Accurate, Robust, and Scalable Machine Abstraction of Mayo Endoscopic Subscores From Colonoscopy Reports.

BACKGROUND: The Mayo endoscopic subscore (MES) is an important quantitative measure of disease activity in ulcerative colitis. Colonoscopy reports in routine clinical care usually characterize ulcerative colitis disease activity using free text description, limiting their utility for clinical research and quality improvement. We sought to develop algorithms to classify colonoscopy reports according to their MES. METHODS: We annotated 500 colonoscopy reports from 2 health systems. We trained and evaluated 4 classes of algorithms. Our primary outcome was accuracy in identifying scorable reports (binary) and assigning an MES (ordinal). Secondary outcomes included learning efficiency, generalizability, and fairness. RESULTS: Automated machine learning models achieved 98% and 97% accuracy on the binary and ordinal prediction tasks, outperforming other models. Binary models trained on the University of California, San Francisco data alone maintained accuracy (96%) on validation data from Zuckerberg San Francisco General. When using 80% of the training data, models remained accurate for the binary task (97% [n = 320]) but lost accuracy on the ordinal task (67% [n = 194]). We found no evidence of bias by gender (P = .65) or area deprivation index (P = .80). CONCLUSIONS: We derived a highly accurate pair of models capable of classifying reports by their MES and recognizing when to abstain from prediction. Our models were generalizable on outside institution validation. There was no evidence of algorithmic bias. Our methods have the potential to enable retrospective studies of treatment effectiveness, prospective identification of patients meeting study criteria, and quality improvement efforts in inflammatory bowel diseases.

Our accurate pair of models automatically classify colonoscopy reports by Mayo endoscopic subscore and abstain from prediction appropriately. Our methods can enable large-scale electronic health record studies of treatment effectiveness, prospective identification of patients for clinical trials, and quality improvement efforts in ulcerative colitis.

Outcomes for expanded polytetrafluoroethylene strip in frontalis suspension surgery.

PURPOSE: This study evaluates surgical outcomes and complication rates of frontalis suspension with expanded polytetrafluoroethylene (ePTFE). METHODS: This retrospective cohort study reviewed all patients undergoing frontalis suspension surgery using ePTFE as the sling material from January 1 2012 to March 3 2020 by a single surgeon at a single academic center. Two different surgical techniques were evaluated in the placement of the sling material. Demographic, clinical, and operative data were extracted. Outcome data including postoperative lid height, reoperation, and complication rate were extracted for the cohort and compared between the two surgical techniques. Descriptive statistics were utilized. RESULTS: Sixty-four eyes from 49 unique patients were included in this study. Forty-three (67.2%) patients had isolated congenital blepharoptosis; 14 (21.9%) had blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES); and 2 (3.1%) had cranial nerve III palsy. Fifty-one (79.7%) patients had no prior blepharoptosis surgery. Lid crease incision and stab incision techniques were utilized for 24 (37.5%) and 40 (62.5%) eyes, respectively. Overall, 21 (32.8%) eyes required reoperation with ePTFE to achieve appropriate eyelid height or contour. Only one patient experienced implant infection, requiring removal of ePTFE sling after a second reoperation. There were no cases of implant exposure or granuloma formation noted during the study period. CONCLUSION: An ePTFE strip soaked in cefazolin prior to utilization in surgery is a viable material for frontalis suspension surgery, with a lower infectious or inflammatory complication rate than previously reported. However, reoperation rate was still relatively high.

Personalizing treatment selection in Crohn's disease: a meta-analysis of individual participant data from fifteen randomized controlled trials.

BACKGROUND: Meta-analyses have found anti-TNF drugs to be the best treatment, on average, for Crohn's disease. We performed a subgroup analysis to determine if it is possible to achieve more efficacious outcomes by individualizing treatment selection. METHODS: We obtained participant-level data from 15 trials of FDA-approved treatments (N=5703). We used sequential regression and simulation to model week six disease activity as a function of drug class, demographics, and disease-related features. We performed hypothesis testing to define subgroups based on rank-ordered preferences for treatments. We queried health records from University of California Health (UCH) to estimate the impacts these models could have on practice. We computed the sample size needed to prospectively test a prediction of our models. RESULTS: 45% of the participants (N=2561) showed greater efficacy with at least one drug class (anti-TNF, anti-IL-12/23, anti-integrin) over another. They were classifiable into 6 subgroups, two showing greatest efficacy with anti-TNFs (36%, N=2064). Women over 50 showed superior responses with anti-IL-12/23s. Although they represented only 2% of the trial-based cohort, 25% of Crohn's patients at UCH are women over 50 (N=5,647), consistent with potential selection bias in trials. Moreover, 75% of biologic-exposed women over 50 did not receive an anti-IL12/23 first-line, supporting the potential value of these models. A future trial with 250 patients per arm will have 97% power to confirm the superiority of anti-IL-12/23s over anti-TNFs in these patients. A treatment recommendation tool is available at https://crohnsrx.org. CONCLUSIONS: Personalizing treatment can improve outcomes in Crohn's disease. Future work is needed to confirm these findings, and improve representativeness in Crohn's trials.

Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group.

BACKGROUND: The advent of clinical trial data sharing platforms has created opportunities for making new discoveries and answering important questions using already collected data. However, existing methods for meta-analyzing these data require the presence of shared control groups across studies, significantly limiting the number of questions that can be confidently addressed. We sought to develop a method for meta-analyzing potentially heterogeneous clinical trials even in the absence of a common control group. METHODS: This work was conducted within the context of a broader effort to study comparative efficacy in Crohn's disease. Following a search of clnicaltrials.gov we obtained access to the individual participant data from nine trials of FDA-approved treatments in Crohn's Disease (N = 3392). We developed a method involving sequences of regression and simulation to separately model the placebo- and drug-attributable effects, and to simulate head-to-head trials against an appropriately normalized background. We validated this method by comparing the outcome of a simulated trial comparing the efficacies of adalimumab and ustekinumab against the recently published results of SEAVUE, an actual head-to-head trial of these drugs. This study was pre-registered on PROSPERO (#157,827) prior to the completion of SEAVUE. RESULTS: Using our method of sequential regression and simulation, we compared the week eight outcomes of two virtual cohorts subject to the same patient selection criteria as SEAVUE and treated with adalimumab or ustekinumab. Our primary analysis replicated the corresponding published results from SEAVUE (p = 0.9). This finding proved stable under multiple sensitivity analyses. CONCLUSIONS: This new method may help reduce the bias of individual participant data meta-analyses, expand the scope of what can be learned from these already-collected data, and reduce the costs of obtaining high-quality evidence to guide patient care.

Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study.

BACKGROUND: Randomized trials are the gold-standard for clinical evidence generation, but they can sometimes be limited by infeasibility and unclear generalizability to real-world practice. External control arm (ECA) studies may help address this evidence gaps by constructing retrospective cohorts that closely emulate prospective ones. Experience in constructing these outside the context of rare diseases or cancer is limited. We piloted an approach for developing an ECA in Crohn's disease using electronic health records (EHR) data. METHODS: We queried EHR databases and manually screened records at the University of California, San Francisco to identify patients meeting the eligibility criteria of TRIDENT, a recently completed interventional trial involving an ustekinumab reference arm. We defined timepoints to balance missing data and bias. We compared imputation models by their impacts on cohort membership and outcomes. We assessed the accuracy of algorithmic data curation against manual review. Lastly, we assessed disease activity following treatment with ustekinumab. RESULTS: Screening identified 183 patients. 30% of the cohort had missing baseline data. Nonetheless, cohort membership and outcomes were robust to the method of imputation. Algorithms for ascertaining non-symptom-based elements of disease activity using structured data were accurate against manual review. The cohort consisted of 56 patients, exceeding planned enrollment in TRIDENT. 34% of the cohort was in steroid-free remission at week 24. CONCLUSION: We piloted an approach for creating an ECA in Crohn's disease from EHR data by using a combination of informatics and manual methods. However, our study reveals significant missing data when standard-of-care clinical data are repurposed. More work will be needed to improve the alignment of trial design with typical patterns of clinical practice, and thereby enable a future of more robust ECAs in chronic diseases like Crohn's disease.

When the Neighboring Village is Not Treated: Role of Geographic Proximity to Communities Not Receiving Mass Antibiotics for Trachoma.

BACKGROUND: Mass administration of azithromycin is an established strategy for decreasing the prevalence of trachoma in endemic areas. However, nearby untreated communities could serve as a reservoir that may increase the chances of chlamydia reinfection in treated communities. METHODS: As part of a cluster-randomized trial in Ethiopia, 60 communities were randomized to receive mass azithromycin distributions and 12 communities were randomized to no treatments until after the first year. Ocular chlamydia was assessed from a random sample of children per community at baseline and month 12. Distances between treated and untreated communities were assessed from global positioning system coordinates collected for the study. RESULTS: The pretreatment prevalence of ocular chlamydia among 0 to 9 year olds was 43% (95% confidence interval [CI], 39%-47%), which decreased to 11% (95% CI, 9%-14%) at the 12-month visit. The posttreatment prevalence of chlamydia was significantly higher in communities that were closer to an untreated community after adjusting for baseline prevalence and the number of mass treatments during the year (odds ratio, 1.12 [95% CI, 1.03-1.22] for each 1 km closer to an untreated community). CONCLUSIONS: Mass azithromycin distributions to wide, contiguous geographic areas may reduce the likelihood of continued ocular chlamydia infection in the setting of mass antibiotic treatments.

Longitudinal Use of Telehealth During the COVID-19 Pandemic and Utility of Asynchronous Testing for Subspecialty-Level Ophthalmic Care.

Importance: Telehealth in ophthalmology has traditionally focused on preventive disease screening with limited use in outpatient evaluation. The unique conditions of the COVID-19 pandemic afforded the opportunity to evaluate different implementations of teleophthalmology at scale, providing insight into expanding teleophthalmology care. Objective: To compare telehealth use in ophthalmology with other specialties and assess the feasibility of augmenting ophthalmic telehealth encounters with asynchronous testing during the COVID-19 pandemic. Design, Setting, and Participants: This quality improvement study evaluated retrospective, longitudinal, observational data from the first 18 months of the COVID-19 pandemic (January 1, 2020, through July 31, 2021) for 881 080 patients receiving care from outpatient primary care, cardiology, neurology, gastroenterology, surgery, neurosurgery, urology, orthopedic surgery, otolaryngology, obstetrics/gynecology, and ophthalmology clinics of the University of California, San Francisco. Asynchronous testing was evaluated for teleophthalmology encounters. Interventions: A hybrid care model wherein ophthalmic testing data were acquired asynchronously and used to augment telehealth encounters. Main Outcomes and Measures: Telehealth as a percentage of total volume of ambulatory care and use of asynchronous testing for ophthalmic conditions. Results: The volume of in-person outpatient visits dropped by 83.3% (39 488 of 47 390) across the evaluated specialties at the onset of shelter-in-place orders for the COVID-19 pandemic, and the initial use of telehealth increased for these specialties before stabilizing over the 18-month study period. In ophthalmology, telehealth use peaked at 488 of 1575 encounters (31.0%) early in the pandemic and returned to mostly in-person visits as COVID-19 restrictions lifted. Elective use of telehealth was highest in gastroenterology, urology, neurology, and neurosurgery and lowest in ophthalmology. Asynchronous testing was combined with 126 teleophthalmology encounters, resulting in change of clinical management for 32 patients (25.4%) and no change for 91 (72.2%). Conclusions and Relevance: Telehealth increased across various specialties during the COVID-19 pandemic. Combining teleophthalmic visits with asynchronous testing suggested that this approach is feasible for subspecialty-level evaluation. Additional study is needed to evaluate whether asynchronous testing outside the same institution could provide an effective and lasting approach for expanding the reach of ophthalmic telehealth.

Concordance of ompA types in children re-infected with ocular Chlamydia trachomatis following mass azithromycin treatment for trachoma.

BACKGROUND: The chlamydial major outer membrane protein, encoded by the ompA gene, is a primary target for chlamydial vaccine research. However, human studies of ompA-specific immunity are limited, and prior studies have been limited in differentiating re-infection from persistent infection. The purpose of this study was to assess whether children living in trachoma-endemic communities with re-infections of ocular chlamydia were more likely to be infected with a different or similar genovar. METHODOLOGY AND FINDINGS: The study included 21 communities from a trachoma-hyperendemic area of Ethiopia that had been treated with a mass azithromycin distribution for trachoma. Conjunctival swabbing was offered to all children younger than 5 years of age at baseline (i.e., pre-treatment), and then at follow-up visits 2 and 6 months later. Swabs were subjected to polymerase chain reaction (PCR) to detect C. trachomatis. A random sample of 359 PCR-positive swabs, stratified by study visit and study community, was chosen for ompA sequencing. In addition, ompA sequencing was performed on all swabs of 24 children who experienced chlamydial re-infection (i.e., positive chlamydial test before treatment, negative test 2 months following mass distribution of azithromycin, and again a positive test 6 months post-treatment). ompA sequencing was successful for 351 of 359 swabs of the random sample and 44 of 48 swabs of the re-infection sample. In the random sample, ompA types clustered within households more than would be expected by chance. Among the 21 re-infected children with complete ompA data, 14 had the same ompA type before and after treatment. CONCLUSION: The high frequency of ompA concordance suggests incomplete genovar-specific protective immunity and the need for multiple antigens as vaccine targets.

Nocardia sienata: a new causative species of infectious keratitis.

A 25-year-old man presented with a 2-month history of progressively worsening left eye pain and an atypical corneal ring infiltrate. His condition deteriorated despite topical antibiotic therapy. Cultures for bacteria, fungus and acanthamoeba, repeated twice, all demonstrated no growth. On third corneal scraping, culture on Middlebrook agar grew colonies after 3 weeks of incubation. Sixteen-second deep sequencing identified Nocardia sienata as the pathogen. This species of Nocardia has not previously been described as a causative pathogen for infectious keratitis. Sloughing and loose epithelium with recurrent filament formation are unusual in infectious keratitis and could be associated with this species. In culture-negative cases, clinicians should consider Nocardia as a cause of keratitis despite its rarity outside of south Asia and use steroids cautiously. Next generation sequencing technology may facilitate identification of the causate of keratitis and can be especially useful in culture-negative cases and with unexpected pathogens.

Polymicrobial odontogenic periorbital and orbital necrotizing fasciitis (PONF): A case report.

PURPOSE: To present a case of periorbital and orbital necrotizing fasciitis (PONF) from an odontogenic source with a distinct microbiologic profile and highlight the need for emergent multidisciplinary management. OBSERVATIONS: A 39-year-old man presented with periorbital swelling, pain, and erythema following facial trauma. Imaging revealed peri-dental collections, accompanying maxillary sinusitis, and pre- and post-septal involvement. Immediate surgical debridement of necrotic tissue along with broad-spectrum antibiotics were pursued for management. Cultures grew multiple organisms, most notably Streptococcus milleri group and Staphylococcus lugdunensis. CONCLUSIONS AND IMPORTANCE: PONF is a rare yet potentially fatal disease. Streptococcus milleri group and a fulminant course are to be suspected when the source is odontogenic. Timely multidisciplinary surgical debridement and medical management with intravenous antibiotics is critical for best outcomes.

Keratoprosthesis, silicone oil placement, and fluocinolone acetonide implant for treatment of uveitis-associated hypotony and keratopathy.

PURPOSE: To describe a case series of combined Boston Type 1 Keratoprosthesis with pars plana vitrectomy, silicone oil placement, and fluocinolone acetonide intravitreal 0.59 mg implant (RETISERT®), and report its safety and efficacy in preventing phthisis bulbi in patients with uveitis-associated hypotony and concurrent corneal edema. FINDINGS: A retrospective review of patients with chronic uveitis, corneal decompensation and concurrent hypotony who underwent the combined approach described here between 2015 and 2020 was conducted. Three patients were treated using the combined approach. Post-operative recovery was unremarkable in all cases and the patients' corneal condition remained stable on follow up. No patient developed phthisis, retroprosthetic membrane, or infectious endophthalmitis. Average intraocular pressure one year after intervention was 2.7 to 6.4 mmHg higher compared to a year prior. CONCLUSIONS: The approach described is potentially safe and effective in preventing phthisis and membrane formation in uveitis-associated hypotony and keratopathy.

Multifocal pancreatic PPoma in the setting of MEN1: Case report and review of literature.

INTRODUCTION AND IMPORTANCE: Functioning pancreatic neuroendocrine tumors (pNETs) that express pancreatic polypeptide-PPomas-do not yet have a pathognomonic clinical syndrome associated with them due to their overall rarity and diverse symptoms. Moreover, in patients with MEN1, the often multifocal nature of pNETs presents a unique clinical issue. CASE PRESENTATION: We report a case of a 22-year-old man with a known MEN1 gene mutation who was suffering from severe diarrhea (7-8 bowel movements per day) and was found to have only elevated PP levels on biochemical work-up. Ga68-DOTATATE PET/CT showed multifocal tumors in the body and tail of the pancreas that were not evident on contrast-enhanced CT. The patient underwent a successful laparoscopic radical antegrade modular pancreatosplenectomy (RAMP) and recovered well post-operatively with complete resolution of his diarrhea. Immunohistochemistry showed multiple pure PPomas. CLINICAL DISCUSSION: This case highlights the unique propensity for multifocal disease in patients with MEN1 mutations and the utility of functional imaging by somatostatin analogs, i.e., Ga68-DOTATATE PET/CT, in order to perform oncologic laparoscopic pancreatic resections. CONCLUSION: PPomas in the setting of MEN1 mutations are a unique clinical entity due to their diverse associated clinical syndromes and propensity for multifocal disease.

CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties.

Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work.

CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties.

Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work.

A Triple-Fluorophore-Labeled Nucleic Acid pH Nanosensor to Investigate Non-viral Gene Delivery.

There is a need for new tools to better quantify intracellular delivery barriers in high-throughput and high-content ways. Here, we synthesized a triple-fluorophore-labeled nucleic acid pH nanosensor for measuring intracellular pH of exogenous DNA at specific time points in a high-throughput manner by flow cytometry following non-viral transfection. By including two pH-sensitive fluorophores and one pH-insensitive fluorophore in the nanosensor, detection of pH was possible over the full physiological range. We further assessed possible correlation between intracellular pH of delivered DNA, cellular uptake of DNA, and DNA reporter gene expression at 24 hr post-transfection for poly-L-lysine and branched polyethylenimine polyplex nanoparticles. While successful transfection was shown to clearly depend on median cellular pH of delivered DNA at the cell population level, surprisingly, on an individual cell basis, there was no significant correlation between intracellular pH and transfection efficacy. To our knowledge, this is the first reported instance of high-throughput single-cell analysis between cellular uptake of DNA, intracellular pH of delivered DNA, and gene expression of the delivered DNA. Using the nanosensor, we demonstrate that the ability of polymeric nanoparticles to avoid an acidic environment is necessary, but not sufficient, for successful transfection.

Continuous microfluidic assembly of biodegradable poly(beta-amino ester)/DNA nanoparticles for enhanced gene delivery.

Translation of biomaterial-based nanoparticle formulations to the clinic faces significant challenges including efficacy, safety, consistency and scale-up of manufacturing, and stability during long-term storage. Continuous microfluidic fabrication of polymeric nanoparticles has the potential to alleviate the challenges associated with manufacture, while offering a scalable solution for clinical level production. Poly(beta-amino esters) (PBAE)s are a class of biodegradable cationic polymers that self-assemble with anionic plasmid DNA to form polyplex nanoparticles that have been shown to be effective for transfecting cancer cells specifically in vitro and in vivo. Here, we demonstrate the use of a microfluidic device for the continuous and scalable production of PBAE/DNA nanoparticles followed by lyophilization and long term storage that results in improved in vitro efficacy in multiple cancer cell lines compared to nanoparticles produced by bulk mixing as well as in comparison to widely used commercially available transfection reagents polyethylenimine and Lipofectamine® 2000. We further characterized the nanoparticles using nanoparticle tracking analysis (NTA) to show that microfluidic mixing resulted in fewer DNA-free polymeric nanoparticles compared to those produced by bulk mixing. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1813-1825, 2017.