Joanna Nelson

All Publications

• Almanac - Retrieval-Augmented Language Models for Clinical Medicine. NEJM AI Zakka, C., Shad, R., Chaurasia, A., Dalal, A. R., Kim, J. L., Moor, M., Fong, R., Phillips, C., Alexander, K., Ashley, E., Boyd, J., Boyd, K., Hirsch, K., Langlotz, C., Lee, R., Melia, J., Nelson, J., Sallam, K., Tullis, S., Vogelsong, M. A., Cunningham, J. P., Hiesinger, W. 2024; 1 (2)

  Abstract

  Large language models (LLMs) have recently shown impressive zero-shot capabilities, whereby they can use auxiliary data, without the availability of task-specific training examples, to complete a variety of natural language tasks, such as summarization, dialogue generation, and question answering. However, despite many promising applications of LLMs in clinical medicine, adoption of these models has been limited by their tendency to generate incorrect and sometimes even harmful statements.We tasked a panel of eight board-certified clinicians and two health care practitioners with evaluating Almanac, an LLM framework augmented with retrieval capabilities from curated medical resources for medical guideline and treatment recommendations. The panel compared responses from Almanac and standard LLMs (ChatGPT-4, Bing, and Bard) versus a novel data set of 314 clinical questions spanning nine medical specialties.Almanac showed a significant improvement in performance compared with the standard LLMs across axes of factuality, completeness, user preference, and adversarial safety.Our results show the potential for LLMs with access to domain-specific corpora to be effective in clinical decision-making. The findings also underscore the importance of carefully testing LLMs before deployment to mitigate their shortcomings. (Funded by the National Institutes of Health, National Heart, Lung, and Blood Institute.).

  View details for DOI 10.1056/aioa2300068

  View details for PubMedID 38343631

  View details for PubMedCentralID PMC10857783

• Sternal wound infection with Mycoplasma salivarium following bilateral lung transplant. Transplant infectious disease : an official journal of the Transplantation Society Rodriguez-Nava, G., Epstein, D., Nelson, J. 2023: e14120

  View details for DOI 10.1111/tid.14120

  View details for PubMedID 37622411

• Almanac: Retrieval-Augmented Language Models for Clinical Medicine. Research square Zakka, C., Chaurasia, A., Shad, R., Dalal, A. R., Kim, J. L., Moor, M., Alexander, K., Ashley, E., Boyd, J., Boyd, K., Hirsch, K., Langlotz, C., Nelson, J., Hiesinger, W. 2023

  Abstract

  Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n= 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

  View details for DOI 10.21203/rs.3.rs-2883198/v1

  View details for PubMedID 37205549

  View details for PubMedCentralID PMC10187428

• Epidemiology of lower respiratory tract infections and community-acquired respiratory viruses in patients with bronchiolitis obliterans syndrome after hematopoietic cell transplant: a retrospective cohort study. Transplantation and cellular therapy Epstein, D. J., Liang, E. C., Sharifi, H., Lai, Y. K., Arai, S., Graber-Naidich, A., Sundaram, V., Nelson, J., Hsu, J. L. 2022

  Abstract

  Among 55 patients with bronchiolitis obliterans syndrome, 34 (61.8%) developed lower respiratory tract infections, which were associated with impaired lung function and a trend toward increased mortality. Rhinovirus/enterovirus and Pseudomonas aeruginosa infections predominated; 10 (18.2%) patients developed non-tuberculous mycobacterial infections.

  View details for DOI 10.1016/j.jtct.2022.07.016

  View details for PubMedID 35872303

• Strongyloides Hyperinfection After Immunosuppression in an Immigrant From El Salvador A Case for Early Diagnosis and Treatment JCR-JOURNAL OF CLINICAL RHEUMATOLOGY Hoppenfeld, M., Kennedy, V., Sheth, K., Chang, A., Nelson, J., Fairchild, R. 2021; 27 (4): E128-+

  View details for Web of Science ID 000657235500003

• Covid-19 in hospitalized lung and non-lung solid organ transplant recipients: a comparative analysis from a multicenter study. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons Heldman, M. R., Kates, O. S., Safa, K., Kotton, C. N., Georgia, S. J., Steinbrink, J. M., Alexander, B. D., Hemmersbach-Miller, M., Blumberg, E. A., Crespo, M. M., Multani, A., Lewis, A. V., Beaird, O. E., Haydel, B., La Hoz, R. M., Moni, L., Condor, Y., Flores, S., Munoz, C. G., Guitierrez, J., Diaz, E. I., Diaz, D., Vianna, R., Guerra, G., Loebe, M., Rakita, R. M., Malinis, M., Azar, M. M., Hemmige, V., McCort, M. E., Chaudhry, Z. S., Singh, P., Hughes, K., Velioglu, A., Yabu, J. M., Morillis, J. A., Mehta, S. A., Tanna, S. D., Ison, M. G., Tomic, R., Derenge, A. C., van Duin, D., Maximin, A., Gilbert, C., Goldman, J. D., Sehgal, S., Weisshaar, D., Girgis, R. E., Nelson, J., Lease, E. D., Fisher, C. E., Limaye, A. P., UW Covid-19 SOT Study Team, Lawrence, C. 2021

  Abstract

  Lung transplant recipients (LTR) with Covid-19 may have higher mortality than non-lung solid organ transplant recipients (SOTR), but direct comparisons are limited. Risk factors for mortality specifically in LTR have not been explored. We performed a multicenter cohort study of adult SOTR with Covid-19 to compare mortality by 28-days between hospitalized LTR and non-lung SOTR. Multivariable logistic regression models were used to assess comorbidity-adjusted mortality among LTR vs. non-lung SOTR and to determine risk factors for death in LTR. Of 1,616 SOTR with Covid-19, 1,051 (65%) were hospitalized including 117/159 (74%) LTR and 934/1457 (64%) non-lung SOTR (p=0.02). Mortality was higher among LTR compared to non-lung SOTR (24% vs. 16%, respectively, p=0.035) and lung transplant was independently associated with death after adjusting for age and comorbidities (aOR 1.7, 95% CI 1.0-2.6, p=0.05). Among LTR, independent risk factors for mortality included single lung transplant (aOR 2.8, 95% CI 1.0-7.7, p=0.04) and chronic lung allograft dysfunction (aOR 3.6, 95% CI 1.0-12.4, p=0.05), but not age >65 years, heart failure, or obesity. Among SOTR hospitalized for Covid-19, LTR had higher mortality than non-lung SOTR. In LTR, single lung transplant and chronic allograft dysfunction were independently associated with mortality.

  View details for DOI 10.1111/ajt.16692

  View details for PubMedID 34008917

• Use of Remdesivir for Pregnant Patients with Severe Novel 2019 Coronavirus Disease. American journal of obstetrics and gynecology Igbinosa, I., Miller, S., Bianco, K., Nelson, J., Kappagoda, S., Blackburn, B. G., Grant, P., Subramanian, A., Lyell, D., El-Sayed, Y., Aziz, N. 2020

  View details for DOI 10.1016/j.ajog.2020.08.001

  View details for PubMedID 32771381

• Challenges in Diagnosis and Management of Nontuberculous Mycobacteria in Solid Organ Transplantation OBM Transplantation Nelson, J. K., Subramanian, A. 2019; 3 (1)

  View details for DOI 10.21926/obm.transplant.1901047

• PROCALCITONIN IS NONSPECIFICALLY ELEVATED IN ADULT HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS Lau, E., Martin, B., Nelson, J. K. WILEY. 2019: S24

  View details for Web of Science ID 000449991100049

• Strongyloides Hyperinfection After Immunosuppression in an Immigrant From El Salvador: A Case for Early Diagnosis and Treatment. Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases Hoppenfeld, M. S., Kennedy, V., Sheth, K., Chang, A., Nelson, J., Fairchild, R. M. 2018

  View details for PubMedID 30074914

• Donor-Derived Coccidioides immitis Endocarditis and Disseminated Infection in the Setting of Solid Organ Transplantation. Open forum infectious diseases Nelson, J. K., Giraldeau, G., Montoya, J. G., Deresinski, S., Ho, D. Y., Pham, M. 2016; 3 (3): ofw086-?

  Abstract

  Background.  Endocarditis is a rare manifestation of infection with Coccidioides. This is the first reported case of donor-derived Coccidioides endocarditis obtained from a heart transplant. Methods.  We present a unique case of donor-derived Coccidioides immitis endocarditis and disseminated infection in a heart transplant patient. We also conducted a review of the literature to identify other cases of donor-derived coccidioidomycosis in solid organ transplant recipients and reviewed their clinical characteristics. Results.  Fifteen prior cases of donor-derived coccidioidomycosis were identified. A majority of these cases were diagnosed by positive culture (83%). Mortality was high at 58%. Conclusions.  Clinicians should maintain a high index of suspicion for disseminated coccidioidomycosis in patients who received transplants with organs from donors with a history of residing in endemic regions.

  View details for DOI 10.1093/ofid/ofw086

  View details for PubMedID 27413765

• Encephalitis caused by chikungunya virus in a traveler from the kingdom of tonga. Journal of clinical microbiology Nelson, J., Waggoner, J. J., Sahoo, M. K., Grant, P. M., Pinsky, B. A. 2014; 52 (9): 3459-3461

  Abstract

  Febrile travelers from countries with unique endemic pathogens pose a significant diagnostic challenge. In this report, we describe the case of a Tongan man presenting with fever, rash, and altered mental status. The diagnosis of Chikungunya encephalitis was made using a laboratory-developed real-time RT-PCR and serologic testing.

  View details for DOI 10.1128/JCM.01288-14

  View details for PubMedID 24958800