A Stacked Generalization of 3D Orthogonal Deep Learning Convolutional Neural Networks for Improved Detection of White Matter Hyperintensities in 3D FLAIR Images

BACKGROUND AND PURPOSE:Accurate and reliable detection of white matter hyperintensities and their volume quantification can provide valuable clinical information to assess neurologic disease progression. In this work, a stacked generalization ensemble of orthogonal 3D convolutional neural networks, StackGen-Net, is explored for improving automated detection of white matter hyperintensities in 3D T2-FLAIR images.MATERIALS AND METHODS:Individual convolutional neural networks in StackGen-Net were trained on 2.5D patches from orthogonal reformatting of 3D-FLAIR (n = 21) to yield white matter hyperintensity posteriors. A meta convolutional neural network was trained to learn the functional mapping from orthogonal white matter hyperintensity posteriors to the final white matter hyperintensity prediction. The impact of training data and architecture choices on white matter hyperintensity segmentation performance was systematically evaluated on a test cohort (n = 9). The segmentation performance of StackGen-Net was compared with state-of-the-art convolutional neural network techniques on an independent test cohort from the Alzheimer’s Disease Neuroimaging Initiative-3 (n = 20).RESULTS:StackGen-Net outperformed individual convolutional neural networks in the ensemble and their combination using averaging or majority voting. In a comparison with state-of-the-art white matter hyperintensity segmentation techniques, StackGen-Net achieved a significantly higher Dice score (0.76 [SD, 0.08], F1-lesion (0.74 [SD, 0.13]), and area under precision-recall curve (0.84 [SD, 0.09]), and the lowest absolute volume difference (13.3% [SD, 9.1%]). StackGen-Net performance in Dice scores (median = 0.74) did not significantly differ (P = .22) from interobserver (median = 0.73) variability between 2 experienced neuroradiologists. We found no significant difference (P = .15) in white matter hyperintensity lesion volumes from StackGen-Net predictions and ground truth annotations.CONCLUSIONS:A stacked generalization of convolutional neural networks, utilizing multiplanar lesion information using 2.5D spatial context, greatly improved the segmentation performance of StackGen-Net compared with traditional ensemble techniques and some state-of-the-art deep learning models for 3D-FLAIR.

White matter hyperintensities (WMHs) correspond to pathologic features of axonal degeneration, demyelination, and gliosis observed within cerebral white matter.¹ Clinically, the extent of WMHs in the brain has been associated with cognitive impairment, Alzheimer’s disease and vascular dementia, and increased risk of stroke.^2,3 The detection and quantification of WMH volumes to monitor lesion burden evolution and its correlation with clinical outcomes have been of interest in clinical research.^4,5 Although the extent of WMHs can be visually scored,⁶ the categoric nature of such scoring systems makes quantitative evaluation of disease progression difficult. Manually segmenting WMHs is tedious, prone to inter- and intraobserver variability, and is, in most cases, impractical. Thus, there is an increased interest in developing fast, accurate, and reliable computer-aided automated techniques for WMH segmentation.Convolutional neural network (CNN)-based approaches have been successful in several semantic segmentation tasks in medical imaging.⁷ Recent works have proposed using deep learning–based methods for segmenting WMHs using 2D-FLAIR images.^8-11 More recently, a WMH segmentation challenge¹² was also organized (http://wmh.isi.uu.nl/) to facilitate comparison of automated segmentation of WMHs of presumed vascular origin in 2D multislice T2-FLAIR images. Architectures that used an ensemble of separately trained CNNs showed promising results in this challenge, with 3 of the top 5 winners using ensemble-based techniques.¹²Conventional 2D-FLAIR images are typically acquired with thick slices (3–4 mm) and possible slice gaps. Partial volume effects from a thick slice are likely to affect the detection of smaller lesions, both in-plane and out-of-plane. 3D-FLAIR images, with isotropic resolution, have been shown to achieve higher resolution and contrast-to-noise ratio¹³ and have shown promising results in MS lesion detection using 3D CNNs.¹⁴ Additionally, the isotropic resolution enables viewing and evaluation of the images in multiple planes. This multiplanar reformatting of 3D-FLAIR without the use of interpolating kernels is only possible due to the isotropic nature of the acquisition. Network architectures that use information from the 3 orthogonal views have been explored in recent works for CNN-based segmentation of 3D MR imaging data.¹⁵ The use of data from multiple planes allows more spatial context during training without the computational burden associated with full 3D training.¹⁶ The use of 3 orthogonal views simultaneously mirrors how humans approach this segmentation task.Ensembles of CNNs have been shown to average away the variances in the solution and the choice of model- and configuration-specific behaviors of CNNs.¹⁷ Traditionally, the solutions from these separately trained CNNs are combined by averaging or using a majority consensus. In this work, we propose the use of a stacked generalization framework (StackGen-Net) for combining multiplanar lesion information from 3D CNN ensembles to improve the detection of WMH lesions in 3D-FLAIR. A stacked generalization¹⁸ framework learns to combine solutions from individual CNNs in the ensemble. We systematically evaluated the performance of this framework and compared it with traditional ensemble techniques, such as averaging or majority voting, and state-of-the-art deep learning techniques.     

Volume control associated with better cardiac function in long-term peritoneal dialysis patients.

BACKGROUND: This study was undertaken to investigate the effect of long-term blood pressure (BP) reduction, achieved with salt restriction and strict volume control, on frequency and regression of left ventricular hypertrophy (LVH) in long-term peritoneal dialysis (PD) patients. METHODS: 56 patients who had been treated for more than 2 years under our care were enrolled. After echocardiographic (Echo) evaluation, 46 patients were included in the follow-up study. In our unit, we aim to keep patients' BP below 130/85 mmHg and cardiothoracic index below 0.50. To reach these targets, moderate salt restriction is advised, and if necessary, hypertonic PD solutions are used. Echo was performed at the beginning of the study (after a mean period of 36 months on PD) and at the end of the prospective follow-up period (24 months later). RESULTS: At the time of the first Echo, LVH was detected in only 8 (21%) patients. Residual urine volume was significantly decreased compared to data taken when they first started PD (658 +/- 795 vs 236 +/- 307 mL/day). Mean left ventricular mass index (LVMI) was 107 +/- 26.5 g/m2. LVMI was significantly decreased at the end of the follow-up in patients who had LVH at baseline. No LVH developed in patients who had normal LVMI at baseline. CONCLUSION: Our results indicate that control of hypertension is possible when extracellular fluid volume is kept under control using hypertonic PD solutions in case of recruitment in addition to salt restriction in long-term PD patients. Sustained normovolemia is associated with low incidence and regression of LVH.     

The problems and advantages of one lung ventilation during surgical intervention in pulmonary hydatid cyst disease

Background Hydatid disease is the most severe helminthic zoonosis, with an important public health problem especially in rural areas in Turkey. The aim of this study was to review the problems and advantages encountered in surgical treatment of 43 patients who were ventilated with one-lung ventilation during last four years. Methods Patients, operated with one-lung ventilation, constitute the study group. Data related to symptoms, radiographic findings, performed surgical procedures, perioperative and postoperative morbidity, hospitalization time, and cyst recurrence were collected from each individual's records. Results Cystotomy and capitonnage were performed in all cases. Perioperative complications were seen in 5 patients. Four of these 5 patients had double-lumen endotracheal tube malpositioning. In one patient hypoxemia developed. The most common postoperative complication was atelectasis. One patient had recurrent cysts. There was no perioperative or postoperative death. Conclusions We prefer cystotomy and capitonnage because it is a fast and effective technique with limited postoperative complications. One-lung ventilation prevents the exposure of lower lung areas from massive aspiration, which may cause acute obstruction of airways, and contamination by cyst contents from the operative part of the lung that causes recurrent disease. One-lung ventilation in pulmonary hydatid cyst surgery may be preferred owing to lower mortality and morbidity rates.     

The effect of metoclopramide on gastric emptying in traumatic brain injury.

OBJECTIVE: Gastric paresis in traumatic brain injury (TBI) hinders the effectiveness of enteral support in this patient group. In this study we have investigated the effect of metoclopramide on gastric emptying in TBI patients. METHOD: In this prospective, randomized, controlled, double-blind study, 19 TBI patients with Glasgow Coma Scale scores of 3-11 were included. In all patients, enteral nutrition was commenced with a nasogastric feeding tube within 48 hours of trauma. Patients were randomized into two groups. In the metoclopramide (M) group, 10 mg metoclopramide was delivered intravenously three times daily for 5 days. In the control (C) group, an equal volume of saline was administered. Besides demographics, gastric emptying according to a paracetamol absorption test at days 0 and 5, time to reach target nutritional requirements, gastric residues, intolerance to feeding, nutritional complications, and clinical outcomes were recorded for each patient. RESULTS: The gastric residue rates were 2.7+/-7.4 mL and 8.1+/-17.7 mL per 100 patient days for groups C and M respectively (p=0.408). Similarly, feeding intolerance and complication rates did not significantly differ between groups C and M, (respectively p=0.543 and 0.930). Gastric emptying parameters also were similar between the study groups. CONCLUSION: We were unable to document any advantage to using metoclopramide in TBI patients. Simple intragastric enteral feeding with close monitoring of the possible complications seems to be sufficient with acceptable morbidity rates.     

Multiple primary malignant neoplasms in urologic patients

Methods: Second primary cancers constitute approximately 9–10% of malignancies diagnosed in the United States. We aimed to show the risk and incidance of second primary tumor occuring associated to urologic tumors and show the distrubution of tumors in Tracia region. We retrospectively examined the patients' files with the diagnosis of malignant disease between the years 1985–2000. Hazard function analysis was performed to estimate the relative risk of secondary malignancy occuring. Age, sex and tumor number were examined to find out if they affect on mortality rate. Results: A total number of 25 MPMNs were diagnosed. In 52 percent of the cases the second primary neoplasm developed within six months. The relative risk of development of a second neoplasm is found as increasing 1.111 times per month. The incidence of secondary malignancy occuring in the patients with one tumor was found as 6.31%. Age (p < 0.001) and tumor number (p < 0.001) are found as statistically effective predictor on mortality rate where the sex is not. Conclusions: In the patients with a primary tumor not only the metastasis must be investigated but also second primary tumors should be taken in to consideration. This revised version was published online in August 2006 with corrections to the Cover Date.     

Optimization of self-reference thermometry using complex field estimation.

Referenceless, or self-reference, thermometry is a technique for mapping temperature differences in the region of interest (ROI) using the baseline phase estimated by extrapolating the field in the surrounding region for estimation (RFE) and subtracting the estimated baseline from the measured field. In the present work a self-reference technique based on complex field estimation using 2D polynomials comprising complex-valued coefficients was proposed and optimized. Numerical simulations with a Gaussian-profiled phase distribution demonstrated that the ROI radius had to be 2.3-2.5 times the standard deviation (SD) of the Gaussian function in order to keep the error below 8% of the peak phase change. The area ratio between the ROI and the RFE had to be larger than 2.0 to maintain the error level. Based on the simulations, and phantom and volunteer experiments, the complex-based method with independently optimized polynomial orders for the two spatial dimensions was compared with the phase-based method using the similar-order optimization strategy. The complex-based method appeared to be useful when phase unwrapping was not removed. Otherwise, the phase-based method yielded equivalent results with less polynomial orders.     

Intracoronary shunt reduces postoperative troponin leaks: a prospective randomized study.

OBJECTIVE: The purpose of this study was to evaluate whether intracoronary shunt usage reduced the myocardial damage on the basis of the cardiac markers when compared with the shuntless anastomosis in off-pump coronary artery bypass grafting (OPCABG) surgery of isolated left anterior descending artery lesions. METHODS: Forty patients who had stable angina with isolated left anterior descending (LAD) coronary artery lesion undergoing OPCABG surgery were randomized into two groups. Shunt group consisted of 20 patients who had OPCABG using intracoronary shunt, whereas the shuntless group consisted of 20 patients who underwent OPCABG without using intracoronary shunt. Cardiac troponin I, CK, and CK-MB before and 24h after the surgery were assessed in the groups. RESULTS: There were no deaths in the study. The two groups were similar with respect to sex and age. Duration of LIMA-LAD anastomosis was significantly higher in the shunt group (p=0.01). There was no significant difference between the groups concerning the preoperative and postoperative CK and CK-MB levels. The preoperative troponin I levels of the groups were not different (p=0.238; NS), whereas postoperative levels of this marker was significantly higher in the shuntless group (p=0.003). CONCLUSION: Intracoronary shunt reduced the postoperative troponin I levels significantly, so it may be indicated in the patients who are thought to be susceptible to transient ischemia.     

Fast decomposition of water and lipid using a GRASE technique with the IDEAL algorithm.

Three-point Dixon techniques achieve good lipid-water separation by estimating the phase due to field inhomogeneities. Recently it was demonstrated that the combination of an iterative algorithm (iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL)) with a fast spin-echo (FSE) three-point Dixon method yielded robust lipid-water decomposition. As an alternative to FSE, the gradient- and spin-echo (GRASE) technique has been developed for efficient data collection. In this work we present a method for lipid-water separation by combining IDEAL with the GRASE technique. An approach to correct for errors in the lipid-water decomposition caused by phase distortions due to the switching of the readout gradient polarities inherent to GRASE is presented. The IDEAL-GRASE technique is demonstrated in phantoms and in vivo for various applications, including pelvic, musculoskeletal, and (breath-hold) cardiac imaging.     

Recurrent retroperitoneal cystic lymphangioma

Retroperitoneal cystic lymphangioma is a rare congenital malformation. The majority of lymphangiomas are present at birth and nearly all present before the age of two years. We report a case of giant cystic retroperitoneal lymphangioma in a patient who first presented with symptoms at the age of 7, underwent surgery, and who then suffered a recurrent mass 11 years later.     

In-vitro activity of rifabutin against rifampicin-resistant Mycobacterium tuberculosis isolates with known rpoB mutations

The relationship between resistance to rifampicin and rifabutin and genetic alterations in the rpoB gene of 41 rifampicin-resistant isolates of Mycobacterium tuberculosis was evaluated. Although 35 isolates with rifampicin MICs > or = 32 mg/L were also rifabutin-resistant, six isolates with rifampicin MICs of 2-16 mg/L were susceptible to rifabutin (MIC < or = 0.5 mg/L). Mutations Asp516Val, Asp516Tyr, Leu533Pro and the double mutation Met515Ile and Leu533Pro influenced susceptibility to rifampicin, but not to rifabutin. All mutations at codons 531 and 526, except one isolate with a His526Cys mutation, correlated with resistance to both compounds.