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1. Acute idiopathic pancreatitis is associated with more aggressive disease course in Crohn’s disease but not in ulcerative colitis

Author

Karim T. Osman, Asahi Hoque, Ravi Teja Pasam, Adel Farhoud, Ahmed Abdelfattah, Vishant Ramadorai, Khadija Chaudrey, and Randall Pellish

Subjects
Prognosis, IBD, Pancreatitis, Crohn’s disease, Extra-intestinal manifestations, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Abstract Purpose Patients with inflammatory bowel disease (IBD), whether Crohn’s disease (CD) or ulcerative colitis (UC), have an increased risk of acute pancreatitis. The prognostic value of diagnosing acute idiopathic pancreatitis in patients with IBD is not well understood. Methods A retrospective review of 56 patients with IBD and acute pancreatitis was conducted in a tertiary center from 2011 to 2020. Aggressive disease course was defined as (i)biologic change, (ii)biologic dose escalation, or (iii)IBD-related surgeries occurring within 1 year of acute pancreatitis diagnosis. Logistic regression modelling identified associations between covariates and an aggressive disease course. Results Baseline characteristics between idiopathic pancreatitis and other causes of acute pancreatitis, in both CD and UC cohorts, were similar. Idiopathic pancreatitis was significantly associated with an aggressive disease course in CD (P = 0.04). No confounding factors were associated with an aggressive disease course in CD. Idiopathic pancreatitis, however, was not associated with an aggressive disease course in UC (P = 0.35). Conclusion The diagnosis of acute idiopathic pancreatitis may provide a prognostic indicator of a more severe disease course in CD. No such association appears to exist with UC. To the best of our knowledge, this is the first study that identifies an association and possible prognostic value between idiopathic pancreatitis and a more severe disease course in CD. More studies with a larger sample size are needed to validate these findings, further define idiopathic pancreatitis as an extraintestinal manifestation of IBD and elucidate a clinical strategy to optimize care in patients with aggressive CD and idiopathic pancreatitis.

Published
2023
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2. HPV vaccination coverage for pediatric, adolescent and young adult patients receiving care in a childhood cancer survivor program

Author

Lauren Thomaier, Danielle A. Aase, Rachel I. Vogel, Helen M. Parsons, Karim T. Sadak, and Deanna Teoh

Subjects
HPV vaccination, Pediatric, Adolescent, Young adult cancer survivors, Survivorship, Secondary cancer prevention, Medicine
Abstract

Pediatric, adolescent and young adult patients undergoing cancer treatment and/or hematopoietic stem cell transplant are at increased risk for developing a secondary human papillomavirus (HPV)-associated malignancy. The objective of this study was to determine HPV vaccination coverage among individuals participating in a childhood cancer survivor program (CCSP). A retrospective cohort study was conducted among CCSP patients age 11–26 years attending a CCSP visit between 2014 and 2019. Survivors were age-, sex-, and race-matched 1:2 with controls without cancer. Data were abstracted from the electronic health record and state-based vaccination registry. Analysis was limited to Minnesota residents to minimize missing vaccination data. Survivorship care plans (SCPs) were reviewed for vaccine recommendations.592 patients were included in the analyses (200 CCSP patients; 392 controls). By study design, mean age (18.4 years), race (72 % white), and sex (49 % female) were similar in the two groups. Among CCSP patients 22 % resided in a rural area compared to 3.8 % of controls. Vaccination coverage among CCSP patients was not statistically significantly different from controls [60.0 % vs 66.3 %, OR = 0.82, 95 % CI: (0.55, 1.23), p = 0.35]. Completion of 3 doses was not different between groups even though 3 doses is recommended for all CCSP patients regardless of age at initiation (28.5 % vs 30.1 %, p = 0.09). Only 8.0 % of SCPs recommended HPV vaccination.Although patients participating in a CCSP did not have significantly different HPV vaccination coverage compared to controls, HPV vaccination initiation and 3-dose series completion are still suboptimal in a patient population at high-risk of a secondary HPV-associated cancer.

Published
2022
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3. Longitudinal Changes in Echocardiographic Parameters of Cardiac Function in Pediatric Cancer Survivors

Author

William L. Border, MBChB, MPH, Ritu Sachdeva, MBBS, Kayla L. Stratton, MS, Saro H. Armenian, DO, MPH, Aarti Bhat, MD, David E. Cox, RDCS, Kasey J. Leger, MD, MS, Wendy M. Leisenring, ScD, Lillian R. Meacham, MD, Karim T. Sadak, MD, Shanthi Sivanandam, MD, Paul C. Nathan, MD, MSc, and Eric J. Chow, MD, MPH

Subjects
cancer survivorship, cardiomyopathy, echocardiography, longitudinal, Diseases of the circulatory (Cardiovascular) system, RC666-701, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Objectives: The purpose of this study was to assess the timing of changes in serial echocardiographic parameters in pediatric cancer survivors and to evaluate their associations with cardiomyopathy development. Background: Pediatric cancer survivors undergo serial echocardiograms to screen for cardiotoxicity. It is not clear whether small longitudinal changes in functional or structural parameters over time have clinical significance. Methods: This is a multicenter, retrospective, case-control study of ≥1-year survivors following the end of cancer therapy. Cardiomyopathy cases (fractional shortening [FS] ≤28% or ejection fraction [EF] ≤50% on ≥2 occasions) were matched to control subjects (FS ≥30%, EF ≥55%, not on cardiac medications) by cumulative anthracycline and chest radiation dose, follow-up duration, and age at diagnosis. Digitally archived clinical surveillance echocardiograms were quantified in a central core laboratory, blinded to patient characteristics. Using mixed models with interaction terms between time and case status, we estimated the least square mean differences of 2-dimensional, M-mode, pulsed wave Doppler, and tissue Doppler imaging–derived parameters over time between cases and control subjects. Results: We identified 50 matched case-control pairs from 5 centers. Analysis of 412 echocardiograms (cases, n = 181; control subjects, n = 231) determined that indices of left ventricular systolic function (FS, biplane EF), diastolic function (mitral E/A ratio), and left ventricular size (end-diastolic dimension z-scores) were significantly different between cases and control subjects, even 4 years prior to the development of cardiomyopathy. Conclusions: Longitudinal changes in cardiac functional parameters can occur relatively early in pediatric cancer survivors and are associated with the development of cardiomyopathy.

Published
2020
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4. The Construction of Large-scale Structure Catalogs for the Dark Energy Spectroscopic Instrument

Author

Ross, A. J., Aguilar, J., Ahlen, S., Alam, S., Anand, A., Bailey, S., Bianchi, D., Brieden, S., Brooks, D., Burtin, E., Rosell, A. Carnero, Chaussidon, E., Claybaugh, T., Cole, S., Dawson, K., de la Macorra, A., de Mattia, A., Dey, Arjun, Dey, Biprateep, Doel, P., Fanning, K., Ferraro, S., Ereza, J., Font-Ribera, A., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Guy, J., Hahn, C., Heydenreich, S., Honscheid, K., Howlett, C., Ishak, M., Karim, T., Kirkby, D., Kisner, T., Kong, H., Kremin, A., Krolewski, A., Lambert, A., Landriau, M., Lasker, J., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., McDonald, P., Meisner, A., Miquel, R., Moon, J., Moustakas, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Newman, J. A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Raichoor, A., Ravoux, C., Rezaie, M., Rosado-Marin, A., Rossi, G., Samushia, L., Sanchez, E., Schlafly, E. F., Schlegel, D., Seo, H., Smith, A., Sprayberry, D., Tarlé, G., Valcin, D., Vargas-Magaña, M., Weaver, B. A., Wilson, M., Yu, J., Zarrouk, P., Zhao, C., Zhou, R., and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present the technical details on how large-scale structure (LSS) catalogs are constructed from redshifts measured from spectra observed by the Dark Energy Spectroscopic Instrument (DESI). The LSS catalogs provide the information needed to determine the relative number density of DESI tracers as a function of redshift and celestial coordinates and, e.g., determine clustering statistics. We produce catalogs that are weighted subsamples of the observed data, each matched to a weighted `random' catalog that forms an unclustered sampling of the probability density that DESI could have observed those data at each location. Precise knowledge of the DESI observing history and associated hardware performance allows for a determination of the DESI footprint and the number of times DESI has covered it at sub-arcsecond level precision. This enables the completeness of any DESI sample to be modeled at this same resolution. The pipeline developed to create LSS catalogs has been designed to easily allow robustness tests and enable future improvements. We describe how it allows ongoing work improving the match between galaxy and random catalogs, such as including further information when assigning redshifts to randoms, accounting for fluctuations in target density, accounting for variation in the redshift success rate, and accommodating blinding schemes., Comment: Accepted (by JCAP) version of supporting publication of DESI 2024II: Sample definitions, characteristics, and two-point clustering statistics

Published
2024

5. Henoch-Schönlein Purpura Presenting in Association With Neuroblastoma: A Case Report

Author

Zineb Alfath, Asmaa Ferdjallah, Emily Greengard, Sabeen K. Askari, Karim T. Sadak, and Colleen K. Correll

Subjects
neuroblastoma, Henoch-Schönlein purpura, rash, pediatrics, case report, Pediatrics, RJ1-570
Abstract

Henoch-Schönlein purpura (HSP) is a common systemic vasculitis affecting children. It is managed in the outpatient setting and rarely associated with malignancy. We present a case of neuroblastoma in a 7-year-old boy diagnosed after suspected HSP. Our case highlights the importance of maintaining a broad differential diagnosis in children with atypical HSP and performing a skin biopsy with immunofluorescence when a rash is present.

Published
2020
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8. The Early Data Release of the Dark Energy Spectroscopic Instrument

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., Della Costa, J., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jacques, A., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Leauthaud, A., Guillou, L. Le, Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Nikutta, R., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Pothier, S., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Soumagnac, M. T., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) completed its five-month Survey Validation in May 2021. Spectra of stellar and extragalactic targets from Survey Validation constitute the first major data sample from the DESI survey. This paper describes the public release of those spectra, the catalogs of derived properties, and the intermediate data products. In total, the public release includes good-quality spectral information from 466,447 objects targeted as part of the Milky Way Survey, 428,758 as part of the Bright Galaxy Survey, 227,318 as part of the Luminous Red Galaxy sample, 437,664 as part of the Emission Line Galaxy sample, and 76,079 as part of the Quasar sample. In addition, the release includes spectral information from 137,148 objects that expand the scope beyond the primary samples as part of a series of secondary programs. Here, we describe the spectral data, data quality, data products, Large-Scale Structure science catalogs, access to the data, and references that provide relevant background to using these spectra., Comment: 43 pages, 7 figures, 17 tables, accepted for publication in the Astronomical Journal

Published
2023
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9. Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Joyce, R., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) was designed to conduct a survey covering 14,000 deg$^2$ over five years to constrain the cosmic expansion history through precise measurements of Baryon Acoustic Oscillations (BAO). The scientific program for DESI was evaluated during a five month Survey Validation (SV) campaign before beginning full operations. This program produced deep spectra of tens of thousands of objects from each of the stellar (MWS), bright galaxy (BGS), luminous red galaxy (LRG), emission line galaxy (ELG), and quasar target classes. These SV spectra were used to optimize redshift distributions, characterize exposure times, determine calibration procedures, and assess observational overheads for the five-year program. In this paper, we present the final target selection algorithms, redshift distributions, and projected cosmology constraints resulting from those studies. We also present a `One-Percent survey' conducted at the conclusion of Survey Validation covering 140 deg$^2$ using the final target selection algorithms with exposures of a depth typical of the main survey. The Survey Validation indicates that DESI will be able to complete the full 14,000 deg$^2$ program with spectroscopically-confirmed targets from the MWS, BGS, LRG, ELG, and quasar programs with total sample sizes of 7.2, 13.8, 7.46, 15.7, and 2.87 million, respectively. These samples will allow exploration of the Milky Way halo, clustering on all scales, and BAO measurements with a statistical precision of 0.28% over the redshift interval $z<1.1$, 0.39% over the redshift interval $1.1

Published
2023
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11. Target Selection and Validation of DESI Emission Line Galaxies

Author

Raichoor, A., Moustakas, J., Newman, Jeffrey A., Karim, T., Ahlen, S., Alam, Shadab, Bailey, S., Brooks, D., Dawson, K., de la Macorra, A., de Mattia, A., Dey, A., Dey, Biprateep, Dhungana, G., Eftekharzadeh, S., Eisenstein, D. J., Fanning, K., Font-Ribera, A., Garcia-Bellido, J., Gaztanaga, E., Gontcho, S. Gontcho A, Guy, J., Honscheid, K., Ishak, M., Kehoe, R., Kisner, T., Kremin, A., Lan, Ting-Wen, Landriau, M., Guillou, L. Le, Levi, Michael E., Magneville, C., Martini, P., Meisner, Aaron M., Myers, Adam D., Nie, Jundan, Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Ross, A. J., Ruhlmann-Kleider, V., Sabiu, C. G., Schlafly, E. F., Schlegel, D., Tarle, Gregory, Weaver, B. A., Yeche, Christophe, Zhou, Rongpu, Zhou, Zhimin, and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) will precisely constrain cosmic expansion and the growth of structure by collecting $\sim$40 million extra-galactic redshifts across $\sim$80\% of cosmic history and one third of the sky. The Emission Line Galaxy (ELG) sample, which will comprise about one-third of all DESI tracers, will be used to probe the Universe over the $0.6 < z < 1.6$ range, which includes the $1.1

Published
2022
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12. Target Selection and Validation of DESI Emission Line Galaxies

Author

Raichoor, A, Moustakas, J, Newman, Jeffrey A, Karim, T, Ahlen, S, Alam, Shadab, Bailey, S, Brooks, D, Dawson, K, de la Macorra, A, de Mattia, A, Dey, A, Dey, Biprateep, Dhungana, G, Eftekharzadeh, S, Eisenstein, DJ, Fanning, K, Font-Ribera, A, García-Bellido, J, Gaztañaga, E, Gontcho, S Gontcho A, Guy, J, Honscheid, K, Ishak, M, Kehoe, R, Kisner, T, Kremin, Anthony, Lan, Ting-Wen, Landriau, M, Le Guillou, L, Levi, Michael E, Magneville, C, Manera, M, Martini, P, Meisner, Aaron M, Myers, Adam D, Nie, Jundan, Palanque-Delabrouille, N, Percival, WJ, Poppett, C, Prada, F, Ross, AJ, Ruhlmann-Kleider, V, Sabiu, CG, Schlafly, EF, Schlegel, D, Tarlé, Gregory, Weaver, BA, Yèche, Christophe, Zhou, Rongpu, Zhou, Zhimin, and Zou, H

Subjects
Space Sciences, Physical Sciences, Astronomical and Space Sciences, Astronomy & Astrophysics, Astronomical sciences, Particle and high energy physics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) will precisely constrain cosmic expansion and the growth of structure by collecting ∼40 million extragalactic redshifts across ∼80% of cosmic history and one-third of the sky. The Emission Line galaxy (ELG) sample, which will comprise about one-third of all DESI tracers, will be used to probe the universe over the 0.6 < z < 1.6 range, including the 1.1 < z < 1.6 range, which is expected to provide the tightest constraints. We present the target selection for the DESI Survey Validation (SV) and Main Survey ELG samples, which relies on the imaging of the Legacy Surveys. The Main ELG selection consists of a g-band magnitude cut and a (g − r) versus (r − z) color box, while the SV selection explores extensions of the Main selection boundaries. The Main ELG sample is composed of two disjoint subsamples, which have target densities of about 1940 deg−2 and 460 deg−2, respectively. We first characterize their photometric properties and density variations across the footprint. We then analyze the DESI spectroscopic data that have been obtained from 2020 December to 2021 December in the SV and Main Survey. We establish a preliminary criterion for selecting reliable redshifts, based on the [O ii] flux measurement, and assess its performance. Using this criterion, we are able to present the spectroscopic efficiency of the Main ELG selection, along with its redshift distribution. We thus demonstrate that the Main selection 1940 deg−2 subsample alone should provide 400 deg−2 and 460 deg−2 reliable redshifts in the 0.6 < z < 1.1 and the 1.1 < z < 1.6 ranges, respectively.

Published
2023

13. Overview of the Instrumentation for the Dark Energy Spectroscopic Instrument

Author

Abareshi, B., Aguilar, J., Ahlen, S., Alam, Shadab, Alexander, David M., Alfarsy, R., Allen, L., Prieto, C. Allende, Alves, O., Ameel, J., Armengaud, E., Asorey, J., Aviles, Alejandro, Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Beltran, S. F., Benavides, B., BenZvi, S., Berti, A., Besuner, R., Beutler, Florian, Bianchi, D., Blake, C., Blanc, P., Blum, R., Bolton, A., Bose, S., Bramall, D., Brieden, S., Brodzeller, A., Brooks, D., Brownewell, C., Buckley-Geer, E., Cahn, R. N., Cai, Z., Canning, R., Rosell, A. Carnero, Carton, P., Casas, R., Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chuang, C., Circosta, C., Cole, S., Cooper, A. P., da Costa, L., Cousinou, M. -C., Cuceu, A., Davis, T. M., Dawson, K., de la Cruz-Noriega, R., de la Macorra, A., de Mattia, A., Della Costa, J., Demmer, P., Derwent, M., Dey, A., Dey, B., Dhungana, G., Ding, Z., Dobson, C., Doel, P., Donald-McCann, J., Donaldson, J., Douglass, K., Duan, Y., Dunlop, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Enriquez-Vargas, M., Escoffier, S., Evatt, M., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Romero, J. E., Frenk, C. S., Fromenteau, S., Gänsicke, B. T., Garcia-Quintero, C., Garrison, L., Gaztañaga, E., Gerardi, F., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, Alma X., Gonzalez-de-Rivera, G., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Grove, C., Gruen, D., Gutierrez, G., Guy, J., Hahn, C., Harris, S., Herrera, D., Herrera-Alcantar, Hiram K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jelinsky, P., Jiang, L., Jimenez, J., Jing, Y. P., Joyce, R., Jullo, E., Juneau, S., Karaçaylı, N. G., Karamanis, M., Karcher, A., Karim, T., Kehoe, R., Kent, S., Kirkby, D., Kisner, T., Kitaura, F., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, Alex, L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, Ting-Wen, Landriau, M., Lane, S., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Van Suu, A. Le, Levi, Michael E., Li, T. S., Magneville, C., Manera, M., Manser, Christopher J., Marshall, B., McCollam, W., McDonald, P., Meisner, Aaron M., Mezcua, J. Mena-Fernández M., Miller, T., Miquel, R., Montero-Camacho, P., Moon, J., Martini, J. Paul, Meneses-Rizo, J., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, Andrea, Myers, Adam D., Nadathur, S., Najita, J., Napolitano, L., Neilsen, E., Newman, Jeffrey A., Nie, J. D., Ning, Y., Niz, G., Norberg, P., Noriega, Hernán E., O'Brien, T., Obuljen, A., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Pappalardo, D., Peng, X., Percival, W. J., Perruchot, S., Pogge, R., Poppett, C., Porredon, A., Prada, F., Prochaska, J., Pucha, R., Pérez-Fernández, A., Pérez-Ráfols, I., Rabinowitz, D., Raichoor, A., Ramirez-Solano, S., Ramírez-Pérez, César, Ravoux, C., Reil, K., Rezaie, M., Rocher, A., Rockosi, C., Roe, N. A., Roodman, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Safonova, S., Said, K., Saintonge, A., Catonga, Javier Salas, Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E., Schlegel, D., Schmoll, J., Scholte, D., Schubnell, M., Secroun, A., Seo, H., Serrano, S., Sharples, Ray M., Sholl, Michael J., Silber, Joseph Harry, Silva, D. R., Sirk, M., Siudek, M., Smith, A., Sprayberry, D., Staten, R., Stupak, B., Tan, T., Tarlé, Gregory, Tie, Suk Sien, Tojeiro, R., Ureña-López, L. A., Valdes, F., Valenzuela, O., Valluri, M., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, C., Wechsler, R., Wilson, Michael J., Yang, J., Yu, Y., Yuan, S., Yèche, Christophe, Zhang, H., Zhang, K., Zhao, Cheng, Zhou, Rongpu, Zhou, Zhimin, Zou, H., Zou, J., Zou, S., and Zu, Y.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) has embarked on an ambitious five-year survey to explore the nature of dark energy with spectroscopy of 40 million galaxies and quasars. DESI will determine precise redshifts and employ the Baryon Acoustic Oscillation method to measure distances from the nearby universe to z > 3.5, as well as measure the growth of structure and probe potential modifications to general relativity. In this paper we describe the significant instrumentation we developed for the DESI survey. The new instrumentation includes a wide-field, 3.2-deg diameter prime-focus corrector that focuses the light onto 5020 robotic fiber positioners on the 0.812 m diameter, aspheric focal surface. The positioners and their fibers are divided among ten wedge-shaped petals. Each petal is connected to one of ten spectrographs via a contiguous, high-efficiency, nearly 50 m fiber cable bundle. The ten spectrographs each use a pair of dichroics to split the light into three channels that together record the light from 360 - 980 nm with a resolution of 2000 to 5000. We describe the science requirements, technical requirements on the instrumentation, and management of the project. DESI was installed at the 4-m Mayall telescope at Kitt Peak, and we also describe the facility upgrades to prepare for DESI and the installation and functional verification process. DESI has achieved all of its performance goals, and the DESI survey began in May 2021. Some performance highlights include RMS positioner accuracy better than 0.1", SNR per \sqrt{\AA} > 0.5 for a z > 2 quasar with flux 0.28e-17 erg/s/cm^2/A at 380 nm in 4000s, and median SNR = 7 of the [OII] doublet at 8e-17 erg/s/cm^2 in a 1000s exposure for emission line galaxies at z = 1.4 - 1.6. We conclude with highlights from the on-sky validation and commissioning of the instrument, key successes, and lessons learned. (abridged), Comment: 78 pages, 32 figures, submitted to AJ

Published
2022
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14. Dynamics of Liver Stiffness Measurement and Clinical Course of Primary Biliary Cholangitis

Author

Lam, Laurent, Soret, Pierre-Antoine, Lemoinne, Sara, Hansen, Bettina, Hirschfield, Gideon, Gulamhusein, Aliya, Montano-Loza, Aldo J., Lytvyak, Ellina, Parés, Albert, Olivas, Ignasi, Londono, Maria-Carlota, Rodríguez-Tajes, Sergio, Eaton, John E., Osman, Karim T., Schramm, Christoph, Sebode, Marcial, Lohse, Ansgar W., Dalekos, George, Gatselis, Nikolaos, Nevens, Frederik, Cazzagon, Nora, Zago, Alessandra, Russo, Francesco Paolo, Floreani, Annarosa, Abbas, Nadir, Trivedi, Palak, Thorburn, Douglas, Saffioti, Francesca, Barkai, Laszlo, Roccarina, Davide, Calvaruso, Vicenza, Fichera, Anna, Delamarre, Adèle, Sobenko, Natalia, Villamil, Alejandra Maria, Medina-Morales, Esli, Bonder, Alan, Patwardhan, Vilas, Rigamonti, Cristina, Carbone, Marco, Invernizzi, Pietro, Cristoferi, Laura, van der Meer, Adriaan, de Veer, Rozanne, Zigmond, Ehud, Yehezkel, Eyal, Kremer, Andreas E., Deibel, Ansgar, Bruns, Tony, Große, Karsten, Wetten, Aaron, Dyson, Jessica Katharine, Jones, David, Levy, Cynthia, Tanaka, Atsushi, Dumortier, Jérôme, Pageaux, Georges-Philippe, de Lédinghen, Victor, Carrat, Fabrice, Chazouillères, Olivier, and Corpechot, Christophe

Published
2024
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15. The Generalized Fractional NU Method for the Diatomic Molecules in the Deng-Fan Model

Author

Abu-Shady, M., Khokha, E. M., and Abdel-Karim, T. A.

Subjects
Quantum Physics
Abstract

A solution of the fractional N-dimensional radial Schrodinger equation with the Deng-Fan potential is investigated by the generalized fractional NU method. The analytical formulas of energy eigenvalues and corresponding eigen functions for the Deng-Fan potential are generated. Furthermore, the current results are applied to several diatomic molecules for the Deng-Fan potential as well as the shifted Deng Fan potential. For both the Deng-Fan potential and its shifted potential, the effect of the fractional parameter on the energy levels of various diatomic molecules is examined numerically and graphically. We found that the energy eigenvalues are gradually improved when the fractional parameter increases. The energy spectra of various diatomic molecules are also evaluated in three-dimensional space and higher dimensions. It is worthy to note that the energy spectrum raises as the number of dimensions increases. In addition, the dependence of the energy spectra of the Deng-Fan potential and its shifted potential on the reduced mass, screening parameter, equilibrium bond length, rotational and vibrational quantum numbers is illustrated. To validate our findings, we estimate the energy levels of the Deng-Fan potential and shifted Deng-Fan potential at the classical case for various diatomic molecules and found that they are entirely compatible with earlier studies., Comment: 20 pages, 6 figures

Published
2022
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21. Masses and Thermodynamics Properties of Heavy Mesons in the Non-Relativistic Quark Model Using Nikiforov-Uvarov Method

Author

Abu-Shady, M., Abdel-Karim, T. A., and Ezz-Alarab, Sh. Y.

Subjects
High Energy Physics - Phenomenology
Abstract

Thermodynamics properties of heavy mesons are calculated within the framework of the N-dimensional radial Schrodinger equation. The Cornell potential is extended by including the quadratic potential plus the inverse of quadratic potential. The energy eigenvalues and the corresponding wave functions are calculated in the N-dimensional space using the Nikiforov-Uvarov (NV) method. The obtained results are applied for calculating the mass of spectra of charmonium, bottomonium, bc, and cs mesons. The thermodynamics properties of heavy quarkonia such as, the mean energy, specific heat, free energy, and entropy are calculated. The effect of temperature and the dimensionality number on heavy mesons masses and thermodynamics properties is investigated. The obtained results are improved in comparison with other theoretical approaches and in a good agreement with experimental data. We conclude that the present potential well describes thermodynamic properties in the three-dimensional space and also the higher dimensional space., Comment: 17 pages, 10 Figures, 4 Tables

Published
2019
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23. Exact Solution of the N-dimensional Radial Schr\'odinger Equation via Laplace Transformation Method with the Generalized Cornell Potential

Author

Abu-Shady, M., Abdel-Karim, T. A., and Khokha, E. M.

Subjects
High Energy Physics - Phenomenology
Abstract

The exact solution of N- dimensional radial Schr\"odinger equation with the generalized Cornell potential has been obtained using the Laplace transformation (LT) method. The energy eigenvalues and the corresponding wave functions for any state have been determined. The eigenvalues for some special cases of the generalized Cornell potential are obtained. The present results are applied to calculate the mass spectra of heavy quarkonium systems such as charmonium and bottomonium and the bc meson. A comparison is discussed with the experimental data and recent works. The present results are improved in comparison with other recent studies and are in a good agreement with the experimental data. The effect of the dimensional number (N) on the meson masses has been studied. We note that the meson masses increase in higher dimensions., Comment: 14 pages, 1 figure

Published
2018

24. Liver stiffness measurement by vibration-controlled transient elastography improves outcome prediction in primary biliary cholangitis

Author

Corpechot, Christophe, Carrat, Fabrice, Gaouar, Farid, Chau, Frederic, Hirschfield, Gideon, Gulamhusein, Aliya, Montano-Loza, Aldo J., Lytvyak, Ellina, Schramm, Christoph, Pares, Albert, Olivas, Ignasi, Eaton, John E., Osman, Karim T., Dalekos, George, Gatselis, Nikolaos, Nevens, Frederik, Cazzagon, Nora, Zago, Alessandra, Russo, Francesco Paolo, Abbas, Nadir, Trivedi, Palak, Thorburn, Douglas, Saffioti, Francesca, Barkai, Laszlo, Roccarina, Davide, Calvaruso, Vicenza, Fichera, Anna, Delamarre, Adèle, Medina-Morales, Esli, Bonder, Alan, Patwardhan, Vilas, Rigamonti, Cristina, Carbone, Marco, Invernizzi, Pietro, Cristoferi, Laura, van der Meer, Adriaan, de Veer, Rozanne, Zigmond, Ehud, Yehezkel, Eyal, Kremer, Andreas E., Deibel, Ansgar, Dumortier, Jérôme, Bruns, Tony, Große, Karsten, Pageaux, Georges-Philippe, Wetten, Aaron, Dyson, Jessica, Jones, David, Chazouillères, Olivier, Hansen, Bettina, and de Lédinghen, Victor

Published
2022
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25. Binding Energies and Dissociation Temperatures of Heavy Quarkonia at Finite Temperature and Chemical Potential in the N-dimensional space

Author

Abu-Shady, M., Abdel-Karim, T. A., and Khokha, E. M.

Subjects
High Energy Physics - Phenomenology
Abstract

The N-dimensional radial Schr\"odinger equation has been solved using the analytical exact iteration method (AEIM), in which the Cornell potential is generalized to finite temperature and chemical potential. The energy eigenvalues have been calculated in the N-dimensional space for any state (n, l). The present results have been applied for studying quarkonium properties such as charmonium and bottomonium masses. The binding energies and the mass spectra of heavy quarkonia are studied in the N-dimensional space. The dissociation temperatures for different states of heavy quarkonia are calculated in the three dimensional space. The influence of dimensionality number (N) has been discussed on the dissociation temperatures. A comparison is studied with other recent works. We conclude that the AEIM successes to predict the heavy-quarkonium properties at finite temperature and chemical potential., Comment: 17 Pages, 9 Figures, and 3 Tables

Published
2017
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27. Quarkonium Masses in the N-dimensional Space Using the Analytical Exact Iteration Method

Author

Khokha, E. M., Abu-Shady, M., and Abdel-Karim, T. A.

Subjects
High Energy Physics - Phenomenology
Abstract

The N-dimensional radial Schrodinger equation with an extended Cornell potential is solved. The analytical exact iteration method is applied. The energy eigenvalues are calculated in the N-dimensional space. The charmonium meson, the bottomonium meson and the bc meson masses are calculated in the N-dimensional space. The special cases are obtained from the general case. The study of the effect of dimensionality number is studied. The mean value of the radius and the mean square velocity of charmonium meson, bottomonium meson, and bc meson are calculated. The present results are improved in comparison with other recent studies and are in good agreement with the experimental data. Therefore, the present method with the present potential gives successfully description of heavy quarkonium properties., Comment: 7 pages, 3 figures, and 6 tables

Published
2016
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28. Divergence Measures as Diversity Indices

Author

Abou-Moustafa, Karim T.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Quantitative Methods, Statistics - Methodology
Abstract

Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy-based diversity indices, or diversity indices for short, suffer from three problems. First, when computing the diversity for samples withdrawn from communities with different structures, diversity indices can easily yield non-comparable and hard to interpret results. Second, diversity indices impose weighting schemes on the species distributions that unnecessarily emphasize low abundant rare species, or erroneously identified ones. Third, diversity indices do not allow for comparing distributions against each other, which is necessary when a community has a well-known species' distribution. In this paper we propose a new general methodology based on information theoretic principles to quantify the species diversity of a community. Our methodology, comprised of two steps, naturally overcomes the previous mentioned problems, and yields comparable and easy to interpret diversity values. We show that our methodology retains all the functional properties of any diversity index, and yet is far more flexible than entropy--based diversity indices. Our methodology is easy to implement and is applicable to any community of interest.

Published
2014

48. Utility of apical four‐chamber longitudinal strain in the assessment of childhood cancer survivors: A multicenter study.

Author

Mosgrove, Matthew J., Sachdeva, Ritu, Stratton, Kayla L., Armenian, Saro H., Bhat, Aarti, Leger, Kasey J., Yang, Christina, Leisenring, Wendy M., Meacham, Lillian R., Sadak, Karim T., Narasimhan, Shanti L., Nathan, Paul C., Chow, Eric J., and Border, William L.

Subjects
RESEARCH, ECHOCARDIOGRAPHY, CONFIDENCE intervals, LEFT ventricular dysfunction, GLOBAL longitudinal strain, RETROSPECTIVE studies, TUMORS in children, CANCER patients, PEARSON correlation (Statistics), COMPARATIVE studies, DESCRIPTIVE statistics, RESEARCH funding, STATISTICAL correlation, SENSITIVITY & specificity (Statistics), LONGITUDINAL method
Abstract

Background: A previous multicenter study showed that longitudinal changes in standard cardiac functional parameters were associated with the development of cardiomyopathy in childhood cancer survivors (CCS). Evaluation of the relationship between global longitudinal strain (GLS) changes and cardiomyopathy risk was limited, largely due to lack of quality apical 2‐ and 3‐chamber views in addition to 4‐chamber view. We sought to determine whether apical 4‐chamber longitudinal strain (A4LS) alone can serve as a suitable surrogate for GLS in this population. Methods: A4LS and GLS were measured in echocardiograms with acceptable apical 2‐, 3‐, and 4‐chamber views. Correlation was evaluated using Pearson and Spearman coefficients, and agreement was evaluated with Bland–Altman plots. The ability of A4LS to identify normal and abnormal values compared to GLS as the reference was evaluated. Results: Among a total of 632 reviewed echocardiograms, we identified 130 echocardiograms from 56 patients with adequate views (38% female; mean age at cancer diagnosis 8.3 years; mean follow‐up 9.4 years). Correlation coefficients between A4LS and GLS were.89 (Pearson) and.85 (Spearman), with Bland–Altman plot of GLS—A4LS showing a mean difference of −.71 ± 1.8. Compared with GLS as the gold standard, A4LS had a sensitivity of 86% (95% CI 79%–93%) and specificity of 82% (69%–95%) when using normal range cutoffs and 90% (82%–97%) and 70% (58%–81%) when using ±2 standard deviations. Conclusion: A4LS performs well when compared with GLS in this population. Given the more recent adoption of apical 2‐ and 3‐chamber views in most pediatric echocardiography laboratories, A4LS is a reasonable stand‐alone measurement in retrospective analyses of older study cohorts and echocardiogram biorepositories. [ABSTRACT FROM AUTHOR]

Published
2024
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