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1. The EUSO-SPB2 Fluorescence Telescope for the Detection of Ultra-High Energy Cosmic Rays

Author

Adams Jr., James H., Allard, Denis, Alldredge, Phillip, Anchordoqui, Luis, Anzalone, Anna, Battisti, Matteo, Belov, Alexander A., Bertaina, Mario, Bertone, Peter F., Blin-Bondil, Sylvie, Burton, Julia, Cafagna, Francesco S., Casolino, Marco, Černý, Karel, Christ, Mark J., Colalillo, Roberta, Crawford, Hank J., Creusot, Alexandre, Cummings, Austin, Diesing, Rebecca, Di Nola, Alessandro, Ebisuzaki, Toshikazu, Eser, Johannes, Ferrarese, Silvia, Filippatos, George, Finch, William W., Flaminio, Flavia, Fornaro, Claudio, Fuehne, Duncan, Fuglesang, Christer, Garg, Diksha, Golzio, Alessio, Guarino, Fausto, Guépin, Claire, Heibges, Tobias, Judd, Eleanor G., Klimov, Pavel A., Krizmanic, John F., Kungel, Viktoria, Kupari, Luke, Kuznetsov, Evgeny, Manfrin, Massimiliano, Marszal, Wlodzimierz, Matthews, John N., Mese, Marco, Meyer, Stephan S., Mignone, Marco, Miyamoto, Hiroko, Murashov, Alexey S., Nachtman, Jane M., Olinto, Angela V., Onel, Yasar, Osteria, Giuseppe, Panico, Beatrice, Parizot, Ètienne, Paul, Tom, Pech, Miroslav, Perfetto, Francesco, Piotrowski, Lech W., Plebaniak, Zbigniew, Posligua, Jonatan, Prévôt, Guillaume, Przybylak, Marika, Reardon, Patrick, Reno, Mary Hall, Ricci, Marco, Sarazin, Fred, Schovánek, P., Scotti, Valentina, Shinozaki, Kenji, Soriano, Jorge F., Stillwell, Ben K., Szabelski, Jacek, Takizawa, Yoshiyuki, Trofimov, Daniil, Unel, Fredrik, Valore, Laura, Venters, Tonia M., Watts Jr., John, Wiencke, Lawrence, Wistrand, Hannah, and Young, Roy

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

The Extreme Universe Space Observatory on a Super Pressure Balloon 2 (EUSO-SPB2) flew on May 13$^{\text{th}}$ and 14$^{\text{th}}$ of 2023. Consisting of two novel optical telescopes, the payload utilized next-generation instrumentation for the observations of extensive air showers from near space. One instrument, the fluorescence telescope (FT) searched for Ultra-High Energy Cosmic Rays (UHECRs) by recording the atmosphere below the balloon in the near-UV with a 1~$\mu$s time resolution using 108 multi-anode photomultiplier tubes with a total of 6,912 channels. Validated by pre-flight measurements during a field campaign, the energy threshold was estimated around 2~EeV with an expected event rate of approximately 1 event per 10 hours of observation. Based on the limited time afloat, the expected number of UHECR observations throughout the flight is between 0 and 2. Consistent with this expectation, no UHECR candidate events have been found. The majority of events appear to be detector artifacts that were not rejected properly due to a shortened commissioning phase. Despite the earlier-than-expected termination of the flight, data were recorded which provide insights into the detectors stability in the near-space environment as well as the diffuse ultraviolet emissivity of the atmosphere, both of which are impactful to future experiments.

Published
2024
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2. EUSO-SPB1 Mission and Science

Author

Collaboration, JEM-EUSO, Abdellaoui, G., Abe, S., Adams. Jr., J. H., Allard, D., Alonso, G., Anchordoqui, L., Anzalone, A., Arnone, E., Asano, K., Attallah, R., Attoui, H., Pernas, M. Ave, Bachmann, R., Bacholle, S., Bagheri, M., Bakiri, M., Baláz, J., Barghini, D., Bartocci, S., Battisti, M., Bayer, J., Beldjilali, B., Belenguer, T., Belkhalfa, N., Bellotti, R., Belov, A. A., Benmessai, K., Bertaina, M., Bertone, P. F., Biermann, P. L., Bisconti, F., Blaksley, C., Blanc, N., Blin-Bondil, S., Bobik, P., Bogomilov, M., Bolmgren, K., Bozzo, E., Briz, S., Bruno, A., Caballero, K. S., Cafagna, F., Cambié, G., Campana, D., Capdevielle, J. N., Capel, F., Caramete, A., Caramete, L., Caruso, R., Casolino, M., Cassardo, C., Castellina, A., Catalano, O., Cellino, A., Černý, K., Chikawa, M., Chiritoi, G., Christl, M. J., Colalillo, R., Conti, L., Cotto, G., Crawford, H. J., Cremonini, R., Creusot, A., Cummings, A., Gónzalez, A. de Castro, de la Taille, C., del Peral, L., Desiato, J., Damian, A. Diaz, Diesing, R., Dinaucourt, P., Djakonow, A., Djemil, T., Ebersoldt, A., Ebisuzaki, T., Eser, J., Fenu, F., Fernández-González, S., Ferrarese, S., Filippatos, G., Finch, W., Fornaro, C., Fouka, M., Franceschi, A., Franchini, S., Fuglesang, C., Fujii, T., Fukushima, M., Galeotti, P., García-Ortega, E., Gardiol, D., Garipov, G. K., Gascón, E., Gazda, E., Genci, J., Golzio, A., Gorodetzky, P., Gregg, R., Green, A., Guarino, F., Guépin, C., Guzmán, A., Hachisu, Y., Haungs, A., Heigbes, T., Carretero, J. Hernández, Hulett, L., Ikeda, D., Inoue, N., Inoue, S., Isgrò, F., Itow, Y., Jammer, T., Jeong, S., Jochum, J., Joven, E., Judd, E. G., Jung, A., Kajino, F., Kajino, T., Kalli, S., Kaneko, I., Kasztelan, M., Katahira, K., Kawai, K., Kawasaki, Y., Kedadra, A., Khales, H., Khrenov, B. A., Kim, Jeong-Sook, Kim, Soon-Wook, Kleifges, M., Klimov, P. A., Kreykenbohm, I., Krizmanic, J. F., Królik, K., Kungel, V., Kurihara, Y., Kusenko, A., Kuznetsov, E., Lahmar, H., Lakhdari, F., Licandro, J., Campano, L. López, Martínez, F. López, Mackovjak, S., Mahdi, M., Mandát, D., Manfrin, M., Marcelli, L., Marcos, J. L., Marszał, W., Martín, Y., Martinez, O., Mase, K., Mastafa, M., Matthews, J. N., Mebarki, N., Medina-Tanco, G., Menshikov, A., Merino, A., Mese, M., Meseguer, J., Meyer, S. S., Mimouni, J., Miyamoto, H., Mizumoto, Y., Monaco, A., Ríos, J. A. Morales de los, Nachtman, J. M., Nagataki, S., Naitamor, S., Napolitano, T., Neronov, A., Nomoto, K., Nonaka, T., Ogawa, T., Ogio, S., Ohmori, H., Olinto, A. V., Onel, Y., Osteria, G., Otte, A. N., Pagliaro, A., Painter, W., Panasyuk, M. I., Panico, B., Parizot, E., Park, I. H., Pastircak, B., Paul, T., Pech, M., Pérez-Grande, I., Perfetto, F., Peter, T., Picozza, P., Pindado, S., Piotrowski, L. W., Piraino, S., Plebaniak, Z., Pollini, A., Popescu, E. M., Prevete, R., Prévôt, G., Prieto, H., Przybylak, M., Puehlhofer, G., Putis, M., Reardon, P., Reno, M. H., Reyes, M., Ricci, M., Frías, M. D. Rodríguez, Matamala, O. F. Romero, Ronga, F., Sabau, M. D., Saccá, G., Sagawa, H., Sahnoune, Z., Saito, A., Sakaki, N., Salazar, H., Sánchez, J. L., Balanzar, J. C. Sanchez, Santangelo, A., Sanz-Andrés, A., Saprykin, O. A., Sarazin, F., Sato, M., Scagliola, A., Schanz, T., Schieler, H., Schovánek, P., Scotti, V., Serra, M., Sharakin, S. A., Shimizu, H. M., Shinozaki, K., Soriano, J. F., Sotgiu, A., Stan, I., Strharský, I., Sugiyama, N., Supanitsky, D., Suzuki, M., Szabelski, J., Tajima, N., Tajima, T., Takahashi, Y., Takeda, M., Takizawa, Y., Talai, M. C., Tameda, Y., Tenzer, C., Thomas, S. B., Tibolla, O., Tkachev, L. G., Tomida, T., Tone, N., Toscano, S., Traïche, M., Tsunesada, Y., Tsuno, K., Turriziani, S., Uchihori, Y., Valdés-Galicia, J. F., Vallania, P., Valore, L., Vankova-Kirilova, G., Venters, T. M., Vigorito, C., Villaseñor, L., Vlcek, B., von Ballmoos, P., Vrabel, M., Wada, S., Watanabe, J., Watts. Jr., J., Muñoz, R. Weigand, Weindl, A., Wiencke, L., Wille, M., Wilms, J., Yamamoto, T., Yang, J., Yano, H., Yashin, I. V., Yonetoku, D., Yoshida, S., Young, R., Zgura, I. S., Zotov, M. Yu., and Marchi, A. Zuccaro

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

The Extreme Universe Space Observatory on a Super Pressure Balloon 1 (EUSO-SPB1) was launched in 2017 April from Wanaka, New Zealand. The plan of this mission of opportunity on a NASA super pressure balloon test flight was to circle the southern hemisphere. The primary scientific goal was to make the first observations of ultra-high-energy cosmic-ray extensive air showers (EASs) by looking down on the atmosphere with an ultraviolet (UV) fluorescence telescope from suborbital altitude (33~km). After 12~days and 4~hours aloft, the flight was terminated prematurely in the Pacific Ocean. Before the flight, the instrument was tested extensively in the West Desert of Utah, USA, with UV point sources and lasers. The test results indicated that the instrument had sensitivity to EASs of approximately 3 EeV. Simulations of the telescope system, telescope on time, and realized flight trajectory predicted an observation of about 1 event assuming clear sky conditions. The effects of high clouds were estimated to reduce this value by approximately a factor of 2. A manual search and a machine-learning-based search did not find any EAS signals in these data. Here we review the EUSO-SPB1 instrument and flight and the EAS search., Comment: 18 pages, 19 figures

Published
2024
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3. JEM-EUSO Collaboration contributions to the 38th International Cosmic Ray Conference

Author

Abe, S., Adams Jr., J. H., Allard, D., Alldredge, P., Aloisio, R., Anchordoqui, L., Anzalone, A., Arnone, E., Bagheri, M., Baret, B., Barghini, D., Battisti, M., Bellotti, R., Belov, A. A., Bertaina, M., Bertone, P. F., Bianciotto, M., Bisconti, F., Blaksley, C., Blin-Bondil, S., Bolmgren, K., Briz, S., Burton, J., Cafagna, F., Cambiè, G., Campana, D., Capel, F., Caruso, R., Casolino, M., Cassardo, C., Castellina, A., Černý, K., Christl, M. J., Colalillo, R., Conti, L., Cotto, G., Crawford, H. J., Cremonini, R., Creusot, A., Cummings, A., Gónzalez, A. de Castro, de la Taille, C., Diesing, R., Dinaucourt, P., Di Nola, A., Ebisuzaki, T., Eser, J., Fenu, F., Ferrarese, S., Filippatos, G., Finch, W. W., Flaminio, F., Fornaro, C., Fuehne, D., Fuglesang, C., Fukushima, M., Gadamsetty, S., Gardiol, D., Garipov, G. K., Gazda, E., Golzio, A., Guarino, F., Guépin, C., Haungs, A., Heibges, T., Isgrò, F., Judd, E. G., Kajino, F., Kaneko, I., Kim, S. -W., Klimov, P. A., Krizmanic, J. F., Kungel, V., Kuznetsov, E., Martínez, F. López, Mandát, D., Manfrin, M., Marcelli, A., Marcelli, L., Marszał, W., Matthews, J. N., Mese, M., Meyer, S. S., Mimouni, J., Miyamoto, H., Mizumoto, Y., Monaco, A., Nagataki, S., Nachtman, J. M., Naumov, D., Neronov, A., Nonaka, T., Ogawa, T., Ogio, S., Ohmori, H., Olinto, A. V., Onel, Y., Osteria, G., Otte, A. N., Pagliaro, A., Panico, B., Parizot, E., Park, I. H., Paul, T., Pech, M., Perfetto, F., Picozza, P., Piotrowski, L. W., Plebaniak, Z., Posligua, J., Potts, M., Prevete, R., Prévôt, G., Przybylak, M., Reali, E., Reardon, P., Reno, M. H., Ricci, M., Matamala, O. F. Romero, Romoli, G., Sagawa, H., Sakaki, N., Saprykin, O. A., Sarazin, F., Sato, M., Schovánek, P., Scotti, V., Selmane, S., Sharakin, S. A., Shinozaki, K., Stepanoff, S., Soriano, J. F., Szabelski, J., Tajima, N., Tajima, T., Takahashi, Y., Takeda, M., Takizawa, Y., Thomas, S. B., Tkachev, L. G., Tomida, T., Toscano, S., Traïche, M., Trofimov, D., Tsuno, K., Vallania, P., Valore, L., Venters, T. M., Vigorito, C., Vrábel, M., Wada, S., Watts Jr., J., Wiencke, L., Winn, D., Wistrand, H., Yashin, I. V., Young, R., and Zotov, M. Yu.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

This is a collection of papers presented by the JEM-EUSO Collaboration at the 38th International Cosmic Ray Conference (Nagoya, Japan, July 26-August 3, 2023)

Published
2023

4. Developments and results in the context of the JEM-EUSO program obtained with the ESAF Simulation and Analysis Framework

Author

Abe, S., Adams Jr., J. H., Allard, D., Alldredge, P., Anchordoqui, L., Anzalone, A., Arnone, E., Baret, B., Barghini, D., Battisti, M., Bayer, J., Bellotti, R., Belov, A. A., Bertaina, M., Bertone, P. F., Bianciotto, M., Biermann, P. L., Bisconti, F., Blaksley, C., Blin-Bondil, S., Bobik, P., Bolmgren, K., Briz, S., Burton, J., Cafagna, F., Cambié, G., Campana, D., Capel, F., Caruso, R., Casolino, M., Cassardo, C., Castellina, A., Černý, K., Christl, M. J., Colalillo, R., Conti, L., Cotto, G., Crawford, H. J., Cremonini, R., Creusot, A., Cummings, A., Gónzalez, A. de Castro, de la Taille, C., del Peral, L., Diesing, R., Dinaucourt, P., Di Nola, A., Ebersoldt, A., Ebisuzaki, T., Eser, J., Fenu, F., Ferrarese, S., Filippatos, G., Finch, W. W., Flaminio, F., Fornaro, C., Fuehne, D., Fuglesang, C., Fukushima, M., Gardiol, D., Garipov, G. K., Golzio, A., Gorodetzky, P., Guarino, F., Guépin, C., Guzmán, A., Haungs, A., Heibges, T., Hernández-Carretero, J., Isgrò, F., Judd, E. G., Kajino, F., Kaneko, I., Kawasaki, Y., Kleifges, M., Klimov, P. A., Kreykenbohm, I., Krizmanic, J. F., Kungel, V., Kuznetsov, E., Martínez, F. López, Mackovjak, S., Mandát, D., Manfrin, M., Marcelli, A., Marcelli, L., Marszał, W., Matthews, J. N., Menshikov, A., Mernik, T., Mese, M., Meyer, S. S., Mimouni, J., Miyamoto, H., Mizumoto, Y., Monaco, A., Ríos, J. A Morales de los, Nagataki, S., Nachtman, J. M., Naumov, D., Neronov, A., Nonaka, T., Ogawa, T., Ogio, S., Ohmori, H., Olinto, A. V., Onel, Y., Osteria, G., Pagliaro, A., Panico, B., Parizot, E., Park, I. H., Pastircak, B., Paul, T., Pech, M., Perfetto, F., Picozza, P., Piotrowski, L. W., Plebaniak, Z., Posligua, J., Prevete, R., Prévôt, G., Prieto, H., Przybylak, M., Putis, M., Reali, E., Reardon, P., Reno, M. H., Ricci, M., Frías, M. Rodríguez, Romoli, G., Cano, G. Sáez, Sagawa, H., Sakaki, N., Santangelo, A., Saprykin, O. A., Sarazin, F., Sato, M., Schieler, H., Schovánek, P., Scotti, V., Selmane, S., Sharakin, S. A., Shinozaki, K., Soriano, J. F., Szabelski, J., Tajima, N., Tajima, T., Takahashi, Y., Takeda, M., Takizawa, Y., Tenzer, C., Thomas, S. B., Tkachev, L. G., Tomida, T., Toscano, S., Traïche, M., Trofimov, D., Tsuno, K., Vallania, P., Valore, L., Venters, T. M., Vigorito, C., von Ballmoos, P., Vrabel, M., Wada, S., Watts Jr., J., Weindl, A., Wiencke, L., Wilms, J., Winn, D., Wistrand, H., Yashin, I. V., Young, R., and Zotov, M. Yu.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment
Abstract

JEM--EUSO is an international program for the development of space-based Ultra-High Energy Cosmic Ray observatories. The program consists of a series of missions which are either under development or in the data analysis phase. All instruments are based on a wide-field-of-view telescope, which operates in the near-UV range, designed to detect the fluorescence light emitted by extensive air showers in the atmosphere. We describe the simulation software ESAFin the framework of the JEM--EUSO program and explain the physical assumptions used. We present here the implementation of the JEM--EUSO, POEMMA, K--EUSO, TUS, Mini--EUSO, EUSO--SPB1 and EUSO--TA configurations in ESAF. For the first time ESAF simulation outputs are compared with experimental data.

Published
2023
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6. SSRI use during acute COVID-19 and risk of Long COVID among patients with depression

Author

Zachary Butzin-Dozier, Yunwen Ji, Sarang Deshpande, Eric Hurwitz, A. Jerrod Anzalone, Jeremy Coyle, Junming Shi, Andrew Mertens, Mark J. van der Laan, John M. Colford, Rena C. Patel, Alan E. Hubbard, and the National COVID Cohort Collaborative (N3C) Consortium

Subjects
COVID-19, Long COVID, SSRI, Medicine
Abstract

Abstract Background Long COVID, also known as post-acute sequelae of COVID-19 (PASC), is a poorly understood condition with symptoms across a range of biological domains that often have debilitating consequences. Some have recently suggested that lingering SARS-CoV-2 virus particles in the gut may impede serotonin production and that low serotonin may drive many Long COVID symptoms across a range of biological systems. Therefore, selective serotonin reuptake inhibitors (SSRIs), which increase synaptic serotonin availability, may be used to prevent or treat Long COVID. SSRIs are commonly prescribed for depression, therefore restricting a study sample to only include patients with depression can reduce the concern of confounding by indication. Methods In an observational sample of electronic health records from patients in the National COVID Cohort Collaborative (N3C) with a COVID-19 diagnosis between September 1, 2021, and December 1, 2022, and a comorbid depressive disorder, the leading indication for SSRI use, we evaluated the relationship between SSRI use during acute COVID-19 and subsequent 12-month risk of Long COVID (defined by ICD-10 code U09.9). We defined SSRI use as a prescription for SSRI medication beginning at least 30 days before acute COVID-19 and not ending before SARS-CoV-2 infection. To minimize bias, we estimated relationships using nonparametric targeted maximum likelihood estimation to aggressively adjust for high-dimensional covariates. Results We analyzed a sample (n = 302,626) of patients with a diagnosis of a depressive condition before COVID-19 diagnosis, where 100,803 (33%) were using an SSRI. We found that SSRI users had a significantly lower risk of Long COVID compared to nonusers (adjusted causal relative risk 0.92, 95% CI (0.86, 0.99)) and we found a similar relationship comparing new SSRI users (first SSRI prescription 1 to 4 months before acute COVID-19 with no prior history of SSRI use) to nonusers (adjusted causal relative risk 0.89, 95% CI (0.80, 0.98)). Conclusions These findings suggest that SSRI use during acute COVID-19 may be protective against Long COVID, supporting the hypothesis that serotonin may be a key mechanistic biomarker of Long COVID.

Published
2024
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7. Neuroprotective Effects of Pulsed Electromagnetic Fields in Acute Stroke

Author

Fioravante Capone, Andrea Zini, Franco Valzania, Marina Diomedi, Valeria Tugnoli, Letizia Leocani, Giancarlo Comi, Nicoletta Anzalone, Sara Contardi, Micol Colella, Micaela Liberti, Simona Salati, Stefania Setti, Ruggero Cadossi, and Vincenzo Di Lazzaro

Subjects
Diseases of the circulatory (Cardiovascular) system, RC666-701
Published
2024
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9. Triggering Dark Showers with Conditional Dual Auto-Encoders

Author

Anzalone, Luca, Chhibra, Simranjit Singh, Maier, Benedikt, Chernyavskaya, Nadezda, and Pierini, Maurizio

Subjects
High Energy Physics - Experiment, Computer Science - Machine Learning
Abstract

We present a family of conditional dual auto-encoders (CoDAEs) for generic and model-independent new physics searches at colliders. New physics signals, which arise from new types of particles and interactions, are considered in our study as anomalies causing deviations in data with respect to expected background events. In this work, we perform a normal-only anomaly detection, which employs only background samples, to search for manifestations of a dark version of strong force applying (variational) auto-encoders on raw detector images, which are large and highly sparse, without leveraging any physics-based pre-processing or strong assumption on the signals. The proposed CoDAE has a dual-encoder design, which is general and can learn an auxiliary yet compact latent space through spatial conditioning, showing a neat improvement over competitive physics-based baselines and related approaches, therefore also reducing the gap with fully supervised models. It is the first time an unsupervised model is shown to exhibit excellent discrimination against multiple dark shower models, illustrating the suitability of this method as an accurate, fast, model-independent algorithm to deploy, e.g., in the real-time event triggering systems of Large Hadron Collider experiments such as ATLAS and CMS., Comment: 24 pages, 6 figures, and 4 tables; journal version

Published
2023
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10. Common Iliac Artery Mycotic Pseudoaneurysm Associated with a Prevertebral Infection: A Case Report

Author

Davis, Will, Greene, Christopher, and Anzalone, Brendan

Subjects
proteus mirabilis, case report, mycotic pseudoaneurysm
Abstract

Introduction: Mycotic pseudoaneurysms are rare but severe sequelae of an arterial wall infection. If undiagnosed and untreated they can lead to significant morbidity and mortality through complications such as arterial rupture or dissection.Case report: This report details the case of a 64-year-old-male who developed a left common iliac artery mycotic pseudoaneurysm from Proteus mirabilis, which was associated with a prevertebral abscess. The patient presented with isolated, left lower extremity edema and intermittent fevers. The case is unique in both the pathogen (P mirabilis) and in its association with presumed direct arterial wall infection from an adjacent prevertebral abscess.Conclusion: The obscure presentation highlights the need for a high clinical suspicion of such a diagnosis when a patient presents with a certain constellation of symptoms and the right predisposing risk factors in their history.

Published
2023

13. A prime editor mouse to model a broad spectrum of somatic mutations in vivo

Author

Ely, Zackery A., Mathey-Andrews, Nicolas, Naranjo, Santiago, Gould, Samuel I., Mercer, Kim L., Newby, Gregory A., Cabana, Christina M., Rideout, III, William M., Jaramillo, Grissel Cervantes, Khirallah, Jennifer M., Holland, Katie, Randolph, Peyton B., Freed-Pastor, William A., Davis, Jessie R., Kulstad, Zachary, Westcott, Peter M. K., Lin, Lin, Anzalone, Andrew V., Horton, Brendan L., Pattada, Nimisha B., Shanahan, Sean-Luc, Ye, Zhongfeng, Spranger, Stefani, Xu, Qiaobing, Sánchez-Rivera, Francisco J., Liu, David R., and Jacks, Tyler

Published
2024
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16. The prevalence of postacute sequelae of coronavirus disease 2019 in solid organ transplant recipients: Evaluation of risk in the National COVID Cohort Collaborative

Author

Wilcox, Adam B., Lee, Adam M., Graves, Alexis, Anzalone, Alfred Jerrod, Manna, Amin, Saha, Amit, Olex, Amy, Zhou, Andrea, Williams, Andrew E., Southerland, Andrew, Girvin, Andrew T., Walden, Anita, Sharathkumar, Anjali A., Amor, Benjamin, Bates, Benjamin, Hendricks, Brian, Patel, Brijesh, Alexander, Caleb, Bramante, Carolyn, Ward-Caviness, Cavin, Madlock-Brown, Charisse, Suver, Christine, Chute, Christopher, Dillon, Christopher, Wu, Chunlei, Schmitt, Clare, Takemoto, Cliff, Housman, Dan, Gabriel, Davera, Eichmann, David A., Mazzotti, Diego, Brown, Don, Boudreau, Eilis, Hill, Elaine, Zampino, Elizabeth, Marti, Emily Carlson, Pfaff, Emily R., French, Evan, Koraishy, Farrukh M., Mariona, Federico, Prior, Fred, Sokos, George, Martin, Greg, Lehmann, Harold, Spratt, Heidi, Mehta, Hemalkumar, Liu, Hongfang, Sidky, Hythem, Hayanga, J.W. Awori, Pincavitch, Jami, Clark, Jaylyn, Harper, Jeremy Richard, Islam, Jessica, Ge, Jin, Gagnier, Joel, Saltz, Joel H., Saltz, Joel, Loomba, Johanna, Buse, John, Mathew, Jomol, Rutter, Joni L., McMurry, Julie A., Guinney, Justin, Starren, Justin, Crowley, Karen, Bradwell, Katie Rebecca, Walters, Kellie M., Wilkins, Ken, Gersing, Kenneth R., Cato, Kenrick Dwain, Murray, Kimberly, Kostka, Kristin, Northington, Lavance, Pyles, Lee Allan, Misquitta, Leonie, Cottrell, Lesley, Portilla, Lili, Deacy, Mariam, Bissell, Mark M., Clark, Marshall, Emmett, Mary, Saltz, Mary Morrison, Palchuk, Matvey B., Haendel, Melissa A., Adams, Meredith, Temple-O'Connor, Meredith, Kurilla, Michael G., Morris, Michele, Qureshi, Nabeel, Safdar, Nasia, Garbarini, Nicole, Sharafeldin, Noha, Sadan, Ofer, Francis, Patricia A., Burgoon, Penny Wung, Robinson, Peter, Payne, Philip R.O., Fuentes, Rafael, Jawa, Randeep, Erwin-Cohen, Rebecca, Patel, Rena, Moffitt, Richard A., Zhu, Richard L., Kamaleswaran, Rishi, Hurley, Robert, Miller, Robert T., Pyarajan, Saiju, Michael, Sam G., Bozzette, Samuel, Mallipattu, Sandeep, Vedula, Satyanarayana, Chapman, Scott, O'Neil, Shawn T., Setoguchi, Soko, Hong, Stephanie S., Johnson, Steve, Bennett, Tellen D., Callahan, Tiffany, Topaloglu, Umit, Sheikh, Usman, Gordon, Valery, Subbian, Vignesh, Kibbe, Warren A., Hernandez, Wenndy, Beasley, Will, Cooper, Will, Hillegass, William, Zhang, Xiaohan Tanner, Vinson, Amanda J., Schissel, Makayla, Anzalone, Alfred J., Dai, Ran, French, Evan T., Olex, Amy L., Lee, Stephen B., Ison, Michael, and Mannon, Roslyn B.

Published
2024
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17. Crowd-sourced machine learning prediction of long COVID using data from the National COVID Cohort CollaborativeResearch in context

Author

Timothy Bergquist, Johanna Loomba, Emily Pfaff, Fangfang Xia, Zixuan Zhao, Yitan Zhu, Elliot Mitchell, Biplab Bhattacharya, Gaurav Shetty, Tamanna Munia, Grant Delong, Adbul Tariq, Zachary Butzin-Dozier, Yunwen Ji, Haodong Li, Jeremy Coyle, Seraphina Shi, Rachael V. Philips, Andrew Mertens, Romain Pirracchio, Mark van der Laan, John M. Colford, Jr., Alan Hubbard, Jifan Gao, Guanhua Chen, Neelay Velingker, Ziyang Li, Yinjun Wu, Adam Stein, Jiani Huang, Zongyu Dai, Qi Long, Mayur Naik, John Holmes, Danielle Mowery, Eric Wong, Ravi Parekh, Emily Getzen, Jake Hightower, Jennifer Blase, Ataes Aggarwal, Joseph Agor, Amera Al-Amery, Oluwatobiloba Aminu, Adit Anand, Corneliu Antonescu, Mehak Arora, Sayed Asaduzzaman, Tanner Asmussen, Mahdi Baghbanzadeh, Frazier Baker, Bridget Bangert, Laila Bekhet, Jenny Blase, Brian Caffo, Hao Chang, Zeyuan Chen, Jiandong Chen, Jeffrey Chiang, Peter Cho, Robert Cockrell, Parker Combs, Ciara Crosby, Ran Dai, Anseh Danesharasteh, Elif Yildirim, Ryan Demilt, Kaiwen Deng, Sanjoy Dey, Rohan Dhamdhere, Andrew Dickson, Phoebe Dijour, Dong Dinh, Richard Dixon, Albi Domi, Souradeep Dutta, Mirna Elizondo, Zeynep Ertem, Solomon Feuerwerker, Danica Fliss, Jennifer Fowler, Sunyang Fu, Kelly Gardner, Neil Getty, Mohamed Ghalwash, Logan Gloster, Phil Greer, Yuanfang Guan, Colby Ham, Samer Hanoudi, Jeremy Harper, Nathaniel Hendrix, Leeor Hershkovich, Junjie Hu, Yu Huang, Tongtong Huang, Junguk Hur, Monica Isgut, Hamid Ismail, Grant Izmirlian, Kuk Jang, Christianah Jemiyo, Hayoung Jeong, Xiayan Ji, Ming Jiang, Sihang Jiang, Xiaoqian Jiang, Yuye Jiang, Akin Johnson, Zach Analyst, Saarthak Kapse, Uri Kartoun, Dukka KC, Zahra Fard, Tim Kosfeld, Spencer Krichevsky, Mike Kuo, Dale Larie, Lauren Lederer, Shan Leng, Hongyang Li, Jianfu Li, Tiantian Li, Xinwen Liang, Hengyue Liang, Feifan Liu, Daniel Liu, Gang Luo, Ravi Madduri, Vithal Madhira, Shivali Mani, Farzaneh Mansourifard, Robert Matson, Vangelis Metsis, Pablo Meyer, Catherine Mikhailova, Dante Miller, Christopher Milo, Gourav Modanwal, Ronald Moore, David Morgenthaler, Rasim Musal, Vinit Nalawade, Rohan Narain, Saideep Narendrula, Alena Obiri, Satoshi Okawa, Chima Okechukwu, Toluwanimi Olorunnisola, Tim Ossowski, Harsh Parekh, Jean Park, Saaya Patel, Jason Patterson, Chetan Paul, Le Peng, Diana Perkins, Suresh Pokharel, Dmytro Poplavskiy, Zach Pryor, Sarah Pungitore, Hong Qin, Salahaldeen Rababa, Mahbubur Rahman, Elior Rahmani, Gholamali Rahnavard, Md Raihan, Suraj Rajendran, Sarangan Ravichandran, Chandan Reddy, Abel Reyes, Ali Roghanizad, Sean Rouffa, Xiaoyang Ruan, Arpita Saha, Sahil Sawant, Melody Schiaffino, Diego Seira, Saurav Sengupta, Ruslan Shalaev, Linh Shinguyen, Karnika Singh, Soumya Sinha, Damien Socia, Halen Stalians, Charalambos Stavropoulos, Jan Strube, Devika Subramanian, Jiehuan Sun, Ju Sun, Chengkun Sun, Prathic Sundararajan, Salmonn Talebi, Edward Tawiah, Jelena Tesic, Mikaela Thiess, Raymond Tian, Luke Torre-Healy; Ming-Tse Tsai, David Tyus, Madhurima Vardhan, Benjamin Walzer, Jacob Walzer, Junda Wang, Lu Wang, Will Wang, Jonathan Wang, Yisen Wang, Chad Weatherly, Fanyou Wu, Yifeng Wu, Hao Yan, Zhichao Yang, Biao Ye, Rui Yin, Changyu Yin, Yun Yoo, Albert You, June Yu, Martin Zanaj, Zachary Zaiman, Kai Zhang, Xiaoyi Zhang, Tianmai Zhang, Degui Zhi, Yishan Zhong, Huixue Zhou, Andrea Zhou, Yuanda Zhu, Sophie Zhu, Meredith Adams, Caleb Alexander, Benjamin Amor, Alfred Anzalone, Benjamin Bates, Will Beasley, Tellen Bennett, Mark Bissell, Eilis Boudreau, Samuel Bozzette, Katie Bradwell, Carolyn Bramante, Don Brown, Penny Burgoon, John Buse, Tiffany Callahan, Kenrick Cato, Scott Chapman, Christopher Chute, Jaylyn Clark, Marshall Clark, Will Cooper, Lesley Cottrell, Karen Crowley, Mariam Deacy, Christopher Dillon, David Eichmann, Mary Emmett, Rebecca Erwin-Cohen, Patricia Francis, Evan French, Rafael Fuentes, Davera Gabriel, Joel Gagnier, Nicole Garbarini, Jin Ge, Kenneth Gersing, Andrew Girvin, Valery Gordon, Alexis Graves, Justin Guinney, Melissa Haendel, J.W. Hayanga, Brian Hendricks, Wenndy Hernandez, Elaine Hill, William Hillegass, Stephanie Hong, Dan Housman, Robert Hurley, Jessica Islam, Randeep Jawa, Steve Johnson, Rishi Kamaleswaran, Warren Kibbe, Farrukh Koraishy, Kristin Kostka, Michael Kurilla, Adam Lee, Harold Lehmann, Hongfang Liu, Charisse Madlock-Brown; Sandeep Mallipattu, Amin Manna, Federico Mariona, Emily Marti, Greg Martin, Jomol Mathew, Diego Mazzotti, Julie McMurry, Hemalkumar Mehta, Sam Michael, Robert Miller, Leonie Misquitta, Richard Moffitt, Michele Morris, Kimberly Murray, Lavance Northington, Shawn O’Neil, Amy Olex, Matvey Palchuk, Brijesh Patel, Rena Patel, Philip Payne, Jami Pincavitch, Lili Portilla, Fred Prior, Saiju Pyarajan, Lee Pyles, Nabeel Qureshi, Peter Robinson, Joni Rutter, Ofer Sadan, Nasia Safdar, Amit Saha, Joel Saltz, Mary Saltz, Clare Schmitt, Soko Setoguchi, Noha Sharafeldin, Anjali Sharathkumar, Usman Sheikh, Hythem Sidky, George Sokos, Andrew Southerland, Heidi Spratt, Justin Starren, Vignesh Subbian, Christine Suver, Cliff Takemoto, Meredith Temple-O'Connor, Umit Topaloglu, Satyanarayana Vedula, Anita Walden, Kellie Walters, Cavin Ward-Caviness, Adam Wilcox, Ken Wilkins, Andrew Williams, Chunlei Wu, Elizabeth Zampino, Xiaohan Zhang, and Richard Zhu

Subjects
Long COVID, PASC, Machine learning, COVID-19, Evaluation, Community challenge, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: While many patients seem to recover from SARS-CoV-2 infections, many patients report experiencing SARS-CoV-2 symptoms for weeks or months after their acute COVID-19 ends, even developing new symptoms weeks after infection. These long-term effects are called post-acute sequelae of SARS-CoV-2 (PASC) or, more commonly, Long COVID. The overall prevalence of Long COVID is currently unknown, and tools are needed to help identify patients at risk for developing long COVID. Methods: A working group of the Rapid Acceleration of Diagnostics-radical (RADx-rad) program, comprised of individuals from various NIH institutes and centers, in collaboration with REsearching COVID to Enhance Recovery (RECOVER) developed and organized the Long COVID Computational Challenge (L3C), a community challenge aimed at incentivizing the broader scientific community to develop interpretable and accurate methods for identifying patients at risk of developing Long COVID. From August 2022 to December 2022, participants developed Long COVID risk prediction algorithms using the National COVID Cohort Collaborative (N3C) data enclave, a harmonized data repository from over 75 healthcare institutions from across the United States (U.S.). Findings: Over the course of the challenge, 74 teams designed and built 35 Long COVID prediction models using the N3C data enclave. The top 10 teams all scored above a 0.80 Area Under the Receiver Operator Curve (AUROC) with the highest scoring model achieving a mean AUROC of 0.895. Included in the top submission was a visualization dashboard that built timelines for each patient, updating the risk of a patient developing Long COVID in response to clinical events. Interpretation: As a result of L3C, federal reviewers identified multiple machine learning models that can be used to identify patients at risk for developing Long COVID. Many of the teams used approaches in their submissions which can be applied to future clinical prediction questions. Funding: Research reported in this RADx® Rad publication was supported by the National Institutes of Health. Timothy Bergquist, Johanna Loomba, and Emily Pfaff were supported by Axle Subcontract: NCATS-STSS-P00438.

Published
2024
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19. The Relative Risk of COVID-19 in Solid Organ Transplant Recipients Over Waves of the Pandemic

Author

Amanda J. Vinson, Alfred J. Anzalone, Makayla Schissel, Ran Dai, Gaurav Agarwal, Stephen B. Lee, Amy Olex, and Roslyn B. Mannon

Subjects
COVID-19, pandemic, Sars-CoV-2, transplant, outcomes, variant strain, Specialties of internal medicine, RC581-951
Abstract

Solid organ transplant recipients (SOTR) are at increased risk from COVID-19. Over time, the absolute risk of adverse outcomes after COVID-19 has decreased in both the non-immunosuppressed/immunocompromised (non-ISC) general population, and amongst SOTR. Using the N3C, we examined the absolute risk of mortality, major adverse renal or cardiac events, and hospitalization after COVID-19 diagnosis amongst non-ISC and SOTR populations over five waves of the pandemic (Wave 1: Ancestral COVID; Wave 2: Alpha; Wave 3: Delta; Wave 4: Omicron; Wave 5: Omicron). Within each wave, we determined the relative risk of each outcome for SOTR versus the non-ISC population based on crude event rates, and then used multivariable cox proportional hazards models and logistic regression to determine the adjusted risk of each outcome based on SOT status. Throughout the pandemic, including during the Omicron wave (Wave 5), SOTR were at greater absolute risk for each outcome than non-ISC patients (p-values all

Published
2024
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20. Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome

Author

Daniele Nicotra, Farideh Ghadamgahi, Samrat Ghosh, Alice Anzalone, Giulio Dimaria, Alexandros Mosca, Maria Elena Massimino, Ramesh Raju Vetukuri, and Vittoria Catara

Subjects
tomato, microbiome, endophytes, rhizosphere, PGPR, BCA, Plant culture, SB1-1110
Abstract

IntroductionDespite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health.MethodsWe therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits.ResultsBacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth.DiscussionThis study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.

Published
2024
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23. Development of the ELISSA array: prototype testing at Laboratori Nazionali del Sud

Author

Guardo G. L., Anzalone A., Balabanski D., Chesnevskaya S., Crucillá W., Filipescu D., Gulino M., La Cognata M., Lattuada D., Matei C., Pizzone R. G., Rapisarda G. G., Romano S., Spitaleri C., Taffara A., Tumino A., and Xu Y.

Subjects
Physics, QC1-999
Abstract

The Extreme Light Infrastructure-Nuclear Physics (ELI-NP) facility, underconstruction in Magurele near Bucharest in Romania, will provide high-intensity andhigh-resolution gamma ray beams that can be used to address hotly debated problems in nuclear astrophysics, such as the accurate measurements of the cross sections of the24Mg(γ,α)20Ne reaction For this purpose, a silicon strip detector array (named ELISSA) will be realized in acommon effort by ELI-NP and Laboratori Nazionali del Sud (INFN-LNS), in order to measure excitation functions and angular distributions over a wide energy and angular range. A prototype of ELISSA was built and tested at INFN-LNS in Catania (Italy) with the support of ELI-NP. In this occasion, we have carried out experiments with alpha sources and with a 11 MeV 7Li beam that show up a very good energy resolution (better than 1%) and very good position resolution, of the order of 1 mm. Moreover, a threshold of 150 keV can be easily achieved with no cooling.

Published
2018
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24. A Geant4-based Monte Carlo Tool for Nuclear Astrophysics

Author

Lattuada D., La Cognata M., Anzalone A., Balabanski D.L., Chesnevskaya S., Costa M., Crucillà V., Guardo G.L., Gulino M., Matei C., Pizzone R.G., Romano S., Spitaleri C., Tumino A., and Xu Y

Subjects
Physics, QC1-999
Abstract

Present and future gamma-beam facilities represent a great opportunity to validate and evaluate the cross-sections of many photonuclear reactions at near-threshold energies, whose data mostly come from theoretical calculations. We developed a Monte Carlo (MC) software that makes use of the validatedtracking Geant4 libraries and the n-body event generator of ROOT libraries in order to provide a fast, realiable and complete MC tool to be used for nuclear physics experiments, with a particular focus on photo-nuclear processes. We discuss the results of the MC simulations performed in order to evaluate the effects of the electromagnetic background, the straggling of the emitted particles due to the target thickness and the resolution of the silicon detectors. Finally we present the preliminary results on some nuclear reactions involved in the p-process, which will be studied with ELISSA and the GBS at ELI-NP.

Published
2018
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25. Liquid biopsy of cerebrospinal fluid enabling the detection and therapeutic targeting of the BRAFV600E mutation in a patient with overlapping Erdheim-Chester/Rosai-Dorfman disease

Author

Pieri, Valentina, Berzero, Giulia, Paterra, Rosina, Ferré, Laura, Tomelleri, Alessandro, Campochiaro, Corrado, Esposito, Federica, Calimeri, Teresa, Cangi, Maria Giulia, Tenace, Nazario Pio, Ferreri, Andrés José María, Castellano, Antonella, Barbera, Maurizio, Anzalone, Nicoletta, Gay, Lorenzo Gabriel, Bello, Lorenzo, Colecchia, Maurizio, Ponzoni, Maurilio, Finocchiaro, Gaetano, and Filippi, Massimo

Published
2024
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28. A Call for a Health Data–Informed Workforce Among Clinicians

Author

Joy Doll, A Jerrod Anzalone, Martina Clarke, Kathryn Cooper, Ann Polich, and Jacob Siedlik

Subjects
Special aspects of education, LC8-6691, Medicine (General), R5-920
Abstract

AbstractA momentous amount of health data has been and is being collected. Across all levels of health care, data are driving decision-making and impacting patient care. A new field of knowledge and role for those in health care is emerging—the need for a health data–informed workforce. In this viewpoint, we describe the approaches needed to build a health data–informed workforce, a new and critical skill for the health care ecosystem.

Published
2024
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29. Evaluating COVID-19 vaccine effectiveness during pre-Delta, Delta and Omicron dominant periods among pregnant people in the U.S.: Retrospective cohort analysis from a nationally sampled cohort in National COVID Collaborative Cohort (N3C)

Author

Nasia Safdar, Harold Lehmann, Jing Sun, Brijesh Patel, Hongfang Liu, Peter Robinson, Elaine Hill, Justin Guinney, Joel Gagnier, Cavin Ward-Caviness, Noha Sharafeldin, Justin Starren, Amit Saha, Lesley Cottrell, Melissa A Haendel, Vignesh Subbian, Kristin Kostka, Farrukh M Koraishy, Andrew E Williams, Robert Hurley, Steve Johnson, Usman Sheikh, Rishi Kamaleswaran, Christopher Dillon, Rena C Patel, Michele Morris, Randeep Jawa, Hemalkumar Mehta, Benjamin Bates, Tellen D Bennett, Nabeel Qureshi, Qiuyuan Qin, Kenneth Wilkins, Sara E Jones, Katie Rebecca Bradwell, Lauren Chan, Jerrod Anzalone, Qulu Zheng, Michael Liebman, Federico Mariona, Emily A Groene Faherty, Anup P Challa, Adam B Wilcox, Adam M Lee, Alexis Graves, Alfred Anzalone, Amin Manna, Amy Olex, Andrea Zhou, Andrew Southerland, Andrew T Girvin, Anita Walden, Anjali A Sharathkumar, Benjamin Amor, Brian Hendricks, Caleb Alexander, Caroline Signore, Carolyn Bramante, Charisse Madlock-Brown, Christine Suver, Christopher Chute, Chunlei Wu, Clare Schmitt, Cliff Takemoto, Dan Housman, Davera Gabriel, David A Eichmann, Diego Mazzotti, Eilis Boudreau Don Brown, Elizabeth Zampino, Emily Carlson Marti, Emily R Pfaff, Evan French, Fred Prior, George Sokos, Greg Martin, Heidi Spratt, Hythem Sidky, JW Awori Hayanga, Jami Pincavitch, Jaylyn Clark, Jeremy Richard Harper, Jessica Islam, Jin Ge, Joel H Saltz, Joel Saltz, Johanna Loomba, John Buse, Jomol Mathew, Joni L Rutter, Julie A McMurry, Karen Crowley, Kellie M Walters, Ken Wilkins, Kenneth R Gersing, Kenrick Dwain Cato, Kimberly Murray, Lavance Northington, Lee Allan Pyles, Leonie Misquitta, Lili Portilla, Mariam Deacy, Mark M Bissell, Marshall Clark, Mary Emmett, Mary Morrison Saltz, Matvey B Palchuk, Meredith Adams, Meredith Temple-O'Connor, Michael G Kurilla, Nicole Garbarini, Ofer Sadan, Patricia A Francis, Penny Wung Burgoon, Philip RO Payne, Rafael Fuentes, Rebecca Erwin-Cohen, Richard A Moffitt, Richard L Zhu, Robert T Miller, Saiju Pyarajan, Sam G Michael, Samuel Bozzette, Sandeep Mallipattu, Satyanarayana Vedula, Scott Chapman, T Shawn, Soko Setoguchi O'Neil, Stephanie S Hong, Tiffany Callahan, Umit Topaloglu, Valery Gordon, Warren A Kibbe, Wenndy Hernandez, Will Beasley, Will Cooper, William Hillegass, and Xiaohan Tanner Zhang

Subjects
Public aspects of medicine, RA1-1270
Abstract

Objectives To evaluate the effectiveness of COVID-19 vaccinations (initial and booster) during pre-Delta, Delta and Omicron dominant periods among pregnant people via (1) COVID-19 incident and severe infections among pregnant people who were vaccinated versus unvaccinated and (2) post-COVID-19 vaccination breakthrough infections and severe infections among vaccinated females who were pregnant versus non-pregnant.Design Retrospective cohort study using nationally sampled electronic health records data from the National COVID Cohort Collaborative, 10 December 2020 –7 June 2022.Participants Cohort 1 included pregnant people (15–55 years) and cohort 2 included vaccinated females of reproductive age (15–55 years).Exposures (1) COVID-19 vaccination and (2) pregnancy.Main outcome measures Adjusted HRs (aHRs) for COVID-19 incident or breakthrough infections and severe infections (ie, COVID-19 infections with related hospitalisations).Results In cohort 1, 301 107 pregnant people were included. Compared with unvaccinated pregnant people, the aHRs for pregnant people with initial vaccinations during pregnancy of incident COVID-19 were 0.77 (95% CI 0.62 to 0.96) and 0.88 (95% CI 0.73 to 1.07) and aHRs of severe COVID-19 infections were 0.65 (95% CI 0.47 to 0.90) and 0.79 (95% CI 0.51 to 1.21) during the Delta and Omicron periods, respectively. Compared with pregnant people with full initial vaccinations, the aHR of incident COVID-19 for pregnant people with booster vaccinations was 0.64 (95% CI 0.58 to 0.71) during the Omicron period. In cohort 2, 934 337 vaccinated people were included. Compared with vaccinated non-pregnant females, the aHRs of severe COVID-19 infections for people with initial vaccinations during pregnancy was 2.71 (95% CI 1.31 to 5.60) during the Omicron periods.Conclusions Pregnant people with initial and booster vaccinations during pregnancy had a lower risk of incident and severe COVID-19 infections compared with unvaccinated pregnant people across the pandemic stages. However, vaccinated pregnant people still had a higher risk of severe infections compared with non-pregnant females.

Published
2024
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30. Improving Parametric Neural Networks for High-Energy Physics (and Beyond)

Author

Anzalone, Luca, Diotalevi, Tommaso, and Bonacorsi, Daniele

Subjects
High Energy Physics - Experiment, Computer Science - Machine Learning
Abstract

Signal-background classification is a central problem in High-Energy Physics (HEP), that plays a major role for the discovery of new fundamental particles. A recent method -- the Parametric Neural Network (pNN) -- leverages multiple signal mass hypotheses as an additional input feature to effectively replace a whole set of individual classifiers, each providing (in principle) the best response for the corresponding mass hypothesis. In this work we aim at deepening the understanding of pNNs in light of real-world usage. We discovered several peculiarities of parametric networks, providing intuition, metrics, and guidelines to them. We further propose an alternative parametrization scheme, resulting in a new parametrized neural network architecture: the AffinePNN; along with many other generally applicable improvements, like the balanced training procedure. Finally, we extensively and empirically evaluate our models on the HEPMASS dataset, along its imbalanced version (called HEPMASS-IMB) we provide here for the first time, to further validate our approach. Provided results are in terms of the impact of the proposed design decisions, classification performance, and interpolation capability, as well., Comment: Published at MLST. Code available at: https://github.com/Luca96/affine-parametric-networks

Published
2022
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31. Crowd-sourced machine learning prediction of long COVID using data from the National COVID Cohort Collaborative

Author

Aggarwal, Ataes, Agor, Joseph, Al-Amery, Amera, Aminu, Oluwatobiloba, Anand, Adit, Antonescu, Corneliu, Arora, Mehak, Asaduzzaman, Sayed, Asmussen, Tanner, Baghbanzadeh, Mahdi, Baker, Frazier, Bangert, Bridget, Bekhet, Laila, Bhattacharya, Biplab, Blase, Jenny, Butzin-Dozier, Zachary, Caffo, Brian, Chang, Hao, Chen, Zeyuan, Chen, Jiandong, Chiang, Jeffrey, Cho, Peter, Cockrell, Robert, Combs, Parker, Coyle, Jeremy, Crosby, Ciara, Dai, Zongyu, Dai, Ran, Danesharasteh, Anseh, Yildirim, Elif, Delong, Grant, Demilt, Ryan, Deng, Kaiwen, Dey, Sanjoy, Dhamdhere, Rohan, Dickson, Andrew, Dijour, Phoebe, Dinh, Dong, Dixon, Richard, Domi, Albi, Dutta, Souradeep, Elizondo, Mirna, Ertem, Zeynep, Feuerwerker, Solomon, Fliss, Danica, Fowler, Jennifer, Fu, Sunyang, Gardner, Kelly, Getty, Neil, Ghalwash, Mohamed, Gloster, Logan, Greer, Phil, Guan, Yuanfang, Ham, Colby, Hanoudi, Samer, Harper, Jeremy, Hendrix, Nathaniel, Hershkovich, Leeor, Hightower, Jake, Hu, Junjie, Huang, Jiani, Huang, Yu, Huang, Tongtong, Hur, Junguk, Isgut, Monica, Ismail, Hamid, Izmirlian, Grant, Jang, Kuk, Jemiyo, Christianah, Jeong, Hayoung, Ji, Yunwen, Ji, Xiayan, Jiang, Ming, Jiang, Sihang, Jiang, Xiaoqian, Jiang, Yuye, Johnson, Akin, Analyst, Zach, Kapse, Saarthak, Kartoun, Uri, KC, Dukka, Fard, Zahra, Kosfeld, Tim, Krichevsky, Spencer, Kuo, Mike, Larie, Dale, Lederer, Lauren, Leng, Shan, Li, Ziyang, Li, Hongyang, Li, Haodong, Li, Jianfu, Li, Tiantian, Liang, Xinwen, Liang, Hengyue, Liu, Feifan, Liu, Daniel, Luo, Gang, Munia, Tamanna, Madduri, Ravi, Madhira, Vithal, Mani, Shivali, Mansourifard, Farzaneh, Matson, Robert, Mertens, Andrew, Metsis, Vangelis, Meyer, Pablo, Mikhailova, Catherine, Miller, Dante, Milo, Christopher, Mitchell, Elliot, Modanwal, Gourav, Moore, Ronald, Morgenthaler, David, Musal, Rasim, Naik, Mayur, Nalawade, Vinit, Narain, Rohan, Narendrula, Saideep, Obiri, Alena, Okawa, Satoshi, Okechukwu, Chima, Olorunnisola, Toluwanimi, Ossowski, Tim, Parekh, Harsh, Park, Jean, Patel, Saaya, Patterson, Jason, Paul, Chetan, Peng, Le, Perkins, Diana, Pokharel, Suresh, Poplavskiy, Dmytro, Pryor, Zach, Pungitore, Sarah, Qin, Hong, Rababa, Salahaldeen, Rahman, Mahbubur, Rahmani, Elior, Rahnavard, Gholamali, Raihan, Md, Rajendran, Suraj, Ravichandran, Sarangan, Reddy, Chandan, Reyes, Abel, Roghanizad, Ali, Rouffa, Sean, Ruan, Xiaoyang, Saha, Arpita, Sawant, Sahil, Schiaffino, Melody, Seira, Diego, Sengupta, Saurav, Shalaev, Ruslan, Shetty, Gaurav, Shi, Seraphina, Shinguyen, Linh, Singh, Karnika, Sinha, Soumya, Socia, Damien, Stalians, Halen, Stavropoulos, Charalambos, Strube, Jan, Subramanian, Devika, Sun, Jiehuan, Sun, Ju, Sun, Chengkun, Sundararajan, Prathic, Talebi, Salmonn, Tawiah, Edward, Tesic, Jelena, Thiess, Mikaela, Tian, Raymond, Torre-Healy; Ming-Tse Tsai, Luke, Tyus, David, Vardhan, Madhurima, Velingker, Neelay, Walzer, Benjamin, Walzer, Jacob, Wang, Junda, Wang, Lu, Wang, Will, Wang, Jonathan, Wang, Yisen, Weatherly, Chad, Wu, Fanyou, Wu, Yifeng, Wu, Yinjun, Xia, Fangfang, Yan, Hao, Yang, Zhichao, Ye, Biao, Yin, Rui, Yin, Changyu, Yoo, Yun, You, Albert, Yu, June, Zanaj, Martin, Zaiman, Zachary, Zhang, Kai, Zhang, Xiaoyi, Zhang, Tianmai, Zhao, Zixuan, Zhi, Degui, Zhong, Yishan, Zhou, Huixue, Zhou, Andrea, Zhu, Yuanda, Zhu, Yitan, Zhu, Sophie, Adams, Meredith, Alexander, Caleb, Amor, Benjamin, Anzalone, Alfred, Bates, Benjamin, Beasley, Will, Bennett, Tellen, Bissell, Mark, Boudreau, Eilis, Bozzette, Samuel, Bradwell, Katie, Bramante, Carolyn, Brown, Don, Burgoon, Penny, Buse, John, Callahan, Tiffany, Cato, Kenrick, Chapman, Scott, Chute, Christopher, Clark, Jaylyn, Clark, Marshall, Cooper, Will, Cottrell, Lesley, Crowley, Karen, Deacy, Mariam, Dillon, Christopher, Eichmann, David, Emmett, Mary, Erwin-Cohen, Rebecca, Francis, Patricia, French, Evan, Fuentes, Rafael, Gabriel, Davera, Gagnier, Joel, Garbarini, Nicole, Ge, Jin, Gersing, Kenneth, Girvin, Andrew, Gordon, Valery, Graves, Alexis, Guinney, Justin, Haendel, Melissa, Hayanga, J.W., Hendricks, Brian, Hernandez, Wenndy, Hill, Elaine, Hillegass, William, Hong, Stephanie, Housman, Dan, Hurley, Robert, Islam, Jessica, Jawa, Randeep, Johnson, Steve, Kamaleswaran, Rishi, Kibbe, Warren, Koraishy, Farrukh, Kostka, Kristin, Kurilla, Michael, Lee, Adam, Lehmann, Harold, Liu, Hongfang, Loomba, Johanna, Madlock-Brown; Sandeep Mallipattu, Charisse, Manna, Amin, Mariona, Federico, Marti, Emily, Martin, Greg, Mathew, Jomol, Mazzotti, Diego, McMurry, Julie, Mehta, Hemalkumar, Michael, Sam, Miller, Robert, Misquitta, Leonie, Moffitt, Richard, Morris, Michele, Murray, Kimberly, Northington, Lavance, O’Neil, Shawn, Olex, Amy, Palchuk, Matvey, Patel, Brijesh, Patel, Rena, Payne, Philip, Pfaff, Emily, Pincavitch, Jami, Portilla, Lili, Prior, Fred, Pyarajan, Saiju, Pyles, Lee, Qureshi, Nabeel, Robinson, Peter, Rutter, Joni, Sadan, Ofer, Safdar, Nasia, Saha, Amit, Saltz, Joel, Saltz, Mary, Schmitt, Clare, Setoguchi, Soko, Sharafeldin, Noha, Sharathkumar, Anjali, Sheikh, Usman, Sidky, Hythem, Sokos, George, Southerland, Andrew, Spratt, Heidi, Starren, Justin, Subbian, Vignesh, Suver, Christine, Takemoto, Cliff, Temple-O'Connor, Meredith, Topaloglu, Umit, Vedula, Satyanarayana, Walden, Anita, Walters, Kellie, Ward-Caviness, Cavin, Wilcox, Adam, Wilkins, Ken, Williams, Andrew, Wu, Chunlei, Zampino, Elizabeth, Zhang, Xiaohan, Zhu, Richard, Bergquist, Timothy, Tariq, Adbul, Philips, Rachael V., Pirracchio, Romain, van der Laan, Mark, Colford, John M., Jr., Hubbard, Alan, Gao, Jifan, Chen, Guanhua, Stein, Adam, Long, Qi, Holmes, John, Mowery, Danielle, Wong, Eric, Parekh, Ravi, Getzen, Emily, and Blase, Jennifer

Published
2024
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33. From Alpha to Omicron and Beyond: Associations Between SARS-CoV-2 Variants and Surgical Outcomes

Author

Wilcox, Adam B., Lee, Adam M., Graves, Alexis, Anzalone, Alfred, Manna, Amin, Saha, Amit, Olex, Amy, Zhou, Andrea, Williams, Andrew E., Southerland, Andrew, Girvin, Andrew T., Walden, Anita, Sharathkumar, Anjali A., Amor, Benjamin, Bates, Benjamin, Hendricks, Brian, Patel, Brijesh, Alexander, Caleb, Bramante, Carolyn, Ward-Caviness, Cavin, Madlock-Brown, Charisse, Suver, Christine, Chute, Christopher, Dillon, Christopher, Wu, Chunlei, Schmitt, Clare, Takemoto, Cliff, Housman, Dan, Gabriel, Davera, Eichmann, David A., Mazzotti, Diego, Brown, Don, Boudreau, Eilis, Hill, Elaine, Zampino, Elizabeth, Marti, Emily Carlson, Pfaff, Emily R., French, Evan, Koraishy, Farrukh M., Mariona, Federico, Prior, Fred, Sokos, George, Martin, Greg, Lehmann, Harold, Spratt, Heidi, Mehta, Hemalkumar, Liu, Hongfang, Sidky, Hythem, Hayanga, J.W. Awori, Pincavitch, Jami, Clark, Jaylyn, Harper, Jeremy Richard, Islam, Jessica, Ge, Jin, Gagnier, Joel, Saltz, Joel H., Saltz, Joel, Loomba, Johanna, Buse, John, Mathew, Jomol, Rutter, Joni L., McMurry, Julie A., Guinney, Justin, Starren, Justin, Crowley, Karen, Bradwell, Katie Rebecca, Walters, Kellie M., Wilkins, Ken, Gersing, Kenneth R., Cato, Kenrick Dwain, Murray, Kimberly, Kostka, Kristin, Northington, Lavance, Pyles, Lee Allan, Misquitta, Leonie, Cottrell, Lesley, Portilla, Lili, Deacy, Mariam, Bissell, Mark M., Clark, Marshall, Emmett, Mary, Saltz, Mary Morrison, Palchuk, Matvey B., Haendel, Melissa A., Adams, Meredith, Temple-O'Connor, Meredith, Kurilla, Michael G., Morris, Michele, Qureshi, Nabeel, Safdar, Nasia, Garbarini, Nicole, Sharafeldin, Noha, Sadan, Ofer, Francis, Patricia A., Burgoon, Penny Wung, Robinson, Peter, Payne, Philip R.O., Fuentes, Rafael, Jawa, Randeep, Erwin-Cohen, Rebecca, Patel, Rena, Moffitt, Richard A., Zhu, Richard L., Kamaleswaran, Rishi, Hurley, Robert, Miller, Robert T., Pyarajan, Saiju, Michael, Sam G., Bozzette, Samuel, Mallipattu, Sandeep, Vedula, Satyanarayana, Chapman, Scott, O'Neil, Shawn T., Setoguchi, Soko, Hong, Stephanie S., Johnson, Steve, Bennett, Tellen D., Callahan, Tiffany, Topaloglu, Umit, Sheikh, Usman, Gordon, Valery, Subbian, Vignesh, Kibbe, Warren A., Hernandez, Wenndy, Beasley, Will, Cooper, Will, Hillegass, William, Zhang, Xiaohan Tanner, Verhagen, Nathaniel B., Geissler, Thomas, SenthilKumar, Gopika, Gehl, Carson, Shaik, Tahseen, Flitcroft, Madelyn A., Yang, Xin, Taylor, Bradley W., Ghaferi, Amir A., Gould, Jon C., and Kothari, Anai N.

Published
2024
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34. JEM-EUSO Collaboration contributions to the 37th International Cosmic Ray Conference

Author

Abdellaoui, G., Abe, S., Adams Jr., J. H., Allard, D., Alonso, G., Anchordoqui, L., Anzalone, A., Arnone, E., Asano, K., Attallah, R., Attoui, H., Pernas, M. Ave, Bagheri, M., Baláz, J., Bakiri, M., Barghini, D., Bartocci, S., Battisti, M., Bayer, J., Beldjilali, B., Belenguer, T., Belkhalfa, N., Bellotti, R., Belov, A. A., Benmessai, K., Bertaina, M., Bertone, P. F., Biermann, P. L., Bisconti, F., Blaksley, C., Blanc, N., Blin-Bondil, S., Bobik, P., Bogomilov, M., Bolmgren, K., Bozzo, E., Briz, S., Bruno, A., Caballero, K. S., Cafagna, F., Cambié, G., Campana, D., Capdevielle, J-N., Capel, F., Caramete, A., Caramete, L., Carlson, P., Caruso, R., Casolino, M., Cassardo, C., Castellina, A., Catalano, O., Cellino, A., Černý, K., Chikawa, M., Chiritoi, G., Christl, M. J., Colalillo, R., Conti, L., Cotto, G., Crawford, H. J., Cremonini, R., Creusot, A., Gónzalez, A. de Castro, de la Taille, C., del Peral, L., Damian, A. Diaz, Diesing, R., Dinaucourt, P., Djakonow, A., Djemil, T., Ebersoldt, A., Ebisuzaki, T., Eser, J., Fenu, F., Fernández-González, S., Ferrarese, S., Filippatos, G., Fornaro, W. I. Finch C., Fouka, M., Franceschi, A., Franchini, S., Fuglesang, C., Fujii, T., Fukushima, M., Galeotti, P., García-Ortega, E., Gardiol, D., Garipov, G. K., Gascón, E., Gazda, E., Genci, J., Golzio, A., Alvarado, C. González, Gorodetzky, P., Green, A., Guarino, F., Guépin, C., Guzmán, A., Hachisu, Y., Haungs, A., Carretero, J. Hernández, Hulett, L., Ikeda, D., Inoue, N., Inoue, S., Isgrò, F., Itow, Y., Jammer, T., Jeong, S., Joven, E., Judd, E. G., Jochum, J., Kajino, F., Kajino, T., Kalli, S., Kaneko, I., Karadzhov, Y., Kasztelan, M., Katahira, K., Kawai, K., Kawasaki, Y., Kedadra, A., Khales, H., Khrenov, B. A., Kim, Jeong-Sook, Kim, Soon-Wook, Kleifges, M., Klimov, P. A., Kolev, D., Kreykenbohm, I., Krizmanic, J. F., Królik, K., Kungel, V., Kurihara, Y., Kusenko, A., Kuznetsov, E., Lahmar, H., Lakhdari, F., Licandro, J., Campano, L. López, Martínez, F. López, Mackovjak, S., Mahdi, M., Mandát, D., Manfrin, M., Marcelli, L., Marcos, J. L., Marszał, W., Martín, Y., Martinez, O., Mase, K., Matev, R., Matthews, J. N., Mebarki, N., Medina-Tanco, G., Menshikov, A., Merino, A., Mese, M., Meseguer, J., Meyer, S. S., Mimouni, J., Miyamoto, H., Mizumoto, Y., Monaco, A., Ríos, J. A. Morales de los, Mastafa, M., Nagataki, S., Naitamor, S., Napolitano, T., Neronov, J. M. Nachtman A., Nomoto, K., Nonaka, T., Ogawa, T., Ogio, S., Ohmori, H., Olinto, A. V., Osteria, Y. Onel G., Otte, A. N., Pagliaro, A., Painter, W., Panasyuk, M. I., Panico, B., Parizot, E., Park, I. H., Pastircak, B., Paul, T., Pech, M., Pérez-Grande, I., Perfetto, F., Peter, T., Picozza, P., Pindado, S., Piotrowski, L. W., Piraino, S., Plebaniak, Z., Pollini, A., Popescu, E. M., Prevete, R., Prévôt, G., Prieto, H., Przybylak, M., Puehlhofer, G., Putis, M., Reardon, P., Reno, M. H., Reyes, M., Ricci, M., Frías, M. D. Rodríguez, Matamala, O. F. Romero, Ronga, F., Sabau, M. D., Saccá, G., Cano, G. Sáez, Sagawa, H., Sahnoune, Z., Saito, A., Sakaki, N., Salazar, H., Balanzar, J. C. Sanchez, Sánchez, J. L., Santangelo, A., Sanz-Andrés, A., Palomino, M. Sanz, Saprykin, O. A., Sarazin, F., Sato, M., Scagliola, A., Schanz, T., Schieler, H., Schovánek, P., Scotti, V., Serra, M., Sharakin, S. A., Shimizu, H. M., Shinozaki, K., Soriano, J. F., Sotgiu, A., Stan, I., Strharský, I., Sugiyama, N., Supanitsky, D., Suzuki, M., Szabelski, J., Tajima, N., Tajima, T., Takahashi, Y., Takeda, M., Takizawa, Y., Talai, M. C., Tameda, Y., Tenzer, C., Thomas, S. B., Tibolla, O., Tkachev, L. G., Tomida, T., Tone, N., Toscano, S., Traïche, M., Tsunesada, Y., Tsuno, K., Turriziani, S., Uchihori, Y., Vaduvescu, O., Valdés-Galicia, J. F., Vallania, P., Valore, L., Vankova-Kirilova, G., Venters, T. M., Vigorito, C., Villaseñor, L., Vlcek, B., von Ballmoos, P., Vrabel, M., Wada, S., Watanabe, J., Watts Jr., J., Muñoz, R. Weigand, Weindl, A., Wiencke, L., Wille, M., Wilms, J., Yamamoto, D. Winn T., Yang, J., Yano, H., Yashin, I. V., Yonetoku, D., Yoshida, S., Young, R., Zgura, I. S., Zotov, M. Yu., and Marchi, A. Zuccaro

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

Compilation of papers presented by the JEM-EUSO Collaboration at the 37th International Cosmic Ray Conference (ICRC), held on July 12-23, 2021 (online) in Berlin, Germany., Comment: html page with links to the JEM-EUSO Collaboration papers presented at ICRC-2021, Berlin, Germany

Published
2022

35. Laser Driven Nuclear physics at ELINP

Author

Negoita, F., Roth, M., Thirolf, P. G., Tudisco, S., Hannachi, F., Moustaizis, S., Pomerantz, I., Mckenna, P., Fuchs, J., Sphor, K., Acbas, G., Anzalone, A., Audebert, P., Balascuta, S., Cappuzzello, F., Cernaianu, M. O., Chen, S., Dancus, I., Freeman, R., Geissel, H., Ghenuche, P., Gizzi, L., Gobet, F., Gosselin, G., Gugiu, M., Higginson, D., D¶Humiêres, E., Ivan, C., Jaroszynski, D., Kar, S., Lamia, L., Leca, V., Neagu, L., Lanzalone, G., Meot, V., Mirfayzi, S. R., Mitu, I. O., Morel, P., Murphy, C., Petcu, C., Petrascu, H., Petrone, C., Raczka, P., Risca, M., Rotaru, F., Santos, J. J., Schumacher, D., Stutman, D., Tarisien, M., Tataru, M., Tatulea, B., Turcu, I. C. E., Versteegen, M., Ursescu, D., Gales, S., and Zamfir, N. V.

Subjects
Physics - Instrumentation and Detectors, Nuclear Experiment
Abstract

High power lasers have proven being capable to produce high energy gamma rays, charged particles and neutrons to induce all kinds of nuclear reactions. At ELI, the studies with high power lasers will enter for the first time into new domains of power and intensities.

Published
2022

38. Nonelective coronary artery bypass graft outcomes are adversely impacted by Coronavirus disease 2019 infection, but not altered processes of care: A National COVID Cohort Collaborative and National Surgery Quality Improvement Program analysisCentral MessagePerspective

Author

Emily A. Grimsley, MD, Johnathan V. Torikashvili, BS, Haroon M. Janjua, MS, Meagan D. Read, MD, Anai N. Kothari, MD, MS, Nate B. Verhagen, BS, Ricardo Pietrobon, MD, PhD, Paul C. Kuo, MD, MS, MBA, Michael P. Rogers, MD, MS, Adam B. Wilcox, Adam M. Lee, Alexis Graves, Alfred (Jerrod) Anzalone, Amin Manna, Amit Saha, Amy Olex, Andrea Zhou, Andrew E. Williams, Andrew Southerland, Andrew T. Girvin, Anita Walden, Anjali A. Sharathkumar, Benjamin Amor, Benjamin Bates, Brian Hendricks, Brijesh Patel, Caleb Alexander, Carolyn Bramante, Cavin Ward-Caviness, Charisse Madlock-Brown, Christine Suver, Christopher Chute, Christopher Dillon, Chunlei Wu, Clare Schmitt, Cliff Takemoto, Dan Housman, Davera Gabriel, David A. Eichmann, Diego Mazzotti, Don Brown, Eilis Boudreau, Elaine Hill, Elizabeth Zampino, Emily Carlson Marti, Emily R. Pfaff, Evan French, Farrukh M. Koraishy, Federico Mariona, Fred Prior, George Sokos, Greg Martin, Harold Lehmann, Heidi Spratt, Hemalkumar Mehta, Hongfang Liu, Hythem Sidky, J.W. Awori Hayanga, Jami Pincavitch, Jaylyn Clark, Jeremy Richard Harper, Jessica Islam, Jin Ge, Joel Gagnier, Joel H. Saltz, Joel Saltz, Johanna Loomba, John Buse, Jomol Mathew, Joni L. Rutter, Julie A. McMurry, Justin Guinney, Justin Starren, Karen Crowley, Katie Rebecca Bradwell, Kellie M. Walters, Ken Wilkins, Kenneth R. Gersing, Kenrick Dwain Cato, Kimberly Murray, Kristin Kostka, Lavance Northington, Lee Allan Pyles, Leonie Misquitta, Lesley Cottrell, Lili Portilla, Mariam Deacy, Mark M. Bissell, Marshall Clark, Mary Emmett, Mary Morrison Saltz, Matvey B. Palchuk, Melissa A. Haendel, Meredith Adams, Meredith Temple-O'Connor, Michael G. Kurilla, Michele Morris, Nabeel Qureshi, Nasia Safdar, Nicole Garbarini, Noha Sharafeldin, Ofer Sadan, Patricia A. Francis, Penny Wung Burgoon, Peter Robinson, Philip R.O. Payne, Rafael Fuentes, Randeep Jawa, Rebecca Erwin-Cohen, Rena Patel, Richard A. Moffitt, Richard L. Zhu, Rishi Kamaleswaran, Robert Hurley, Robert T. Miller, Saiju Pyarajan, Sam G. Michael, Samuel Bozzette, Sandeep Mallipattu, Satyanarayana Vedula, Scott Chapman, Shawn T. O'Neil, Soko Setoguchi, Stephanie S. Hong, Steve Johnson, Tellen D. Bennett, Tiffany Callahan, Umit Topaloglu, Usman Sheikh, Valery Gordon, Vignesh Subbian, Warren A. Kibbe, Wenndy Hernandez, Will Beasley, Will Cooper, William Hillegass, and Xiaohan Tanner Zhang

Subjects
nonelective coronary artery bypass grafting, COVID-19, pandemic, outcomes, Diseases of the circulatory (Cardiovascular) system, RC666-701, Surgery, RD1-811
Abstract

Objective: The effects of Coronavirus disease 2019 (COVID-19) infection and altered processes of care on nonelective coronary artery bypass grafting (CABG) outcomes remain unknown. We hypothesized that patients with COVID-19 infection would have longer hospital lengths of stay and greater mortality compared with COVID-negative patients, but that these outcomes would not differ between COVID-negative and pre-COVID controls. Methods: The National COVID Cohort Collaborative 2020-2022 was queried for adult patients undergoing CABG. Patients were divided into COVID-negative, COVID-active, and COVID-convalescent groups. Pre-COVID control patients were drawn from the National Surgical Quality Improvement Program database. Adjusted analysis of the 3 COVID groups was performed via generalized linear models. Results: A total of 17,293 patients underwent nonelective CABG, including 16,252 COVID-negative, 127 COVID-active, 367 COVID-convalescent, and 2254 pre-COVID patients. Compared to pre-COVID patients, COVID-negative patients had no difference in mortality, whereas COVID-active patients experienced increased mortality. Mortality and pneumonia were higher in COVID-active patients compared to COVID-negative and COVID-convalescent patients. Adjusted analysis demonstrated that COVID-active patients had higher in-hospital mortality, 30- and 90-day mortality, and pneumonia compared to COVID-negative patients. COVID-convalescent patients had a shorter length of stay but a higher rate of renal impairment. Conclusions: Traditional care processes were altered during the COVID-19 pandemic. Our data show that nonelective CABG in patients with active COVID-19 is associated with significantly increased rates of mortality and pneumonia. The equivalent mortality in COVID-negative and pre-COVID patients suggests that pandemic-associated changes in processes of care did not impact CABG outcomes. Additional research into optimal timing of CABG after COVID infection is warranted.

Published
2023
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41. Study of two- and multi-particle correlations in 12C+24Mg and 12C+208Pb reactions at E=35 AMeV

Author

Quattrocchi L., Acosta L., Amorini F., Anzalone A., Auditore L., Berceanu I., Cardella G., Chbihi A., De Filippo E., Dell’ Aquila D., Francalanza L., Gnoffo B., Grzeszczuk A., Lanzalone G., Lombardo I., Martel I., Minniti T., Norella S., Pagano A., Pagano E.V., Papa M., Pirrone S., Politi G., Porto F., Rizzo F., Rosato E., Russotto P., Trifirò A., Trimarchi M., Verde G., Veselsky M., and Vigilante M.

Subjects
Physics, QC1-999
Abstract

Two and multi particle correlations from the decay of sources produced in 12C+24Mg and 12C+208Pb collisions at E=35 AMeV have been studied by using the forward part (1° < θlab < 30°) of the CHIMERA multi-detector. Correlations and invariant mass spectroscopy are used to explore simultaneous and sequential decays of resonances in light isotopes with Z∼3-6, produced in peripheral collisions via the break-up of excited quasi-projectiles. Among them we mention 5Li, 6Li, 6Be, 8Be and the astrophysically important state in 12C decaying into three alpha particles. Results and future perspectives at the INFN-LNS will be presented.

Published
2016
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42. Study of nuclear reactions in laser plasmas at future ELI-NP facility

Author

Lanzalone G., Altana C., Anzalone A., Cappuzzello F., Cavallaro M., Gizzi L. A., Labate L., Lamia L., Mascali D., Muoio A., Negoita F., Odorici F., Petrascu H., Trifirò A., Trimarchi M., and Tudisco S.

Subjects
Physics, QC1-999
Abstract

In this contribution we will present the future activities that our collaboration will carry out at ELI-NP (Extreme Light Infrastructure Nuclear Physics), the new multi peta-watt Laser facility, currently under construction at Bucharest (Romania). The activities concerns the study of nuclear reactions in laser plasmas. In this framework we proposed the construction of a new, general-purpose experimental set-up able to detect and identify neutrons and charged particles.

Published
2016
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47. Genetic strategies for sex-biased persistence of gut microbes across human life

Author

Tarracchini, Chiara, Alessandri, Giulia, Fontana, Federico, Rizzo, Sonia Mirjam, Lugli, Gabriele Andrea, Bianchi, Massimiliano Giovanni, Mancabelli, Leonardo, Longhi, Giulia, Argentini, Chiara, Vergna, Laura Maria, Anzalone, Rosaria, Viappiani, Alice, Turroni, Francesca, Taurino, Giuseppe, Chiu, Martina, Arboleya, Silvia, Gueimonde, Miguel, Bussolati, Ovidio, van Sinderen, Douwe, Milani, Christian, and Ventura, Marco

Published
2023
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48. Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota

Author

Chiara Argentini, Gabriele Andrea Lugli, Chiara Tarracchini, Federico Fontana, Leonardo Mancabelli, Alice Viappiani, Rosaria Anzalone, Leonora Angelini, Giulia Alessandri, Giulia Longhi, Massimiliano G. Bianchi, Giuseppe Taurino, Ovidio Bussolati, Christian Milani, Douwe van Sinderen, Francesca Turroni, and Marco Ventura

Subjects
Bifidobacteria, microbiome, genomics, metagenomics, host-microbe interaction, Microbiology, QR1-502
Abstract

Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.

Published
2024
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49. Immunogenicity and reactogenicity of modified vaccinia Ankara pre-exposure vaccination against mpox according to previous smallpox vaccine exposure and HIV infection: prospective cohort studyResearch in context

Author

Valentina Mazzotta, Alessandro Cozzi Lepri, Giulia Matusali, Eleonora Cimini, Pierluca Piselli, Camilla Aguglia, Simone Lanini, Francesca Colavita, Stefania Notari, Alessandra Oliva, Silvia Meschi, Rita Casetti, Vanessa Mondillo, Alessandra Vergori, Aurora Bettini, Germana Grassi, Carmela Pinnetti, Daniele Lapa, Eleonora Tartaglia, Paola Gallì, Annalisa Mondi, Giulia Montagnari, Roberta Gagliardini, Emanuele Nicastri, Miriam Lichtner, Loredana Sarmati, Enrica Tamburrini, Claudio Mastroianni, Christof Stingone, Andrea Siddu, Alessandra Barca, Carla Fontana, Chiara Agrati, Enrico Girardi, Francesco Vaia, Fabrizio Maggi, Andrea Antinori, Enza Anzalone, Marta Camici, Fabio Cannone, Priscilla Caputi, Claudia Cimaglia, Rita Corso, Flavia Cristofanelli, Stefania Cruciani, Nicola De Marco, Chiara De Ponte, Giulia Del Duca, Paolo Faccendini, Francesca Faraglia, Augusto Faticoni, Marisa Fusto, Saba Gebremeskel, Maria Letizia Giancola, Giuseppina Giannico, Simona Gili, Maria Rosaria Iannella, Angela Junea, Alessandra Lamonaca, Alessandra Marani, Erminia Masone, Ilaria Mastrorosa, Stefania Mazzotta, Alessandra Nappo, Giorgia Natalini, Alfredo Parisi, Sara Passacantilli, Jessica Paulicelli, Maria Maddalena Plazzi, Adriano Possi, Gianni Preziosi, Silvia Rosati, Marika Rubino, Pietro Scanzano, Laura Scorzolini, Virginia Tomassi, Maurizio Vescovo, Serena Vita, Luciano Caterini, Luigi Coppola, Dimitra Kontogiannis, Gabriella D'Ettorre, Marco Ridolfi, Simona Di Giambenedetto, Damiano Farinacci, Alessandra Latini, Mauro Marchili, and Raffaella Marocco

Subjects
mpox, MVA-BN immunogenicity, Reactogenicity, Cellular response, Humoral response, HIV, Medicine (General), R5-920
Abstract

Summary: Background: Pre-exposure vaccination with MVA-BN has been widely used against mpox to contain the 2022 outbreak. Many countries have defined prioritized strategies, administering a single dose to those historically vaccinated for smallpox, to achieve quickly adequate coverage in front of low supplies. Using epidemiological models, real-life effectiveness was estimated at approximately 36%–86%, but no clinical trials were performed. Few data on MVA-BN immunogenicity are currently available, and there are no established correlates of protection. Immunological response in PLWH in the context of the 2022 outbreak was also poorly described. Methods: Blood samples were collected from participants eligible for pre-exposure MVA-BN vaccination before (T1) receiving a full course of vaccine (single-dose for vaccine-experienced or smallpox-primed and two-dose for smallpox vaccine-naïve or smallpox non-primed) and one month after the last dose (T2 and T3, respectively). MPXV-specific IgGs were measured by in-house immunofluorescence assay, using 1:20 as screening dilution, MPXV-specific nAbs by 50% plaque reduction neutralization test (PRNT50, starting dilution 1:10), and IFN-γ-producing specific T cells to MVA-BN vaccine, by ELISpot assay. Paired or unpaired t-test and Wilcoxon or Mann–Whitney test were used to analyse IgG and nAbs, and T-cell response, as appropriate. The probability of IgG and nAb response in vaccine-experienced vs. vaccine-naïve was estimated in participants not reactive at T1. The McNemar test was used to evaluate vaccination's effect on humoral response both overall and by smallpox vaccination history. In participants who were not reactive at T1, the proportion of becoming responders one month after full-cycle completion by exposure groups was compared by logistic regression and then analysed by HIV status strata (interaction test). The response was also examined in continuous, and the Average Treatment Effect (ATE) of the difference from baseline to schedule completion according to previous smallpox vaccination was estimated after weighting for HIV using a linear regression model. Self-reports of adverse effects following immunization (AEFIs) were prospectively collected after the first MVA-BN dose (T1). Systemic (S-AEFIs: fatigue, myalgia, headache, GI effects, chills) and local (L-AEFIs: redness, swelling, pain) AEFIs were graded as absent (grade 0), mild (1), moderate (2), or severe (3). The maximum level of severity for S-AEFIs and L-AEFIs ever experienced over the 30 days post-dose by vaccination exposure groups were analysed using a univariable multinomial logistic regression model and after adjusting for HIV status; for each of the symptoms, we also compared the mean duration by exposure group using an unpaired t-test. Findings: Among the 164 participants included, 90 (54.8%) were smallpox vaccine-experienced. Median age was 49 years (IQR 41–55). Among the 76 (46%) PLWH, 76% had a CD4 count >500 cells/μL. There was evidence that both the IgG and nAbs titers increased after administration of the MVA-BN vaccine. However, there was no evidence for a difference in the potential mean change in humoral response from baseline to the completion of a full cycle when comparing primed vs. non-primed participants. Similarly, there was no evidence for a difference in the seroconversion rate after full cycle vaccination in the subset of participants not reactive for nAbs at T1 (p = 1.00 by Fisher's exact test). In this same analysis and for the nAbs outcome, there was some evidence of negative effect modification by HIV (interaction p-value = 0.17) as primed people living with HIV (PLWH) showed a lower probability of seroconversion vs. non-primed, and the opposite was seen in PLWoH. When evaluating the response in continuous, we observed an increase in T-cell response after MVA-BN vaccination in both primed and non-primed. There was evidence for a larger increase when using the 2-dose vs. one-dose strategy with a mean difference of −2.01 log2 (p ≤ 0.0001), after controlling for HIV. No evidence for a difference in the risk of developing any AEFIs of any grade were observed by exposure group, except for the lower risk of grade 2 (moderate) fatigue, induration and local pain which was lower in primed vs. non-primed [OR 0.26 (0.08–0.92), p = 0.037; OR 0.30 (0.10–0.88), p = 0.029 and OR 0.19 (0.05–0.73), p = 0.015, respectively]. No evidence for a difference in symptom duration was also detected between the groups. Interpretation: The evaluation of the humoral and cellular response one month after the completion of the vaccination cycle suggested that MVA-BN is immunogenic and that the administration of a two-dose schedule is preferable regardless of the previous smallpox vaccination history, especially in PLWH, to maximize nAbs response. MVA-BN was safe as well tolerated, with grade 2 reactogenicity higher after the first administration in vaccine-naïve than in vaccine-experienced individuals, but with no evidence for a difference in the duration of these adverse effects. Further studies are needed to evaluate the long-term duration of immunity and to establish specific correlates of protection. Funding: The study was supported by the National Institute for Infectious Disease Lazzaro Spallanzani IRCCS “Advanced grant 5 × 1000, 2021” and by the Italian Ministry of Health “Ricerca Corrente Linea 2”.

Published
2024
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50. Hormone replacement therapy and COVID-19 outcomes in solid organ transplant recipients compared with the general population

Author

Wilcox, Adam B., Lee, Adam M., Graves, Alexis, Anzalone, Alfred (Jerrod), Manna, Amin, Saha, Amit, Olex, Amy, Zhou, Andrea, Williams, Andrew E., Southerland, Andrew, Girvin, Andrew T., Walden, Anita, Sharathkumar, Anjali A., Amor, Benjamin, Bates, Benjamin, Hendricks, Brian, Patel, Brijesh, Alexander, Caleb, Bramante, Carolyn, Ward-Caviness, Cavin, Madlock-Brown, Charisse, Suver, Christine, Chute, Christopher, Dillon, Christopher, Wu, Chunlei, Schmitt, Clare, Takemoto, Cliff, Housman, Dan, Gabriel, Davera, Eichmann, David A., Mazzotti, Diego, Brown, Don, Boudreau, Eilis, Hill, Elaine, Zampino, Elizabeth, Marti, Emily Carlson, Pfaff, Emily R., French, Evan, Koraishy, Farrukh M., Mariona, Federico, Prior, Fred, Sokos, George, Martin, Greg, Lehmann, Harold, Spratt, Heidi, Mehta, Hemalkumar, Liu, Hongfang, Sidky, Hythem, Hayanga, J.W. Awori, Pincavitch, Jami, Clark, Jaylyn, Harper, Jeremy Richard, Islam, Jessica, Ge, Jin, Gagnier, Joel, Saltz, Joel H., Saltz, Joel, Loomba, Johanna, Buse, John, Mathew, Jomol, Rutter, Joni L., McMurry, Julie A., Guinney, Justin, Starren, Justin, Crowley, Karen, Bradwell, Katie Rebecca, Walters, Kellie M., Wilkins, Ken, Gersing, Kenneth R., Cato, Kenrick Dwain, Murray, Kimberly, Kostka, Kristin, Northington, Lavance, Pyles, Lee Allan, Misquitta, Leonie, Cottrell, Lesley, Portilla, Lili, Deacy, Mariam, Bissell, Mark M., Clark, Marshall, Emmett, Mary, Saltz, Mary Morrison, Palchuk, Matvey B., Haendel, Melissa A., Adams, Meredith, Temple-O'Connor, Meredith, Kurilla, Michael G., Morris, Michele, Qureshi, Nabeel, Safdar, Nasia, Garbarini, Nicole, Sharafeldin, Noha, Sadan, Ofer, Francis, Patricia A., Burgoon, Penny Wung, Robinson, Peter, Payne, Philip R.O., Fuentes, Rafael, Jawa, Randeep, Erwin-Cohen, Rebecca, Patel, Rena, Moffitt, Richard A., Zhu, Richard L., Kamaleswaran, Rishi, Hurley, Robert, Miller, Robert T., Pyarajan, Saiju, Michael, Sam G., Bozzette, Samuel, Mallipattu, Sandeep, Vedula, Satyanarayana, Chapman, Scott, O'Neil, Shawn T., Setoguchi, Soko, Hong, Stephanie S., Johnson, Steve, Bennett, Tellen D., Callahan, Tiffany, Topaloglu, Umit, Sheikh, Usman, Gordon, Valery, Subbian, Vignesh, Kibbe, Warren A., Hernandez, Wenndy, Beasley, Will, Cooper, Will, Hillegass, William, Zhang, Xiaohan Tanner, Vinson, Amanda J., Anzalone, Alfred, Schissel, Makayla, Dai, Ran, French, Evan T., Olex, Amy L., and Mannon, Roslyn B.

Published
2023
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