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EpiModel in the Scientific Literature

Samuel Jenness edited this page Sep 30, 2022 · 68 revisions
  1. Delaney KP, Rosenberg ES, Kramer MR, Waller LA, Sullivan PS. Optimizing Human Immunodeficiency Virus Testing Interventions for Men Who Have Sex With Men in the United States: A Modeling Study. Open Forum Infect Dis. 2015;2(4): ofv153. [LINK]

  2. Ezenwa VO, Archie EA, Craft ME, Hawley DM, Martin LB, Moore J, White L. Host behaviour-parasite feedback: an essential link between animal behaviour and disease ecology. Proc Biol Sci. 2016; 283(1828). [LINK]

  3. Webber QM, Brigham RM, Park AD, Gillam EH, O’Shea TJ, Willis CK. Social network characteristics and predicted pathogen transmission in summer colonies of female big brown bats (Eptesicus fuscus). Behavioral Ecology and Sociobiology. 2016;70(5): 701-12. [LINK]

  4. Jenness SM, Goodreau SM, Morris M, Cassels S. Effectiveness of Combination Packages for HIV-1 Prevention in Sub-Saharan Africa Depends on Partnership Network Structure. Sexually Transmitted Infections. 2016; 92(8): 619-624. [LINK]

  5. Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan P. Impact of CDC’s HIV Preexposure Prophylaxis Guidelines among MSM in the United States. Journal of Infectious Diseases. 2016; 214(12): 1800-1807. [LINK]

  6. Goldstein ND, Eppes SC, Mackley A, Tuttle D, Paul DA. A Network Model of Hand Hygiene: How Good Is Good Enough to Stop the Spread of MRSA? Infect Control Hosp Epidemiol. 2017; 38(8): 945-52. [LINK]

  7. Jenness SM, Sharma A, Goodreau SM, Rosenberg ES, Weiss KM, Hoover KW, Smith DK, Sullivan P. Individual HIV Risk versus Population Impact of Risk Compensation after HIV Preexposure Prophylaxis Initiation among Men Who Have Sex with Men. PLoS One. 2017; 12(1): e0169484. [LINK]

  8. Goodreau SM, Rosenberg ES, Jenness SM, Luisi N, Stansfield SE, Millett G, Sullivan P. Sources of Racial Disparities in HIV Prevalence among Men Who Have Sex with Men in Atlanta, GA: A Modeling Study. Lancet HIV. 2017; 4(7):e311-e320. [LINK]

  9. Jenness SM, Weiss KM, Goodreau SM, Rosenberg E, Gift T, Chesson H, Hoover KW, Smith DK, Liu AY, Sullivan P. Incidence of Gonorrhea and Chlamydia Following HIV Preexposure Prophylaxis among Men Who Have Sex with Men: A Modeling Study. Clinical Infectious Diseases. 2017; 65(5): 712-718. [LINK]

  10. White LA, Forester JD, Craft ME. Covariation between the physiological and behavioral components of pathogen transmission: Host heterogeneity determines epidemic outcomes. Oikos. 2018; 127(4): 538-52. [LINK]

  11. Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM. HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine. Vaccine. 2018;36(4): 514-520. [LINK]

  12. Robinson SJ, Barbieri MM, Murphy S, Baker JD, Harting AL, Craft ME, Littnan CL. Model recommendations meet management reality: implementation and evaluation of a network-informed vaccination effort for endangered Hawaiian monk seals. Proceeding of the Royal Society B. 2018; 285(1870): 20171899. [LINK]

  13. Vandormael A, Dobra A, Bärnighausen T, de Oliveira T, Tanser F. Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach. International Journal of Epidemiology. 2018; 47(1): 236-245. [LINK]

  14. Goodreau SM, Hamilton DT, Jenness SM, Sullivan PS, Valencia RK, Wang LY, Dunville RL, Barrios LC, Rosenberg ES. Targeting Human Immunodeficiency Virus Pre-Exposure Prophylaxis to Adolescent Sexual Minority Males in Higher Prevalence Areas of the United States: A Modeling Study. J Adolesc Health. 2018; 62(3): 311-319. [LINK]

  15. Luo W, Katz DA, Hamilton DT, McKenney J, Jenness SM, Goodreau SM, Stekler JD, Rosenberg ES, Sullivan P, Cassels S. Development of an Agent-Based Model to Investigate the Impact of HIV Self-Testing Programs for Men Who Have Sex with Men in Atlanta and Seattle. Journal of Medical Internet Research Public Health Surveillance. 2018; 4(2): e58. [LINK]

  16. Goodreau SM, Stansfield SE, Murphy JT, Peebles KC, Gottlieb GS, Abernethy NF, Herbeck JT, Mittler JE. Relational concurrency, stages of infection, and the evolution of HIV set point viral load. Virus Evolution. 2018; 4(2): vey032. [LINK]

  17. Goldstein ND, Jenness SM, Tuttle D, Power M, Paul DA, Eppes SC. Evaluating a neonatal intensive care unit MRSA surveillance programme using agent-based network modeling. Journal of Hospital Infection. 2018; 100(3): 337-43. [LINK]

  18. Hamilton DT, Goodreau SM, Jenness SM, Sullivan PS, Wang LY, Dunville RL, Barrios LC, Rosenberg ES. Potential Impact of HIV Preexposure Prophylaxis Among Black and White Adolescent Sexual Minority Males: A Modeling Study. American Journal of Public Health. 2018; 108(S4): S284–S291. [LINK]

  19. Haeussler K, den Hout A van, Baio G. A dynamic Bayesian Markov model for health economic evaluations of interventions in infectious disease. BMC Medical Research Methodology. 2018;18(1):82. [LINK]

  20. Everton SF, Schroeder R. Plagues, Pagans, and Christians: Differential Survival, Social Networks, and the Rise of Christianity. Journal for the Scientific Study of Religion. 2019; DOI: 10.1111/jssr.12631. [LINK]

  21. Hamilton DT, Rosenberg ES, Jenness SM, Sullivan PS, Wang LY, Dunville RL, Barrios LC, Aslam M, Goodreau SM. Modeling the Joint Effects of Adolescent and Adult PrEP for Sexual Minority Males in the United States. PloS One. 2019; 14(5): e0217315. [LINK]

  22. Milwid RM, O'Sullivan TL, Poljak Z, Laskowski M, Greer AL. Comparing the effects of non-homogenous mixing patterns on epidemiological outcomes in equine populations: A mathematical modelling study. Sci Rep. 2019; 9(1): 3227. [LINK]

  23. Stansfield SE, Mittler JE, Gottlieb GS, Murphy JT, Hamilton DT, Detels R, Wolinsky SM, Jacobson LP, Margolick JB, Rinaldo CR, Herbeck JT, Goodreau SM. Sexual Role and HIV-1 Set Point Viral Load among Men who Have Sex with Men. Epidemics. 2019; 26: 68-76. [LINK]

  24. Jenness SM, Maloney K, Smith SK, Hoover KW, Rosenberg ES, Goodreau SM, Weiss KM, Liu AY, Rao D, Sullivan PS. Addressing Gaps in HIV Preexposure Prophylaxis Care to Reduce Racial Disparities in HIV Incidence in the United States. American Journal of Epidemiology. 2019; 188(4): 743-752. [LINK]

  25. Jones J, Weiss K, Mermin J, Dietz P, Rosenberg ES, Gift TL, Chesson H, Sullivan PS, Lyles C, Bernstein KT, Jenness SM. Proportion of Incident Human Immunodeficiency Virus Cases Among Men Who Have Sex With Men Attributable to Gonorrhea and Chlamydia: A Modeling Analysis. Sexually Transmitted Diseases. 2019; 46(6): 357-63. [LINK]

  26. Wilson-Aggarwal JK, Ozella L, Tizzoni M, Cattuto C, Swan GJ, Moundai T, Silk MJ, Zingeser JA, McDonald RA. High-resolution contact networks of free-ranging domestic dogs Canis familiaris and implications for transmission of infection. PLoS Neglected Tropical Diseases. 2019; 13(7): e0007565. [LINK]

  27. Weiss KM, Jones J, Katz DA, Gift TL, Bernstein K, Workowski K, Rosenberg E, Jenness SM. Epidemiological Impact of Expedited Partner Therapy for Men Who Have Sex with Men: A Modeling Study. Sexually Transmitted Diseases. 2019; 46(11): 697–705. [LINK]

  28. Mittler JE, Murphy JT, Stansfield SE, Peebles KC, Gottlieb GS, Abernethy NF, Reid MC, Goodreau SM, Herbeck JT. Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model. PLoS Comput Biol. 2019;15(12):e1007561. [LINK]

  29. Amirpour Haredasht S, Tavornpanich S, Jansen MD, Lyngstad TM, Yatabe T, Brun E, Martínez-López B. A stochastic network-based model to simulate the spread of pancreas disease (PD) in the Norwegian salmon industry based on the observed vessel movements and seaway distance between marine farms. Prev Vet Med. 2019; 167: 174-181. [LINK]

  30. Goldstein ND, LeVasseur MT, Tran NK, Purtle J, Welles SL, Eppes SC. Modeling HPV vaccination scale-up among urban young men who have sex with men in the context of HIV. Vaccine. 2019; 37(29): 3883-3891. [LINK]

  31. Weiss KM, Jones JS, Anderson EJ, Gift T, Chesson H, Bernstein K, Workowski K, Tuite A, Rosenberg ES, Sullivan PS, Jenness SM. Optimizing Coverage versus Frequency for Sexually Transmitted Infection Screening of Men Who Have Sex with Men. Open Forum Infectious Diseases. 2019; 6(10): ofz405. [LINK]

  32. Almeshal AM, Almazrouee AI, Alenizi MR, Alhajeri SN. Forecasting the Spread of COVID-19 in Kuwait Using Compartmental and Logistic Regression Models. Applied Sciences. 2020;10(10):3402. [LINK]

  33. Wang LY, Hamilton DT, Rosenberg ES, Aslam MV, Sullivan PS, Katz DA, Dunville RL, Barrios LC, Goodreau SM. Cost-Effectiveness of Pre-Exposure Prophylaxis Among Adolescent Sexual Minority Males. J Adolesc Health. 2020; 66(1): 100-106. [LINK]

  34. Amusan O, Thompson AF, Aderinola TB, Alese BK. Modelling Malicious Attack in Social Networks. Network and Communication Technologies. 2020; 5(1): 37-43. [LINK]

  35. Jenness SM, Johnson JA, Hoover KW, Smith DK, Delaney K. Modeling an Integrated HIV Prevention and Care Continuum to Achieve the Ending the HIV Epidemic Goals. AIDS. 2020; 34(14): 2103–2113. [LINK]

  36. Baker E, Challenor P, Eames M. Predicting the Output From a Stochastic Computer Model When a Deterministic Approximation is Available. Journal of Computational and Graphical Statistics. 2020: 1-12. [LINK]

  37. Ghosh P, Basheer S, Paul S, Chakrabarti P, Sarkar J. Increased Detection coupled with Social Distancing and Health Capacity Planning Reduce the Burden of COVID-19 Cases and Fatalities: A Proof of Concept Study using a Stochastic Computational Simulation Model. medRxiv. 2020; DOI: 10.1101/2020.04.05.20054775. [LINK]

  38. Yap WA, Raja DB. Time-variant strategies for optimizing the performance of non-pharmaceutical interventions (NPIs) in protecting lives and livelihoods during the COVID-19 pandemic. medRxiv. 2020; DOI: 10.1101/2020.04.13.20063248. [LINK]

  39. Yu X. Modeling return of the epidemic: Impact of population structure, asymptomatic infection, case importation and personal contacts. Travel Medicine and Infectious Disease. 2020; 37:101858. [LINK]

  40. Bhutta ZA, Harari O, Park JJ, et al. Evaluation of effects of public health interventions on COVID-19 transmission for Pakistan: A mathematical simulation study. medRxiv. 2020; DOI: 10.1101/2020.04.30.20086447. [LINK]

  41. Earnest R, Rönn MM, Bellerose M, Gift TL, Berruti AA, Hsu KK, Testa C, Zhu L, Malyuta Y, Menzies NA, Salomon JA. Population-level Benefits of Extragenital Gonorrhea Screening Among Men Who Have Sex With Men: An Exploratory Modeling Analysis. Sexually Transmitted Diseases. 2020; 2020; 47(7): 484-490. [LINK]

  42. Nguemdjo UK, Meno F, Dongfack A, Ventelou B. Simulating the progression of the COVID-19 disease in Cameroon using SIR models. PLOS ONE. 2020; DOI: 10.1371/journal.pone.0237832. [LINK]

  43. Turk PJ, Chou S-H, Kowalkowski MA, et al. Modeling COVID-19 latent prevalence to assess a public health intervention at a state and regional scale. JMIR Public Health Surveill 2020; 6(2): e19353. [LINK]

  44. Al-Khani AM, Khalifa MA, Almazrou A, Saquib N. The SARS-CoV-2 pandemic course in Saudi Arabia: A dynamic epidemiological model. Infectious Disease Modelling. 2020;5:766-771. [LINK]

  45. Bhavani DSD, Rani DTS, Rapolu T, Nutakki B. A Time-Dependent SEIRD Model for Forecasting the COVID-19 Transmission Dynamics. medRxiv. 2020; DOI: 10.1101/2020.05.29.20113571. [LINK]

  46. Churches T, Jorm L. “COVOID”: A flexible, freely available stochastic individual contact model for exploring COVID-19 intervention and control strategies. JMIR Public Health Surveill. 2020; 6(3): e18965. [LINK]

  47. López-Abente J, Valor-Suarez C, López-Abente G. Massive application of the SARS-CoV-2 diagnostic test: Simulation of its effect on the evolution of the epidemic in Spain. Epidemiology & Infection. 2020; 148: e233. [LINK]

  48. DeFries R, Agarwala M, Baquie S, et al. Post-lockdown spread of COVID-19 from cities to vulnerable forest-fringe villages in central India. Current Science. 2020; 119(1):52-58. DOI: 10.18520/cs/v119/i1/52-58. [LINK]

  49. Adeiza SS, Shuaibu Bello A, Shuaibu MG, Abdulraheem U. COVID -19 in a Nigerian University: Modelling the Spread of SARS-CoV-2 on an Average University Campus. Social Science Research Network. 2020; DOI: 10.2139/ssrn.3701542. [LINK]

  50. Vermeer W, Hjorth A, Jenness SM, Brown CH, Wilensky U. Leveraging Modularity During Replication of High-Fidelity Models: Lessons from Replicating an Agent-Based Model for HIV Prevention. Journal of Artificial Societies and Social Simulation. 2020; DOI: 10.18564/jasss.4352. [LINK]

  51. Fang Z, Zhao P, Xu M, Xu S, Hu T, Fang X. Statistical modeling of computer malware propagation dynamics in cyberspace. Journal of Applied Statistics. 2020; DOI: 10.1080/02664763.2020.1845621. [LINK]

  52. Wang Y, Li B, Gouripeddi R, Facelli JC. Human Activity Pattern Implications for Modeling SARS-CoV-2 Transmission. Computer Methods and Programs in Biomedicine. 2020; DOI: 10.1016/j.cmpb.2020.105896. [LINK]

  53. Ogunbiyi N, Basukoski A, Chaussalet T. Investigating the Diffusion of Workload-Induced Stress—A Simulation Approach. Information. 2020; DOI: 10.3390/info12010011. [LINK]

  54. Lopman B, Liu CY, Le Guillou A, Handel A, Lash TL, Isakov AP, et al. A modeling study to inform screening and testing interventions for the control of SARS-CoV-2 on university campuses. Scientific Reports. 2021 Mar 15;11(1):5900. [LINK]

  55. Hamilton DT, Rosenberg ES, Sullivan PS, et al. Modeling the Impact of PrEP Programs for Adolescent Sexual Minority Males Based on Empirical Estimates for the PrEP Continuum of Care. Journal of Adolescent Health. 2021; 68(3): 488-496. [LINK]

  56. Jenness SM, Willebrand KS, Malik AA, Lopman BA, Omer S. Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship. Epidemics. 2021; 37: 100488. [LINK]

  57. Jenness SM, Le Guillou A, Chandra C, Mann L, Sanchez T, Westreich D, Marcus JL. Projected HIV and Bacterial STI Incidence Following COVID-Related Sexual Distancing and Clinical Service Interruption. Journal of Infectious Diseases. 2021; 223(6): 1019–28. [LINK]

  58. Anderson EJ, Weiss KM, Morris MM, Sanchez TH, Prasad P, Jenness SM. HIV and Sexually Transmitted Infection Epidemic Potential of Networks of Men Who Have Sex with Men in Two Cities. Epidemiology. 2021; 32(5):681-9. [LINK]

  59. Stansfield SE, Herbeck JT, Gottlieb GS, Abernethy NF, Murphy JT, Mittler JE, Goodreau SM. Test-and-Treat Coverage and HIV Virulence Evolution among Men who have Sex with Men. Virus Evolution. 2021; 7(1): veab011. [LINK]

  60. Lee HS, Thakur KK, Pham-Thanh L, Dao TD, Bui AN, Bui VN, et al. A stochastic network-based model to simulate farm-level transmission of African swine fever virus in Vietnam. PLoS One. 2021; DOI: 10.1371/journal.pone.0247770. [LINK]

  61. Le Guillou A, Buchbinder S, Scott H, Liu A, Havlir D, Scheer S, Jenness SM. Population Impact and Efficiency of Improvements to HIV PrEP Under Conditions of High ART Coverage among San Francisco Men Who Have Sex with Men. Journal of Acquired Immune Deficiency Syndromes. 2021; 88(4): 340 - 347. [LINK]

  62. Bhattacharyya R, Banerjee S, Mohammed S, Baladandayuthapani V. Network-based Modeling of COVID-19 Dynamics: Early Pandemic Spread in India. medRxiv. 2021 Mar 20;2021.03.16.21253772. [LINK]

  63. Peebles K, Mittler JE, Goodreau SM, Murphy JT, Reid MC, Abernethy N, et al. Risk compensation after HIV-1 vaccination may accelerate viral adaptation and reduce cost-effectiveness: a modeling study. Sci Rep. 2021; 11(1): 6798. [LINK]

  64. Lovick S, Dite GS, Allman R. The health effects in the US of quarantine policies based on predicted individual risk of severe COVID-19 outcomes. medRxiv. 2021 Mar 26;2021.03.21.21254065. [LINK]

  65. Kauk J, Kreysa H, Schweinberger SR. Understanding and countering the spread of conspiracy theories in social networks: Evidence from epidemiological models of Twitter data. PLoS One. 2021; 16(8): e0256179. [LINK]

  66. Maloney KM, Driggers R, Sarkar S, Anderson EA, Malik AA, Jenness SM. Projected Impact of Concurrently Available Long-Acting Injectable and Daily-Oral HIV Pre-Exposure Prophylaxis. Journal of Infectious Diseases. 2021; 223(1): 72–82. [LINK]

  67. Jenness SM, Knowlton G, Smith DK, Marcus JL, Anderson EJ, Siegler AJ, Jones J, Sullivan PS, Enns E. A Decision Analytics Model to Optimize Investment in Interventions Targeting the HIV PrEP Cascade of Care. AIDS. 2021; 35(9): 1479–89. [LINK]

  68. Katz DA, Hamilton DT, Rosenthal EM, Wang LY, Dunville RL, Aslam M, Barrios LC, Zlotorzynska M, Sanchez TH, Sullivan PS, Rosenberg ES, Goodreau SM. Effects of Condom Use on Human Immunodeficiency Virus Transmission Among Adolescent Sexual Minority Males in the United States: A Mixed Epidemiology and Epidemic Modeling Study. Sexually Transmitted Diseases. 2021; 48(12): 973-980. [LINK]

  69. Hu Y, Guo J, Li G, Lu X, Li X, Zhang Y, et al. Role of efficient testing and contact tracing in mitigating the COVID-19 pandemic: a network modeling study. BMJ Open. 2021 Jul 7;11(7):e045886. [LINK]

  70. Wheatley MM, Knowlton G, Kao SY, Jenness SM, Enns E. Cost-Effectiveness of Interventions to Improve HIV Pre-Exposure Prophylaxis Initiation, Adherence, and Persistence among Men Who Have Sex with Men. Journal of Acquired Immune Deficiency Syndromes. 2022; 90(1): 41-49. [LINK]

  71. Earnest R, Rönn MM, Bellerose M, Menon-Johansson AS, Berruti AA, Chesson HW, Gift TL, Hsu KK, Testa C, Zhu L, Malyuta Y, Menzies NA, Salomon JA. Modeling the Cost-Effectiveness of Express Multisite Gonorrhea Screening Among Men Who Have Sex With Men in the United States. Sex Transm Dis. 2021; 48(11): 805-812. [LINK]

  72. Hamilton DT, Katz DA, Luo W, Stekler JD, Rosenberg ES, Sullivan PS, Goodreau SM, Cassels S. Effective strategies to promote HIV self-testing for men who have sex with men: Evidence from a mathematical model. Epidemics. 2021; 37: 100518. [LINK]

  73. Tran NK, Goldstein ND, Welles SL. Countering the rise of syphilis: A role for doxycycline post-exposure prophylaxis? International Journal of STD & AIDS. 2022; 33(1): 18-30. [LINK]

  74. Sahnan D, Goel V, Masud S, Jain C, Goyal V, Chakraborty T. DiVA: A Scalable, Interactive and Customizable Visual Analytics Platform for Information Diffusion on Large Networks. arXiv. 2021; DOI: 10.48550/arXiv.2112.06267. [LINK]

  75. AlJohani NI, Mutai K. Effect of non-pharmacological interventions on the COVID-19 epidemic in Saudi Arabia. Epidemiology and Infection. 2021; 149: e252. [LINK]

  76. Zeng P. On the Transmission of COVID-19 and Its Prevention and Control Management. Discrete Dynamics in Nature and Society. 2021; DOI: 10.1155/2021/9629816. [LINK]

  77. Jones J, Le Guillou A, Gift TL, Chesson H, Bernstein K, Delaney K, Lyles C, Berruit A, Sullivan PS, Jenness SM. Effect of Screening and Treatment for Gonorrhea and Chlamydia on HIV Incidence among Men who Have Sex with Men in the United States: A Modeling Analysis. Sexually Transmitted Diseases. 2022; 49(10): 663–668. [LINK]

  78. Jenness SM, Le Guillou A, Lyles C, Bernstein KT, Krupinsky K, Enns EA, Sullivan PS, Delaney KP. The Role of HIV Partner Services in the Modern Biomedical HIV Prevention Era: A Network Modeling Study. Pre-Print: DOI: 10.1101/2022.05.20.22275395. [LINK]

  79. Nguyen D, Wakhare T, Jiao J, Myers K, Udiani O, Fefferman NH. Seasonality in multi-host disease systems. Ecological Modelling. 2022; 470:109973. [LINK]

  80. Goodreau SM, Stansfield SE, Mittler JE, Murphy JT, Abernethy NF, Gottlieb GS, Reid MC, Burke JC, Pollock ED, Herbeck JT. Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis. Epidemics. 2022; 41:100629. [LINK]

  81. Spicknall IH, Pollock ED, Clay PA, Oster AM, Charniga K, Masters N, Nakazawa YJ, Rainisch G, Bundlapalli AV, Gift TL. Modeling the impact of sexual networks in the transmission of Monkeypox virus among gay, bisexual, and other men who have sex with men—United States, 2022. MMWR: Morbidity and Mortality Weekly Report. 2022;71. [LINK]

  82. Higgins SS, Luna AH, Rabelo AM, Dos Santos RO, Ferreira VC. A structural method to assess the course of the SARS-CoV-2 pandemic in school environments. Pan American Journal of Public Health. 2022; 46:e117. [LINK]

  83. Man I, Georges D, de Carvalho TM, Saraswati LR, Bhandari P, Kataria I, Siddiqui M, Muwonge R, Lucas E, Berkhof J, Sankaranarayanan R, Bogaards JA, Basu P, Baussano I. Evidence-based impact projections of single-dose human papillomavirus vaccination in India: a modelling study. Lancet Oncol. 2022; S1470-2045(22)00543-5. doi: 10.1016/S1470-2045(22)00543-5. Online ahead of print. [LINK]