Publications by authors named "Deniz Alis"

Background: Explainable Artificial Intelligence (XAI) is prominent in the diagnostics of opaque deep learning (DL) models, especially in medical imaging. Saliency methods are commonly used, yet there's a lack of quantitative evidence regarding their performance.

Objectives: To quantitatively evaluate the performance of widely utilized saliency XAI methods in the task of breast cancer detection on mammograms.

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Background: Being digitally literate allows health-based science students to access reliable, up-to-date information efficiently and expands the capacity for continuous learning. Digital literacy facilitates effective communication and collaboration among other healthcare providers. It helps to navigate the ethical implications of using digital technologies and aids the use of digital tools in managing healthcare processes.

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Objective: Robot-assisted minimally invasive coronary bypass surgery is one of the least invasive approaches that offers multivessel revascularization and accelerated recovery. We investigated the benefits of computed tomography angiography (CTA) guidance in robotic coronary bypass (RCAB) by analyzing perioperative outcomes.

Methods: Between April 2022 and April 2023, 60 consecutive patients who underwent RCAB under preoperative CTA guidance were included.

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Background: Although systems such as Prostate Imaging Quality (PI-QUAL) have been proposed for quality assessment, visual evaluations by human readers remain somewhat inconsistent, particularly among less-experienced readers.

Objectives: To assess the feasibility of deep learning (DL) for the automated assessment of image quality in bi-parametric MRI scans and compare its performance to that of less-experienced readers.

Methods: We used bi-parametric prostate MRI scans from the PI-CAI dataset in this study.

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Objective: To evaluate the effectiveness of a self-adapting deep network, trained on large-scale bi-parametric MRI data, in detecting clinically significant prostate cancer (csPCa) in external multi-center data from men of diverse demographics; to investigate the advantages of transfer learning.

Methods: We used two samples: (i) Publicly available multi-center and multi-vendor Prostate Imaging: Cancer AI (PI-CAI) training data, consisting of 1500 bi-parametric MRI scans, along with its unseen validation and testing samples; (ii) In-house multi-center testing and transfer learning data, comprising 1036 and 200 bi-parametric MRI scans. We trained a self-adapting 3D nnU-Net model using probabilistic prostate masks on the PI-CAI data and evaluated its performance on the hidden validation and testing samples and the in-house data with and without transfer learning.

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Background: The Prostate Imaging Quality (PI-QUAL) score is the first step toward image quality assessment in multi-parametric prostate MRI (mpMRI). Previous studies have demonstrated moderate to excellent inter-rater agreement among expert readers; however, there is a need for studies to assess the inter-reader agreement of PI-QUAL scoring in basic prostate readers.

Objectives: To assess the inter-reader agreement of the PI-QUAL score amongst basic prostate readers on multi-center prostate mpMRI.

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The use of deep learning (DL) techniques for automated diagnosis of large vessel occlusion (LVO) and collateral scoring on computed tomography angiography (CTA) is gaining attention. In this study, a state-of-the-art self-configuring object detection network called nnDetection was used to detect LVO and assess collateralization on CTA scans using a multi-task 3D object detection approach. The model was trained on single-phase CTA scans of 2425 patients at five centers, and its performance was evaluated on an external test set of 345 patients from another center.

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Article Synopsis
  • - Hidradenitis suppurativa (HS) is linked to a higher risk of subclinical atherosclerosis, and while TNF inhibitors are effective for severe HS, their impact on atherosclerosis in these patients hasn't been studied before.
  • - This study involved 30 HS patients and 30 healthy controls, examining changes in blood glucose, cholesterol, and carotid intima-media thickness (CIMT) after 6 months of TNF inhibitor therapy.
  • - Findings revealed that HS patients had higher CIMT values than healthy controls; after treatment, blood glucose levels decreased, but total cholesterol and CIMT increased, signaling a potential risk for worsening atherosclerosis in HS patients on TNF inhibitors.
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Objective: The aim of the study is to investigate the role of whole-body magnetic resonance imaging (MRI) in assessing extrapulmonary metastases in primary osteosarcoma staging.

Methods: We retrospectively reviewed medical data to identify primary osteosarcoma patients with available preoperative whole-body MRI obtained in the staging or restaging. Histopathology was the reference test for assessing the diagnostic performance, if available.

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Objective: To investigate whether commercially available deep learning (DL) software improves the Prostate Imaging-Reporting and Data System (PI-RADS) scoring consistency on bi-parametric MRI among radiologists with various levels of experience; to assess whether the DL software improves the performance of the radiologists in identifying clinically significant prostate cancer (csPCa).

Methods: We retrospectively enrolled consecutive men who underwent bi-parametric prostate MRI at a 3 T scanner due to suspicion of PCa. Four radiologists with 2, 3, 5, and > 20 years of experience evaluated the bi-parametric prostate MRI scans with and without the DL software.

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Background: Lesional posterior cortex epilepsy (PCE) is often drug resistant and may benefit from surgical intervention. In this study, we aimed to identify potential predictive factors associated with seizure recurrence after epilepsy surgery in lesional PCE.

Methods: We retrospectively reviewed patients with PCE who underwent surgery between 1998 and 2021.

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Objectives: To compare the effectiveness of individual multiparametric prostate MRI (mpMRI) sequences-T2W, diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC), and dynamic contrast-enhanced (DCE)-in assessing prostate cancer (PCa) index lesion volume using whole-mount pathology as the ground-truth; to assess the impact of an endorectal coil (ERC) on the measurements.

Materials And Methods: We retrospectively enrolled 72 PCa patients who underwent 3T mpMRI with (n = 39) or without (n = 33) an ERC. A pathologist drew the index lesion borders on whole-mount pathology using planimetry (whole-mount).

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Objectives: To describe F-fluorodeoxyglucose positron emission tomography/magnetic resonance imaging ( F-FDG PET/MRI) along with semiology and electroencephalography (EEG) in patients with gray matter heterotopia (GMH); to evaluate the concordance between F-FDG PET/MRI and clinical epileptogenic zone (EZ).

Materials & Methods: GMH (subcortical heterotopia [SCH] and periventricular nodular heterotopia [PNH]) patients with epilepsy who underwent F-FDG PET/MRI were retrospectively enrolled. Two radiologists evaluated brain MRI, while two nuclear medicine specialists assessed the F-FDG PET.

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Purpose: In this study, we assessed the performance of apparent diffusion coefficient (ADC) and diffusion-weighted imaging (DWI) metrics and their ratios across different magnetic resonance imaging (MRI) acquisition settings, with or without an endorectal coil (ERC), for the evaluation of prostate cancer (PCa) aggressiveness using whole-mount specimens as a reference.

Methods: We retrospectively reviewed the data of prostate carcinoma patients with a Gleason score (GS) of 3+4 or higher who underwent prostate MRI using a 3T unit at our institution. They were divided into two groups based on the use of ERC for MRI acquisition, and patients who underwent prostate MRI with an ERC constituted the ERC (n = 55) data set, while the remaining patients accounted for the non-ERC data set (n = 41).

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To investigate the performance of a joint convolutional neural networks-recurrent neural networks (CNN-RNN) using an attention mechanism in identifying and classifying intracranial hemorrhage (ICH) on a large multi-center dataset; to test its performance in a prospective independent sample consisting of consecutive real-world patients. All consecutive patients who underwent emergency non-contrast-enhanced head CT in five different centers were retrospectively gathered. Five neuroradiologists created the ground-truth labels.

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Objective: To explore the image quality and radiation exposure associated with coronary angiography obtained with a third-generation dual-source computed tomography, using body mass index (BMI)- and heart rate (HR)-adapted protocols in real-world patients.

Methods: Three scan protocols were implemented with regard to HR: prospective turbo high-pitch spiral, sequential, and retrospective spiral modes. We adapted the reference kilovoltage value according to BMI.

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Diastolic dysfunction in hypertrophic cardiomyopathy (HCM) patients is a frequent, yet poorly understood phenomenon. The purpose of this study is to assess the relationship between the myocardial fibrosis and diastolic dysfunction in patients with HCM. We retrospectively investigated the impact of the myocardial fibrosis, as assessed by the extent of late gadolinium enhancement (LGE-%) on cardiac magnetic resonance imaging (CMRI), on diastolic dysfunction in 110 patients with HCM.

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Objectives: We aimed to determine the parameters that predict Gleason Score (GS) upgrading in patients undergoing robot-assisted laparoscopic radical prostatectomy (RARP) and especially the ability of neutrophile to lymphocyte ratio (NLR) in predicting the upgrading.

Methods: Patients who underwent RARP for prostate cancer in our clinic between January 2013 and January 2018 were retrospectively analyzed. Patients' demographic data, preoperative and postoperative parameters were all recorded in the database.

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There is little evidence on the applicability of deep learning (DL) in the segmentation of acute ischemic lesions on diffusion-weighted imaging (DWI) between magnetic resonance imaging (MRI) scanners of different manufacturers. We retrospectively included DWI data of patients with acute ischemic lesions from six centers. Dataset A (n = 2986) and B (n = 3951) included data from Siemens and GE MRI scanners, respectively.

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Purpose: To investigate whether prostate cancer (PCa) lesions regarding histopathological composition exhibit different morphological features on multiparametric prostate MRI (mpMRI).

Methods: We investigated men with PCa with available mpMRI and whole-mount specimens between June 2015 to December 2020.The acquisition protocol consistent with the Prostate Imaging Reporting and Data System (PI-RADS).

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Background: To test the hypothesis that making a diagnosis of left ventricular noncompaction (LVNC) on cardiac magnetic resonance imaging (CMRI) using a noncompacted-to-compacted (NC/C) myocardium ratio > 2.3 would yield significant errors, and also to test a diagnostic flowchart in patients who undergo CMRI and have clinical and echocardiographic findings suggesting LVNC could improve the diagnosis of LVNC.

Methods: A total of 84 patients with LVNC and 162 controls consisting of patients with other diseases and healthy participants who had CMRI and echocardiograms were selected.

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Objective: Epicardial adipose tissue (EAT) is a metabolically active visceral fat depot that plays an important role in coronary atherosclerosis. In this study, our aim was to investigate the relationship between long-term major adverse cardiovascular events (MACEs) and EAT volume detected by coronary computed tomography angiography (CCTA) in patients with Type 2 diabetes mellitus (T2-DM) without previous coronary events.

Methods: A total of 127 patients with diabetes who underwent CCTA between 2012 and 2014 were enrolled retrospectively.

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Objective: To evaluate the utility of cardiac magnetic resonance feature tracking-derived left ventricular strain in assessing cardiac dysfunction and investigate the correlation between left ventricular strain and myocardial T2* in patients with beta-thalassaemia major.

Methods: Forty-two patients with beta-thalassaemia major, having a mean age of 22.49 ± 8.

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