Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas

BACKGROUND AND PURPOSE

The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation.

MATERIALS AND METHODS

MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 (IDH1) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification.

RESULTS

Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features.

CONCLUSIONS

Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training.

Features of diffuse gliomas that are misdiagnosed on initial neuroimaging: a case control study

PURPOSE

The neuroimaging diagnosis of diffuse gliomas can be challenging owing to their variable clinical and radiologic presentation. The purpose of this study was to identify factors that are associated with imaging errors in the diagnosis of diffuse gliomas.

METHODS

A retrospective case-control analysis was undertaken. 18 misdiagnosed diffuse gliomas on initial neuroimaging (cases) and 108 accurately diagnosed diffuse gliomas on initial neuroimaging (controls) were collected. Clinical, pathological, and imaging metrics were tabulated for each patient. The tabulated metrics were compared between cases and controls to determine factors associated with misdiagnosis.

RESULTS

Cases of misdiagnosed diffuse glioma (vs controls) were more likely to undergo initial triage as a stroke workup [OR 14.429 (95% CI 4.345, 47.915), p < 0.0001], were less likely to enhance [OR 0.283 (95% CI 0.098, 0.812), p = 0.02], were smaller (mean diameter 4.4 vs 6.0 cm, p = 0.0008), produced less midline shift (median midline shift 0.0 vs 2.0 mm, p = 0.003), were less likely to demonstrate necrosis [OR 0.156 (95% CI 0.034-0.713), p = 0.008], and were less likely to have IV contrast administered on the initial MRI [OR 0.100 (95% CI 0.020, 0.494), p = 0.008].

CONCLUSION

Several clinical and radiologic metrics are associated with diffuse gliomas that are missed or misdiagnosed on the initial neuroimaging study. Knowledge of these associations may aid in avoiding misinterpretation and accurately diagnosing such cases in clinical practice.

"Left to my own devices, I don't know": using theory and patient-reported barriers to move from physical activity recommendations to practice

Knowledge exchange with community-dwelling individuals across Ontario revealed barriers to implementation of physical activity recommendations that reflected capability, opportunity, and motivation; barriers unique to individuals with osteoporosis include fear of fracturing, trust in providers, and knowledge of exercise terminology. Using the Behaviour Change Wheel, we identified interventions (training, education, modeling) and policy categories (communication/marketing, guidelines, service provision).

INTRODUCTION

Physical activity recommendations exist for individuals with osteoporosis; however, to change behavior, we must address barriers and facilitators to their implementation. The purposes of this project are (1) to identify barriers to and facilitators of uptake of disease-specific physical activity recommendations (2) to use the findings to identify behavior change strategies using the Behaviour Change Wheel (BCW).

METHODS

Focus groups and semi-structured interviews were conducted with community-dwelling individuals attending osteoporosis-related programs or education sessions in Ontario. They were stratified by geographic area, urban/rural, and gender, and transcribed verbatim. Two researchers coded data and identified emerging themes. Using the Behaviour Change Wheel framework, themes were categorized into capability, opportunity, and motivation, and interventions were identified.

RESULTS

Two hundred forty community-dwelling individuals across Ontario participated (mean ± SD age = 72 ± 8.28). Barriers were as follows: capability: disease-related symptoms hinder exercise and physical activity participation, lack of exercise-related knowledge, low exercise self-efficacy; opportunity: access to exercise programs that meet needs and preferences, limited resources and time, physical activity norms and preferences; motivation: incentives to exercise, fear of fracturing, trust in exercise providers. Interventions selected were training, education, and modeling. Policy categories selected were communication/marketing, guidelines, and service provision.

CONCLUSIONS

Barriers unique to individuals with osteoporosis included the following: lack of knowledge on key exercise concepts, fear of fracturing, and trust in providers. Behavior change techniques may need tailoring to gender, age, or presence of comorbid conditions.

Combined immunosuppression and radiotherapy in thyroid eye disease (CIRTED): a multicentre, 2 × 2 factorial, double-blind, randomised controlled trial

BACKGROUND

Standard treatment for thyroid eye disease is with systemic corticosteroids. We aimed to establish whether orbital radiotherapy or antiproliferative immunosuppression would confer any additional benefit.

METHODS

CIRTED was a multicentre, double-blind, randomised controlled trial with a 2 × 2 factorial design done at six centres in the UK. Adults with active moderate-to-severe thyroid eye disease associated with proptosis or ocular motility restriction were recruited to the trial. Patients all received a 24 week course of oral prednisolone (80 mg per day, reduced to 20 mg per day by 6 weeks, 10 mg per day by 15 weeks, and 5 mg per day by 21 weeks) and were randomly assigned via remote computerised randomisation to receive either radiotherapy or sham radiotherapy and azathioprine or placebo in a 2 × 2 factorial design. Randomisation included minimisation to reduce baseline disparities in potential confounding variables between trial interventions. Patients and data analysts were masked to assignment, whereas trial coordinators (who monitored blood results), pharmacists, and radiographers were not. The radiotherapy dose was 20 Gy administered to the retrobulbar orbit in ten to 12 fractions over 2 to 3 weeks. Azathioprine treatment was provided for 48 weeks at 100-200 mg per day (dispensed as 50 mg tablets), depending on bodyweight (100 mg for <50 kg, 150 mg 50-79 kg, 200 mg for ≥80 kg). The primary outcomes were a binary composite clinical outcome score and an ophthalmopathy index at 48 weeks, and a clinical activity score at 12 weeks. The primary analysis was based on the intention-to-treat allocation and safety was assessed in all participants. This study is registered with ISRCTN, number 22471573.

FINDINGS

Between Feb 15, 2006, and Oct 3, 2013, 126 patients were recruited and randomly assigned to groups: 31 patients to radiotherapy plus azathioprine, 31 to sham radiotherapy and azathioprine, 32 to radiotherapy and placebo, and 32 to sham radiotherapy and placebo. Outcome data were available for 103 patients (54 for sham radiotherapy vs 49 for radiotherapy and 53 for placebo vs 50 for azathioprine), of whom 84 completed their allocated treatment of radiotherapy or sham radiotherapy and 57 continued to take azathioprine or placebo up to 48 weeks. There was no interaction betweeen azathioprine and radiotherapy (p_interaction=0·86). The adjusted odds ratio (OR_adj) for improvement in the binary clinical composite outcome measure was 2·56 (95% CI 0·98-6·66, p=0·054) for azathioprine and 0·89 (0·36-2·23, p=0·80) for radiotherapy. In a post-hoc analysis of patients who completed their allocated therapy the OR_adj for improvement was 6·83 (1·66-28·1, p=0·008) for azathioprine and 1·32 (0·30-4·84, p=0·67) for radiotherapy. The ophthalmopathy index, clinical activity score, and numbers of adverse events (161 with azathioprine and 156 with radiotherapy) did not differ between treatment groups. In both groups, the most common adverse events were mild infections. No patients died during the study.

INTERPRETATION

In patients receiving oral prednisolone for 24 weeks, radiotherapy did not have added benefit. We also did not find added benefit for addition of azathioprine in the primary analysis; however, our conclusions are limited by the high number of patients who withdrew from treatment. Results of post-hoc analysis of those who completed the assigned treatment suggest improved clinical outcome at 48 weeks with azathioprine treatment.

FUNDING

National Eye Research Centre, Above and Beyond, and Moorfields Eye Charity.

Facile Fabrication of Durable Copper-Based Superhydrophobic Surfaces via Electrodeposition

Superhydrophobic surfaces have myriad industrial applications, yet their practical utilization has been limited by their poor mechanical durability and longevity. We present a low-cost, facile process to develop superhydrophobic copper-based coatings via an electrodeposition route, that addresses this limitation. Through electrodeposition, a stable, multiscale, cauliflower shaped fractal morphology was obtained and upon modification by stearic acid, the prepared coatings show extreme water repellency with contact angle of 162 ± 2° and roll-off angle of about 3°. Systematic studies are presented on coatings fabricated under different processing conditions to demonstrate good durability, mechanical and underwater stability, corrosion resistance, and self-cleaning effect. The study also presents an approach for rejuvenation of slippery superhydrophobic nature (roll-off angle <10°) on the surfaces after long-term water immersion. The presented process can be scaled to larger, durable coatings with controllable wettability for diverse applications.

p-Hexafluoroisopropanol phenyl functionalized graphene for QCM based detection of dimethyl methylphosphonate, a simulant of the nerve agent sarin

The detection of DMMP (dimethyl methylphosphonate, a simulant of nerve agent sarin) was performed by using p-hexafluoroisopropanol phenyl (HFIPP) functionalized graphene (GR) via hydrogen bond interactions. For this, the HFIPP moiety was covalently functionalized on the surface of GR by a diazo reaction. The HFIPP-GR film-modified QCM electrodes were fabricated and their sensing characteristics towards DMMP were investigated. The proposed sensor showed good response towards sensing DMMP vapor at room temperature. In order to see the effect of HFIPP derivatives on DMMP vapor sensing, a comparative study was also conducted with unfunctionalized graphene. The sensitivity and detection limit of the HFIPP-GR sensor against DMMP vapors were 12.24 Hz ppm-1 and 150 ppb respectively. The HFIPP-GR coated sensors showed good selectivity towards sensing DMMP vapors when compared with common organic vapors.

Optimization of antimicrobial therapy in vancomycin-resistant enterococcal bacteraemia using a rapid detection Gram-positive blood culture assay

Rapid molecular blood culture Gram-positive (BC-GP) assay can promptly identify vancomycin-resistant enterococcal (VRE) bloodstream infections (BSIs). We sought to evaluate patients with VRE BSI following the pre (N = 44) and post (N = 20) implementation of Verigene BC-GP assay. The average time to detection of VRE was 25.9 ± 4.1h (95% confidence interval (CI): 17.6-34.1; P < 0.001) earlier with Verigene BC-GP assay. Compared to patients in the pre-Verigene BC-GP period, the mean adjusted difference in time to administration of anti-VRE therapy was 18.2 ± 7.8h (95% CI: 2.5-33.8; P = 0.024) earlier among patients in the post-Verigene BC-GP period.

Equal treatment: no evidence of gender inequity in osteoporosis management in a coordinator-based fragility fracture screening program

We evaluated gender imbalance in osteoporosis management in a provincial coordinator-based fracture prevention program and found no difference by gender in treatment of high-risk fragility fracture patients. This establishes that a systemic approach with interventions for all fragility fracture patients can eliminate the gender inequity that is often observed.

INRODUCTION

The purpose of this study was to evaluate an Ontario-based fracture prevention program for its ability to address the well-documented gender imbalance in osteoporosis (OP) management, by incorporating its integrated fracture risk assessments within a needs-based evaluation of equity.

METHODS

Fragility fracture patients (≥ 50 years) who were treatment naïve at screening and completed follow-up within 6 months of screening were studied. Patients who underwent bone mineral density (BMD) testing done in the year prior to their current fracture were excluded. All participants had BMD testing conducted through the Ontario OP Strategy Fracture Screening and Prevention program, thus providing us with fracture risk assessment data. Our primary study outcome was treatment initiation at follow-up within 6 months of screening. Gender differences were compared using Fisher's exact test, at p < 0.05.

RESULTS

After adjusting for subsequent fracture risk, study participants did not show a statistically significant gender difference in pharmacotherapy initiation at follow-up (p > 0.05). 68.4% of women and 66.2% of men at high risk were treated within 6 months of screening.

CONCLUSION

Needs-based analyses show no difference by gender in treatment of high-risk fragility fracture patients. An intensive coordinator-based fracture prevention model adopted in Ontario, Canada was not associated with gender inequity in OP treatment of fragility fracture patients after fracture risk adjustment.

Engraftment Syndrome: Clinical Features and Predictive Factors in Autologous Stem Cell Transplant

Engraftment Syndrome (ES) maybe observed in patients who undergo autologous stem cell transplant (SCT). To investigate clinical criteria for ES diagnosis and analyse the risk factors for this complication, we reviewed all auto-SCT cases (Lymphoma and Myeloma) performed during the past 9 years at two tertiary care centres. We analysed all patients with a non-infectious fever, developed within 7 days of engraftment (first day of ANC of 500 on two consecutive days) in 178 patients undergoing autologous stem cell transplant. A total of 46/178 (25.8%) patients developed non-infectious fever and one or more clinical signs of ES within 7 days of engraftment. In all, 29 (61%) fulfilled the Maiolino and 12 (26%) the Spitzer criteria. The incidence of engraftment syndrome using the Maiolino criteria in our study was 29 (15%), which compares well with Spanish study (13% using same criteria) and the original Maiolino study (20%). All patients with ES satisfactorily recovered and discharged with a median of 20 days from hospital. There was no significant difference in number of days of hospitalisation and days of antibiotics between the ES and non ES arms. All patients recovered without any morbidity and only 1 (2%) patient required readmission for fungal pneumonitis. 8 (17%) patients required ICU admission due to delay in initiation of steroids. None of the factors including number of chemotherapy cycles, conditioning regime, disease status, CD34 collection, growth factors and day of WBC engraftment except female (p = 0.064) were statistically significant (in univariate or multivariate analysis). Our study shows that engraftment syndrome is common in autologous transplant setting. Maiolino criteria to diagnose ES is more sensitive in our setting. If detected and treated early there is not much morbidity or mortality related to ES.

Diagnostic Accuracy of Neuroimaging to Delineate Diffuse Gliomas within the Brain: A Meta-Analysis

BACKGROUND

Brain imaging in diffuse glioma is used for diagnosis, treatment planning, and follow-up.

PURPOSE

In this meta-analysis, we address the diagnostic accuracy of imaging to delineate diffuse glioma.

DATA SOURCES

We systematically searched studies of adults with diffuse gliomas and correlation of imaging with histopathology.

STUDY SELECTION

Study inclusion was based on quality criteria. Individual patient data were used, if available.

DATA ANALYSIS

A hierarchic summary receiver operating characteristic method was applied. Low- and high-grade gliomas were analyzed in subgroups.

DATA SYNTHESIS

Sixty-one studies described 3532 samples in 1309 patients. The mean Standard for Reporting of Diagnostic Accuracy score (13/25) indicated suboptimal reporting quality. For diffuse gliomas as a whole, the diagnostic accuracy was best with T2-weighted imaging, measured as area under the curve, false-positive rate, true-positive rate, and diagnostic odds ratio of 95.6%, 3.3%, 82%, and 152. For low-grade gliomas, the diagnostic accuracy of T2-weighted imaging as a reference was 89.0%, 0.4%, 44.7%, and 205; and for high-grade gliomas, with T1-weighted gadolinium-enhanced MR imaging as a reference, it was 80.7%, 16.8%, 73.3%, and 14.8. In high-grade gliomas, MR spectroscopy (85.7%, 35.0%, 85.7%, and 12.4) and ¹¹C methionine-PET (85.1%, 38.7%, 93.7%, and 26.6) performed better than the reference imaging.

LIMITATIONS

True-negative samples were underrepresented in these data, so false-positive rates are probably less reliable than true-positive rates. Multimodality imaging data were unavailable.

CONCLUSIONS

The diagnostic accuracy of commonly used imaging is better for delineation of low-grade gliomas than high-grade gliomas on the basis of limited evidence. Improvement is indicated from advanced techniques, such as MR spectroscopy and PET.

Emergence of dalbavancin non-susceptible, vancomycin-intermediate Staphylococcus aureus (VISA) after treatment of MRSA central line-associated bloodstream infection with a dalbavancin- and vancomycin-containing regimen

OBJECTIVES

Dalbavancin is a long-acting lipoglycopeptide with activity against gram-positives, including methicillin-resistant Staphylococcus aureus (MRSA). The potential for lipoglycopeptides, with half-lives greater than 1 week, to select for resistance is unknown. Here we explore a case of MRSA central line-associated bloodstream infection in which dalbavancin and vancomycin non-susceptibility emerged in a urine isolate collected after the patient was treated with vancomycin and dalbavancin sequentially.

METHODS

Isolates from blood and urine underwent susceptibility testing, and whole genome sequencing (WGS). The blood isolate was subjected to successive passage in vitro in the presence of escalating dalbavancin concentrations and the emergent isolate was subjected to repeat susceptibility testing and WGS.

RESULTS

The blood isolate was fully susceptible to vancomycin; however, MICs of the urine isolate to dalbavancin, vancomycin, telavancin, and daptomycin were at least fourfold higher than the blood-derived strain. Both strains were indistinguishable by spa and variable number tandem repeat (VNTR) typing, and WGS revealed only seven variants, indicating clonality. Four variants affected genes, including a 3bp in-frame deletion in yvqF, a gene which has been implicated in glycopeptide resistance. Vancomycin and dalbavancin non-susceptibility emerged in the blood isolate after successive passage in vitro in the presence of dalbavancin, and WGS identified a single non-synonymous variant in yvqF.

CONCLUSIONS

This is the first case in which VISA has emerged in the context of a dalbavancin-containing regimen. The selection for cross-resistance to vancomycin in vitro by dalbavancin exposure alone is troubling. Clinicians should be aware of the possibility for emergence of dalbavancin non-susceptibility and glycopeptide cross-resistance arising following therapy.