About

James F. Holmes, Jr., M.D., M.P.H., is an Interim Chair and Professor in the Department of Emergency Medicine at UC Davis Health. His medical practice involves providing care for patients of all agents in the Emergency Department. His research primarily focuses on the initial evaluation and care of injured patients, with a specific interest in the initial care of injured children. He has a particular focus on the utilization of CT scans following trauma. Dr. Holmes has received several awards, including the SAEM Organizational Advancement Award in 2022, the UC Davis Diamond Doc Award in 2021, and the UC Davis Dean’s Excellence in Mentoring Award in 2014. His scholarly work includes research on emergent cardiac outcomes, COVID-19 testing in emergency settings, trauma transport and long-term functional outcomes, and the cost of emergency department wait times. Dr. Holmes's educational background includes a B.S. from Auburn University, an M.D. from the University of Alabama School of Medicine, and an M.P.H. in Epidemiology from UC Berkeley. He completed his internship and residency in Emergency Medicine at UC Davis. His contributions to emergency medicine research and education are recognized through his leadership and numerous publications.

Research topics

• Medicine
• Emergency medicine
• Medical emergency
• Internal medicine
• Cardiology
• Surgery
• Gerontology
• Psychiatry
• Family medicine

Selected publications

• Perceived Race and Ethnicity on CT Use in Children With Minor Head or Abdominal Trauma

  PEDIATRICS · 2026-01-12 · 2 citations

  article

  OBJECTIVE: To determine whether race or ethnicity is associated with computed tomography (CT) use in children after minor blunt head trauma (BHT) or blunt abdominal trauma (BAT). METHODS: This was a prospective secondary analysis of children (<18 years) with BHT and/or BAT at 6 pediatric trauma centers. Injury severity was assessed using the Pediatric Emergency Care Applied Research Network prediction rules. We performed multivariable logistic regression, controlling for site, age, sex, Social Deprivation Index, and injury severity. RESULTS: In total, 17 339 patients with BHT were enrolled. For patients aged 2 years or older, compared with the reference group (∼85% non-Hispanic white patients), there was no difference in CT use for Hispanic ethnicity (adjusted odds ratio [aOR], 0.96; 95% CI, 0.86-1.08), non-Hispanic Asian (aOR, 1.06; 95% CI, 0.82, 1.37), or Black race (aOR, 1.03; 95% CI, 0.89-1.19). For patients aged younger than 2 years, there was no difference in CT use for Asian (aOR, 1.07; 95% CI, 0.70-1.63) or Black race (aOR, 1.20; 95% CI, 0.89-1.62) but less CT use for Hispanic patients (aOR, 0.75; 95% CI, 0.59-0.96). In all, 6821 patients with BAT were enrolled. Compared with the reference group (∼95% non-Hispanic white), there were no significant differences in CT use for patients who were Asian (aOR, 0.98; 95% CI, 0.68-1.40), Black (aOR, 0.89; 95% CI, 0.73-1.40), or Hispanic (aOR, 0.96; 95% CI, 0.81-1.13). CONCLUSIONS: CT use in children with BAT was similar across racial and ethnic groups. However, head CT rates in Hispanic children aged younger than 2 years may reflect disparities in imaging practices.

  PublisherDOI

• Methylation Score Could Improve Prediction of Clinical Outcomes in COVID-19

  American Journal of Respiratory and Critical Care Medicine · 2025-05-01

  article

  Abstract Rationale: Identifying patients at high risk for severe COVID-19 is important to optimize clinical outcomes and resource allocation. We hypothesized that inclusion of methylation data would improve performance of a clinical prediction model. Methods: We performed a retrospective cohort study of adults (≥18 years) with COVID-19 who presented to the University of Colorado Hospital emergency department from March 2020 to June 2020. Patient data were derived from Health Data Compass, an electronic warehouse that includes clinical and biological data from UCHealth patients. The outcome of interest was a modified version of the WHO ordinal score for clinical improvement, which stratifies severity based on respiratory support required. We performed univariate and bivariate analyses to further select variables for inclusion (p&amp;lt;0.05). We used ordinal logistic regression to develop a model predicting WHO score. Methylation scores were measured at presentation using Infinium MethylationEPIC Array analyses immune-targeted to 262 genes and 7831 additional probes. We assessed the methylation score's impact on the model, using the estimated logit-hat for the predictive model derived for the entire cohort as an independent variable in a pair of models fit to the methylation subsample, one with and the other without the score as a variable. The Wald test was used to quantify the predictive value of the methylation score. The areas under the curve (AUC) for the two models were computed and compared using the somersd package in Stata. Results: A total of 1,400 patients were included, 123 with methylation scores. The derived model for the entire cohort included the following variables: age ≥65 years (OR 9.6, 95% CI 5.8-16), male sex (OR 1.8, 95% CI 1.4-2.5), BMI &amp;lt;18 or ≥30 (OR 2.2, 95% CI 1.5-3.2), neutrophil:lymphocyte ratio &amp;lt;0.7 or &amp;gt;3.0 (OR 1.9, 95% CI 1.3-2.7), and glucose ≤70 or ≥120 (OR 1.8, 95% CI 1.3-2.5). In the 123 patients with methylation scores, methylation score had an odds ratio of 6.9 (95% CI 1.5-31.6). In comparing models with and without methylation score, the AUC was 0.87 (95% CI 0.81-0.92) without and 0.90 (95% CI 0.85, 0.94) with the methylation score, a difference in AUC=0.02 (95% CI -0.003, 0.05), p=0.085. Conclusions: Five variables were associated with severity. The addition of methylation scores at presentation statistically significantly improved prediction but not model discrimination in this small sample. Further investigation is warranted to identify the utility of methylation scores in predicting outcomes in this and other emerging infections.

  PublisherDOI

• Performance of individual criteria of the <scp>Pediatric Emergency Care Applied Research Network</scp> (<scp>PECARN</scp>) intraabdominal injury prediction rule

  Academic Emergency Medicine · 2025-01-13 · 1 citations

  articleSenior author

  Abstract Objective The Pediatric Emergency Care Applied Research Network (PECARN) derived and externally validated a clinical prediction rule to identify children with blunt torso trauma at low risk for intraabdominal injuries undergoing acute intervention (IAI AI ). Little is known about the risk for IAI AI when only one or two prediction rule variables are positive. We sought to determine the risk for IAI AI when either one or two PECARN intraabdominal injury rule variables are positive. Methods We performed a planned secondary analysis of a prospective, multicenter study that included 7542 children (&lt;18 years old) with blunt torso trauma evaluated in six emergency departments from December 2016 to August 2021. Patients with only one or two PECARN rule variables positive were included. The outcome was IAI AI (IAI undergoing therapeutic laparotomy, angiographic embolization, blood transfusion, or two or more nights of intravenous fluids). Results Among the 7542 children enrolled, 2986 (39.6%, 95% confidence interval [CI] 38.5%–40.7%) had one or two PECARN variables positive and were included. Of this subpopulation, 227 (7.6%, 95% CI 6.7%–8.6%) had intraabdominal injuries. In the 1639 patients with only one rule variable positive, 21 (1.3%, 95% CI 0.8%–2.0%) had IAI AI . In the 1347 patients with two rule variables positive, 27 (2.0%, 95% CI 1.3%–2.9%) had IAI AI . Risk for IAI AI for each variable was highest for Glasgow Coma Scale (GCS) score &lt;14 (16/291, 5.5%, 95% CI 3.2%–8.8%) and abdominal wall trauma (three of 321, 0.9%, 95% CI 0.2%–2.7%). Risk for IAI AI when two variables were present was highest when decreased breath sounds (three of 44, 6.8%, 95% CI 1.4%–18.7%) and GCS &lt;14 (10/207, 4.8%, 95% CI 2.3%–8.7%) were present with one other variable. Conclusions Few children with blunt torso trauma and one or two PECARN predictor variables present have IAI AI . Those with GCS score &lt;14, however, are at highest risk for IAI AI .

  PublisherDOI

• Abdominal ultrasound (FAST) in hemodynamically stable children with blunt abdominal trauma: study protocol for a randomized controlled trial

  Trials · 2025-12-12

  articleOpen access1st authorCorresponding

  BACKGROUND: Hemorrhage from intra-abdominal injuries (IAI) is a leading cause of traumatic deaths in children. Concern over misdiagnosing IAIs has resulted in excessive use of abdominal computed tomography (CT). Despite its many benefits, CT presents risks to children most notably radiation-induced malignancies. Thus, we must safely limit abdominal CT evaluation to those at non-negligible risk. The focused assessment with sonography for trauma (FAST) examination uses abdominal ultrasonography to detect the presence of intraperitoneal fluid in injured patients and may decrease abdominal CT use in some children. Limited and conflicting data exists on the utility of the FAST examination in children. A large multicenter study is thus necessary to determine if the FAST examination should routinely be included in the diagnostic evaluation of injured children. METHODS: This is a multicenter, randomized controlled clinical trial to assess the impact of the FAST examination on the initial evaluation of children with blunt abdominal trauma. Enrolled participants will be randomized 1:1 to the FAST examination plus routine care or routine care alone during their initial emergency department (ED) evaluation. The study will enroll 3194 (initial sample size) to 4346 (second sample size) children at six diverse sites. The primary outcomes are as follows: (1) The proportion of abdominal CT in the initial 24 h of care and (2) the proportion of missed or delayed diagnoses of IAIs. Secondary outcomes include (1) ED length of stay, (2) hospitalization proportion and length of hospital stay, (3) physician suspicion of IAI, (4) the proportion of abdominal CT use in the subgroup of children 0 to 3 years old, and (5) laparotomy proportion. Hospitalized participants will be followed through their stay, and guardians of those discharged from the ED will be contacted after 1 week to assess their status. DISCUSSION: The study will determine if the FAST examination results in a safe reduction of CT use in injured children and will provide definitive evidence if the FAST examination should be routinely implemented in the initial evaluation of children with blunt abdominal trauma. TRIAL REGISTRATION: ClinicalTrials.gov NCT05910567. Registered on May 9, 2023.

  PublisherOA PDFDOI

• Racial Differences in the Identification of Seat Belt Signs Among Pediatric Motor Vehicle Crash Occupants

  Pediatric Emergency Care · 2025-08-06 · 1 citations

  articleOpen access

  OBJECTIVE: To determine if there are racial differences in the identification of seat belt signs (SBS) among children with motor vehicle crash (MVC)-related blunt torso trauma. METHODS: This was a secondary analysis of a de-identified, public-use data set from a Pediatric Emergency Care Applied Research Network (PECARN) prospective cohort study of children with blunt torso trauma between May 2007 and January 2010. Children <18 years in MVCs were included. Patient demographics, documentation of an abdominal SBS presence, MVC crash speed, and restraint status were analyzed. Descriptive statistics, χ 2 analyses, and the Cochran-Armitage test for trend were performed. RESULTS: There were 3832 children in MVCs. The mean age was 10.6 years (SD: 5.5), 52.6% of patients were White, 31.1% Black, 16.3% other/unknown, and 2.3% Asian. Restraint status differed significantly by race ( P <0.001), with 74.1% of White children (95% CI: 72.2%-76.0%), 64.5% of Black children (95% CI: 61.7%-67.2%), 83.0% of Asian children (95% CI: 75.1%-90.8%), and 68.3% of other/unknown race children (95% CI: 64.4%-72.3%) reported as restrained. There was a significant difference in the proportion of restrained Black children with SBS (7.2% [95% CI: 5.3%-9.0%]) compared with White children (27.0% [95% CI: 24.7%-29.2%]) ( P <0.001) and Asian children (26.0% [95% Cl: 16.0%-36.1%]). When adjusting for age, MVC speed, and restraint status, Black patients were 74% less likely than White patients to have SBS observed (OR: 0.26, 95% CI: 0.18-0.36). CONCLUSIONS: There were significant differences in SBS identification among Black children compared with other race children after MVCs. Prospective studies accounting for skin tone are necessary to further investigate these findings.

  PublisherOA PDFDOI

• PECARN prediction rules for CT imaging of children presenting to the emergency department with blunt abdominal or minor head trauma: a multicentre prospective validation study

  The Lancet Child & Adolescent Health · 2024-04-10 · 44 citations

  article1st authorCorresponding
  PublisherDOI

• Assessment of a COVID-19 vaccination protocol for unhoused patients in the emergency department

  Vaccine · 2023-01-02

  articleOpen accessSenior authorCorresponding

  BACKGROUND: We aimed to evaluate the feasibility of implementing an emergency department (ED)-based Coronavirus Disease of 2019 (COVID-19) vaccination protocol in a population of unhoused patients. METHODS: On June 10, 2021, a best practice alert (BPA) was implemented that fired when an ED provider opened the charts of unhoused patients and prompted the provider to order COVID-19 vaccination for eligible patients. We downloaded electronic medical record data of patients who received a COVID-19 vaccine in the ED between June 10, 2021 and August 26, 2021. The outcomes of interest were the number of unhoused, and the total number of patients vaccinated for COVID-19 during the study period. Data were described with simple descriptive statistics. RESULTS: There were 25,871 patient encounters in 19,992 unique patients (mean 1.3 visits/patient) in the emergency department during the study period. There were 1,474 (6% of total ED population) visits in 1,085 unique patients who were unhoused (mean 1.4 visits/patient). The BPA fired in 1,046 unhoused patient encounters (71% of PEH encounters) and was accepted in 79 (8%). Forty-three unhoused patients were vaccinated as a result of the BPA (4% of BPA fires) and 18 unhoused patients were vaccinated without BPA prompting. An additional 76 domiciled patients were vaccinated in the ED. CONCLUSIONS: Implementing an ED-based COVID-19 vaccination program is feasible, however, only a small number of patients underwent COVID-19 vaccination. Further studies are needed to explore the utility of using the ED as a setting for COVID-19 vaccination.

  PublisherDOI

• Sports-related traumatic brain injuries and acute care costs in children

  BMJ Paediatrics Open · 2023-01-01 · 4 citations

  articleOpen access

  OBJECTIVE: To estimate traumatic brain injuries (TBIs) and acute care costs due to sports activities. METHODS: A planned secondary analysis of 7799 children from 5 years old to <18 years old with head injuries enrolled in a prospective multicentre study between 2011 and 2014. Sports-related TBIs were identified by the epidemiology codes for activity, place and injury mechanism. The sports cohort was stratified into two age groups (younger: 5-11 and older: 12-17 years). Acute care costs from the publicly funded Australian health system perspective are presented in 2018 pound sterling (£). RESULTS: There were 2903 children (37%) with sports-related TBIs. Mean age was 12.0 years (95% CI 11.9 to 12.1 years); 78% were male. Bicycle riding was associated with the most TBIs (14%), with mean per-patient costs of £802 (95% CI £644 to £960) and 17% of acute costs. The highest acute costs (21%) were from motorcycle-related TBIs (3.8% of injuries), with mean per-patient costs of £3795 (95% CI £1850 to £5739). For younger boys and girls, bicycle riding was associated with the highest TBIs and total costs; however, the mean per-patient costs were highest for motorcycle and horse riding, respectively. For older boys, rugby was associated with the most TBIs. However, motorcycle riding had the highest total and mean per-patient acute costs. For older girls, horse riding was associated with the most TBIs and highest total acute costs, and motorcycle riding was associated with the highest mean per-patient costs. CONCLUSION: Injury prevention strategies should focus on age-related and sex-related sports activities to reduce the burden of TBIs in children. TRIAL REGISTRATION NUMBER: ACTRN12614000463673.

  PublisherOA PDFDOI

• Validation of Prediction Rules for Computed Tomography Use in Children With Blunt Abdominal or Blunt Head Trauma: Protocol for a Prospective Multicenter Observational Cohort Study

  JMIR Research Protocols · 2022-11-24 · 9 citations

  articleOpen accessSenior authorCorresponding

  BACKGROUND: Traumatic brain injuries (TBIs) and intra-abdominal injuries (IAIs) are 2 leading causes of traumatic death and disability in children. To avoid missed or delayed diagnoses leading to increased morbidity, computed tomography (CT) is used liberally. However, the overuse of CT leads to inefficient care and radiation-induced malignancies. Therefore, to maximize precision and minimize the overuse of CT, the Pediatric Emergency Care Applied Research Network (PECARN) previously derived clinical prediction rules for identifying children at high risk and very low risk for IAIs undergoing acute intervention and clinically important TBIs after blunt trauma in large cohorts of children who are injured. OBJECTIVE: This study aimed to validate the IAI and age-based TBI clinical prediction rules for identifying children at high risk and very low risk for IAIs undergoing acute intervention and clinically important TBIs after blunt trauma. METHODS: This was a prospective 6-center observational study of children aged <18 years with blunt torso or head trauma. Consistent with the original derivation studies, enrolled children underwent routine history and physical examinations, and the treating clinicians completed case report forms prior to knowledge of CT results (if performed). Medical records were reviewed to determine clinical courses and outcomes for all patients, and for those who were discharged from the emergency department, a follow-up survey via a telephone call or SMS text message was performed to identify any patients with missed IAIs or TBIs. The primary outcomes were IAI undergoing acute intervention (therapeutic laparotomy, angiographic embolization, blood transfusion, or intravenous fluid for ≥2 days for pancreatic or gastrointestinal injuries) and clinically important TBI (death from TBI, neurosurgical procedure, intubation for >24 hours for TBI, or hospital admission of ≥2 nights due to a TBI on CT). Prediction rule accuracy was assessed by measuring rule classification performance, using standard point and 95% CI estimates of the operational characteristics of each prediction rule (sensitivity, specificity, positive and negative predictive values, and diagnostic likelihood ratios). RESULTS: The project was funded in 2016, and enrollment was completed on September 1, 2021. Data analyses are expected to be completed by December 2022, and the primary study results are expected to be submitted for publication in 2023. CONCLUSIONS: This study will attempt to validate previously derived clinical prediction rules to accurately identify children at high and very low risk for clinically important IAIs and TBIs. Assuming successful validation, widespread implementation is then indicated, which will optimize the care of children who are injured by better aligning CT use with need. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/43027.

  PublisherOA PDFDOI

• Time required for electrocardiogram interpretation in the emergency department

  Academic Emergency Medicine · 2022-01-30 · 4 citations

  letterSenior authorCorresponding
  PublisherDOI

Recent grants

• NIH Grant R49CE001002

  NIH · $1.3M · 2010

• NIH Grant K12HL108964

  NIH · $3.1M · 2017

Frequent coauthors

• Craig D. Newgard

  467 shared

• Renee Y. Hsia

  University of California, San Francisco

  447 shared

• Eileen M. Bulger

  Harborview Injury Prevention and Research Center

  361 shared

• Nathan Kuppermann

  University of California, Davis

  327 shared

• Ross J. Fleischman

  University of California, Los Angeles

  252 shared

• Jason S. Haukoos

  University of Colorado Denver

  246 shared

• Dana Zive

  Oregon Health & Science University

  234 shared

• Michael M. Liao

  Denver Health Medical Center

  229 shared

Labs

• Emergency Medicine Department, UC Davis HealthPI

Awards & honors

• SAEM Organizational Advancement Award, 2022
• UC Davis Diamond Doc Award, 2021
• UC Davis Dean’s Excellence in Mentoring Award, 2014