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MotivationCells contain dozens of major organelles and thousands of other structures, many of which vary extensively in their number, size, shape and spatial distribution. This complexity and variation dramatically complicates the use of both traditional and deep learning methods to build accurate models of cell organization. Most cellular organelles are distinct objects with defined boundaries that do not overlap, while the pixel resolution of most imaging methods is not sufficient to resolve these boundaries. Thus while cell organization is conceptually object-based, most current methods are pixel-based. Using extensive image collections in which particular organelles were fluorescently-labeled, deep learning methods can be used to build conditional autoencoder models for particular organelles. A major advance occurred with the use of a U-net approach to make multiple models all conditional upon a common reference, unlabeled image, allowing the relationships between different organelles to be at least partially inferred.ResultsWe have developed improved GAN-based approaches for learning these models and have also developed novel criteria for evaluating how well synthetic cell images reflect the properties of real images. The first set of criteria measure how well models preserve the expected property that organelles do not overlap. We also developed a modified loss function that allows retraining of the models to minimize that overlap. The second set of criteria uses object-based modeling to compare object shape and spatial distribution between synthetic and real images. Our work provides the first demonstration that, at least for some organelles, deep learning models can capture object-level properties of cell images.AvailabilityA Reproducible Research Archive containing all source code, generated images and analysis results will be made available at http://murphylab.cbd.cmu.edu/Software upon publication.Contactmurphy@cmu.eduSupplementary informationSupplementary data are available at Bioinformatics online.

An automated image analysis pipeline to map cell geometry and basal body organization in the ciliate Tetrahymena thermophila is described. Generative modeling was used to computationally reconstruct cell cycle progression from images of cells at single time points. The results reveal novel aspects of basal body distribution and replication.

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Purpose: Our preclinical studies showed that the PARP inhibitor, olaparib, prior to carboplatin attenuated carboplatin cytotoxicity. We evaluated sequence-specific pharmacokinetic and pharmacodynamic effects, safety, and activity of the combination.Experimental Design: Eligible patients had metastatic or recurrent women's cancer. Olaparib tablets were introduced (100 or 200 mg twice daily, days 1–7) in a 3 + 3 dose escalation with carboplatin AUC4 or 5 every 21 days, up to eight cycles, followed by olaparib 300 mg twice daily maintenance. Patients were randomly assigned to starting schedule: cohort A (olaparib days 1–7, carboplatin on day 8) or B (carboplatin on day 1, olaparib days 2–8) during cycle 1. Patients received the reversed scheme in cycle 2. Blood was collected for olaparib pharmacokinetics, platinum–DNA adducts, comet assay, and PAR concentrations. The primary objectives were to examine schedule-dependent effects on olaparib pharmacokinetics and platinum–DNA adducts.Results: A total of 77 (60 ovarian, 14 breast, and 3 uterine cancer) patients were treated. Dose-limiting toxicity was thrombocytopenia and neutropenia, defining olaparib 200 mg twice daily + carboplatin AUC4 as the MTD. Olaparib clearance was increased approximately 50% when carboplatin was given 24 hours before olaparib. In vitro experiments demonstrated carboplatin preexposure increased olaparib clearance due to intracellular olaparib uptake. Quantities of platinum–DNA adducts were not different as a function of the order of drug administration. Responses included 2 CRs and 31 PRs (46%) with a higher RR in BRCA mutation carriers compared with nonmutation carriers (68% vs. 19%).Conclusions: Tablet olaparib with carboplatin is a safe and active combination. Carboplatin preexposure causes intracellular olaparib accumulation reducing bioavailable olaparib, suggesting carboplatin should be administered prior to olaparib. Clin Cancer Res; 23(6); 1397–406. ©2016 AACR.

Supplementary method 1. DNA platinum-adducts measurement

While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML Level 3 Core specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Spatial Processes package for SBML Level 3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes.

MotivationMultiplexed protein imaging methods provide valuable information on complex tissue structure and cellular heterogeneity. However, costs increase and image quality decreases with the number of biomarkers imaged, and the number of markers that can be measured in the same tissue sample is limited.ResultsIn this work, we propose an efficient algorithm to choose a minimal predictive subset of markers that for the first time allows the prediction of full images for a much larger set of markers. We demonstrate that our approach also outperforms previous methods for predicting cell-level marker composition. We also demonstrate that an effective minimal subset can be selected even if the desired full set is too large to be imaged on the same samples.AvailabilityAll code and intermediate results are available in a Reproducible Research Archive athttps://github.com/murphygroup/CODEXPanelOptimization.

Patients with early-onset scoliosis (EOS) and spasticity may receive treatment with an intrathecal baclofen pump. We assessed how baclofen pumps are associated with the odds of complications and secondary interventions after growth-friendly (GF) spine surgery for EOS and analyzed infectious complications within the pump cohort.Using a prospectively maintained, international multicenter database, we studied patients with neuromuscular EOS with baclofen pumps who underwent GF spine surgery from 2002 through 2019 (n=25). Baclofen pumps were implanted before GF instrumentation in 18 patients, during in 2 patients, and after in 5 patients. Patients with existing pumps at initial GF spine surgery were matched 1:3 with 54 patients (control group) without pumps according to treatment center, year of surgery, diagnosis, surgery type, and preoperative curve magnitude. Univariate analysis and multivariate logistic regression were performed to compare complications and secondary interventions between the 2 cohorts.Patients with baclofen pumps had 4.8 times the odds [95% confidence interval (CI): 1.5-16] of experiencing any complication within 1 year after initial GF spine surgery compared with controls. During mean follow-up of 6.9±4.3 years, they had 4.7 times the odds (95% CI: 1.3-16) of deep surgical site infection and 5.6 times the odds (95% CI: 1.2-26) of spinal rod removal after any complication. Differences in rates of mechanical complication, such as rod migration and breakage, were nonsignificant between the 2 groups. For the 9 patients (50%) with pumps who experienced infections, the most common microorganisms were Staphylococcus aureus (4 patients) and Pseudomonas aeruginosa (2). The pump/catheter was revised or removed, in addition to antibiotic therapy or surgical irrigation and debridement, in 2 patients.Among patients with neuromuscular EOS, those with baclofen pumps are much more likely to experience complications within 1 year after GF spine surgery. They are also more likely to have deep surgical site infections, with S. aureus and P. aeruginosa being the most common causative organisms, and to require spinal rod removal.Level III-retrospective comparative study.

Objective To evaluate institutional opioid prescribing patterns following percutaneous fixation of pediatric supracondylar humerus fractures before and after implementation of a standardized discharge order set. Design A retrospective review of patients who underwent closed reduction and percutaneous skeletal fixation of a Type II or III supracondylar humerus fracture in 2017 (prior to pain protocol implementation) and again in 2019 (after pain protocol implementation) Setting Single Tertiary Care Children's Hospital Participants In total, 106 patients met inclusion criteria between years 2017 (n = 49) and 2019 (n = 57). Exclusion criteria included miscoded patients, open fractures, patients who presented with vascular injury or nerve palsy, polytrauma patients with multiple fractures in the same upper extremity, and supracondylar humerus fractures that underwent an open procedure. Results There were no significant differences between inpatient pain scores (p = 0.91) and MDE prescribed (p = 0.75) between the 2 cohorts. In 2017, large variability was noted in day supply of opioids (0-11.4 days) and MDE (0-8.45 mg/kg), with significant differences between prescribing patterns of junior and senior level residents (mean day supply of opioids (p = 0.045), mean MDE prescribed on discharge (p = 0.001)). After implementation of a standardized opioid discharge order set, there was a tenfold increase in the number of patients discharged without an opioid prescription (2017: 4%, 2019: 44%). Additionally, any discrepancies between prescribing practices of junior and senior level residents were eliminated (mean day supply of opioids (p = 0.65), mean MDE prescribed on discharge (p = 0.69)). Conclusions The introduction of a standardized post-operative opioid discharge order set led to a 10-fold increase in the number of patients discharged without an opioid prescription. Additionally, the order set decreased the variability in the prescribing patterns of discharge opioid medications without change in pain control. The resident prescribing variability based upon level of experience resolved with the use of the order set.

Because of the relative rarity of Early Onset Scoliosis (EOS) cases, patient registries were developed to combine clinical information from multiple institutions to maximize patient care and outcomes. This study examines the history and trends regarding the use of growth-friendly devices for index surgical procedures in EOS patients within the Pediatric Spine Study Group database.All index growth-friendly implants were queried from registry inception until October 2020. EOS etiology, device/implant type, and geographic area/institution for each procedure were recorded.From 1994 to 2020, 2786 patients underwent index surgery at a mean age of 6.2±2.9 years. There were 908 traditional growing rods (TGR) (32.3%), 922 vertical expandable prosthetic titanium rib devices (VEPTR) (33.1%), 5 hybrid VEPTR/TGR (0.18%), and 951 magnetically controlled growing rods (MCGR) (34.2%) index implants. Fifty-six different institutions reported an index implant, and 5 accounted for 823 (30%) of the cases during the study period. Institutions in the Northeast accounted for more index implants than other regions of the United States. There was a 40% increase in index implant insertions annually when comparing 1994 (3 implants/1 center) to 2018 (234 implants/56 centers), ( P0.001). Beginning in 2009, there was a 90.9% decrease in the number of TGR/VEPTR procedures (2009: 156 implants/32 centers; 2019: 22 implants/49 centers P =0.001), and a 479% increase in MCGR (2009: 1 implant/1 center; 2018: 197 implants/34 centers ( P =0.005). The overall number of growth-friendly index procedures performed in 2019 (150/49 centers) decreased 34.5% when compared to 2018 (234/48 centers).The number of growth-friendly implants reported in the Pediatric Spine Study Group registry as the initial surgical management of EOS increased markedly over the past 20 years. MCGR is currently the predominant type of device utilized for index surgical procedures by group members, surpassing the use of VEPTR and TGR in 2014. There was a significant decrease in index growth-friendly procedures in 2019 compared to 2018.Level IV.