3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation

Background

Cell segmentation is crucial in bioimage informatics, as its accuracy directly impacts conclusions drawn from cellular analyses. While many approaches to 2D cell segmentation have been described, 3D cell segmentation has received much less attention. 3D segmentation faces significant challenges, including limited training data availability due to the difficulty of the task for human annotators, and inherent three-dimensional complexity. As a result, existing 3D cell segmentation methods often lack broad applicability across different imaging modalities.

Results

To address this, we developed a generalizable approach for using 2D cell segmentation methods to produce accurate 3D cell segmentations. We implemented this approach in 3DCellComposer, a versatile, open-source package that allows users to choose any existing 2D segmentation model appropriate for their tissue or cell type(s) without requiring any additional training. Importantly, we have enhanced our open source CellSegmentationEvaluator quality evaluation tool to support 3D images. It provides metrics that allow selection of the best approach for a given imaging source and modality, without the need for human annotations to assess performance. Using these metrics, we demonstrated that our approach produced high-quality 3D segmentations of tissue images, and that it could outperform an existing 3D segmentation method on the cell culture images with which it was trained.

Conclusions

3DCellComposer, when paired with well-trained 2D segmentation models, provides an important alternative to acquiring human-annotated 3D images for new sample types or imaging modalities and then training 3D segmentation models using them. It is expected to be of significant value for large scale projects such as the Human BioMolecular Atlas Program.

Expanding the coverage of spatial proteomics: a machine learning approach

MOTIVATION

Multiplexed protein imaging methods use a chosen set of markers and provide valuable information about complex tissue structure and cellular heterogeneity. However, the number of markers that can be measured in the same tissue sample is inherently limited.

RESULTS

In this paper, we present an efficient method 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 protein composition. Most importantly, we demonstrate that our approach can be used to select a marker set that enables prediction of a much larger set than could be measured concurrently.

AVAILABILITY AND IMPLEMENTATION

All code and intermediate results are available in a Reproducible Research Archive at https://github.com/murphygroup/CODEXPanelOptimization.

Learning Morphological, Spatial, and Dynamic Models of Cellular Components

In this chapter, we describe protocols for using the CellOrganizer software on the Jupyter Notebook platform to analyze and model cell and organelle shape and spatial arrangement. CellOrganizer is an open-source system for using microscope images to learn statistical models of the structure of cell components and how those components are organized relative to each other. Such models capture the statistical variation in the organization of cellular components by jointly modeling the distributions of their number, shape, and spatial distributions. These models can be created for different cell types or conditions and compared to reflect differences in their spatial organizations. The models are also generative, in that they can be used to synthesize new cell instances reflecting what a model learned and to provide well-structured cell geometries that can be used for biochemical simulations.

Intraoperative Radiation Exposure in Adolescent Idiopathic and Neuromuscular Scoliosis

BACKGROUND

Intraoperative imaging is often used to aid pedicle screw placement during scoliosis operations. Higher rates of cancer and death have been observed in orthopaedic surgeons and radiation technologists, including a fourfold higher rate of breast cancer in female orthopaedic surgeons. The purpose of this study was to evaluate variability in intraoperative radiation during spinal fusions for both adolescent idiopathic scoliosis (AIS) and neuromuscular scoliosis (NMS).

METHODS

A retrospective review of posterior spinal fusion and segmental spinal instrumentation for scoliosis performed by pediatric orthopaedic surgeons from 2017 to 2019 at a single institution was performed. Inclusion criteria included: a diagnosis of AIS or NMS and patients between 8 and 18 years of age. Exclusion criteria included: revision surgery, use of intraoperative navigation, and patients younger than 10 at the time of scoliosis onset within the AIS cohort. Data collected included: preoperative curve, body mass index (BMI), number of levels fused, number of Ponte osteotomies, and fluoroscopy time. One-way analysis of variance tests, Bonferroni post hoc tests, independent t tests, and Pearson correlations were utilized with significance determined at the 95% confidence level ( a = 0.05).

RESULTS

A total of 148 patients were included in the study. The average fluoroscopy time was 143 ± 67 seconds. Patients with NMS had higher average fluoroscopy times (193 ± 75 s) compared with patients with AIS (129 ± 58 s, P < 0.001). In patients with AIS, fluoroscopy time correlated to the patient's preoperative curve ( r = 0.182, P = 0.050). Patients with AIS with fewer than 12 levels fused had significantly less radiation exposure than those with 12 or more levels fused ( P = 0.01). When controlling for the number of levels fused, patients with AIS with higher BMIs had significantly greater fluoroscopy times ( P = 0.001). In patients with NMS, fluoroscopy time negatively correlated with BMI ( r = -0.459, P = 0.009) and positively correlated with a preoperative curve ( r = 0.475, P = 0.007).

CONCLUSION

Fluoroscopy times vary greatly during adolescent spinal fusions for scoliosis. Longer fluoroscopy times are correlated with: NMS diagnosis, larger preoperative curve, BMI, and number of levels fused. Surgeons' knowledge of factors affecting fluoroscopy time will increase awareness and may be the first step in decreasing intraoperative radiation risks.

LEVEL OF EVIDENCE

Level III; Therapeutic-a retrospective study.

Five Inhibitory Receptors Display Distinct Vesicular Distributions in Murine T Cells

T cells can express multiple inhibitory receptors. Upon induction of T cell exhaustion in response to a persistent antigen, prominently in the anti-tumor immune response, many are expressed simultaneously. Key inhibitory receptors are CTLA-4, PD-1, LAG3, TIM3, and TIGIT, as investigated here. These receptors are important as central therapeutic targets in cancer immunotherapy. Inhibitory receptors are not constitutively expressed on the cell surface, but substantial fractions reside in intracellular vesicular structures. It remains unresolved to which extent the subcellular localization of different inhibitory receptors is distinct. Using quantitative imaging of subcellular distributions and plasma membrane insertion as complemented by proximity proteomics and biochemical analysis of the association of the inhibitory receptors with trafficking adaptors, the subcellular distributions of the five inhibitory receptors were discrete. The distribution of CTLA-4 was most distinct, with preferential association with lysosomal-derived vesicles and the sorting nexin 1/2/5/6 transport machinery. With a lack of evidence for the existence of specific vesicle subtypes to explain divergent inhibitory receptor distributions, we suggest that such distributions are driven by divergent trafficking through an overlapping joint set of vesicular structures. This extensive characterization of the subcellular localization of five inhibitory receptors in relation to each other lays the foundation for the molecular investigation of their trafficking and its therapeutic exploitation.

Five inhibitory receptors display distinct vesicular distributions in T cells

T cells can express multiple inhibitory receptors. Upon induction of T cell exhaustion in response to persistent antigen, prominently in the anti-tumor immune response, many are expressed simultaneously. Key inhibitory receptors are CTLA-4, PD-1, LAG3, TIM3 and TIGIT, as investigated here. These receptors are important as central therapeutic targets in cancer immunotherapy. Inhibitory receptors are not constitutively expressed on the cell surface, but substantial fractions reside in intracellular vesicular structures. It remains unresolved to which extent the subcellular localization of different inhibitory receptors is distinct. Using quantitative imaging of subcellular distributions and plasma membrane insertion as complemented by proximity proteomics and a biochemical analysis of the association of the inhibitory receptors with trafficking adaptors, the subcellular distributions of the five inhibitory receptors were discrete. The distribution of CTLA-4 was most distinct with preferential association with lysosomal-derived vesicles and the sorting nexin 1/2/5/6 transport machinery. With a lack of evidence for the existence of specific vesicle subtypes to explain divergent inhibitory receptor distributions, we suggest that such distributions are driven by divergent trafficking through an overlapping joint set of vesicular structures. This extensive characterization of the subcellular localization of five inhibitory receptors in relation to each other lays the foundation for the molecular investigation of their trafficking and its therapeutic exploitation.

A Comparative Analysis of Revision Surgery Before or After 2 Years After Graduation From Growth-friendly Surgery for Early Onset Scoliosis

INTRODUCTION

After discontinuation of growth-friendly (GF) surgery for early onset scoliosis, patients are termed graduates: they undergo a spinal fusion, are observed after final lengthening with GF implant maintenance, or are observed after GF implant removal. The purpose of this study was to compare the rates of and reasons for revision surgery in two cohorts of GF graduates: before or after 2 years of follow-up from graduation.

METHODS

A pediatric spine registry was queried for patients who underwent GF spine surgery with a minimum of 2 years of follow-ups after graduation by clinical and/or radiographic evidence. Scoliosis etiology, graduation strategy, number of, and reasons for revision surgery were queried.

RESULTS

There were 834 patients with a minimum of 2-year follow-up after graduation who were analyzed. There were 241 (29%) congenital, 271 (33%) neuromuscular, 168 (20%) syndromic, and 154 (18%) idiopathic. 803 (96%) had traditional growing rod/vertical expandable titanium rib as their GF construct and 31 (4%) had magnetically controlled growing rod. Five hundred ninety-six patients (71%) underwent spinal fusion at graduation, 208 (25%) had GF implants retained, and 30 (4%) had GF implants removed.In the entire cohort, there were 108/834 (13%) patients who underwent revision surgery. Of the revisions, 71/108 (66%) occurred as acute revisions (ARs) between 0 and 2 years from graduation (mean 0.6 y), and the most common AR indication was infection (26/71, 37%). The remaining 37/108 (34%) patients underwent delayed revision (DR) surgery >2 years (mean 3.8 y) from graduation, and the most common DR indication was implant issues (17/37, 46%).Graduation strategy affected revision rates. Of the 596 patients with spinal fusion as a graduation strategy, 98/596 (16%) underwent revision, compared with only 8/208 (4%) patients who had their GF implants retained, and 2/30 (7%) that had their GF implants removed (P ≤ 0.001).A significantly higher percentage of the ARs had a spinal fusion as the graduation strategy (68/71, 96%) compared with 30/37 DRs, (81%, P = 0.015). In addition, the 71 patients who underwent AR undergo more revision surgeries (mean: 2, range: 1 to 7) than 37 patients who underwent DR (mean: 1, range: 1 to 2) (P = 0.001).

CONCLUSION

In this largest reported series of GF graduates to date, the overall risk of revision was 13%. Patients who undergo a revision at any time, as well as ARs in particular, are more likely to have a spinal fusion as their graduation strategy. Patients who underwent AR, on average, undergo more revision surgeries than patients who underwent DR.

LEVEL OF EVIDENCE

Level III, comparative.

SBML level 3 package: spatial processes, version 1, release 1

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.

Definition of Tweener: Consensus Among Experts in Treating Early-onset Scoliosis

BACKGROUND

The term "Tweener" is colloquially used to refer to early-onset scoliosis (EOS) patients whose age and development make them candidates for multiple surgical options. The purpose of this study was to establish expert consensus on a definition to formally characterize the Tweener population.

METHODS

A 3-round survey of surgeons in an international EOS study group was conducted. Surgeons were provided with various patient characteristics and asked if each was part of their definition for Tweener patients. Responses were analyzed for consensus (≥70%), near-consensus (60% to 69%), and no consensus (<60%).

RESULTS

Consensus was reached (89% of respondents) for including chronological age in the Tweener definition; 8 to 10 years for females and 9 to 11 years for males. Surgeons agreed for inclusion of Sanders score, particularly Sanders 2 (86.0%). Patients who have reached Sanders 4, postmenarche, or have closed triradiate cartilage should not be considered Tweeners. Bone age range of 8 years and 10 months to 10 years and 10 months for females (12 y for males) could be part of the Tweener definition.

CONCLUSIONS

This study suggests that the Tweener definition could be the following: patients with open triradiate cartilage who are not postmenarche and have not reached Sanders 4, and if they have one of the following: Sanders 2 or chronological age 8 to 10 years for females (9 to 11 y for males) or bone age 8 years and 10 months to 10 years and 10 months for females (12 y for males). This definition will allow for more focused and comparative research on this population.

LEVEL OF EVIDENCE

Level V-expert opinion.

Basal body organization and cell geometry during the cell cycle in Tetrahymena thermophila

Tetrahymena thermophila possesses arrays of motile cilia that promote fluid flow for cell motility. These consist of intricately organized basal bodies (BBs) that nucleate and position cilia at the cell cortex. Tetrahymena cell geometry and spatial organization of BBs play important roles in cell size, swimming, feeding, and division. How cell geometry and BB organization are established and maintained remains poorly understood, and prior studies have been limited due to difficulties in accurate BB identification and small sample size. We therefore developed an automated image processing pipeline that segments single cells, distinguishes unique BB populations, assigns BBs into distinct ciliary rows, and distinguishes new from mature BBs. We identified unique features to describe the variation of cell shape and BB spatial organization in unsynchronized single-cell images. The results reveal asymmetries in BB distribution and positioning of the cytokinetic furrow within the cell. Moreover, we establish novel spatial and temporal waves in new BB assembly through the cell cycle. Lastly, we used measurements from single cells across the cell cycle to construct a generative model that allows synthesis of movies depicting single cells progressing through the cell cycle. Our approach is expected to be of particular value for characterizing Tetrahymena mutants. [Media: see text].

Evaluation of cell segmentation methods without reference segmentations

Cell segmentation is a cornerstone of many bioimage informatics studies and inaccurate segmentation introduces error in downstream analysis. Evaluating segmentation results is thus a necessary step for developing segmentation methods as well as for choosing the most appropriate method for a particular type of sample. The evaluation process has typically involved comparison of segmentations to those generated by humans, which can be expensive and subject to unknown bias. We present here an approach to evaluating cell segmentation methods without relying upon comparison to results from humans. For this, we defined a number of segmentation quality metrics that can be applied to multichannel fluorescence images. We calculated these metrics for 14 previously-described segmentation methods applied to datasets from 4 multiplexed microscope modalities covering 5 tissues. Using principal component analysis to combine the metrics we defined an overall cell segmentation quality score and ranked the segmentation methods. We found that two deep learning-based methods performed the best overall, but that results for all methods could be significantly improved by postprocessing to ensure proper matching of cell and nuclear masks. Our evaluation tool is available as open source and all code and data are available in a Reproducible Research Archive.

Contraindications to magnetically controlled growing rods: consensus among experts in treating early onset scoliosis

PURPOSE

The purpose of this study was to describe contraindications to the magnetically controlled growing rod (MCGR) in patients with early onset scoliosis (EOS) by establishing consensus amongst expert surgeons who treat these patients frequently.

METHODS

Nine pediatric spine surgeons from an international EOS study group participated in semi-structured interviews via email to identify factors that influence decision making in the use of MCGR. A 39-question survey was then developed to specify these factors as contraindications for MCGR-these included patient age and size, etiology, medical comorbidities, coronal and sagittal curve profiles, and skin and soft tissue characteristics. Pediatric spine surgeons from the EOS international study group were invited to complete the survey. A second 29-item survey was created to determine details and clarify results from the first survey. Responses were analyzed for consensus (> 70%), near consensus (60-69%), and no consensus/variability (< 60%) for MCGR contraindication.

RESULTS

56 surgeons of 173 invited (32%) completed the first survey, and 64 (37%) completed the second survey. Responders had a mean of over 15 years in practice (range 1-45) with over 6 years of experience with using MCGR (range 2-12). 71.4% of respondents agreed that patient size characteristics should be considered as contraindications, including BMI (81.3%) and spinal height (84.4%), although a specific BMI range or a specific minimum spinal height were not agreed upon. Among surgeons who agreed that skin and soft tissue problems were contraindications (78.6%), insufficient soft tissue (98%) and skin (89%) to cover MCGR were specified. Among surgeons who reported curve stiffness as a contraindication (85.9%), there was agreement that this curve stiffness should be defined by clinical evaluation (78.2%) and by traction films (72.3%). Among surgeons who reported sagittal curve characteristics as contraindications, hyperkyphosis (95.3%) and sagittal curve apex above T3 (70%) were specified. Surgeons who indicated the need for repetitive MRI as a contraindication (79.7%) agreed that image quality (72.9%) and not patient safety (13.6%) was the concern. In the entire cohort, consensus was not achieved on the following factors: patient age (57.4%), medical comorbidities (46.4%), etiology (53.6%), and coronal curve characteristics (58.9%).

CONCLUSION

Surgeon consensus suggests that MCGR should be avoided in patients who have insufficient spinal height to accommodate the MCGR, have potential skin and soft tissue inadequacy, have too stiff a spinal curve, have too much kyphosis, and require repetitive MRI, particularly of the spine. Future data-driven studies using this framework are warranted to generate more specific criteria (e.g. specific degrees of kyphosis) to facilitate clinical decision making for EOS patients.

LEVEL OF EVIDENCE

Level V-expert opinion.

Improving and evaluating deep learning models of cellular organization

MOTIVATION

Cells 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 n 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.

RESULTS

We have developed improved Generative Adversarial Networks-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.

AVAILABILITY AND IMPLEMENTATION

http://murphylab.cbd.cmu.edu/Software/2022_insilico.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Trends in the Utilization of Implants in Index Procedures for Early Onset Scoliosis From the Pediatric Spine Study Group

INTRODUCTION

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.

METHODS

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.

RESULTS

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), ( P <0.001). 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).

CONCLUSION

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 OF EVIDENCE

Level IV.

Mechanical Failure of 2 Cannulated Screw Fixation for Unstable SCFE: A Case Report

CASE

A 13-year-old obese boy presented with an acute-on-chronic unstable left slipped capital femoral epiphysis (SCFE). He underwent in situ surgical fixation with two 6.5-mm fully threaded cannulated screws. At 6 months, he presented with mechanical failure of both screws. He underwent screw removal, revision in situ fixation, a peritrochanteric flexion and internal rotational osteotomy, and an open femoroplasty. The osteotomy healed at 6 weeks. The femoral physis took an additional year to close.

CONCLUSION

This case highlights an uncommon complication of in situ pinning of SCFE, discusses revision fixation options, and suggests possible prolonged physeal closure in severe slips.

A Standardized Order-Set Improves Variability in Opioid Discharge Prescribing Patterns After Surgical Fixation of Pediatric Supracondylar Humerus Fractures

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.

A Single Sugar-Tong Splint Can Maintain Pediatric Forearm Fractures

Displaced pediatric forearm fractures often are treated with closed reduction and immobilization. Recent literature demonstrates no difference in maintaining alignment or needing repeat intervention in patients immobilized with either a single sugar-tong splint or a long-arm cast, but most series include patients with distal fractures. This study included patients 3 to 15 years old who underwent closed reduction and immobilization for displaced midshaft or proximal forearm fractures. Radiographs from the time of injury, after reduction, and at 4-week follow-up were reviewed for coronal and sagittal plane angular alignment. Secondary interventions also were recorded. A total of 121 patients (70 long-arm cast, 51 simple sugar-tong splint) met inclusion criteria. Groups were matched in terms of age (P=.95), sex (P=.41), body mass index (P=.12), and angular deformity prior to reduction in the sagittal (P=.78) and coronal (P=.83) planes. Following closed reduction, sagittal (P=.003) and coronal (P=.002) alignment improved significantly in all patients. At 4-week follow-up, there were no significant differences in sagittal (P=.15) or coronal (P=.68) alignment between the 2 groups. Nine patients underwent a secondary intervention after the index reduction (long-arm cast, n=7; simple sugar-tong splint, n=2), with no statistically significant difference between groups (P=.30). There were no statistically significant differences between patients managed with long-arm cast or simple sugar-tong splint regarding residual sagittal or coronal plane deformity at 4-week follow-up or incidence of secondary intervention. These findings indicate simple sugar-tong splint and long-arm cast appear to be acceptable and equivalent methods of immobilization for these injuries. [Orthopedics. 2021;44(2):e178-e182.].

Evaluation of Categorical Matrix Completion Algorithms: Towards Improved Active Learning for Drug Discovery

MOTIVATION

High throughput and high content screening are extensively used to determine the effect of small molecule compounds and other potential therapeutics upon particular targets as part of the early drug development process. However, screening is typically used to find compounds that have a desired effect but not to identify potential undesirable side effects. This is because the size of the search space precludes measuring the potential effect of all compounds on all targets. Active machine learning has been proposed as a solution to this problem.

RESULTS

In this article, we describe an improved imputation method, Impute By Committee, for completion of matrices containing categorical values. We compare this method to existing approaches in the context of modeling the effects of many compounds on many targets using latent similarities between compounds and conditions. We also compare these methods for the task of driving active learning in well-characterized settings for synthetic and real datasets. Our new approach performed the best overall both in the accuracy of matrix completion itself and in the number of experiments needed to train an accurate predictive model compared to random selection of experiments. We further improved upon the performance of our new method by developing an adaptive switching strategy for active learning that iteratively chooses between different matrix completion methods.

AVAILABILITY

A Reproducible Research Archive containing all data and code will be made available upon acceptance at http://murphylab.cbd.cmu.edu/software.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

An initial effort to define an early onset scoliosis "graduate"-The Pediatric Spine Study Group experience

PURPOSE

Increasingly, patients with early onset scoliosis (EOS) are completing a growth friendly surgical program followed by observation, removal of implants or a definitive spinal fusion. These patients are colloquially referred to as "graduates". A standardized definition of a graduate is needed for research and comparing the outcomes, family counseling, and a better understanding of the population.

METHODS

A 15-question electronic survey was completed by 39 experienced pediatric spine surgeons to identify factors salient to the definition of a graduate of EOS surgical programs. A Delphi/Nominal group technique session with nine questions was then performed face-to-face with 21 members of the Pediatric Spine Study Group to discuss and refine the definition. A follow-up electronic survey was then distributed to these same 21 members to gain consensus on the final definition.

RESULTS

From the initial survey, it was identified that a graduate did not require definitive spinal fusion after a growing program. From the Delphi session, it was determined that skeletal maturity was the most important factor in defining a graduate. A strictly defined minimum length of follow-up was not felt to be a prerequisite for qualification of graduation. After the final electronic version was distributed, > 80% of respondents agreed upon the final definition, thereby achieving consensus.

CONCLUSION

The Pediatric Spine Study Group recommends adoption of the following definition: a "graduate" is a patient who has undergone any surgical program to treat early onset scoliosis, and has reached skeletal maturity and does not have a planned surgical intervention for EOS in the future.

LEVEL OF EVIDENCE

V.

Interactions between programmable shunt valves and magnetically controlled growing rods for scoliosis

OBJECTIVE

Although the advent of magnetic growing rod technology for scoliosis has provided a means to bypass multiple hardware lengthening operations, it is important to be aware that many of these same patients have a codiagnosis of hydrocephalus with magnet-sensitive programmable ventricular shunts. As the magnetic distraction of scoliosis rods has not previously been described to affect the shunt valve setting, the authors conducted an investigation to characterize the interaction between the two devices.

METHODS

In this ex vivo study, the authors carried out 360 encounters between four different shunt valve types at varying distances from the magnetic external remote control (ERC) used to distract the growing rods. Valve settings were examined before and after every interaction with the remote control to determine if there was a change in the setting.

RESULTS

The Medtronic Strata and Codman Hakim valves were found to have setting changes at distances of 3 and 6 inches but not at 12 inches. The Aesculap proGAV and Codman Certas valves, typically described as MRI-resistant, did not have any setting changes due to the magnetic ERC regardless of distance.

CONCLUSIONS

Although it is not necessary to check a shunt valve after every magnetic distraction of scoliosis growing rods, if there is concern that the magnetic ERC may have been within 12 inches (30 cm) of a programmable ventricular shunt valve, the valve should be checked at the bedside with a programmer or with a skull radiograph along with postdistraction scoliosis radiographs.

Consistency and variation of protein subcellular location annotations

A major challenge for protein databases is reconciling information from diverse sources. This is especially difficult when some information consists of secondary, human-interpreted rather than primary data. For example, the Swiss-Prot database contains curated annotations of subcellular location that are based on predictions from protein sequence, statements in scientific articles, and published experimental evidence. The Human Protein Atlas (HPA) consists of millions of high-resolution microscopic images that show protein spatial distribution on a cellular and subcellular level. These images are manually annotated with protein subcellular locations by trained experts. The image annotations in HPA can capture the variation of subcellular location across different cell lines, tissues, or tissue states. Systematic investigation of the consistency between HPA and Swiss-Prot assignments of subcellular location, which is important for understanding and utilizing protein location data from the two databases, has not been described previously. In this paper, we quantitatively evaluate the consistency of subcellular location annotations between HPA and Swiss-Prot at multiple levels, as well as variation of protein locations across cell lines and tissues. Our results show that annotations of these two databases differ significantly in many cases, leading to proposed procedures for deriving and integrating the protein subcellular location data. We also find that proteins having highly variable locations are more likely to be biomarkers of diseases, providing support for incorporating analysis of subcellular location in protein biomarker identification and screening.

Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images

MOTIVATION

Systematic and comprehensive analysis of protein subcellular location as a critical part of proteomics ('location proteomics') has been studied for many years, but annotating protein subcellular locations and understanding variation of the location patterns across various cell types and states is still challenging.

RESULTS

In this work, we used immunohistochemistry images from the Human Protein Atlas as the source of subcellular location information, and built classification models for the complex protein spatial distribution in normal and cancerous tissues. The models can automatically estimate the fractions of protein in different subcellular locations, and can help to quantify the changes of protein distribution from normal to cancer tissues. In addition, we examined the extent to which different annotated protein pathways and complexes showed similarity in the locations of their member proteins, and then predicted new potential proteins for these networks.

AVAILABILITY AND IMPLEMENTATION

The dataset and code are available at: www.csbio.sjtu.edu.cn/bioinf/complexsubcellularpatterns.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

PD-1 suppresses the maintenance of cell couples between cytotoxic T cells and target tumor cells within the tumor

The killing of tumor cells by CD8⁺ T cells is suppressed by the tumor microenvironment, and increased expression of inhibitory receptors, including programmed cell death protein-1 (PD-1), is associated with tumor-mediated suppression of T cells. To find cellular defects triggered by tumor exposure and associated PD-1 signaling, we established an ex vivo imaging approach to investigate the response of antigen-specific, activated effector CD8⁺ tumor-infiltrating lymphocytes (TILs) after interaction with target tumor cells. Although TIL-tumor cell couples readily formed, couple stability deteriorated within minutes. This was associated with impaired F-actin clearing from the center of the cellular interface, reduced Ca²⁺ signaling, increased TIL locomotion, and impaired tumor cell killing. The interaction of CD8⁺ T lymphocytes with tumor cell spheroids in vitro induced a similar phenotype, supporting a critical role of direct T cell-tumor cell contact. Diminished engagement of PD-1 within the tumor, but not acute ex vivo blockade, partially restored cell couple maintenance and killing. PD-1 thus contributes to the suppression of TIL function by inducing a state of impaired subcellular organization.

Evaluation of methods for generative modeling of cell and nuclear shape

MOTIVATION

Cell shape provides both geometry for, and a reflection of, cell function. Numerous methods for describing and modeling cell shape have been described, but previous evaluation of these methods in terms of the accuracy of generative models has been limited.

RESULTS

Here we compare traditional methods and deep autoencoders to build generative models for cell shapes in terms of the accuracy with which shapes can be reconstructed from models. We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings. As expected, much higher accuracies were observed using high dimensional encodings, with outline-based methods significantly outperforming image-based autoencoders. The latter tended to encode all cells as having smooth shapes, even for high dimensions. For complex 3D cell shapes, we developed a significant improvement of a method based on the spherical harmonic transform that performs significantly better than other methods. We obtained similar results for the joint modeling of cell and nuclear shape. Finally, we evaluated the modeling of shape dynamics by interpolation in the shape space. We found that our modified method provided lower deformation energies along linear interpolation paths than other methods. This allows practical shape evolution in high dimensional shape spaces. We conclude that our improved spherical harmonic based methods are preferable for cell and nuclear shape modeling, providing better representations, higher computational efficiency and requiring fewer training images than deep learning methods.

AVAILABILITY AND IMPLEMENTATION

All software and data is available at http://murphylab.cbd.cmu.edu/software.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Image-derived models of cell organization changes during differentiation and drug treatments

PC12 cells are a popular model system to study changes driving and accompanying neuronal differentiation. While attention has been paid to changes in transcriptional regulation and protein signaling, much less is known about the changes in organization that accompany PC12 differentiation. Fluorescence microscopy can provide extensive information about these changes, although it is difficult to continuously observe changes over many days of differentiation. We describe a generative model of differentiation-associated changes in cell and nuclear shape and their relationship to mitochondrial distribution constructed from images of different cells at discrete time points. We show that the model accurately represents complex cell and nuclear shapes and learn a regression model that relates cell and nuclear shape to mitochondrial distribution; the predictive accuracy of the model increases during differentiation. Most importantly, we propose a method, based on cell matching and interpolation, to produce realistic simulations of the dynamics of cell differentiation from only static images. We also found that the distribution of cell shapes is hollow: most shapes are very different from the average shape. Finally, we show how the method can be used to model nuclear shape changes of human-induced pluripotent stem cells resulting from drug treatments.

Prospectively collected surgeon indications for discontinuation of a lengthening program for early-onset scoliosis

INTRODUCTION

At some point after children with early-onset scoliosis (EOS) undergo implantation of a distraction construct to control deformity and promote growth, a decision is made to discontinue lengthening. The purpose of this study was to evaluate surgeon indications for discontinuation of a lengthening program and to evaluate patient outcomes.

METHODS

As a part of a multicenter database, surgeons prospectively completed a questionnaire at the completion of growth-friendly treatment. Surgeon indications for discontinuation included patient age, pain/functional status, implant status, and spinal deformity parameters. Patient demographics, scoliosis type, deformity parameters, and length of time in a growing program were queried. Patients were treated with a final fusion or observation, and rate of secondary surgeries was analyzed.

RESULTS

Questionnaires were completed on 121 patients (61% female). EOS etiology was 31% neuromuscular, 43% congenital, 16% idiopathic, and 10% syndromic. Average age at initiation of growing program was 6.8 ± 3.1 years, and average age at discontinuation was 12.7 ± 2.5 years. The most commonly cited indications for discontinuation of a lengthening program included bone age/skeletal maturity (n = 46), patient age (n = 33), and diminishing returns with expansions (n = 33). A larger coronal Cobb angle was found in patients who underwent definitive fusion (65°) when compared with continued observation (55°, p = 0.001). Twenty-nine (24%) patients were initially treated with observation after completion of a growing construct. In this subgroup, at a minimum of 2 years' (average 3.8 years') follow-up, 26/29 (90%) patients remained stable with observation alone; whereas, three (10%) underwent delayed final fusion surgery.

CONCLUSIONS

The most common surgeon-cited indications for discontinuation of a lengthening program in EOS patients are skeletal maturity and patient age. The majority of patients (76%) underwent definitive spinal fusion after discontinuation of a lengthening program; whereas, those treated with observation alone had a survivorship of 90% at a minimum follow-up of two years.

Hemiepiphyseodesis for Juvenile and Adolescent Tibia Vara Utilizing Percutaneous Transphyseal Screws

BACKGROUND

In juvenile and adolescent tibia vara patients with sufficient growth remaining, implant-controlled hemiepiphyseodesis, or guided growth, can be used to correct deformity. Recent reports have described hardware failure of certain hemiepiphyseodesis implants in overweight patients with tibia vara. We describe our experience using transphyseal screws to correct deformity in this patient population.

METHODS

A retrospective chart and radiograph review was conducted on all juvenile and adolescent tibia vara patients who underwent lateral proximal tibial hemiepiphyseodesis using a single transphyseal screw. Charts were queried for preoperative and postoperative mechanical axis deviation, medial proximal tibial angle, lateral distal femoral angle, and postoperative complications or need for further surgery.

RESULTS

In total, 14 affected limbs in 9 patients (6 males) who underwent lateral proximal tibial transphyseal screw hemiepiphyseodesis were considered. Average chronologic age at implantation was 10.4 years and average body mass index was 31.7 kg/m. At average 23-month follow-up, the average mechanical axis deviation improved from 46 to 0 mm (P<0.001), and the average medial proximal tibial angle improved from 81 to 92 degrees (P<0.001). No limbs underwent further surgery to correct residual deformity. There were no complications or instances of implant failure associated with the transphyseal screws.

CONCLUSIONS

Hemiepiphyseodesis using transphyseal screws is an effective technique to correct deformity in juvenile and adolescent tibia vara patients with sufficient growth remaining. This method can be used safely with few complications and with minimal risk of mechanical failure, even in overweight patients.

LEVEL OF EVIDENCE

Level IV-therapeutic.

Diagnosis and Management of Common Conditions of the Pediatric Spine

Back pain and spinal deformity in the pediatric and adolescent patient population are common reasons for presentation to the orthopaedic surgeon, and although most conditions are benign and self-limiting, a standardized approach to the history and physical examination can identify concerning signs and symptoms as well as aid in determining the final diagnosis and a recommended treatment plan. The most common and concerning etiologies of back pain and spinal deformity will be reviewed, along with nonsurgical and surgical management of these conditions.

Transient protein accumulation at the center of the T cell antigen-presenting cell interface drives efficient IL-2 secretion

Supramolecular signaling assemblies are of interest for their unique signaling properties. A µm scale signaling assembly, the central supramolecular signaling cluster (cSMAC), forms at the center of the interface of T cells activated by antigen-presenting cells. We have determined that it is composed of multiple complexes of a supramolecular volume of up to 0.5 µm³ and associated with extensive membrane undulations. To determine cSMAC function, we have systematically manipulated the localization of three adaptor proteins, LAT, SLP-76, and Grb2. cSMAC localization varied between the adaptors and was diminished upon blockade of the costimulatory receptor CD28 and deficiency of the signal amplifying kinase Itk. Reconstitution of cSMAC localization restored IL-2 secretion which is a key T cell effector function as dependent on reconstitution dynamics. Our data suggest that the cSMAC enhances early signaling by facilitating signaling interactions and attenuates signaling thereafter through sequestration of a more limited set of signaling intermediates.

Cells receive dozens of signals at different times and in different places. Integrating incoming information and deciding how to respond is no easy task. Signaling molecules on the cell surface pass messages inwards using chemical messengers that interact in complicated networks within the cell. One way to unravel the complexity of these networks is to look at specific groups of signaling molecules in test tubes to see how they interact. But the interior of a living cell is a very different environment. Molecules inside cells are tightly packed and, under certain conditions, they interact with each other by the thousands. They form structures known as ‘supramolecular complexes’, which changes their behavior.

One such supramolecular complex is the ‘central supramolecular activation cluster’, or cSMAC for short. It forms under the surface of immune cells called T cells when they are getting ready to fight an infection. Under the microscope, the cSMAC looks like the bullseye of a dartboard, forming a crowd of signaling molecules at the center of the interface between the T cell and another cell. Its exact role is not clear, but evidence suggests it helps to start and stop the signals that switch T cells on. The cSMAC contains two key protein adaptors called LAT and SLP-76 that help to hold the structure together. So, to find out what the cSMAC does, Clark et al. genetically modified these adaptors to gain control over when the cSMAC forms.

Clark et al. examined mouse T cells using super-resolution microscopy and electron microscopy, watching as other immune cells delivered the signal to switch on. As the T cells started to activate, the composition of the cSMAC changed. In the first two minutes after the cells started activating, the cSMAC included a large number of different components. This made T cell activation more efficient, possibly because the supramolecular complex was helping the network of signals to interact. Later, the cSMAC started to lose many of these components. Separating components may have helped to stop the activation signals.

Understanding how T cells activate could lead to the possibility of turning them on or off in immune-related diseases. But these findings are not just relevant to immune cells. Other cells also use supramolecular complexes to control their signaling. Investigating how these complexes change over time could help us to understand how other cell types make decisions.

A rare case of type 2 entrapment of the median nerve after posterior elbow dislocation with MRI and ultrasound correlation

A 9-year-old boy sustained an ulnohumeral dislocation with a medial epicondyle fracture and experienced incomplete post-traumatic median nerve palsy in addition to post-traumatic stiffness following closed reduction and cast immobilization. When his motor palsy and stiffness did not improve, MRI and ultrasound were obtained, which demonstrated entrapment of the median nerve in an osseous tunnel at the fracture site, compatible with type 2 median nerve entrapment. Subsequently, the patient underwent surgery to mobilize the medial epicondyle and free the median nerve, resulting in improved range of motion, near complete restoration of motor function, and complete restoration of sensory function in the median nerve distribution within 6 months of surgery. Median nerve entrapment, particularly intraosseous, is a rare complication of posterior elbow dislocation and medial epicondyle fracture that may result in significant, sometimes irreversible, nerve damage if there is a delay in diagnosis and treatment. A high degree of clinical suspicion with early imaging is indicated in patients with persistent stiffness or nerve deficits following reduction of an elbow dislocation. Intra-articular entrapment diagnosed on ultrasound has been reported and intraosseous entrapment diagnosed clinically and on MR neurography have been reported; however, to our knowledge, this is the first reported case of intraosseous (type 2) median nerve entrapment clearly visualized and diagnosed on traditional MRI and ultrasound. The use of ultrasound for diagnosing median nerve entrapment is an accurate, accessible, and non-invasive imaging option for patients presenting with suspected nerve entrapment following elbow dislocation.

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions.

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes

Protein complexes play a significant role in the core functionality of cells. These complexes are typically identified by detecting densely connected subgraphs in protein-protein interaction (PPI) networks. Recently, multiple large-scale mass spectrometry-based experiments have significantly increased the availability of PPI data in order to further expand the set of known complexes. However, high-throughput experimental data generally are incomplete, show limited agreement between experiments, and show frequent false positive interactions. There is a need for computational approaches that can address these limitations in order to improve the coverage and accuracy of human protein complexes. Here, we present a new method that integrates data from multiple heterogeneous experiments and sources in order to increase the reliability and coverage of predicted protein complexes. We first fused the heterogeneous data into a feature matrix and trained classifiers to score pairwise protein interactions. We next used graph based methods to combine pairwise interactions into predicted protein complexes. Our approach improves the accuracy and coverage of protein pairwise interactions, accurately identifies known complexes, and suggests both novel additions to known complexes and entirely new complexes. Our results suggest that integration of heterogeneous experimental data helps improve the reliability and coverage of diverse high-throughput mass-spectrometry experiments, leading to an improved global map of human protein complexes.

Current concepts in neuromuscular scoliosis

PURPOSE OF REVIEW

Spinal deformity is a common issue in pediatric patients with an underlying neurological diagnosis or syndrome. Management of neuromuscular scoliosis (NMS) is a major part of the orthopedic care of such patients, as the deformity is often progressive, and may affect gait, seating and positioning. In addition, untreated large spinal deformities may be associated with pain and/or cardiopulmonary issues over time.

RECENT FINDINGS

Recent changes in medical management of the underlying disease process appears to alter the natural history of certain neuromuscular conditions, and in the case of patients with Duchenne's muscular dystrophy significantly diminish the incidence of spinal deformity. In the most common diagnosis associated with NMS, cerebral palsy, there is evidence that despite a high complication rate, surgical management of spinal deformity is associated with measurable improvements in validated health-related quality-of-life measures. Spinal deformity is a common finding in patients with neurological diagnoses. It is important for those involved in the care of these patients to understand the natural history of NMS, as well as the potential risks and benefits to the patient and caregivers, of surgical and non-surgical interventions.

Learning Generative Models of Tissue Organization with Supervised GANs

A key step in understanding the spatial organization of cells and tissues is the ability to construct generative models that accurately reflect that organization. In this paper, we focus on building generative models of electron microscope (EM) images in which the positions of cell membranes and mitochondria have been densely annotated, and propose a two-stage procedure that produces realistic images using Generative Adversarial Networks (or GANs) in a supervised way. In the first stage, we synthesize a label "image" given a noise "image" as input, which then provides supervision for EM image synthesis in the second stage. The full model naturally generates label-image pairs. We show that accurate synthetic EM images are produced using assessment via (1) shape features and global statistics, (2) segmentation accuracies, and (3) user studies. We also demonstrate further improvements by enforcing a reconstruction loss on intermediate synthetic labels and thus unifying the two stages into one single end-to-end framework.

Sagittal plane parameters in growing rod patients following final fusion

Almost half of growing rod (GR) patients that undergo final fusion (FF) have an extension of instrumented levels. The purpose of this study was to review sagittal plane radiographic parameters of patients with distal extension of instrumented levels at FF to those whose levels remained the same. Radiographs were assessed preoperatively, after GR insertion/first lengthening, following GR treatment before FFs, and after FF. Measurements included sagittal balance, lumbar lordosis, thoracic kyphosis, and distal junction angle (DJA). Twenty-one patients were included. There was no change in sagittal balance. There was a significant decrease in lordosis and kyphosis following initial GR implantation. Kyphosis and lordosis increased during the GR period, but remained unchanged at time of FF. DJA increased 8° on average. Seven patients had distal extension of instrumented levels at time of FF (average 2 levels, range: 1-4). Indication for distal extension was sagittal plane decompensation in four cases. When comparing patients who had distal extension at the time of FF to those whose levels remained the same, there was no difference in the change in sagittal balance, lordosis, or kyphosis. Final DJA was significantly smaller in those patients with distal extension. Most GR patients that undergo FF demonstrate acceptable correction of sagittal plane radiographic parameters. A small cohort of patients requires distal extension at FF due to sagittal plane decompensation.

LEVEL OF EVIDENCE

Level IV, Therapeutic.

Periacetabular osteotomy for developmental hip dysplasia with labral tears: is arthrotomy or arthroscopy required?

Patients with developmental dysplasia of the hip (DDH) who undergo periacetabular osteotomy (PAO) often have labral tears. The objective of this retrospective study was to compare PAO alone with PAO combined with arthrotomy or arthroscopy in DDH patients who had a full-thickness labral tear on magnetic resonance imaging. In total, 47 hips in the PAO group (PAO) were compared with 60 hips in the PAO with concomitant arthrotomy or arthroscopy (PAO-A) with respect to Hip Disability and Osteoarthritis Outcome Score (HOOS), modified Harris Hip Score (mHHS), Visual Analog Scale (VAS), clinical and radiographic outcomes at a median of 29 months. Reoperation rate and complications were compared between two groups of treatment. The PAO group was younger than the PAO-A group (25.2 ± 9.7 versus 31.3 ± 8.3). The PAO group was more likely to have worse dysplasia: lateral center edge angle (7.6°±9.63° versus 10.8°±6.85°) and anterior center edge angle (4°±12.92° versus 10.8°±9.92°). The PAO group had a higher preoperative mHHS (65.2 ± 15.3 versus 57.8 ± 14.8) and HOOS (66.3 ± 17.5 versus 55.8 ± 20.1). There were no significant differences in final functional outcome scores across treatment groups: mHHS (PAO; 86.8 ± 12.4 versus PAO-A, 83.3 ± 17.2), HOOS (86.5 ± 13.3 versus 82.5 ± 16.8) and VAS (2.5 ± 2.8 versus 2.5 ± 3.1). There was no difference in reoperation rate between two groups (6.4% versus 11.6%, P = 0.51). The overall complication rate was lower in the PAO group (26% versus 68%), but major complications were comparable. On the basis of our data, we were not able to conclusively demonstrate a clear benefit for the routine treatment of all labral tears; however, arthrotomy or arthroscopy may play a role in some conditions.

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

Upstream open reading frames (uORFs), located in transcript leaders (5' UTRs), are potent cis-acting regulators of translation and mRNA turnover. Recent genome-wide ribosome profiling studies suggest that thousands of uORFs initiate with non-AUG start codons. Although intriguing, these non-AUG uORF predictions have been made without statistical control or validation; thus, the importance of these elements remains to be demonstrated. To address this, we took a comparative genomics approach to study AUG and non-AUG uORFs. We mapped transcription leaders in multiple Saccharomyces yeast species and applied a novel machine learning algorithm (uORF-seqr) to ribosome profiling data to identify statistically significant uORFs. We found that AUG and non-AUG uORFs are both frequently found in Saccharomyces yeasts. Although most non-AUG uORFs are found in only one species, hundreds have either conserved sequence or position within Saccharomyces uORFs initiating with UUG are particularly common and are shared between species at rates similar to that of AUG uORFs. However, non-AUG uORFs are translated less efficiently than AUG-uORFs and are less subject to removal via alternative transcription initiation under normal growth conditions. These results suggest that a subset of non-AUG uORFs may play important roles in regulating gene expression.

Image-based spatiotemporal causality inference for protein signaling networks

Motivation

Efforts to model how signaling and regulatory networks work in cells have largely either not considered spatial organization or have used compartmental models with minimal spatial resolution. Fluorescence microscopy provides the ability to monitor the spatiotemporal distribution of many molecules during signaling events, but as of yet no methods have been described for large scale image analysis to learn a complex protein regulatory network. Here we present and evaluate methods for identifying how changes in concentration in one cell region influence concentration of other proteins in other regions.

Results

Using 3D confocal microscope movies of GFP-tagged T cells undergoing costimulation, we learned models containing putative causal relationships among 12 proteins involved in T cell signaling. The models included both relationships consistent with current knowledge and novel predictions deserving further exploration. Further, when these models were applied to the initial frames of movies of T cells that had been only partially stimulated, they predicted the localization of proteins at later times with statistically significant accuracy. The methods, consisting of spatiotemporal alignment, automated region identification, and causal inference, are anticipated to be applicable to a number of biological systems.

Availability and implementation

The source code and data are available as a Reproducible Research Archive at http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/

Orthobiologics in Pediatric Orthopedics

Orthobiologics are biologic devices or products used in orthopedic surgery to augment or enhance bone formation. The use of orthobiologics in pediatric orthopedics is less frequent than in other orthopedic subspecialties, mainly due to the naturally abundant healing potential and bone formation in children compared with adults. However, orthobiologics are used in certain situations in pediatric orthopedics, particularly in spine and foot surgery. Other uses have been reported in conjunction with specific procedures involving the tibia and pelvis. The use of bioabsorable implants to stabilize children's fractures is an emerging concept but has limited supporting data.

Plasma and cerebrospinal fluid pharmacokinetics of doxil after intravenous administration in adults with primary CNS lymphoma

e14067

Background: Doxil, a pegylated liposomal doxorubicin (PLD) has excellent CNS penetration in rodent brain tumor models and is active in patients with lymphoma. The CNS penetration of doxil in humans is unknown. We evaluated the plasma and cerebrospinal fluid (CSF) pharmacokinetics (PK) of doxil in adults primary CNS lymphoma (PCNSL) as a surrogate for CNS penetration. Methods: Adults with PCNSL enrolled on a NCI phase I study of ibrutinib and multi-agent immune-chemotherapy (NCT02203526) received doxil 50 mg/m2 IV over 1 hour on day 2 of 21-day cycles of chemotherapy. In 4 patients with indwelling Ommaya reservoirs serial blood and CSF samples were obtained prior to infusion and until a median of 345 hours, (range 72-477 hours) after doxil administration. Total doxorubicin concentration (liposome bound + protein bound + free) was quantified with a validated liquid chromatography/tandem mass spectrometry assay (lower limit of quantification plasma=0.29 ng/mL, and CSF=0.06 ng/mL). PK parameters were estimated using non-compartmental methods. CSF penetration was calculated from the AUCCSF:AUCplasma. Results:Total doxorubicin plasma concentration time curves were characterized by sustained drug exposure and a median terminal half-life of 64.5 hours. (range, 61.9-65.1 hours). Doxorubicin was measurable in CSF in all patients, but CSF penetration was low. The terminal half-life of doxorubicin in CSF could not be calculated due to persistently measurable concentrations throughout the sampling times. Conclusions: In patients with PCNSL doxorubicin was measurable in CSF for prolonged time periods after doxil administration, but CSF penetration is low. Clinical trial information: NCT02203526. [Table: see text]

Degradation of protein translation machinery by amino acid starvation-induced macroautophagy

Macroautophagy is regarded as a nonspecific bulk degradation process of cytoplasmic material within the lysosome. However, the process has mainly been studied by nonspecific bulk degradation assays using radiolabeling. In the present study we monitor protein turnover and degradation by global, unbiased approaches relying on quantitative mass spectrometry-based proteomics. Macroautophagy is induced by rapamycin treatment, and by amino acid and glucose starvation in differentially, metabolically labeled cells. Protein dynamics are linked to image-based models of autophagosome turnover. Depending on the inducing stimulus, protein as well as organelle turnover differ. Amino acid starvation-induced macroautophagy leads to selective degradation of proteins important for protein translation. Thus, protein dynamics reflect cellular conditions in the respective treatment indicating stimulus-specific pathways in stress-induced macroautophagy.

A method for characterizing phenotypic changes in highly variable cell populations and its application to high content screening of Arabidopsis thaliana protoplasts

Quantitative image analysis procedures are necessary for the automated discovery of effects of drug treatment in large collections of fluorescent micrographs. When compared to their mammalian counterparts, the effects of drug conditions on protein localization in plant species are poorly understood and underexplored. To investigate this relationship, we generated a large collection of images of single plant cells after various drug treatments. For this, protoplasts were isolated from six transgenic lines of A. thaliana expressing fluorescently tagged proteins. Eight drugs at three concentrations were applied to protoplast cultures followed by automated image acquisition. For image analysis, we developed a cell segmentation protocol for detecting drug effects using a Hough transform-based region of interest detector and a novel cross-channel texture feature descriptor. In order to determine treatment effects, we summarized differences between treated and untreated experiments with an L₁ Cramér-von Mises statistic. The distribution of these statistics across all pairs of treated and untreated replicates was compared to the variation within control replicates to determine the statistical significance of observed effects. Using this pipeline, we report the dose dependent drug effects in the first high-content Arabidopsis thaliana drug screen of its kind. These results can function as a baseline for comparison to other protein organization modeling approaches in plant cells. © 2017 International Society for Advancement of Cytometry.

Allograft Bone Use in Pediatric Subaxial Cervical Spine Fusions

BACKGROUND

The use of freeze-dried allograft as a bone graft substitute for pediatric spine surgery is safe and efficacious in the thoracic and lumbar spines. Allograft bone use in segmental instrumented fusions in the subaxial cervical spine has not been well reported in the literature. We sought to describe our experience with allograft bone in this patient cohort, and to compare union rates to patients treated with autograft.

METHODS

Medical records were queried over a 10-year time period (2004 to 2014). Inclusion criteria were all pediatric patients (18 y old and below) who underwent subaxial cervical spine fusion with minimum follow-up of 24 months. Variables queried included demographics, type of graft material used, diagnosis, approach (anterior, posterior, combined), levels instrumented, placement of postoperative halo, surgical-related complications, and achievement of fusion.

RESULTS

A total of 26 patients qualified for inclusion (18 allograft, 8 autograft). No differences existed between the 2 groups regarding age, sex, or number of fused levels. In the allograft cohort, average age at initial surgery was 13.3 years (range, 5 to 18 y). The most common reasons for surgery included trauma (6), tumor (3), and syndrome-associated kyphosis (3). The average number of instrumented levels was 4 (range, 2 to 13). Four patients (22%) developed a postoperative surgical complication. There were 2 asymptomatic pseudarthroses not requiring revision. At a minimum of 24-month follow-up (average, 45 mo; range, 24 to 121 mo), the allograft group demonstrated a fusion rate of 88%, which was comparable with a fusion rate of 87% in the autograft group.

CONCLUSIONS

The use of allograft bone for pediatric subaxial instrumented cervical spine fusions is safe in a variety of conditions, with the same rate of fusion as autograft. Rates of complications are acceptable. To avoid donor-site morbidity from autogenous graft harvest, we recommend considering allograft bone in subaxial cervical spine fusions with modern segmental instrumentation.

LEVEL OF EVIDENCE

Level IV-case series; therapeutic.

Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition

As a central element within the RAS/ERK pathway, the serine/threonine kinase BRAF plays a key role in development and homeostasis and represents the most frequently mutated kinase in tumors. Consequently, it has emerged as an important therapeutic target in various malignancies. Nevertheless, the BRAF activation cycle still raises many mechanistic questions as illustrated by the paradoxical action and side effects of RAF inhibitors. By applying SEC-PCP-SILAC, we analyzed protein-protein interactions of hyperactive BRAF^V600E and wild-type BRAF (BRAF^WT). We identified two macromolecular, cytosolic BRAF complexes of distinct molecular composition and phosphorylation status. Hyperactive BRAF^V600E resides in large complexes of higher molecular mass and activity, while BRAF^WT is confined to smaller, slightly less active complexes. However, expression of oncogenic K-Ras^G12V, either by itself or in combination with RAF dimer promoting inhibitors, induces the incorporation of BRAF^WT into large, active complexes, whereas pharmacological inhibition of BRAF^V600E has the opposite effect. Thus, the quaternary structure of BRAF complexes is shaped by its activation status, the conformation of its kinase domain, and clinically relevant inhibitors.

Systems Imaging of the Immune Synapse

Three-dimensional live cell imaging of the interaction of T cells with antigen-presenting cells (APCs) visualizes the subcellular distributions of signaling intermediates during T cell activation at thousands of resolved positions within a cell. These information-rich maps of local protein concentrations are a valuable resource in understanding T cell signaling. Here, we describe a protocol for the efficient acquisition of such imaging data and their computational processing to create four-dimensional maps of local concentrations. This protocol allows quantitative analysis of T cell signaling as it occurs inside live cells with resolution in time and space across thousands of cells.

Complications following spine fusion for adolescent idiopathic scoliosis

Complications following spine fusion for adolescent idiopathic scoliosis can be characterized as either intra-operative or post-operative. The most serious and feared complication is neurologic injury, both in the intra- and post-operative period. Other intra-operative complications include dural tears and ophthalmologic or peripheral nerve deficits, which may be related to positioning. Among the most common post-operative complications are surgical site infection, venous thromboembolism, gastrointestinal complications, and implant-related complications. Significant blood loss requiring transfusion, traditionally considered a known sequelae of spine fusion, is now being recognized as a "complication" in large national databases. Pediatric spine surgeons who care for patients with AIS must be thoroughly familiar with all potential complications and their management.

Sequence-Specific Pharmacokinetic and Pharmacodynamic Phase I/Ib Study of Olaparib Tablets and Carboplatin in Women's Cancer

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.

Point process models for localization and interdependence of punctate cellular structures

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry.

Use of Vertical Expandable Prosthetic Titanium Rib (VEPTR) in the Treatment of Congenital Scoliosis Without Fused Ribs

BACKGROUND

Although the vertical expandable prosthetic titanium rib (VEPTR) has been shown to be useful in treating congenital scoliosis (CS) with fused ribs, no studies to date have specifically evaluated the efficacy of VEPTR in the treatment of CS without fused ribs. The purpose of this study was to determine the effectiveness of VEPTR in sagittal/coronal curve correction and spine growth and compare its complication rate to the use of VEPTR in other conditions and to other treatment methods used for CS.

METHODS

A multicenter database was queried for patients with CS without fused ribs treated with VEPTR. Anteroposterior (AP) and lateral radiographs were used to measure parameters at 3 timepoints (preoperative, immediate postoperative, and latest follow-up): coronal Cobb angle, sagittal kyphosis, and thoracic and lumbar spine heights. Clinical data included age, time to follow-up, and complications.

RESULTS

Twenty-five patients (13 females, 12 males) were identified. The average age at implantation was 5.7 years, with an average follow-up of 50 months. Several parameters improved from preoperative to latest follow-up: coronal Cobb angle (69 to 54 degrees, P<0.0001), thoracic spine height (T1-T12) in the AP (13.3 to 15.9 cm, P<0.0001) and lateral (14.8 to 17.4 cm, P=0.0024) planes, and lumbar spine height (L1-S1) in the AP (8.8 to 11.4 cm, P<0.0001) and lateral (9.9 to 11.9 cm, P=0.0002) planes. Kyphosis increased over the study period (36 to 41 degrees, P=0.6). Fifteen patients (60%) had 41 complications (average 2.75; range, 1 to 12). Twenty-eight complications (68%) were device-related, and 13 (32%) were disease-related. The most common complications were infection, wound dehiscence, and device migration. Six complications (15%) altered the course of treatment. Thoracic spine height increased 79% of expected growth.

CONCLUSION

VEPTR is an effective treatment for patients with CS without fused ribs, as evidenced by improved radiographic parameters and increased spinal height, with a complication rate which is high but similar to other methods of treatment.

LEVEL OF EVIDENCE

Level IV-case series.

Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics

Fluorescence microscopy is one of the most important tools in cell biology research because it provides spatial and temporal information to investigate regulatory systems inside cells. This technique can generate data in the form of signal intensities at thousands of positions resolved inside individual live cells. However, given extensive cell-to-cell variation, these data cannot be readily assembled into three- or four-dimensional maps of protein concentration that can be compared across different cells and conditions. We have developed a method to enable comparison of imaging data from many cells and applied it to investigate actin dynamics in T cell activation. Antigen recognition in T cells by the T cell receptor (TCR) is amplified by engagement of the costimulatory receptor CD28. We imaged actin and eight core actin regulators to generate over a thousand movies of T cells under conditions in which CD28 was either engaged or blocked in the context of a strong TCR signal. Our computational analysis showed that the primary effect of costimulation blockade was to decrease recruitment of the activator of actin nucleation WAVE2 (Wiskott-Aldrich syndrome protein family verprolin-homologous protein 2) and the actin-severing protein cofilin to F-actin. Reconstitution of WAVE2 and cofilin activity restored the defect in actin signaling dynamics caused by costimulation blockade. Thus, we have developed and validated an approach to quantify protein distributions in time and space for the analysis of complex regulatory systems.