Clinical Focus

  • Interventional Endoscopy
  • Gastroenterology
  • Pediatric Interventional Endoscopy
  • Biliary and Pancreatic Disorders in Adults and Children

Academic Appointments

Administrative Appointments

  • Associate Director of Pediatric Endoscopy, Lucille Packard Children's Hospital at Stanford University Medical Center (2020 - Present)

Boards, Advisory Committees, Professional Organizations

  • Endoscopy Committee, North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (2017 - Present)
  • Member, American Gastroenterological Association (2016 - Present)
  • Member, American College of Gastroenterology (2016 - Present)
  • Member, American Society of Gastrointestinal Endoscopy (2015 - Present)

Professional Education

  • Fellowship: Stanford University Gastroenterology Fellowship (2018) CA
  • Residency: Stanford University Internal Medicine Residency (2015) CA
  • Board Certification: American Board of Internal Medicine, Gastroenterology (2018)
  • Board Certification: American Board of Internal Medicine, Internal Medicine (2015)
  • Medical Education: Stanford University Medical Center (2012) CA

Graduate and Fellowship Programs

  • Gastroenterology & Hepatology (Fellowship Program)

All Publications

  • Role of Endoscopic Retrograde Cholangiopancreatography in the Diagnosis and Management of Cholestatic Liver Diseases. Clinics in liver disease Keihanian, T., Barakat, M. T., Tejaswi, S., Mishra, R., Carlson, C. J., Brandabur, J. J., Girotra, M. 2022; 26 (1): 51-67


    Cholestatic liver diseases (CLDs) occur as a result of bile duct injury, emanating into duct obstruction and bile stasis. Advances in radiological imaging in the last decade has replaced endoscopic retrograde cholangiopancreatography (ERCP) as the first diagnostic tool, except in certain groups of patients, such as those with ischemic cholangiopathy (IsC) or early stages of primary sclerosing cholangitis (PSC). ERCP provides an opportunity for targeted tissue acquisition for histopathological evaluation and carries a diverse therapeutic profile to restore bile flow. The aim of this review article is to appraise the diagnostic and therapeutic roles of ERCP in CLDs.

    View details for DOI 10.1016/j.cld.2021.08.006

    View details for PubMedID 34802663

  • Evaluation of multiple fixed in-room air cleaners with ultraviolet germicidal irradiation, in high-occupancy areas of selected commercial indoor environments. Journal of occupational and environmental hygiene Lee, L., Delclos, G., Berkheiser, M. L., Barakat, M., Jensen, P. 2021: 1-14


    The use of ultraviolet germicidal irradiation (UVGI) to combat disease transmission has come into the international spotlight again because of the recent SARS-CoV-2 pandemic and ongoing outbreaks of MDROs (multidrug resistant organisms) in hospitals. Although the implementation of ultraviolet disinfection technology is widely employed in healthcare facilities and its effectiveness has been repeatedly demonstrated, the use of such technology in the commercial sector has been limited. Considering that most disease transmission occurs in commercial, public, and residential indoor environments as opposed to healthcare facilities, there is a need to understand whether ultraviolet (UV) disinfection technology can be effective for mitigating disease transmission in these environments. The results presented here demonstrate that the installation of fixed in-room UVGI air cleaners in commercial buildings, including restaurants and offices, can produce significant reductions in both airborne and surface borne bacterial contamination. Total airborne reductions after UV implementation at six separate commercial sites averaged 73% (p<0.0001) with a range of 71-88%. Total non-high touch surface reductions after implementation averaged 55% (p<0.0001) with a range of 28-88%. All reductions at the mitigated sites were statistically significant. The mean value of indoor airborne bacteria was 320 CFU/m3 before intervention and 76 CFU/m3 after. The mean value of indoor non-high touch surface borne bacteria was 131 CFU/plate before intervention and 47 CFU/plate after. All test locations and controls had their required pandemic cleaning procedures in place for pre- and post-sampling events. Outdoor levels of airborne bacteria were monitored and there was no significant correlation between the levels of airborne bacteria in the outside air as opposed to the indoor air. Rooms with fixed in-room UVGI air cleaners installed had significant CFU reductions on local surface contamination, which is a novel and important finding. Installation of fixed in-room UVGI air cleaners in commercial buildings will decontaminate the indoor environment and reduce hazardous exposure to human pathogens.

    View details for DOI 10.1080/15459624.2021.1991581

    View details for PubMedID 34647857

  • Safety and efficacy of a novel resection system for direct endoscopic necrosectomy of walled-off pancreas necrosis: a prospective, international, multicenter trial. Gastrointestinal endoscopy Stassen, P. M., de Jonge, P. J., Bruno, M. J., Koch, A. D., Trindade, A. J., Benias, P. C., Sejpal, D. V., Siddiqui, U. D., Chapman, C. G., Villa, E., Tharian, B., Inamdar, S., Hwang, J. H., Barakat, M. T., Andalib, I., Gaidhane, M., Sarkar, A., Shahid, H., Tyberg, A., Binmoeller, K., Watson, R. R., Nett, A., Schlag, C., Abdelhafez, M., Friedrich-Rust, M., Schlachterman, A., Chiang, A. L., Loren, D., Kowalski, T., Kahaleh, M. 2021


    BACKGROUND AND AIMS: Direct endoscopic necrosectomy (DEN) of walled-off pancreatic necrosis (WOPN) lacks dedicated instruments and require repetitive and cumbersome procedures. This study evaluated the safety and efficacy of a new powered endoscopic debridement (PED) system designed to simultaneously resect and remove solid debris within WOPN.METHODS: This was a single-arm, prospective, multicenter, international device trial conducted from November 2018 to August 2019 at 10 sites. Patients with WOPN ≥6 cm and ≤22 cm, with >30% solid debris were enrolled. The primary endpoint was safety through 21 days after the last DEN procedure. Efficacy outcomes included clearance of necrosis, procedural time, adequacy of debridement, number of procedures until resolution, hospital stay duration, and quality of life.RESULTS: Thirty patients (mean age 55 years, 60% male) underwent DEN with no device-related adverse events. Fifteen out of 30 (50%) achieved complete debridement in 1 session, and 20 out of 30 (67%) achieved complete debridement within 2 or fewer sessions. A median of 1.5 interventions (range 1-7) were required. Median hospital stay was 10 days (IQR 22). There was an overall reduction of 91% in percent necrosis within WOPN from baseline to follow-up and 85% in collection volume. Baseline WOPN volume was positively correlated to total number of interventions (rho=0.363, p=0.049).CONCLUSION: The new PED system seems to be a safe and effective treatment tool for WOPN resulting in fewer interventions and lower hospital duration when compared with published data on using conventional instruments. Randomized controlled trials comparing the PED system with conventional DEN are needed.

    View details for DOI 10.1016/j.gie.2021.09.025

    View details for PubMedID 34562471

  • Endoscopic ampullectomy: Can expert input shape endoscopic practice? Gastrointestinal endoscopy Barakat, M. T., Adler, D. G. 2021

    View details for DOI 10.1016/j.gie.2021.05.030

    View details for PubMedID 34419246

  • EUS-guided biliary drainage: A realistic perspective. Endoscopic ultrasound Barakat, M. T., Adler, D. G. 2021; 10 (4): 227-229

    View details for DOI 10.4103/EUS-D-21-00173

    View details for PubMedID 34396991

  • A Practical Approach to Management of Acute Pancreatitis: Similarities and Dissimilarities of Disease in Children and Adults. Journal of clinical medicine Sellers, Z. M., Barakat, M. T., Abu-El-Haija, M. 2021; 10 (12)


    Acute pancreatitis (AP) is associated with significant morbidity and mortality, and it substantially contributes to the healthcare burden of gastrointestinal disease and quality of life in children and adults. AP across the lifespan is characterized by similarities and differences in epidemiology, diagnostic modality, etiologies, management, adverse events, long-term outcomes, and areas in greatest need of research. In this review, we touch on each of these shared and distinctive features of AP in children and adults, with an emphasis on recent advances in the conceptualization and management of AP.

    View details for DOI 10.3390/jcm10122545

    View details for PubMedID 34201374

  • EUS-directed transgastric ERCP: A first-line option for ERCP following Roux-en-Y gastric bypass. Endoscopic ultrasound Barakat, M. T., Adler, D. G. 2021; 10 (3): 151-153

    View details for DOI 10.4103/eus.eus_148_20

    View details for PubMedID 34137380

  • Endoscopy in Patients With Surgically Altered Anatomy. The American journal of gastroenterology Barakat, M. T., Adler, D. G. 2021; 116 (4): 657-665


    A comprehensive understanding of gastrointestinal anatomy is essential for performance of any endoscopic procedure. Surgical approaches to therapy have become increasingly common in the past decade, which has resulted in a substantial proportion of patients with surgically altered anatomy who require endoscopy. In parallel with the obesity epidemic, bariatric surgery for obesity management has been widely adopted. In response to these trends, gastroenterologists must become familiar with patient anatomy after these surgical interventions and understand the implications of this altered anatomy on the current array of available endoscopic modalities for diagnosis and therapy. This review describes the range of surgically altered anatomy commonly encountered in the upper gastrointestinal tract. For each foregut location-esophagus, stomach, and small bowel-we describe indications for and specific details of the range of common surgical approaches affecting this regional anatomy. We then provide an endoscopic roadmap through the altered anatomy resulting from these surgical interventions. Finally, we address the impact of postsurgical anatomy on performance of endoscopic ultrasound and endoscopic retrograde cholangiopancreatography, with guidance surrounding how to successfully execute these procedures. Evolution of endoscopic approaches over time might be expected to enhance the safety and efficacy of these interventions in patients with surgically altered anatomy.

    View details for DOI 10.14309/ajg.0000000000001102

    View details for PubMedID 33982931

  • Quality metrics in the performance of EUS: a population-based observational cohort of the United States. Gastrointestinal endoscopy Huang, R. J., Barakat, M. T., Park, W. n., Banerjee, S. n. 2021


    There exist few data on the quality of endoscopic ultrasound (EUS) in the community setting. We characterized EUS performance at the individual facility level in 3 large American states, using need for repeat biopsy (NRB) as a metric for procedural failure, and rate of unplanned hospital encounter (UHE) as a metric for adverse event.We collected data on 76,614 EUS procedures performed at 166 facilities in California, Florida, and New York (2009-2014). The endpoints for the study were 7-day rate of UHE after EUS, and 30-day rate of NRB after EUS with fine-needle aspiration. Facility-level factors analyzed included annual procedure volume, urban/rural location, and free-standing status (facilities not attached to a larger hospital). Predictors for UHE and NRB were analyzed in both multivariable regression and nonparametric local regression.Facility volume did not predict risk for UHE. However, high facility volume protected against NRB (p-trend <0.001) even after adjustment for other facility-level factors. When regressing facility volume against risk for NRB in local regression, a join-point (inflection point) was identified at 97 procedures per annum. Once facilities reached this threshold volume, there appeared little additional protective effect of higher volume. Rural facility location (OR, 1.81; 95% CI, 1.36-2.40) and free-standing status (OR, 1.57; 95% CI, 1.16-2.13) also associated with NRB.Facility volume does not predict risk for adverse events after EUS. However, high facility volume is associated with decreased rates of technical failure (as assessed by NRB). These data provide one of the first descriptions of EUS practice in community settings and highlight opportunities to improve endoscopic quality nationally.

    View details for DOI 10.1016/j.gie.2020.12.055

    View details for PubMedID 33476611

  • Top tips for electrohydraulic lithotripsy (with video). Gastrointestinal endoscopy Barakat, M. 2021

    View details for DOI 10.1016/j.gie.2021.11.005

    View details for PubMedID 34774855

  • The Changing Epidemiology of Liver Disease Among US Children and Adolescents From 1999 to 2016. The American journal of gastroenterology Li, J., Le, M. H., Barakat, M. T., Cheung, R. C., Nguyen, M. H. 2021


    Nonalcoholic fatty liver disease (NAFLD) and infection with hepatitis B virus (HBV) or hepatitis C virus (HCV) are major causes of liver disease in adults. However, data for children and adolescents are limited. Our study aimed to characterize the prevalence, trend, and risk factors of infection of HBV and HCV and possible NAFLD for this population.We analyzed 6,647 children and adolescents (aged 6-21 years) from the 1999-2016 National Health and Nutrition Examination Survey.Among individuals aged 6-21 years, HBV prevalence decreased after 2011, from 0.72% in 1999-2004 and 0.85% in 2005-2010 to 0.27% in 2011-2016 (P < 0.001), whereas HCV prevalence increased to 0.26% in 2011-2016 after an initial decline from 0.15% in 1999-2004 to 0.02% in 2005-2010 (P = 0.01). Possible NAFLD prevalence also increased by approximately 40% in individuals aged 12-21 years, from 8.54% in 1999-2004 to 10.1% in 2005-2010 and then 11.8% in 2011-2016 (P = 0.033), with most possible NAFLD individuals being male, being obese, or having higher glucose, fasting insulin, hemoglobin A1c, homeostatic model assessment of insulin resistance, liver enzymes, lipids, and uric acid (all P < 0.01). On multivariate logistic regression, hypertension (odds ratio 4.79, 95% confidence interval 1.44-15.9) and dyslipidemia (odds ratio 11.6, 95% confidence interval 5.65-23.9) increased risk for possible NAFLD but not income:poverty ratio, hours spent on computer use, or added sugars.Although HBV prevalence has decreased in recent years among US children and adolescents, HCV and possible NAFLD have increased. Public health efforts must seek further understanding of the driving factors of this increase so that age-appropriate interventions can be developed and implemented.

    View details for DOI 10.14309/ajg.0000000000001386

    View details for PubMedID 34328446

  • Incidental biliary dilation in the era of the opiate epidemic: High prevalence of biliary dilation in opiate users evaluated in the Emergency Department. World journal of hepatology Barakat, M. T., Banerjee, S. 2020; 12 (12): 1289–98


    BACKGROUND: Biliary dilation is frequently related to obstruction; however, non-obstructive factors such as age and previous cholecystectomy have also been reported. In the past two decades there has been a dramatic increase in opiate use/dependence and utilization of cross-sectional abdominal imaging, with increased detection of biliary dilation, particularly in patients who use opiates.AIM: To evaluate associations between opiate use, age, cholecystectomy status, ethnicity, gender, and body mass index utilizing our institution's integrated informatics platform.METHODS: One thousand six hundred and eighty-five patients (20% sample) presenting to our Emergency Department for all causes over a 5-year period (2011-2016) who had undergone cross-sectional abdominal imaging and had normal total bilirubin were included and analyzed.RESULTS: Common bile duct (CBD) diameter was significantly higher in opiate users compared to non-opiate users (8.67 mm vs 7.24 mm, P < 0.001) and in patients with a history of cholecystectomy compared to those with an intact gallbladder (8.98 vs 6.72, P < 0.001). For patients with an intact gallbladder who did not use opiates (n = 432), increasing age did not predict CBD diameter (r 2= 0.159,P= 0.873). Height weakly predicted CBD diameter (r 2= 0.561,P= 0.018), but weight, body mass index, ethnicity and gender did not.CONCLUSION: Opiate use and a history of cholecystectomy are associated with CBD dilation in the absence of an obstructive process. Age alone is not associated with increased CBD diameter. These findings suggest that factors such as opiate use and history of cholecystectomy may underlie the previously-reported association of advancing age with increased CBD diameter. Further prospective study is warranted.

    View details for DOI 10.4254/wjh.v12.i12.1289

    View details for PubMedID 33442455

  • Strongyloides Superinfection After Liver Transplantion. Digestive diseases and sciences Ofosu, A., Higgins, J., Frye, J. S., Kumari, R., Barakat, M. T. 2020

    View details for DOI 10.1007/s10620-020-06696-3

    View details for PubMedID 33219458

  • Nationwide evolution of Pediatric ERCP Indications, Utilization and Re-Admissions over Time. The Journal of pediatrics Barakat, M. T., Cholankeril, G., Gugig, R., Berquist, W. E. 2020


    OBJECTIVES: We conducted the present all-capture US population level study of pediatric Endoscopic retrograde cholangiopancreatography (ERCP) P to analyze outcome and utilization trends over time.STUDY DESIGN: Using the National Inpatient Sample (2005-2014) and National Readmission Database (2010-2014), we identified pediatric hospitalizations (age <20 years) where ERCP was performed and assessed ERCP-associated readmissions. ICD-9-CM codes were used to identify hospitalization diagnosis, co-morbidities and patient/hospital characteristics. Multivariate logistic regression analyses were performed to determine significant predictors (P < 0.05) of 30-day readmission.RESULTS: 11,060 hospitalized pediatric patients underwent ERCP from 2005-2014. Most were female (n=8859, 81%), 14-20 years of age (n=9342, 84%), and White (n=4230, 45%). 85% of ERCPs were therapeutic and leading indications were biliary (n=5350, 48%) and pancreatitis (n=3218, 29%). 13% of patients were re-admitted post-ERCP. Odds for 30-day re-admission were highest for patients with a history of liver transplant, ages between 0-4 years, male sex, and obesity (P < .001 for each). Patients in both urban teaching and urban hospitals had much lower odds than rural hospitals for prolonged length of stay associated with ERCP.CONCLUSIONS: These data represent a comprehensive study of nationwide trends in age-specific volumes and outcomes following ERCP in the pediatric population and provide important insights regarding trends in pediatric pancreaticobiliary disease management, as well as practice setting, patient characteristics and patient comorbidities associated with pediatric post-ERCP outcomes including re-admission and length of stay.

    View details for DOI 10.1016/j.jpeds.2020.11.019

    View details for PubMedID 33197494

  • Novel Algorithms for Reprocessing, Drying and Storing Endoscopes. Gastrointestinal endoscopy clinics of North America Barakat, M. T., Banerjee, S. 2020; 30 (4): 677–91


    After outbreaks of duodenoscope-transmitted infection with multidrug-resistant organisms, it has become clear that institutions must optimize their endoscope reprocessing programs. Standard endoscope reprocessing practices may not represent the ideal approach for preventing transmission of infection related to endoscopy. We discuss multiple approaches to enhance and optimize reprocessing, drying, and storage of standard duodenoscopes. The optimal enhanced duodenoscope reprocessing modality remains to be determined. Acknowledging the challenges and limitations in effectively reprocessing duodenoscopes, the FDA issued a safety communique recommending transitioning to either single use disposable duodenoscopes or duodenoscopes with innovative designs that allow more effective reprocessing.

    View details for DOI 10.1016/j.giec.2020.06.003

    View details for PubMedID 32891225

  • Sequential endoscopist-driven phone calls improve capture rate of adverse events after ERCP: a prospective study. Gastrointestinal endoscopy Barakat, M. T., Banerjee, S. 2020


    BACKGROUND AND AIMS: ERCP is a high-risk endoscopic procedure, yet reports of ERCP-related adverse events are largely limited to early adverse events, based on immediate postprocedure assessment. We hypothesize that immediate/1-day follow-up underestimates the true adverse event rate, and later follow-up calls may enable a more accurate assessment of adverse events, leading to enhanced postprocedural patient care.METHODS: Consecutive patients undergoing ERCP at our tertiary care academic medical center from 2018 to 2019 were analyzed. Patients were encouraged to contact us with postprocedure symptoms and additionally received phone calls at 1, 7, 14, and 30 days after the procedure using a standardized script to assess for delayed adverse events and unplanned healthcare encounters.RESULTS: This study is notable for a high rate of successful patient follow-up at day 1 (94%) and day 7 (93%). The assessed overall adverse event rate was 1.9% immediately postprocedure, 3.3% on day 1, and 9.8% on day 7. Increased detection of adverse events was accomplished by the day 7 call relative to the day 1 call (pancreatitis 2% vs 0.5%; bleeding 0.5% vs 0.2%; infection 0.9% vs 0.5%). 14- and 30-day follow-up calls were lower yield in detection of post-ERCP adverse events.CONCLUSIONS: Initial postprocedure assessment and day 1 follow-up calls underestimate adverse event rates/UHE related to ERCP, due to delayed evolution of some adverse events. The day 7 call is optimal in that it resulted in a >3-fold higher rate of detection of adverse events and successful direction of over 10% of symptomatic patients to appropriate assessment and follow-up heath care.

    View details for DOI 10.1016/j.gie.2020.07.036

    View details for PubMedID 32721489

  • Return to Native Drainage: Duodenal Biliary Fistula Formation Following Pediatric Hepatobiliary Surgery with Roux-en-Y Reconstruction. Digestive diseases and sciences Barakat, M. T., Josephs, S., Gugig, R. 2020

    View details for DOI 10.1007/s10620-020-06372-6

    View details for PubMedID 32533541

  • Use of an Ultra-slim Gastroscope to Accomplish Endoscopist-Facilitated Rescue Intubation During ERCP: A Novel Approach to Enhance Patient and Staff Safety. Digestive diseases and sciences Barakat, M. T., Angelotti, T. P., Banerjee, S. 2020


    BACKGROUND: ERCP is often performed under monitored anesthesia care (MAC) rather than general anesthesia (GA), with patients positioned semi-prone on the fluoroscopy table. Rarely, a MAC ERCP must be converted to GA due to hypoxia or retained food in the stomach. In these circumstances, standard intubation is associated with a significant delay and potential for patient/staff injury during repositioning. We report a novel endoscopist-driven approach to intubation during ERCP using an ultra-slim, flexible gastroscope with an endotracheal tube backloaded onto it.MATERIALS AND METHODS: We identified patients who underwent ERCP from 2014 to 2019, and MAC to GA conversion events. Mode of intubation (standard vs. endoscopist-facilitated) and patient/procedure characteristics were evaluated. All endoscopist-facilitated intubations were performed under anesthesiologist supervision.RESULTS: A total of 3409 patients underwent ERCP; 1568 (46%) GA and 1841 (54%) MAC. Of these, 42 (2.3%) required intubation during ERCP and 16 underwent endoscopist-facilitated intubation due to retained food in the stomach and/or hypoxia. In 3 patients, aspirated material was suctioned from the trachea and bronchi using the ultra-slim gastroscope. Immediate post-procedure extubation was successful in all endoscopist-facilitated intubation patients and none exhibited radiographic evidence of aspiration pneumonia.CONCLUSIONS: Endoscopist-facilitated intubation using an ultra-slim flexible gastroscope is feasible and expeditious for MAC to GA conversion during ERCP. This technique is readily accomplished in the semi-prone position, while standard intubation requires patient transfer from fluoroscopy table to gurney, with associated delay/risks. These data suggest that further study of this approach is warranted, and this may be the most favorable approach for intubation during ERCP.

    View details for DOI 10.1007/s10620-020-06360-w

    View details for PubMedID 32504349

  • PROSPECTIVE TRIAL EVALUATING THE SAFETY AND EFFECTIVENESS OF THE INTERSCOPE ENDOROTOR (R) RESECTION SYSTEM FOR DIRECT ENDOSCOPIC NECROSECTOMY OF WALLED-OF PANCREATIC NECROSIS (ENDOROTOR DEN TRIAL) Stassen, P. M., de Jonge, P. F., Koch, A. D., Bruno, M. J., Trindade, A., Benias, P. C., Sejpal, D. V., Siddiqui, U. D., Chapman, C. G., Villa, E., Tharian, B., Inamdar, S., Hwang, J., Barakat, M., Andalib, I., Gaidhane, M., Sarkar, A., Shahid, H. M., Tyberg, A., Binmoeller, K. F., Watson, R. R., Nett, A., Schlag, C., Abdelhafez, M., Friedrich-Rust, M., Schlachterman, A., Chiang, A., Loren, D. E., Kowalski, T. E., Kahaleh, M. MOSBY-ELSEVIER. 2020: AB80–AB81
  • Recent Trends and the Impact of the Affordable Care Act on Emergency Department Visits and Hospitalizations for Gastrointestinal, Pancreatic, and Liver Diseases JOURNAL OF CLINICAL GASTROENTEROLOGY Barakat, M. T., Mithal, A., Huang, R. J., Sehgal, A., Sehgal, A., Singh, G., Banerjee, S. 2020; 54 (3): E21–E29
  • Goff Septotomy Is a Safe and Effective Salvage Biliary Access Technique Following Failed Cannulation at ERCP. Digestive diseases and sciences Barakat, M. T., Girotra, M., Huang, R. J., Choudhary, A., Thosani, N. C., Kothari, S., Sethi, S., Banerjee, S. 2020


    BACKGROUND: Biliary cannulation is readily achieved in>85% of patients undergoing endoscopic retrograde cholangiopancreatography (ERCP). When standard cannulation techniques fail, salvage techniques utilized include the needle knife precut, double wire technique, and Goff septotomy.METHODS: Records of patients undergoing ERCP from 2005 to 2016 were retrospectively examined using a prospectively maintained endoscopy database. Patients requiring salvage techniques for biliary access were analyzed together with a control sample of 20 randomly selected index ERCPs per study year. Demographic and clinical variables including indications for ERCP, cannulation rates, and adverse events were collected.RESULTS: A total of 7984 patients underwent ERCP from 2005 to 2016. Biliary cannulation was successful in 94.9% of control index ERCPs, 87.2% of patients who underwent Goff septotomy (significantly higher than for all other salvage techniques, p≤0.001), 74.5% of patients in the double wire group and 69.6% of patients in the needle knife precut group. Adverse event rates were similar in the Goff septotomy (4.1%) and index ERCP control sample (2.7%) groups. Adverse events were significantly higher in the needle knife group (27.2%) compared with all other groups.CONCLUSIONS: This study represents the largest study to date of Goff septotomy as a salvage biliary access technique. It confirms the efficacy of Goff septotomy and indicates a safety profile similar to standard cannulation techniques and superior to the widely employed needle knife precut sphincterotomy. Our safety and efficacy data suggest that Goff septotomy should be considered as the primary salvage approach for failed cannulation, with needle knife sphincterotomy restricted to Goff septotomy failures.

    View details for DOI 10.1007/s10620-020-06124-6

    View details for PubMedID 32052216

  • Initial Experience with EUS-guided Coil Placement for Pediatric Gastric Variceal Hemostasis. Journal of pediatric gastroenterology and nutrition Barakat, M. T., Foley, M. A., Gugig, R. n. 2020; Publish Ahead of Print


    Gastric variceal (GV) bleeding is among the most morbid sequelae of portal hypertension, with mortality ranging from 30-50%. Pediatric data focused on endoscopic approaches to management are needed. The present study represents the first pediatric case series of endoscopic ultrasound (EUS)-guided coil placement within feeding vessels as monotherapy for management of GV bleeding.Using our prospectively-maintained endoscopy database, we identified patients 18 years and younger who underwent EUS-guided coil placement for management of GV bleeding from 2008-2018. Demographics, indication, procedural interventions/findings, and available clinical outcomes data were analyzed.12 patients (median age 15, range 11-18 years) underwent EUS-guided coil placement for GV bleeding. All had portal hypertension, with EV in 58.3% and prior GV bleeding with attempted endoscopic management in 75%. Coil placement was accomplished using a linear echoendoscope and a 19-gauge needle. A mean of 2.75 (± 0.43) coils were placed in each patient (4, 6, 8, and 10 mm Nester Embolization Coils, Cook Medical). Immediate hemostasis was achieved in all patients, and 25% of patients developed recurrent gastric varices at a median of 5.5 months following the initial EUS-guided coil placement (range 4-6 months) over the median 12 month follow-up period.The present study establishes the feasibility and efficacy of EUS-guided coil placement as monotherapy for GV bleeding in children and adolescents. The technique was technically successful, with primary hemostasis achieved in all patients. EUS-guided embolization with coils may represent an alternative to current approaches for management of highly morbid GV bleeding.

    View details for DOI 10.1097/MPG.0000000000003028

    View details for PubMedID 33394889

  • Protective Effects of Calcineurin on Pancreatitis in Mice Depend on Cellular Source. Gastroenterology Wen, L. n., Javed, T. A., Dobbs, A. K., Brown, R. n., Niu, M. n., Li, L. n., Khalid, A. n., Barakat, M. n., Xiao, X. n., Yimlamai, D. n., Konnikova, L. n., Yu, M. n., Byersdorfer, C. A., Husain, S. Z. 2020


    Calcineurin is a ubiquitously expressed central Ca2+-responsive signaling molecule that mediates acute pancreatitis, but little is known about its effects. We compared the effects of calcineurin expression by hematopoietic cells vs pancreas in mouse models of pancreatitis and pancreatitis-associated lung inflammation.We performed studies with mice with hematopoietic-specific or pancreas-specific deletion of protein phosphatase 3, regulatory subunit B, alpha isoform (PPP3R1, also called CNB1), in mice with deletion of CNB1 (Cnb1UBC△/△), and in the corresponding controls for each deletion of CNB1. Acute pancreatitis was induced in mice by administration of caerulein or high-pressure infusion of radiocontrast into biliopancreatic ducts; some mice were also given intraductal infusions of an adeno-associated virus vector that expressed NFAT-luciferase into pancreas. Pancreas, bone marrow, liver, kidney, heart, and lung were collected and analyzed by histopathology, immunohistochemistry, and immunoblots; levels of cytokines were measured in serum. Mouse and human primary pancreatic acinar cells were transfected with a vector that expressed NFAT-luciferase and incubated with an agent that blocks interaction of NFAT with calcineurin; cells were analyzed by immunofluorescence. Calcineurin-mediated neutrophil chemotaxis and reactive oxygen species (ROS) production were measured in neutrophils from mice.Mice with hematopoietic-specific deletion of CNB1 developed the same level of local pancreatic inflammation as control mice after administration of caerulein or infusion of radiocontrast into biliopancreatic ducts. Cnb1UBC△/△ mice or mice with pancreas-specific deletion of CNB1 developed less severe pancreatitis and reduced pancreatic inflammation after administration of caerulein or infusion of radiocontrast into biliopancreatic ducts compared with control mice. NFAT was activated in pancreas of Swiss Webster mice given caerulein or infusions of radiocontrast into biliopancreatic ducts. Blocking the interaction between calcineurin and NFAT did not reduce pancreatic acinar cell necrosis in response to caerulein or infusions of radiocontrast. Mice with hematopoietic-specific deletion of CNB1 (but not mice with pancreas-specific deletion of CNB1) had reduced infiltration of lung tissues by neutrophils. Neutrophil chemotaxis and production of ROS were decreased following incubation with a calcineurin inhibitor.Hematopoietic and neutrophil expression of calcineurin promotes pancreatitis-associated lung inflammation, whereas pancreatic calcineurin promotes local pancreatic inflammation. The findings indicate that the protective effects of blocking or deleting calcineurin on pancreatitis are mediated by the source of its expression. This information should be used in development of strategies to inhibit calcineurin for prevention of pancreatitis and pancreatitis-associated lung inflammation.

    View details for DOI 10.1053/j.gastro.2020.05.051

    View details for PubMedID 32445858

  • Escalating complexity of endoscopic retrograde cholangiopancreatography over the last decade with increasing reliance on advanced cannulation techniques. World journal of gastroenterology Barakat, M. T., Girotra, M. n., Thosani, N. n., Kothari, S. n., Banerjee, S. n. 2020; 26 (41): 6391–6401


    At our academic tertiary care medical center, we have noted patients referred for endoscopic retrograde cholangiopancreatography (ERCP) who increasingly require advanced cannulation techniques. This trend is noted despite increased endoscopist experience and annual ERCP volume over the same period.To evaluate this phenomenon of perceived escalation in complexity of cannulation at ERCP and assessed potential underlying factors.Demographic/clinical variables and records of ERCP patients at the beginning (2008), middle (2013) and end (2018) of the last decade were reviewed retrospectively. Cannulation approaches were classified as "standard" or "advanced" and duodenoscope position was labeled as "standard" (short position) or "non-standard" (e.g., long, semi-long).Patients undergoing ERCP were older in 2018 compared to 2008 (69.7 ± 15.2 years vs 55.1 ± 14.7, P < 0.05). Increased ampullary distortion and peri-ampullary diverticula were noted in 2018 (P < 0.001). ERCPs were increasingly performed with a non-standard duodenoscope position, from 2.2% (2008) to 5.6% (2013) and 16.1% (2018) (P < 0.001). Utilization of more than one advanced cannulation technique for a given ERCP increased from 0.7% (2008) to 0.9% (2013) to 6.6% (2018) (P < 0.001). Primary mass size > 4 cm, pancreatic uncinate mass, and bilirubin > 10 mg/dL predicted use of advanced cannulation techniques (P < 0.03 for each).Complexity of cannulation at ERCP has sharply increased over the past 5 years, with an increased proportion of elderly patients and those with malignancy requiring advanced cannulation approaches. These data suggest that complexity of cannulation at ERCP may be predicted based on patient/ampulla characteristics. This may inform selection of experienced, high-volume endoscopists to perform these complex procedures.

    View details for DOI 10.3748/wjg.v26.i41.6391

    View details for PubMedID 33244200

    View details for PubMedCentralID PMC7656203

  • Fluoroscopy Time during ERCP performed for Children and Adolescents is Significantly Higher with Low-volume Endoscopists. Journal of pediatric gastroenterology and nutrition Barakat, M. T., Gugig, R. n., Imperial, J. n., Berquist, W. E. 2020


    Endoscopic retrograde cholangiopancreatography (ERCP) is a fluoroscopy and endoscopy-based procedure important for diagnosis and management of pediatric pancreaticobiliary disorders. Patient, procedure, endoscopist and facility characteristics have been shown to influence ERCP complexity and procedure outcomes as well as fluoroscopy utilization in adults, however the extent to which this is true in pediatric patients remains under-studied and there are minimal data regarding fluoroscopy utilization in pediatric ERCP.We retrospectively analyzed ERCPs performed on patients < 18 years of age at our tertiary care children's hospital from 2002-2017 using our institution's paper and electronic medical record system along with a prospectively-maintained radiation exposure database. Procedure complexity was graded using the Stanford Fluoroscopy Complexity Score and the American Society of Gastrointestinal Endoscopy Complexity scale. High volume endoscopists (HVE) were defined as having a cumulative annual ERCP volume > 100 and low volume endoscopists (LVE) as < 100 (pediatric + adult) ERCPs/year.385 ERCPs performed on 321 patients were included in this analysis. The mean patient age was 13.4 years (+/- 4.2 years), 77% were index ERCPs (native ampullas) and 81% were performed with therapeutic intent (87% for biliary indication and 13% for pancreatic indication). Fluoroscopy times varied dramatically between procedures and providers. Median fluoroscopy time was 4.85 (+/- 2.68) minutes. Endoscopist annual ERCP volume was the strongest predictor of fluoroscopy time (p < 0.001). In addition to endoscopist volume, procedure-specific predictors of increased fluoroscopy time included pancreatic indication for the procedure, biliary or pancreatic duct stricture, patient age < 4 years or > 16 years at the time of ERCP (p < 0.01 for each), and native ampulla. ERCP complexity rating based on the Stanford Fluoroscopy Complexity Score correlated with fluoroscopy time.Radiation exposure is higher than desirable for pediatric ERCP and varies with endoscopist as well as patient and procedure-specific factors. HVE perform ERCP with lower fluoroscopy time relative to LVE even though HVE procedure complexity was higher. The Stanford Fluoroscopy Score predicted fluoroscopy time for pediatric ERCP, but the ASGE ERCP complexity scale did not. Adaptation and refinement of pediatric-specific ERCP complexity scales including factors such as patient size and age and indications/interventions more consistent with those encountered in pediatrics could be beneficial.

    View details for DOI 10.1097/MPG.0000000000002914

    View details for PubMedID 32833892

  • Basket Case: Fluoroscopy-Free Capture and Retrieval of Biliary and Pancreatic Duct Stones DIGESTIVE DISEASES AND SCIENCES Barakat, M. T., Banerjee, S. 2019; 64 (10): 2776–79
  • Radiation Training, Radiation Protection, and Fluoroscopy Utilization Practices Among US Therapeutic Endoscopists DIGESTIVE DISEASES AND SCIENCES Sethi, S., Barakat, M. T., Friedland, S., Banerjee, S. 2019; 64 (9): 2455–66
  • Pediatric Endoscopy Practice Patterns in the United States, Canada, and Mexico JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION Barakat, M. T., Triadafilopoulos, G., Berquist, W. E. 2019; 69 (1): 24–31
  • Basket Case: Fluoroscopy-Free Capture and Retrieval of Biliary and Pancreatic Duct Stones. Digestive diseases and sciences Barakat, M. T., Banerjee, S. 2019

    View details for PubMedID 31055718

  • Radiation Training, Radiation Protection, and Fluoroscopy Utilization Practices Among US Therapeutic Endoscopists. Digestive diseases and sciences Sethi, S., Barakat, M. T., Friedland, S., Banerjee, S. 2019


    BACKGROUND: Fluoroscopy use during ERCP exposes patients and providers to deleterious effects of radiation. Formal training in fluoroscopy/radiation protection is not widely emphasized during therapeutic endoscopy training, and radiation use during GI endoscopy has not previously been characterized in the USA. In this study, we evaluated radiation training, fluoroscopy use patterns, and radiation protection practices among US therapeutic endoscopists.METHODS: An anonymous electronic survey was distributed to US therapeutic endoscopists, and responses were analyzed using descriptive statistics. State-specific requirements for fluoroscopy utilization were determined from state radiologic health branches.RESULTS: A total of 159 endoscopists (response rate 67.8%) predominantly those working in university hospitals (69.2%) with >5years of experience performing ERCP (74.9%) completed the questionnaire. Although the majority of endoscopists (61.6%) reported that they personally controlled fluoroscopy during ERCP, most (56.6%) had not received training on operating their fluoroscopy system. Only a minority (18-31%) of all respondents reported consistently utilizing modifiable fluoroscopy system parameters that minimize patient radiation exposure (pulsed fluoroscopy, frame rate modification or collimation). Endoscopists appear to undertake adequate personal radiation protective measures although use of a dosimeter was not consistent in half of respondents. The majority of states (56.8%) do not have any stated requirement for certification of non-radiologist physicians who intend to operate fluoroscopy.CONCLUSIONS: Most US gastroenterologists performing ERCP have not received formal training in operating their fluoroscopy system or in minimizing radiation exposure to themselves and to their patients. Such formal training should be included in all therapeutic endoscopy training programs, and fluoroscopy system-specific training should be offered at all hospitals.

    View details for PubMedID 30911863

  • Pediatric Endoscopy Practice Patterns in the United States, Canada and Mexico. Journal of pediatric gastroenterology and nutrition Barakat, M. T., Triadafilopoulos, G., Berquist, W. E. 2019


    BACKGROUND & AIMS: Endoscopic procedures are important for diagnosis and management of many gastrointestinal, liver and biliary conditions in children. Therapeutic endoscopy procedures, including ERCP, are performed less frequently in children relative to adults. However, a formal study to evaluate institutional volumes and practice patterns for advanced therapeutic pediatric endoscopy procedures has not been previously undertaken.METHODS: A self-administered 16-question (5-minute) online survey assessing practice patterns for performance of pediatric endoscopy procedures was distributed to all registered North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) programs. Results were analyzed using descriptive statistics and thematic analysis of free-text comments.RESULTS: Respondents from 82.9% of NASPGHAN centers completed this survey. Responses revealed that EGD/colonoscopy are performed at the vast majority of centers (>90%), with most performing >50/year. Therapeutic endoscopy procedures are performed less frequently in the pediatric population, with 18.97% reporting that ERCP is not performed at their institution. Where ERCP is performed, 91.38% reported <25/year. EUS is not performed at over half (53.33%) of institutions. 71.67% of respondents do not believe their institution's current arrangement for performing pediatric therapeutic endoscopy procedures is adequate.CONCLUSIONS: Although the range of endoscopic procedures performed in children parallels that performed in adults, there are notable differences in pediatric and adult gastroenterologists' endoscopy training and procedure volumes. Our results and respondent comments suggest that pediatric patients would benefit from a partnership between pediatric and adult gastroenterologists, with adult gastroenterologists performing more complex therapeutic endoscopic procedures.

    View details for PubMedID 30789864

  • When Experts Fail: Use of a Short Turning Radius Colonoscope Facilitates Successful Completion of Colonoscopy in Patients with Bowel Fixity. Digestive diseases and sciences Girotra, M. n., Sethi, S. n., Barakat, M. T., Huang, R. J., Friedland, S. n., Ladabaum, U. n., Banerjee, S. n. 2019


    Rates of incomplete colonoscopy in non-expert settings range up to 13%. Expert colonoscopists can complete ~ 95% colonoscopies when other endoscopists fail; however, a small number remain incomplete even in expert hands, typically due to bowel fixity.Pentax Retroview™ (EC-3490TLi) is a new slim colonoscope with a short turning radius (STR) and greater tip deflection (210°), which allows easy maneuverability across sharply angulated/fixed colonic bends. We evaluated the utility of this colonoscope for completing colonoscopies that fail even in the hands of expert colonoscopists.Retrospective chart review was performed, and main outcomes measured included cecal intubation rate, lesions detected, dosage of sedation used, and complications.Using the STR colonoscope, complete colonoscopy to the cecum was possible in 34/37 patients (91.9%). No loss of lumen/blind advancement was necessary in any of the procedures. No adverse events occurred. Among the completed colonoscopies, 6/34 (17.6%) patients had adenomas, all proximal to the site of prior failure, including one advanced adenoma. All failures (n = 3, 8.1%) had a history of cancer surgeries, with peritoneal carcinomatosis/extensively fixed/frozen bowel (two patients) and an additional diverticular stricture with colo-vesical fistula (one patient).STR colonoscope facilitates completion of a high proportion (91.9%) of colonoscopies that previously failed in expert hands. Its STR allows easy maneuverability across segments of sharp angulation with bowel fixity without need for blind advancement. The use of this colonoscope led to the detection of adenomas in 17.6% of patients, all proximal to the site of prior failed colonoscopy.

    View details for DOI 10.1007/s10620-019-05882-2

    View details for PubMedID 31630343

  • Simethicone is retained in endoscopes despite reprocessing: impact of its use on working channel fluid retention and adenosine triphosphate bioluminescence values GASTROINTESTINAL ENDOSCOPY Barakat, M. T., Huang, R. J., Banerjee, S. 2019; 89 (1): 115–23
  • Comparison of automated and manual drying in the elimination of residual endoscope working channel fluid after reprocessing GASTROINTESTINAL ENDOSCOPY Barakat, M. T., Huang, R. J., Banerjee, S. 2019; 89 (1): 124-+
  • Foregone Inclusion: Neonatal CMV Hepatitis and Cholestasis. Digestive diseases and sciences Martin, M. n., Holmes, S. n., Sim, J. n., Hassan, M. n., Mathew, R. n., Bensen, R. n., Barakat, M. n. 2019

    View details for DOI 10.1007/s10620-019-05691-7

    View details for PubMedID 31187327

  • Unplanned Hospital Encounters After Endoscopic Retrograde Cholangiopancreatography in 3 Large North American States GASTROENTEROLOGY Huang, R. J., Barakat, M. T., Girotra, M., Lee, J. S., Banerjee, S. 2019; 156 (1): 119-+
  • SpyCatcher: Use of a Novel Cholangioscopic Snare for Capture and Retrieval of a Proximally Migrated Biliary Stent DIGESTIVE DISEASES AND SCIENCES Barakat, M. T., Banerjee, S. 2018; 63 (12): 3224–27
  • Recent Trends and the Impact of the Affordable Care Act on Emergency Department Visits and Hospitalizations for Gastrointestinal, Pancreatic, and Liver Diseases. Journal of clinical gastroenterology Barakat, M. T., Mithal, A., Huang, R. J., Sehgal, A., Sehgal, A., Singh, G., Banerjee, S. 2018


    BACKGROUND: The Affordable Care Act (ACA) with Medicaid expansion implemented in 2014, extended health insurance to >20-million previously uninsured individuals. However, it is unclear whether enhanced primary care access with Medicaid expansion decreased emergency department (ED) visits and hospitalizations for gastrointestinal (GI)/pancreatic/liver diseases.METHODS: We evaluated trends in GI/pancreatic/liver diagnosis-specific ED/hospital utilization over a 5-year period leading up to Medicaid expansion and a year following expansion, in California (a state that implemented Medicaid expansion) and compare these with Florida (a state that did not).RESULTS: From 2009 to 2013, GI/pancreatic/liver disease ED visits increased by 15.0% in California and 20.2% in Florida and hospitalizations for these conditions decreased by 2.6% in California and increased by 7.9% in Florida. Following Medicaid expansion, a shift from self-pay/uninsured to Medicaid insurance was seen California; in addition, a new decrease in ED visits for nausea/vomiting and GI infections, was evident, without associated change in overall ED/hospital utilization trends. Total hospitalization charges for abdominal pain, nausea/vomiting, constipation, and GI infection diagnoses decreased in California following Medicaid expansion, but increased over the same time-period in Florida.CONCLUSIONS: We observed a striking payer shift for GI/pancreatic/liver disease ED visits/hospitalizations after Medicaid expansion in California, indicating a shift in the reimbursement burden in self-pay/uninsured patients, from patients and hospitals to the government. ED visits and hospitalization charges decreased for some primary care-treatable GI diagnoses in California, but not for Florida, suggesting a trend toward lower cost of gastroenterology care, perhaps because of decreased hospital utilization for conditions amenable to outpatient management.

    View details for PubMedID 30285976

  • Scoping the scope: endoscopic evaluation of endoscope working channels with a new high-resolution inspection endoscope (with video) GASTROINTESTINAL ENDOSCOPY Barakat, M. T., Girotra, M., Huang, R. J., Banerjee, S. 2018; 88 (4): 601-+
  • Unplanned Hospital Encounters Following Endoscopic Retrograde Cholangiopancreatography in 3 Large American States. Gastroenterology Huang, R. J., Barakat, M. T., Girotra, M., Lee, J. S., Banerjee, S. 2018


    BACKGROUND & AIMS: We have few population-level data on the performance of endoscopic retrograde cholangiopancreatography (ERCP) in the United States. We investigated the numbers of unplanned hospital encounters (UHEs), patient and facility factors associated with UHEs, and variation in quality and outcomes in the performance of ERCP in 3 large American states.METHODS: We collected data on 68,642 ERCPs, performed at 635 facilities in California, Florida, and New York from 2009 through 2014. The primary endpoint was number of UHEs with an ERCP-related event within 7 days of ERCP; secondary endpoints included numbers of UHE within 30 days and mortality within 30 days. Each facility was assigned a risk-standardized cohort, and variations in numbers of UHE were analyzed using multivariable analysis.RESULTS: Among all ERCPs, 5.8% resulted in an UHE within 7 days, and 10.2% by 30 days. Performance of sphincterotomy was significantly associated with a higher risk of UHE at 7 and 30 days (P<.001). Younger age, female sex, and more advanced comorbidity associated with UHE. There was substantial heterogeneity in rates of UHE among facilities: 4.2% at facilities in the lower 5th percentile and 25.2% at facilities in the 95th percentile. Increasing facility volume and ability to perform endoscopic ultrasound associated inversely with risk. The median number of ERCPs performed each year was 68.7, but 69% of facilities performed 100 or fewer ERCPs per year. Risk for UHE following sphincterotomy decreased with increasing facility volume until an inflection point of 157 ERCPs per year was reached.CONCLUSIONS: In an analysis of outcomes of 68,642 ERCPs performed in three states, we found a higher than expected number of UHEs. There is substantial unexplained variation in risk for adverse event following ERCPs among facilities-volume is the strongest predictor of risk. Annual facility volumes above approximately 150 ERCPs per year may protect against UHE.

    View details for PubMedID 30243620

  • Cut and Paste: Endoscopic Management of a Perforating Biliary Stent Utilizing Scissors and Clips DIGESTIVE DISEASES AND SCIENCES Barakat, M. T., Kothari, S., Banerjee, S. 2018; 63 (9): 2202–5
  • Comparison of automated and manual drying in the eliminating residual endoscope working channel fluid after reprocessing (with video). Gastrointestinal endoscopy Barakat, M. T., Huang, R. J., Banerjee, S. 2018


    BACKGROUND: Residual fluid within endoscope working channels after reprocessing may promote growth of pathogens. Current reprocessing guidelines therefore recommend endoscope drying with administration of forced filtered air; however, the duration and modality of administered air are not specified. The new DriScope Aid device enables automated administration of filtered air at controlled pressure through all internal endoscope channels. We systematically compared, for the first time, the impact of manual drying and automated drying on retained working channel fluid and bioburden after reprocessing.METHODS: We assessed for residual working channel fluid after reprocessing/drying using the SteriCam borescope. Drying was performed either manually (forced filtered air) or was automated (DriScope Aid) for either 5 or 10 minutes. ATP bioluminescence testing was performed on working channel rinsates after drying, to evaluate for residual bioburden.RESULTS: Significantly more fluid droplets were evident after manual drying (4.55 ± 6.14) than with automated device-facilitated drying for either 5 minutes (0.83 ± 1.29, p=0.007) or 10 minutes (0±0, p=0.001). ATP bioluminescence values were higher for manual drying compared with automated drying at 48 hours (p=0.001) and 72 hours (p=0.014) after reprocessing.CONCLUSIONS: We demonstrate significantly fewer water droplets and delayed ATP bioluminescence values within endoscope working channels after automated drying compared with manual drying. In particular, virtually no retained fluid was evident within endoscope working channels after automated drying for 10 minutes. These findings support recommendations for automation of as many reprocessing steps as possible. Automated drying may decrease the risk of transmission of infection related to endoscopy.

    View details for PubMedID 30148992

  • Simethicone is retained in endoscopes despite reprocessing: impact of its use on working channel fluid retention and adenosine triphosphate bioluminescence values (with video). Gastrointestinal endoscopy Barakat, M. T., Huang, R. J., Banerjee, S. 2018


    BACKGROUND: Studies from our group and others demonstrate residual fluid in 42% to 95% of endoscope working channels despite high-level disinfection (HLD) and drying. Additionally, persistent simethicone has been reported in endoscope channels despite reprocessing.METHODS: Endoscopy was performed using water or varied simethicone concentrations (0.5%, 1%, 3%) for flushing. After HLD/drying, we inspected endoscope working channels for retained fluid using the SteriCam borescope. Working channel rinsates were evaluated for adenosine triphosphate (ATP) bioluminescence. Fourier transform infrared spectroscopy was performed on fluid droplets gathered from a colonoscope in which low-concentration simethicone was used.RESULTS: Use of medium/high concentration simethicone resulted in higher mean fluid droplets (13.5/17.3 droplets, respectively) and ATP bioluminescence values (20.6/23 RLUs, respectively) compared with procedures using only water (6.3 droplets/10.9 RLUs, p<0.001). Two automated endoscope reprocessing (AER) cycles resulted in return of fluid droplet and ATP bioluminescence values to ranges similar to procedures using only water (p=0.56). Low-concentration simethicone did not increase mean residual fluid or ATP bioluminescence values compared with procedures using only water (5.8 droplets/15.6 RLUs). FTIR analysis revealed simethicone in the endoscope working channel after use of low-concentration simethicone.CONCLUSIONS: Use of medium/high concentration simethicone is associated with retention of increased fluid droplets and higher ATP bioluminescence values in endoscope working channels, compared with endoscopes in which water or low concentration simethicone was used. However, simethicone is detectable in endoscopes despite reprocessing, even when used in low concentration. Our data suggest that when simethicone is used, it should be used in the lowest concentration possible. Facilities may consider 2 AER cycles for reprocessing of endoscopes when simethicone has been used.

    View details for PubMedID 30125574

  • SpyCatcher: Use of a Novel Cholangioscopic Snare for Capture and Retrieval of a Proximally Migrated Biliary Stent. Digestive diseases and sciences Barakat, M. T., Banerjee, S. 2018

    View details for PubMedID 30078117

  • Effects of a Brief Educational Program on Optimization of Fluoroscopy to Minimize Radiation Exposure During Endoscopic Retrograde Cholangiopancreatography CLINICAL GASTROENTEROLOGY AND HEPATOLOGY Barakat, M. T., Thosani, N. C., Huang, R. J., Choudhary, A., Kochar, R., Kothari, S., Banerjee, S. 2018; 16 (4): 550–57


    Fluoroscopy during endoscopic retrograde cholangiopancreatography (ERCP) is increasingly performed by therapeutic endoscopists, many of whom have not received formal training in modulating fluoroscopy use to minimize radiation exposure. Exposure to ionizing radiation has significant health consequences for patients and endoscopists. We aimed to evaluate whether a 20-minute educational intervention for endoscopists would improve use of fluoroscopy and decrease ERCP-associated exposure to radiation for patients.We collected data from 583 ERCPs, performed in California from June 2010 through November 2012; 331 were performed at baseline and 252 following endoscopist education. The educational intervention comprised a 20-minute video explaining best practices for fluoroscopy, coupled with implementation of a formal fluoroscopy time-out protocol before the ERCP was performed. Our primary outcome was the effect of the educational intervention on direct and surrogate markers of patient radiation exposure associated with ERCPs performed by high-volume endoscopists (HVEs) (200 or more ERCPs/year) vs low-volume endoscopists (LVEs) (fewer than 200 ERCPs/year).At baseline, total radiation dose and dose area product were significantly higher for LVEs, but there was no significant difference between HVEs and LVEs following education. Education was associated with significant reductions in median fluoroscopy time (48% reduction for HVEs vs 30% reduction for LVEs), total radiation dose (28% reduction for HVEs vs 52% for LVEs) and dose area product (35% reduction for HVEs vs 48% reduction for LVEs). All endoscopists significantly increased their use of low magnification and collimation following education.A 20-minute educational program with emphasis on ideal use of modifiable fluoroscopy machine settings results in an immediate and significant reduction in ERCP-associated patient radiation exposure for low-volume and high-volume endoscopists. Training programs should consider radiation education for advanced endoscopy fellows.

    View details for PubMedID 28804031

    View details for PubMedCentralID PMC5809234

  • Plastic Surgery: Cholangioscopic Intra-stent Balloon Retrieval of a Proximally Migrated Biliary Stent DIGESTIVE DISEASES AND SCIENCES Barakat, M. T., Girotra, M., Choudhary, A., Banerjee, S. 2018; 63 (4): 851–55

    View details for PubMedID 28965145

    View details for PubMedCentralID PMC5856579

  • Au Naturel: Transpapillary Endoscopic Drainage of an Infected Biloma DIGESTIVE DISEASES AND SCIENCES Barakat, M., Kothari, S., Sethi, S., Banerjee, S. 2018; 63 (3): 597–600

    View details for PubMedID 28856471

    View details for PubMedCentralID PMC5823722

  • Scoping the scope: endoscopic evaluation of endoscope working channels with a new high-resolution inspection endoscope (with video). Gastrointestinal endoscopy Barakat, M. T., Girotra, M., Huang, R. J., Banerjee, S. 2018


    BACKGROUND AND AIMS: Outbreaks of transmission of infection related to endoscopy despite reported adherence to reprocessing guidelines warrant scrutiny of all potential contributing factors. Recent reports from ambulatory surgery centers indicated widespread significant occult damage within endoscope working channels, raising concerns regarding the potential detrimental impact of this damage on the adequacy of endoscope reprocessing.METHODS: We inspected working channels of all 68 endoscopes at our academic institution using a novel flexible inspection endoscope. Inspections were recorded and videos reviewed by 3 investigators to evaluate and rate channel damage and/or debris. Working channel rinsates were obtained from all endoscopes, and adenosine triphosphate (ATP) bioluminescence was measured.RESULTS: Overall endoscope working channel damage was rated as minimal and/or mild and was consistent with expected wear and tear (median 1.59 on our 5-point scale). Our predominant findings included superficial scratches (98.5%) and scratches with adherent peel (76.5%). No channel perforations, stains, or burns were detected. The extent of damage was not predicted by endoscope age. Minor punctate debris was common, and a few small drops of fluid were noted in 42.6% of endoscopes after reprocessing and drying. The presence of residual fluid predicted higher ATP bioluminescence values. The presence of visualized working channel damage or debris was not associated with elevated ATP bioluminescence values.CONCLUSION: The flexible inspection endoscope enables high-resolution imaging of endoscope working channels and offers endoscopy units an additional modality for endoscope surveillance, potentially complementing bacterial cultures and ATP values. Our study, conducted in a busy academic endoscopy unit, indicated predominately mild damage to endoscope working channels, which did not correlate with elevated ATP values.

    View details for PubMedID 29425885

  • Liver transplant-related anastomotic biliary strictures: a novel, rapid, safe, radiation-sparing, and cost-effective management approach GASTROINTESTINAL ENDOSCOPY Barakat, M. T., Huang, R. J., Thosani, N. C., Choudhary, A., Girotra, M., Banerjee, S. 2018; 87 (2): 501–8


    Biliary strictures after orthotopic liver transplantation (OLT) are typically managed by sequential ERCP procedures, with incremental dilation of the stricture and stent exchange (IDSE) and placement of new stents. This approach resolves >80% of strictures after 12 months but requires costly, lengthy ERCPs with significant patient radiation exposure. Increasing awareness of the harmful effects of radiation, escalating healthcare costs, and decreasing reimbursement for procedures mandate maximal efficiency in performing ERCP. We compared the traditional IDSE protocol with a sequential stent addition (SSA) protocol, in which additional stents are placed across the stricture during sequential ERCPs, without stent removal/exchange or stricture dilation.Patients undergoing ERCP for OLT-related anastomotic strictures from 2010 to 2016 were identified from a prospectively maintained endoscopy database. Procedure duration, fluoroscopy time, stricture resolution rates, adverse events, materials fees, and facility fees were analyzed for IDSE and SSA procedures.Seventy-seven patients underwent 277 IDSE and 132 SSA procedures. Mean fluoroscopy time was 64.5% shorter (P < .0001) and mean procedure duration 41.5% lower (P < .0001) with SSA compared with IDSE. SSA procedures required fewer accessory devices, resulting in significantly lower material (63.8%, P < .0001) and facility costs (42.8%, P < .0001) compared with IDSE. Stricture resolution was >95%, and low adverse event rates did not significantly differ.SSA results in shorter, cost-effective procedures requiring fewer accessory devices and exposing patients to less radiation. Stricture resolution rates are equivalent to IDSE, and adverse events do not differ significantly, even in this immunocompromised population.

    View details for PubMedID 28757315

    View details for PubMedCentralID PMC5787034

  • A prospective evaluation of radiation-free direct solitary cholangioscopy for the management of choledocholithiasis GASTROINTESTINAL ENDOSCOPY Barakat, M. T., Girotra, M., Choudhary, A., Huang, R. J., Sethi, S., Banerjee, S. 2018; 87 (2): 584-+


    Endoscopy has replaced many radiologic studies for the GI tract. However, ERCP remains a hybrid endoscopic-fluoroscopic procedure, which limits its portable delivery, creates delays because of fluoroscopy room unavailability, and exposes patients and providers to radiation. We evaluated fluoroscopy/radiation-free management of patients with noncomplex choledocholithiasis using direct solitary cholangioscopy (DSC).Patients underwent fluoroscopy-free biliary cannulation, sphincterotomy, and then cholangioscopy to establish location and number/size of stones and to document distance from ampulla to bifurcation to guide balloon advancement. Stones were extracted using a marked balloon catheter advanced to the bifurcation and inflated to the bile duct diameter, documented on prior imaging. Repeat cholangioscopy was performed to confirm stone clearance.Fluoroscopy-free biliary cannulation was successful in all 40 patients (100%). Advanced cannulation techniques were required in 5 patients. Papillary balloon dilation was performed in 8 patients and electrohydraulic lithotripsy in 3 patients. Discrete stones were visualized in 31 patients and stone debris/sludge in 8 patients. Fluoroscopy-free stone/debris/sludge extraction was successful in all these patients. Brief fluoroscopy was used in 2 patients (5%) to confirm stone clearance. No stone/debris/sludge was noted in 1 patient. Mild pancreatitis was noted in 2 patients (5%) and bleeding in 1 (2.5%).This study establishes the feasibility of fluoroscopy/radiation-free, cholangioscopic management of noncomplex choledocholithiasis with success and adverse event rates similar to standard ERCP. DSC represents a significant procedural advance in the management of biliary disorders that does not need to be confined to the fluoroscopy suite and can be reimagined as bedside procedures in emergency department or intensive care unit settings. (Clinical trial registration number: NCT03074201.).

    View details for PubMedID 28797911

    View details for PubMedCentralID PMC5801123

  • (Re)building the Wall: Recurrent Boerhaave Syndrome Managed by Over-the-Scope Clip and Covered Metallic Stent Placement. Digestive diseases and sciences Barakat, M. T., Girotra, M. n., Banerjee, S. n. 2018; 63 (5): 1139–42

    View details for PubMedID 28948439

    View details for PubMedCentralID PMC5867198

  • Cut and Paste: Endoscopic Management of a Perforating Biliary Stent Utilizing Scissors and Clips. Digestive diseases and sciences Barakat, M. T., Kothari, S., Banerjee, S. 2017

    View details for PubMedID 29127608

  • Practice Patterns for Cholecystectomy Following Endoscopic Retrograde Cholangio-Pancreatography for Patients With Choledocholithiasis. Gastroenterology Huang, R. J., Barakat, M. T., Girotra, M., Banerjee, S. 2017


    Cholecystectomy (CCY) following an episode of choledocholithiasis requiring endoscopic retrograde cholangio-pancreatography (ERCP) with stone extraction reduces recurrent biliary events, compared to expectant management. We studied practice patterns for performance of CCY following ERCP for choledocholithiasis using data from 3 large states and evaluated the effects of delaying CCY.We conducted a retrospective cohort study using the ambulatory surgery, inpatient, and emergency department databases from the states of California (years 2009-2011), New York (2011-2013), and Florida (2012-2014). We collected data from 4516 patients hospitalized with choledocholithiasis who underwent ERCP. We compared outcomes of patients who underwent CCY at index admission (early CCY), elective CCY within 60 days of discharge (delayed CCY), or did not undergo CCY (no CCY), calculating rate of recurrent biliary events (defined as an emergency department visit or unplanned hospitalization due to symptomatic cholelithiasis, cholecystitis, choledocholithiasis, cholangitis, or biliary pancreatitis), mortality, and cost by CCY cohort. We also evaluated risk factors for not undergoing CCY. The primary outcome measure was the rate of recurrent biliary events in the 365 days following discharge from index admission.Of the patients who underwent ERCP for choledocholithiasis, 41.2% underwent early CCY, 10.9% underwent delayed CCY, and 48.0% underwent no CCY. Early CCY reduced relative risk of recurrent biliary events within 60 days by 92%, compared with delayed or no CCY (P<.001). After 60 days following discharge from index admission, patients with early CCY had an 87% lower risk of recurrent biliary events than patients with no CCY (P<.001) and patients with delayed CCY had an 88% lower risk of recurrent biliary events than patients with no CCY (P<.001). A strategy of delayed CCY performed on an outpatient basis was least costly. Performance of early CCY was inversely associated with low facility volume. Hispanic race, Asian race, Medicaid insurance, and no insurance associated inversely with performance of delayed CCY.In a retrospective analysis of over 4500 patients hospitalized with choledocholithiasis, we found that CCY was not performed following ERCP for almost half of the cases. Although early and delayed CCY equally reduce the risk of subsequent recurrent biliary events, patients are at 10-fold higher risk of recurrent biliary event while waiting for a delayed CCY compared with patients who underwent early CCY. Delayed CCY is a cost-effective strategy that must be balanced against the risk of loss to follow up, particularly among patients who are ethnic minorities or have little or no health insurance.

    View details for DOI 10.1053/j.gastro.2017.05.048

    View details for PubMedID 28583822

  • Shaking Off the Shackles of Fluoroscopy - Evolving From Standard ERCP to Radiation-Free Endoscopic Retrograde Cholangioscopy (RF-ERC) Barakat, M. T., Girotra, M., Choudhary, A., Huang, R. J., Sethi, S., Banerjee, S. MOSBY-ELSEVIER. 2017: AB618–AB619
  • High Endoscopist and Facility Volume Protect Against Emergency Department Visits and Unplanned Hospitalizations Following Ambulatory Ercp Huang, R. J., Barakat, M. T., Girotra, M., Banerjee, S. MOSBY-ELSEVIER. 2017: AB84
  • Goff Trans-Pancreatic Septotomy Is an Effective and Safe Salvage Technique Following Failed Standard Biliary Cannulation at ERCP Barakat, M. T., Girotra, M., Huang, R. J., Choudhary, A., Liao, C., Kothari, S., Banerjee, S. MOSBY-ELSEVIER. 2017: AB612
  • Sequential Biliary Stent Addition Without Exchange or Dilation for Post-Operative Biliary Strictures: A Rapid, Cost-Effective Approach that Minimizes Radiation Exposure Barakat, M. T., Choudhary, A., Huang, R. J., Thosani, N., Girotra, M., Banerjee, S. MOSBY-ELSEVIER. 2017: AB88
  • When Experts Fail: Short Turn Radius Colonoscope to the Rescue? Utility of a Novel Colonoscope for Incomplete Colonoscopy Due to Bowel Fixity Girotra, M., Barakat, M. T., Huang, R. J., Sethi, S., Friedland, S., Ladabaum, U., Banerjee, S. MOSBY-ELSEVIER. 2017: AB517
  • Evolution in the utilization of biliary interventions in the United States: results of a nationwide longitudinal study from 1998 to 2013. Gastrointestinal endoscopy Huang, R. J., Thosani, N. C., Barakat, M. T., Choudhary, A., Mithal, A., Singh, G., Sethi, S., Banerjee, S. 2017


    Bile duct surgery (BDS), percutaneous transhepatic cholangiography (PTC), and ERCP are alternative interventions used to treat biliary disease. Our aim was to describe trends in ERCP, BDS, and PTC on a nationwide level in the United States.We used the National Inpatient Sample to estimate age-standardized utilization trends of inpatient diagnostic ERCP, therapeutic ERCP, BDS, and PTC between 1998 and 2013. We calculated average case fatality, length of stay, patient demographic profile (age, gender, payer), and hospital characteristics (hospital size and metropolitan status) for these procedures.Total biliary interventions decreased over the study period from 119.8 to 100.1 per 100,000. Diagnostic ERCP utilization decreased by 76%, and therapeutic ERCP utilization increased by 35%. BDS rates decreased by 78% and PTC rates by 24%. ERCP has almost completely supplanted surgery for the management of choledocholithiasis. Fatality from ERCP, BDS, and PTC have all decreased, whereas mean length of stay has remained stable. The proportion of Medicare-insured, Medicaid-insured, and uninsured patients undergoing biliary procedures has increased over time. Most of the increase in therapeutic ERCP and decrease in BDS occurred in large, metropolitan hospitals.Although therapeutic ERCP utilization has increased over time, the total volume of biliary interventions has decreased. BDS utilization has experienced the most dramatic decrease, possibly a consequence of the increased therapeutic capacity and safety of ERCP. ERCPs are now predominantly therapeutic in nature. Large urban hospitals are leading the shift from surgical to endoscopic therapy of the biliary system.

    View details for DOI 10.1016/j.gie.2016.12.021

    View details for PubMedID 28062313

  • Affordable Care Act and healthcare delivery: A comparison of California and Florida hospitals and emergency departments. PloS one Barakat, M. T., Mithal, A. n., Huang, R. J., Mithal, A. n., Sehgal, A. n., Banerjee, S. n., Singh, G. n. 2017; 12 (8): e0182346


    The Affordable Care Act (ACA) has expanded access to health insurance for millions of Americans, but the impact of Medicaid expansion on healthcare delivery and utilization remains uncertain.To determine the early impact of the Medicaid expansion component of ACA on hospital and ED utilization in California, a state that implemented the Medicaid expansion component of ACA and Florida, a state that did not.Analyze all ED encounters and hospitalizations in California and Florida from 2009 to 2014 and evaluate trends by payer and diagnostic category. Data were collected from State Inpatient Databases, State Emergency Department Databases and the California Office of Statewide Health Planning and Development.Hospital and ED encounters.Population-based study of California and Florida state residents.Implementation of Medicaid expansion component of ACA in California in 2014.Changes in ED visits and hospitalizations by payer, percentage of patients hospitalized after an ED encounter, top diagnostic categories for ED and hospital encounters.In California, Medicaid ED visits increased 33% after Medicaid expansion implementation and self-pay visits decreased by 25% compared with a 5.7% increase in the rate of Medicaid patient ED visits and a 5.1% decrease in rate of self-pay patient visits in Florida. In addition, California experienced a 15.4% increase in Medicaid inpatient stays and a 25% decrease in self pay stays. Trends in the percentage of patients admitted to the hospital from the ED were notable; a 5.4% decrease in hospital admissions originating from the ED in California, and a 2.1% decrease in Florida from 2013 to 2014.We observed a significant shift in payer for ED visits and hospitalizations after Medicaid expansion in California without a significant change in top diagnoses or overall rate of these ED visits and hospitalizations. There appears to be a shift in reimbursement burden from patients and hospitals to the government without a dramatic shift in patterns of ED or hospital utilization.

    View details for PubMedID 28771602

  • Adenosine triphosphate bioluminescence for bacteriological surveillance and reprocessing strategies for minimizing risk of infection transmission by duodenoscopes. Gastrointestinal endoscopy Sethi, S., Huang, R. J., Barakat, M. T., Banaei, N., Friedland, S., Banerjee, S. 2016


    Recent outbreaks of duodenoscope-transmitted infections underscore the importance of adequate endoscope reprocessing. Adenosine triphosphate (ATP) bioluminescence testing allows rapid evaluation of endoscopes for bacteriologic/biologic residue. In this prospective study we evaluate the utility of ATP in bacteriologic surveillance and the effects of endoscopy staff education and dual cycles of cleaning and high-level disinfection (HLD) on endoscope reprocessing.ATP bioluminescence was measured after precleaning, manual cleaning, and HLD on rinsates from suction-biopsy channels of all endoscopes and elevator channels of duodenoscopes/linear echoendoscopes after use. ATP bioluminescence was remeasured in duodenoscopes (1) after re-education and competency testing of endoscopy staff and subsequently (2) after 2 cycles of precleaning and manual cleaning and single cycle of HLD or (3) after 2 cycles of precleaning, manual cleaning, and HLD.The ideal ATP bioluminescence benchmark of <200 relative light units (RLUs) after manual cleaning was achieved from suction-biopsy channel rinsates of all endoscopes, but 9 of 10 duodenoscope elevator channel rinsates failed to meet this benchmark. Re-education reduced RLUs in duodenoscope elevator channel rinsates after precleaning (23,218.0 vs 1340.5 RLUs, P < .01) and HLD (177.0 vs 12.0 RLUs, P < .01). After 2 cycles of manual cleaning/HLD, duodenoscope elevator channel RLUs achieved levels similar to sterile water, with corresponding negative cultures.ATP testing offers a rapid, inexpensive alternative for detection of endoscope microbial residue. Re-education of endoscopy staff and 2 cycles of cleaning and HLD decreased elevator channel RLUs to levels similar to sterile water and may therefore minimize the risk of transmission of infections by duodenoscopes.

    View details for DOI 10.1016/j.gie.2016.10.035

    View details for PubMedID 27818222

  • A Case of Meningococcal Pyomyositis in an Otherwise Healthy Adult. Open forum infectious diseases Barakat, M. T., Gajurel, K., Fischer, K., Stevens, K., Ozdalga, E., Montoya, J. G. 2016; 3 (3): ofw087-?


    The clinical spectrum of Neisseria meningitidis can range from nasopharyngeal colonization to life-threatening invasive diseases such as meningitis. However, its etiologic role in invasive pyomyositis (PM) has never been reported before in the English language. In this study, we report the first case of PM in the English language and the second case in the literature caused by N meningitidis.

    View details for PubMedID 27703989

  • Green Sludge: Intraductal Papillary Mucinous Neoplasm of the Bile Duct Presenting with Intermittent Biliary Obstruction Due to Abundant Mucus. Digestive diseases and sciences Choudhary, A., Barakat, M. T., Leal, J. N., Louie, C. Y., Visser, B. C., Banerjee, S. 2016: -?

    View details for PubMedID 27423887

  • Choledochoscopic Identification of a Hepatic/Cystic Artery Pseudoaneurysm in a Patient with Hematemesis After Laparoscopic Cholecystectomy. Digestive diseases and sciences Choudhary, A., Barakat, M. T., Higgins, L. J., Banerjee, S. 2016: -?

    View details for PubMedID 27423886

  • A Case of Meningococcal Pyomyositis in an Otherwise Healthy Adult OPEN FORUM INFECTIOUS DISEASES Barakat, M. T., Gajurel, K., Fischer, K., Stevens, K., Ozdalga, E., Montoya, J. G. 2016; 3 (3)
  • Kif3a is necessary for initiation and maintenance of medulloblastoma. Carcinogenesis Barakat, M. T., Humke, E. W., Scott, M. P. 2013; 34 (6): 1382-1392


    Medulloblastoma (MB) cells arise from granule neuron precursors (GNPs) that have lost growth control. During normal development, GNPs divide in response to Sonic hedgehog (SHH), a ligand that binds to the patched (PTCH) receptor on GNPs. If one copy of the Ptch gene is lost, as in human Gorlin's syndrome and in Ptch(+/-) mice, MBs may form. Proper transduction of the SHH signal critically depends on primary cilia. Loss of primary cilia results in improper signal reception and failure to properly activate SHH target genes. KIF3a, part of a kinesin motor, is required for formation of primary cilia. Here, we use tamoxifen-induced ablation of Kif3a in GNPs of postnatal Ptch(+/-) mouse cerebella to show that KIF3a is necessary for MB formation. To investigate the importance of primary cilia in established tumors, we deleted Kif3a from cultured cells and from tumor cell grafts. The loss of Kif3a from established tumors led to their growth arrest and regression. MBs behave as if they are addicted to the presence of primary cilia. These results underscore the potential utility of agents that disrupt cilia for the treatment of Hh pathway-related MBs.

    View details for DOI 10.1093/carcin/bgt041

    View details for PubMedID 23389290

    View details for PubMedCentralID PMC3670253

  • Learning from Jekyll to control Hyde: Hedgehog signaling in development and cancer TRENDS IN MOLECULAR MEDICINE Barakat, M. T., Humke, E. W., Scott, M. P. 2010; 16 (8): 337-348


    The Hedgehog (Hh) cascade controls cell proliferation, differentiation and patterning of tissues during embryogenesis but is largely suppressed in the adult. The Hh pathway can become reactivated in cancer. Here, we assimilate data from recent studies to understand how and when the Hh pathway is turned on to aid the neoplastic process. Hh signaling is now known to have a role in established tumors, enabling categorization of tumors based on the role Hh signaling plays in their growth. This categorization has relevance for prognosis and targeted therapeutics. In the first category, abnormal Hh signaling initiates the tumor. In the second category, Hh signaling helps maintain the tumor. In the third category, Hh signaling is implicated but its role is not yet defined.

    View details for DOI 10.1016/j.molmed.2010.05.003

    View details for Web of Science ID 000281273500001

    View details for PubMedID 20696410

    View details for PubMedCentralID PMC3651907

  • Tail Wags Dog: Primary Cilia and Tumorigenesis CANCER CELL Barakat, M. T., Scott, M. P. 2009; 16 (4): 276-277


    Aberrant activation of the Hedgehog (Hh) signaling pathway contributes to many forms of cancer. Primary cilia are Hh signal transduction centers. Two papers in a recent issue of Nature Medicine (Han et al., 2009; Wong et al., 2009) show that mutating cilia can increase or reduce the rates of tumorigenesis depending on how the Hh pathway is disrupted.

    View details for DOI 10.1016/j.ccr.2009.09.019

    View details for Web of Science ID 000270770400005

    View details for PubMedID 19800572

    View details for PubMedCentralID PMC3437380

  • Insulin-like Growth Factor 2 Is Required for Progression to Advanced Medulloblastoma in patched1 Heterozygous Mice CANCER RESEARCH Corcoran, R. B., Raveh, T. B., Barakat, M. T., Lee, E. Y., Scott, M. P. 2008; 68 (21): 8788-8795


    Medulloblastoma (MB) can arise in the cerebellum due to genetic activation of the Sonic Hedgehog (Shh) signaling pathway. During normal cerebellum development, Shh spurs the proliferation of granule neuron precursors (GNP), the precursor cells of MB. Mutations in the Shh receptor gene patched1 (ptc1+/-) lead to increased MB incidence in humans and mice. MB tumorigenesis in mice heterozygous for ptc1+/- shows distinct steps of progression. Most ptc1+/- mice form clusters of preneoplastic cells on the surface of the mature cerebellum that actively transcribe Shh target genes. In approximately 15% of mice, these preneoplastic cells will become fast-growing, lethal tumors. It was previously shown that the loss of function of insulin-like growth factor 2 (igf2) suppresses MB formation in ptc1+/- mice. We found that igf2 is not expressed in preneoplastic lesions but is induced as these lesions progress to more advanced MB tumors. Igf2 is not required for formation of preneoplastic lesions but is necessary for progression to advanced tumors. Exogenous Igf2 protein promoted proliferation of MB precursor cells (GNP) and a MB cell line, PZp53(MED). Blocking igf2 signaling inhibited growth of PZp53(MED) cells, implicating igf2 as a potential clinical target.

    View details for DOI 10.1158/0008-5472.CAN-08-2135

    View details for Web of Science ID 000260698900019

    View details for PubMedID 18974121

    View details for PubMedCentralID PMC2597356

  • NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Franken, P., Dudley, C. A., Estill, S. J., Barakat, M., Thomason, R., O'Haran, B. F., McKnight, S. L. 2006; 103 (18): 7118-7123


    Because the transcription factor neuronal Per-Arnt-Sim-type signal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor and an effector of intracellular energy balance, and because sleep is thought to correct an energy imbalance incurred during waking, we examined NPAS2's role in sleep homeostasis using npas2 knockout (npas2-/-) mice. We found that, under conditions of increased sleep need, i.e., at the end of the active period or after sleep deprivation (SD), NPAS2 allows for sleep to occur at times when mice are normally awake. Lack of npas2 affected electroencephalogram activity of thalamocortical origin; during non-rapid eye movement sleep (NREMS), activity in the spindle range (10-15 Hz) was reduced, and within the delta range (1-4 Hz), activity shifted toward faster frequencies. In addition, the increase in the cortical expression of the NPAS2 target gene period2 (per2) after SD was attenuated in npas2-/- mice. This implies that NPAS2 importantly contributes to the previously documented wake-dependent increase in cortical per2 expression. The data also revealed numerous sex differences in sleep; in females, sleep need accumulated at a slower rate, and REMS loss was not recovered after SD. In contrast, the rebound in NREMS time after SD was compromised only in npas2-/- males. We conclude that NPAS2 plays a role in sleep homeostasis, most likely at the level of the thalamus and cortex, where NPAS2 is abundantly expressed.

    View details for DOI 10.1073/pnas.0602006103

    View details for Web of Science ID 000237399900060

    View details for PubMedID 16636276

    View details for PubMedCentralID PMC1459027

  • Sleep restriction suppresses neurogenesis induced by hippocampus-dependent learning JOURNAL OF NEUROPHYSIOLOGY Hairston, I. S., Little, M. T., Scanlon, M. D., Barakat, M. T., Palmer, T. D., Sapolsky, R. M., Heller, H. C. 2005; 94 (6): 4224-4233


    Sleep deprivation impairs hippocampal-dependent learning, which, in turn, is associated with increased survival of newborn cells in the hippocampus. We tested whether the deleterious effects of sleep restriction on hippocampus-dependent memory were associated with reduced cell survival in the hippocampus. We show that sleep restriction impaired hippocampus-dependent learning and abolished learning-induced neurogenesis. Animals were trained in a water maze on either a spatial learning (hippocampus-dependent) task or a nonspatial (hippocampus-independent) task for 4 days. Sleep-restricted animals were kept awake for one-half of their rest phase on each of the training days. Consistent with previous reports, animals trained on the hippocampus-dependent task expressed increased survival of newborn cells in comparison with animals trained on the hippocampus-independent task. This increase was abolished by sleep restriction that caused overall reduced cell survival in all animals. Sleep restriction also selectively impaired spatial learning while performance in the nonspatial task was, surprisingly, improved. Further analysis showed that in both training groups fully rested animals applied a spatial strategy irrespective of task requirements; this strategy interfered with performance in the nonspatial task. Conversely, in sleep-restricted animals, this preferred spatial strategy was eliminated, favoring the use of nonspatial information, and hence improving performance in the nonspatial task. These findings suggest that sleep loss altered behavioral strategies to those that do not depend on the hippocampus, concomitantly reversing the neurogenic effects of hippocampus-dependent learning.

    View details for DOI 10.1152/jn.00218.2005

    View details for Web of Science ID 000233317100053

    View details for PubMedID 16014798

  • Light induces c-fos and per1 expression in the suprachiasmatic nucleus of arrhythmic hamsters AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY Barakat, M. T., O'Hara, B. F., Cao, V. H., Heller, H. C., Ruby, N. F. 2005; 289 (5): R1381-R1386


    Locomotor activity rhythms in a significant proportion of Siberian hamsters (Phodopus sungorus sungorus) become arrhythmic after the light-dark (LD) cycle is phase-delayed by 5 h. Arrhythmia is apparent within a few days and persists indefinitely despite the presence of the photocycle. The failure of arrhythmic hamsters to regain rhythms while housed in the LD cycle, as well as the lack of any masking of activity, suggested that the circadian system of these animals had become insensitive to light. We tested this hypothesis by examining light-induced gene expression in the suprachiasmatic nucleus (SCN). Several weeks after the phase delay, arrhythmic and re-entrained hamsters were housed in constant darkness (DD) for 24 h and administered a 30-min light pulse 2 h after predicted dark onset because light induces c-fos and per1 genes at this time in entrained animals. Brains were then removed, and tissue sections containing the SCN were processed for in situ hybridization and probed with c-fos and per1 mRNA probes made from Siberian hamster cDNA. Contrary to our prediction, light pulses induced robust expression of both c-fos and per1 in all re-entrained and arrhythmic hamsters. A separate group of animals held in DD for 10 days after the light pulse remained arrhythmic. Thus, even though the SCN of these animals responded to light, neither the LD cycle nor DD restored rhythms, as it does in other species made arrhythmic by constant light (LL). These results suggest that different mechanisms underlie arrhythmicity induced by LL or by a phase delay of the LD cycle. Whereas LL induces arrhythmicity by desynchronizing SCN neurons, phase delay-induced arrhythmicity may be due to a loss of circadian rhythms at the level of individual SCN neurons.

    View details for DOI 10.1152/ajpregu.00695.2004

    View details for Web of Science ID 000232528200020

    View details for PubMedID 16002555

  • Phenotypic differences in reentrainment behavior and sensitivity to nighttime light pulses in Siberian hamsters JOURNAL OF BIOLOGICAL RHYTHMS Ruby, N. F., Barakat, M. T., Heller, H. C. 2004; 19 (6): 530-541


    Spontaneous reentrainment to phase shifts of the photocycle is a fundamental property of all circadian systems. Siberian hamsters are, however, unique in this regard because most fail to reentrain when the LD cycle (16-h light/day) is phase delayed by 5 h. In the present study, the authors compared reentrainment responses in hamsters from 2 colonies. One colony descended from animals trapped in the wild more than 30 years ago (designated "nonentrainers"), and the other colony was outbred as recently as 13 years ago (designated "entrainers"). As reported previously, only 10% of hamsters from the nonentrainer colony reentrained to a 5-h phase delay of the LD cycle. By contrast, 75% of animals from the entrainer colony reentrained to the phase shift. Another goal of this study was to test the hypothesis that failure to reentrain was a consequence of light exposure during the middle of the night on the day of the 5-h phase delay. This hypothesis was tested by exposing animals to 2 h of light during the early, middle, or late part of the night and then subjecting them on the next day to a 3-h phase delay of the photocycle, which is a phase shift to which all hamsters normally reentrain. All animals from both colonies reentrained when light pulses occurred early in the night, but more animals from the entrainer colony, compared to the nonentrainer colony, reentrained when the light pulse occurred in the middle or late part of the night. The phenotypic variation in reentrainment responses is similar to the variation in photoperiodic responsiveness previously reported for these 2 colonies. Phenotypic variation in both traits is due to underlying differences in circadian organization and suggests a common genetic basis for reentrainment responses and photoperiodic responsiveness.

    View details for DOI 10.1177/0748730404268055

    View details for Web of Science ID 000225093900008

    View details for PubMedID 15523114

  • Light pulses do not induce c-fos or per1 in the SCN of hamsters that fail to reentrain to the photocycle JOURNAL OF BIOLOGICAL RHYTHMS Barakat, M. I., O'Hara, B. E., Cao, V. H., Larkin, J. E., Heller, H. C., Ruby, N. F. 2004; 19 (4): 287-297


    Circadian activity rhythms of most Siberian hamsters (Phodopus sungorus sungorus) fail to reentrain to a 5-h phase shift of the light-dark (LD) cycle. Instead, their rhythms free-run at periods close to 25 h despite the continued presence of the LD cycle. This lack of behavioral reentrainment necessarily means that molecular oscillators in the master circadian pacemaker, the SCN, were unable to reentrain as well. The authors tested the hypothesis that a phase shift of the LD cycle rendered the SCN incapable of responding to photic input. Animals were exposed to a 5-h phase delay of the photocycle, and activity rhythms were monitored until a lack of reentrainment was confirmed. Hamsters were then housed in constant darkness for 24 h and administered a 30-min light pulse 2 circadian hours after activity onset. Brains were then removed, and tissue sections containing the SCN were processed for in situ hybridization. Sections were probed with Siberian hamster c-fos and per1 mRNA probes because light rapidly induces these 2 genes in the SCN during subjective night but not at other circadian phases. Light pulses induced robust expression of both genes in all animals that reentrained to the LD cycle, but no expression was observed in any animal that failed to reentrain. None of the animals exhibited an intermediate response. This finding is the first report of acute shift in a photocycle eliminating photosensitivity in the SCN and suggests that a specific pattern of light exposure may desensitize the SCN to subsequent photic input.

    View details for DOI 10.1177/0748730404266771

    View details for Web of Science ID 000222693400004

    View details for PubMedID 15245648