinases in mCRPC as therapeutic targets for existing, approved agents, with the goal of identifying candidate drugs for rapid translation into proof of concept Phase II trials in mCRPC.MethodsTo identify evidence of activation of druggable kinases in these patients, we compared mRNA expression from metastatic biopsies of patients with mCRPC (n = 101) to mRNA expression in localized prostate from TCGA and used this analysis to infer differential kinase activity. In addition, we assessed the differential phosphorylation levels for key MAPK pathway kinases between mCRPC and localized prostate cancers.ResultsTranscriptomic profiling of 101 patients with mCRPC as compared to patients with localized prostate cancer identified evidence of hyperactive ERK1, and whole genome sequencing revealed frequent amplifications of members of the MAPK pathway in 32% of this cohort. Next, we confirmed elevated levels of phosphorylated ERK1/2 in castration resistant prostate cancer as compared to untreated primary prostate cancer. We observed that the presence of detectable phosphorylated ERK1/2 in the primary tumor is associated with biochemical failure after radical prostatectomy independent of clinicopathologic features. ERK1 is the immediate downstream target of MEK1/2, which is druggable with trametinib, an approved therapeutic for melanoma. Trametinib elicited a profound biochemical and clinical response in a patient who had failed multiple prior treatments for mCRPC.ConclusionsWe conclude that pharmacologic targeting of the MEK/ERK pathway may be a viable treatment strategy for patients with refractory metastatic prostate cancer. An ongoing Phase II trial tests this hypothesis.

Published
2019

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