QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at: this https URL

Obesity management for cardiovascular disease prevention

Background: Obesity is a complex disease that leads to higher morbidity and mortality and its rate in the United States is rapidly rising. Targeting obesity management is one of the cornerstones of preventive medicine. Early intervention can significantly reduce the risk of developing cardiovascular disease. While it is well known that lifestyle interventions such as healthful nutrition and routine physical activity are the first and most important step in management, some do not achieve the desired results and require further therapies. Methods: A literature review was conducted, that included clinical documents, public scientific citations and peer review articles to evaluate anti-obesity medications, endoscopic procedures and bariatric surgeries in the management of obesity. We also included effects of these interventions on weight loss, cardiovascular disease risk reduction and side effects. Results: This clinical review summarizes recent evidence for the different approaches in obesity management including medications, common endoscopic procedures and bariatric surgeries. For more detailed review on the different management options discussed, we recommend reviewing Obesity Medicine Association Clinical Practice Statement [1]. Conclusion: Management of obesity reduces cardiovascular risk, improves metabolic parameters and other important health outcomes. Different management approaches are available, hence, a high level of awareness of the growing epidemic of obesity is needed to ensure timely referrals to obesity medicine specialists.</p

The PML-RAR alpha transcript in long-term follow-up of acute promyelocytic leukemia patients

Background and Objectives. Detection of PML-RAR alpha transcripts by RT-PCR is now established as a rapid and sensitive method for diagnosis of acute promyelocytic leukemia (APL), Although the majority of patients in longterm clinical remission are negative by consecutive reverse transcription polymerase chain reaction (RT-PCR) assays, negative tests are still observed in patients who ultimately relapse. Conversion from negative to positive PCR has been observed after consolidation and found to be a much stronger predictor of relapse. This study reports on 47 APL patients to determine the correlation between minimal residual disease (MRD) status and clinical outcome in our cohort of patients. Design and Methods. The presence of PML-RAR alpha t transcripts was investigated in 47 APL patients (37 adults and 10 children) using a semi-nested reverse transcriptase-polymerase chain reaction to evaluate the prognostic value of RT-PCR tests. Results. All patients achieved complete clinical remission (CCR) following induction treatment with all-trans retinoic acid (ATRA) and chemotherapy (CHT) or ATRA alone. Patients were followed up between 2 and 117.6 months (median: 37 months). Relapses occurred in 11 patients (9 adults and 2 children) between 11.4 and 19 months after diagnosis (median: 15.1 months) while 36 patients (28 adults and 8 children) remained in CCR, Seventy-five percent of patients carried the PML-RARa long isoform (bcr 1/2) which also predominated among the relapsed cases (9 of 11) but did not associate with any adverse outcome (p = 0.37), For the purpose of this analysis, minimal residual disease tests were clustered into four time-intervals: 0-2 months, 3-5 months, 5-9 months and 10-24 months. Interpretation and Conclusions. Children showed persisting disease for longer than adults during the first 2 months of treatment, At 2 months, 10 (50%) of 20 patients who remained in CCR and 4 (80%) of 5 patients who subsequently relapsed were positive. Patients who remained in CCR had repeatedly negative results beyond 5.5 months from diagnosis. A positive MRD test preceded relapse in 3 of 4 tested patients. The ability of a negative test to predict CCR (predictive negative value, PNV) was greater after 6 months (> 83%), while the ability of a positive test to predict relapse (predictive positive value, PPV) was most valuable only beyond 10 months (100%). This study (i) highlights the prognostic value of RT-PCR monitoring after treatment of APL patients but only from the end of treatment, (ii) shows an association between conversion to a positive test and relapse and (iii) suggests that PCR assessments should be carried out at 3-month intervals to provide a more accurate prediction of hematologic relapses but only after the end of treatment, (C) 2001, Ferrata Storti Foundatio

The effect of nuclear deformation on level statistics

We analyze the nearest neighbor spacing distributions of low-lying 2+ levels of even-even nuclei. We grouped the nuclei into classes defined by the quadrupole deformation parameter (Beta2). We calculate the nearest neighbor spacing distributions for each class. Then, we determine the chaoticity parameter for each class with the help of the Bayesian inference method. We compare these distributions to a formula that describes the transition to chaos by varying a tuning parameter. This parameter appears to depend in a non-trivial way on the nuclear deformation, and takes small values indicating regularity in strongly deformed nuclei and especially in those having an oblate deformation.Comment: 10 Pages, 6 figure

Level statistics of deformed even-even nuclei

The nearest neighbor spacing distribution of levels of deformed even-even nuclei classified according to their quadrupole deformation parameter is investigated. The results suggest that the oblate deformed nuclei have more regular spectra than prolate ones.Comment: 6 pages, 1 figur

Integrable theory of quantum transport in chaotic cavities

The problem of quantum transport in chaotic cavities with broken time-reversal symmetry is shown to be completely integrable in the universal limit. This observation is utilised to determine the cumulants and the distribution function of conductance for a cavity with ideal leads supporting an arbitrary number $n$ of propagating modes. Expressed in terms of solutions to the fifth Painlev\'e transcendent and/or the Toda lattice equation, the conductance distribution is further analysed in the large-$n$ limit that reveals long exponential tails in the otherwise Gaussian curve.Comment: 4 pages; final version to appear in Physical Review Letter

Are Bosonic Replicas Faulty?

Motivated by the ongoing discussion about a seeming asymmetry in the performance of fermionic and bosonic replicas, we present an exact, nonperturbative approach to zero-dimensional replica field theories belonging to the broadly interpreted "beta=2" Dyson symmetry class. We then utilise the formalism developed to demonstrate that the bosonic replicas do correctly reproduce the microscopic spectral density in the QCD inspired chiral Gaussian unitary ensemble. This disproves the myth that the bosonic replica field theories are intrinsically faulty.Comment: 4.3 pages; final version to appear in PR