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Article ; Online: COVID-19 Diagnosis from Chest CT Scans

Mustafa Kara / Zeynep Öztürk / Sergin Akpek / Ayşegül Turupcu

AI, Vol 2, Iss 20, Pp 330-

A Weakly Supervised CNN-LSTM Approach

2021 Volume 341

Abstract: Advancements in deep learning and availability of medical imaging data have led to the use of CNN-based architectures in disease diagnostic assisted systems. In spite of the abundant use of reverse transcription-polymerase chain reaction-based tests in ... ...

Abstract	Advancements in deep learning and availability of medical imaging data have led to the use of CNN-based architectures in disease diagnostic assisted systems. In spite of the abundant use of reverse transcription-polymerase chain reaction-based tests in COVID-19 diagnosis, CT images offer an applicable supplement with their high sensitivity rates. Here, we study the classification of COVID-19 pneumonia and non-COVID-19 pneumonia in chest CT scans using efficient deep learning methods to be readily implemented by any hospital. We report our deep network framework design that encompasses Convolutional Neural Networks and bidirectional Long Short Term Memory architectures. Our study achieved high specificity (COVID-19 pneumonia: 98.3%, non-COVID-19 pneumonia: 96.2% Healthy: 89.3%) and high sensitivity (COVID-19 pneumonia: 84.0%, non-COVID-19 pneumonia: 93.9% Healthy: 94.9%) in classifying COVID-19 pneumonia, non-COVID-19 pneumonia and healthy patients. Next, we provide visual explanations for the Convolutional Neural Network predictions with gradient-weighted class activation mapping (Grad-CAM). The results provided a model explainability by showing that Ground Glass Opacities, indicators of COVID-19 pneumonia disease, were captured by our convolutional neural network. Finally, we have implemented our approach in three hospitals proving its compatibility and efficiency.
Keywords	deep learning ; computed tomography ; image classification ; COVID-19 ; medical image analysis ; pneumonia ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	006
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Giant Celiac Arteri Aneurysm Treated with a Flow-Divertıng Multilayer Stent: Early Rupture as a Fatal Complication.

Coskun, Bilgen / Rozanes, Izzet / Erkan, Mert / Ates, Sanser / Akpek, Sergin

Journal of vascular and interventional radiology : JVIR

2017 Volume 28, Issue 3, Page(s) 468–470

MeSH term(s)	Aged ; Aneurysm/diagnostic imaging ; Aneurysm/therapy ; Aneurysm, Ruptured ; Angiography, Digital Subtraction ; Celiac Artery ; Computed Tomography Angiography ; Coronary Angiography ; Fatal Outcome ; Female ; Humans ; Radiography, Interventional ; Stents
Language	English
Publishing date	2017
Publishing country	United States
Document type	Case Reports ; Letter
ZDB-ID	1137756-2
ISSN	1535-7732 ; 1051-0443
ISSN (online)	1535-7732
ISSN	1051-0443
DOI	10.1016/j.jvir.2016.11.036
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Article: A 52-Year-Old Man With Progressive Weakness and Incontinence.

Altintas, Ayse / Danyeli, Ayca Ersen / Bozkurt, Subutay Berke / Uysal, Sanem Pinar / Akpek, Sergin / Aygun, Murat Serhat / Akay, Olga Meltem / Kahyaoglu, Bulent / Peker, Selcuk / Ure, Umit Barbaros / Ferhanoglu, Burhan

The Neurohospitalist

2021 Volume 12, Issue 2, Page(s) 307–311

Abstract: Here we report a challenging case of a 52-year-old man presenting with subacute constipation, urinary retention, impotence, absent Achilles reflexes, and hypoesthesia in S2-S5 dermatomes. We review the clinical decision-making as the symptoms evolved and ...

Abstract	Here we report a challenging case of a 52-year-old man presenting with subacute constipation, urinary retention, impotence, absent Achilles reflexes, and hypoesthesia in S2-S5 dermatomes. We review the clinical decision-making as the symptoms evolved and diagnostic testing changed over time. Once the diagnosis is settled, we discuss the sign and symptoms, additional diagnostic tools, treatment options and prognosis.
Language	English
Publishing date	2021-08-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2629083-2
ISSN	1941-8752 ; 1941-8744
ISSN (online)	1941-8752
ISSN	1941-8744
DOI	10.1177/19418744211039586
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Article ; Online: Accuracy of Sampling PI-RADS 4-5 Index Lesions Alone by MRI-guided In-bore Biopsy in Biopsy-naive Patients Undergoing Radical Prostatectomy.

Kilic, Mert / Vural, Metin / Coskun, Bilgen / Acar, Ömer / Saglican, Yesim / Akpek, Sergin / Esen, Tarik

European urology focus

2019 Volume 6, Issue 2, Page(s) 249–254

Abstract: Background: Targeting multiparametric magnetic resonance imaging (MP-MRI)-suspicious regions alone in biopsy-naive patients is not common practice, since it may miss clinically significant prostate cancer (PCa).: Objective: To investigate the ... ...

Abstract	Background: Targeting multiparametric magnetic resonance imaging (MP-MRI)-suspicious regions alone in biopsy-naive patients is not common practice, since it may miss clinically significant prostate cancer (PCa). Objective: To investigate the accuracy of in-bore MRI-guided biopsy of Prostate Imaging Reporting and Data System (PI-RADS) 4 and 5 index lesions alone in biopsy-naive patients undergoing radical prostatectomy (RP). Design, setting, and participants: A total of 170 patients underwent MRI-guided in-bore biopsy for PI-RADS 4 and 5 index lesions alone between 2013 and 2018, of whom 136 patients were diagnosed with PCa. Fifty-two patients without prior biopsy who underwent RP were included in this study. MP-MRI findings, biopsy results, and whole-mount step-section specimen evaluation were retrospectively analyzed. Outcome measurements and statistical analysis: Continuous variables were reported as mean (standard deviation) or median (range). Differences in parametric variables were calculated by Student t test. Results and limitations: Overall International Society of Urological Pathology grade group (GG) up- and downgrading rates were 23.0% and 7.6% per patient and 24.5% and 6.5% per focus, respectively. Ten of 12 biopsy-detected GG 1 foci were upgraded in the final pathology. In 30 patients, a total of 43 different tumor foci were identified outside the sampled index lesion. Average biopsied and nonbiopsied tumor volumes were found to be 2.02 and 0.45 cm³, respectively (p < 0.001). The index lesion was the largest focus of tumor in all patients' final histopathological examination; upgrading was identified in only one nonbiopsied focus in a single patient. Limitations include retrospective design and nonstandard indications of in-bore MRI biopsy. Conclusions: In-bore MRI-guided biopsy of PI-RADS 4-5 index lesions alone in biopsy-naive patients is a safe and accurate diagnostic modality allowing appropriate patient selection for individualized treatment. Patient summary: In-bore magnetic resonance imaging-guided prostate biopsy of suspicious lesions alone allows accurate risk stratification of patients and reduces the detection of insignificant prostate cancer.
MeSH term(s)	Aged ; Data Systems ; Humans ; Image-Guided Biopsy/methods ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Prostatectomy/methods ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms/surgery ; Reproducibility of Results ; Retrospective Studies ; Specimen Handling/methods
Language	English
Publishing date	2019-05-02
Publishing country	Netherlands
Document type	Journal Article
ISSN	2405-4569
ISSN (online)	2405-4569
DOI	10.1016/j.euf.2019.04.010
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Article ; Online: Crossing Y-Solitaire thrombectomy as a rescue treatment for refractory acute occlusions of the middle cerebral artery.

Aydin, Kubilay / Barburoglu, Mehmet / Oztop Cakmak, Ozgur / Yesilot, Nilufer / Vanli, Ebru Nur Yavuz / Akpek, Sergin

Journal of neurointerventional surgery

2018 Volume 11, Issue 3, Page(s) 246–250

Abstract: Background: Mechanical thrombectomy using a stent retriever has become the standard of care for acute large-vessel occlusions in the anterior circulation. Clots that are refractory to single stent retriever thrombectomy remain a challenge for ... ...

Abstract	Background: Mechanical thrombectomy using a stent retriever has become the standard of care for acute large-vessel occlusions in the anterior circulation. Clots that are refractory to single stent retriever thrombectomy remain a challenge for neurointerventionalists. Objective: To assess the efficacy and safety of double stent retriever (crossing Y-Solitaire) thrombectomy as a rescue treatment for acute middle cerebral artery (MCA) occlusions that are refractory to single stent retriever thrombectomy. Methods: We retrospectively reviewed the databases of our hospitals to identify patients who presented with an acute MCA occlusion and were treated with crossing Y-Solitaire thrombectomy. The angiographic (Thrombolysis in Cerebral Infarction (TICI) scale) and clinical outcomes (National Institutes of Health Stroke Scale (NIHSS) and modified Rankin Scale (mRS) scores) and complications were assessed. Results: Ten patients were included in the study. The median initial NIHSS score and Alberta Stroke Program Early CT Score (ASPECTS) were 19.0 and 9.6, respectively. Crossing Y-Solitaire thrombectomy was performed as a rescue technique after unsuccessful single Solitaire thrombectomy passes in all cases. Successful recanalization (TICI 2b/3) was achieved in 8 (80%) patients. We observed asymptomatic reperfusion hemorrhages in 2 (20%) patients. No procedural related complications were seen other than reversible vasospasms in 5 (50%) patients. Sixty percent of the patients had a mRS score of between 2 and 0 at 90 days after the procedure. There was no mortality. Conclusion: Crossing Y-Solitaire thrombectomy seems to be an effective and safe alternative rescue technique to treat refractory MCA bifurcation occlusions that are refractory to standard thrombectomy procedures.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Angiography/methods ; Female ; Follow-Up Studies ; Humans ; Infarction, Middle Cerebral Artery/diagnostic imaging ; Infarction, Middle Cerebral Artery/surgery ; Male ; Middle Aged ; Reperfusion/instrumentation ; Reperfusion/methods ; Retrospective Studies ; Stents ; Thrombectomy/instrumentation ; Thrombectomy/methods ; Treatment Outcome
Language	English
Publishing date	2018-09-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2514982-9
ISSN	1759-8486 ; 1759-8478
ISSN (online)	1759-8486
ISSN	1759-8478
DOI	10.1136/neurintsurg-2018-014288
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Zs.A 6845: Show issues

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Article ; Online: Free-floating intra-aortic thrombus causing coronary artery occlusion: appearance in ECG-gated computed tomography with cine-images.

Gümüş, Terman / Akpek, Sergin / Yücel, Genco

Anadolu kardiyoloji dergisi : AKD = the Anatolian journal of cardiology

2013 Volume 13, Issue 3, Page(s) E18–9

MeSH term(s)	Adult ; Aorta, Thoracic ; Chest Pain/etiology ; Coronary Artery Disease/complications ; Coronary Artery Disease/diagnosis ; Humans ; Magnetic Resonance Imaging ; Male ; Thrombosis/complications ; Thrombosis/diagnosis ; Tomography, X-Ray Computed
Language	English
Publishing date	2013-05-10
Publishing country	Turkey
Document type	Case Reports ; Journal Article
ZDB-ID	2278670-3
ISSN	1308-0032 ; 1302-8723
ISSN (online)	1308-0032
ISSN	1302-8723
DOI	10.5152/akd.2013.095
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Article ; Online: In-bore MRI-guided prostate biopsy in a patient group with PI-RADS 4 and 5 targets: A single center experience.

Vural, Metin / Coskun, Bilgen / Kilic, Mert / Durmaz, Selahattin / Gumus, Terman / Cengiz, Duygu / Onay, Aslihan / Saglican, Yesim / Colakoglu, Bulent / Akpek, Sergin / Yildirim, Hakan / Esen, Tarik / Rozanes, Izzet

European journal of radiology

2021 Volume 141, Page(s) 109785

Abstract: Purpose: To determine the diagnostic yield of magnetic resonance imaging (MRI) guided in-bore biopsy in patients with high likelihood multiparametric MRI (mpMRI) findings, regarding overall and clinically significant prostate cancer (csPCa) detection ... ...

Abstract	Purpose: To determine the diagnostic yield of magnetic resonance imaging (MRI) guided in-bore biopsy in patients with high likelihood multiparametric MRI (mpMRI) findings, regarding overall and clinically significant prostate cancer (csPCa) detection rates and concordance of biopsy and radical prostatectomy (RP) Gleason scores (GS). Methods: This retrospective study consisted of 277 Prostate Imaging Reporting and Data System (PI-RADS) assessment category 4 and 5 targets in 246 patients (mean age, 65.7 years; median prostate specific antigen value, 7.75 ng/mL) who had undergone in-bore biopsy at our institution between 2012 and 2020. Eighty-one patients who underwent RP were eligible for the concordance analysis of biopsy and RP specimen GS. Results: Overall PCa detection rates were 80.5 % per patient (198/246) and 78 % per target (216/277) and 83.5 % and 67.4 % in primary (biopsy naive) and secondary (at least one negative prior biopsy) settings. csPCa was found in 63 % overall, 66 % of patients (132/200) in the primary, and 50 % of patients (23/46) in the secondary biopsy settings (p < 0.001). The prostate cancer detection rate was 68 % and 92 % in PI-RADS 4 and 5, respectively (p < 0.001). In the radical prostatectomy subcohort, 27.2 % of patients were upgraded, 8.6 % of patients were downgraded from needle biopsy. Significant complications occurred in 1.2 % of patients. Conclusions: MRI-guided in-bore prostate biopsy has a high detection rate of csPCa in primary and secondary biopsy cohorts. Biopsy results were satisfactory in terms of the number of positive cores, cancer percentage in positive cores, and concordance of GS in needle biopsy and RP specimen.
MeSH term(s)	Aged ; Humans ; Image-Guided Biopsy ; Magnetic Resonance Imaging ; Male ; Neoplasm Grading ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/surgery ; Retrospective Studies
Language	English
Publishing date	2021-05-21
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	138815-0
ISSN	1872-7727 ; 0720-048X
ISSN (online)	1872-7727
ISSN	0720-048X
DOI	10.1016/j.ejrad.2021.109785
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Zs.A 1630: Show issues

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Article ; Online: Evaluation of Peripheral Zone Prostate Cancer Aggressiveness Using the Ratio of Diffusion Tensor Imaging Measures.

Onay, Aslihan / Ertas, Gokhan / Vural, Metin / Acar, Omer / Saglican, Yesim / Coskun, Bilgen / Akpek, Sergin

Contrast media & molecular imaging

2017 Volume 2017, Page(s) 5678350

Abstract: Purpose: To evaluate the aggressiveness of peripheral zone prostate cancer by correlating the Gleason score (GS) with the ratio of the diffusion tensor imaging (DTI) measures.: Materials and methods: Forty-two peripheral zone prostate tumors were ... ...

Abstract	Purpose: To evaluate the aggressiveness of peripheral zone prostate cancer by correlating the Gleason score (GS) with the ratio of the diffusion tensor imaging (DTI) measures. Materials and methods: Forty-two peripheral zone prostate tumors were imaged using DTI. Regions of interest focusing on the center of tumor foci and noncancerous tissue were used to extract statistical measures of mean diffusivity (MD) and fractional anisotroy (FA). Measure ratio was calculated by dividing tumor measure by noncancerous tissue measure. Results: Strong correlations are observable between GS and MD measures while weak correlations are present between GS and FA measures. Minimum tumor MD (MD Conclusion: Ratios of MD measures can be used in evaluation of peripheral zone prostate cancer aggressiveness; however tumor MD measures alone perform similarly.
MeSH term(s)	Anisotropy ; Diffusion Tensor Imaging/methods ; Humans ; Male ; Neoplasm Grading ; Prostatic Neoplasms/diagnostic imaging
Language	English
Publishing date	2017-09-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2232678-9
ISSN	1555-4317 ; 1555-4309
ISSN (online)	1555-4317
ISSN	1555-4309
DOI	10.1155/2017/5678350
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Zs.A 6273: Show issues

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Article ; Online: Clinical and Radiological Outcomes in Arthroscopic Repair of Shoulder Rotator İnterval Lesions

İlker EREN / Hakan ÖZBEN / Nazan CANBULAT / Şule Meral EREN / Ayla UÇAK / Sergin AKPEK / Mehmet DEMİRHAN

Bezmiâlem Science, Vol 7, Iss 3, Pp 204-

2019 Volume 207

Abstract: Objective:Rotator interval lesion (RIL) is a distinct rotator cuff (RC) injury patern consisting of subscapularis and supraspinatus tear with biceps problem. This pathology is an underdiagnosed RC entitiy and not studied in-depth. Aim of this study is to ...

Abstract	Objective:Rotator interval lesion (RIL) is a distinct rotator cuff (RC) injury patern consisting of subscapularis and supraspinatus tear with biceps problem. This pathology is an underdiagnosed RC entitiy and not studied in-depth. Aim of this study is to report the functional and radiological results of RIL surgeries performed.Methods:Surgeries performed in a single center, in a 7-yearperiod were retrospectively reviewed. Sixteen cases (n=16) who underwent arthroscopic RC repair including subscapularis with biceps tenodesis or tenotomy were called for an up-to-date assessment. Fourteen shoulders of 13 patients (3 females, 10 males) were included. Constant, disabilities of the arm shoulder and hand (DASH), standardized shoulder assessment form (ASES) scores, and RC thickness measurements with magnetic resonance imaging (MRI) were recorded. Preoperative and postoperative results were compared.Results:Average age of the patients were 60.6 (47-74), and followup period was 3.2±1.9 years. Average preoperative Constant, DASH and ASES scores were 44.43±15.4, 22.11±17.21 and 51.37±27.6, respectively. Postoperative values improved to 90.45±6.44, 6±13.68 and 95.82±7.82, respectively (p<0.05). Average subscapularis and supraspinatus thicknesses measured with MRI were 3.85±0.87 and 4.60±0.65 mm respectively. MRI revealed subscapularis tendinitis in 1 patient. Re-tear was not observed in any patients.Conclusion:Arthroscopic subscapularis and supraspinatus repair with biceps tenodesis or tenotomy is an effective treatment method in RIL. No retear was observed with MRI. Clinical results are similar with other RC pathologies.
Keywords	Rotator cuff ; rotator interval ; subscapularis ; magnetic resonance imaging ; Medicine (General) ; R5-920
Subject code	610 ; 616
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Galenos Publishing House
Document type	Article ; Online
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Article: Nephron-Sparing Surgery for Renal Masses Measuring Larger Than 7 cm on Preoperative Imaging: A Single Surgeon, Single Center Experience.

Esen, Tarık / Acar, Omer / Musaoğlu, Ahmet / Vural, Metin / Akpek, Sergin

ISRN surgery

2013 Volume 2013, Page(s) 691080

Abstract: Objectives. To document the feasibility of nephron-sparing surgery (NSS) for the surgical treatment of renal masses measuring larger than 7 cm (cT2) on preoperative imaging. Methods. A total of 139 patients have undergone NSS between 2001 and 2012 by a ... ...

Abstract	Objectives. To document the feasibility of nephron-sparing surgery (NSS) for the surgical treatment of renal masses measuring larger than 7 cm (cT2) on preoperative imaging. Methods. A total of 139 patients have undergone NSS between 2001 and 2012 by a single surgeon in our clinic. Of these, we identified 17 patients whose tumors were measuring greater than 7 cm on preoperative imaging studies and were limited to the kidney. Their charts were retrospectively reviewed. Results. Mean age of the study population was 49.8 ± 11.3 years. Thirteen patients were managed by open NSS, while 4 patients have undergone robot-assisted NSS. Mean diameter and mean R.E.N.A.L. score of the tumors that were enucleoresected were 8.2 cm and 8.5, respectively. A total of 5 Clavien grade 2 and higher complications were recorded within 30 days of surgery. Histopathologic examination revealed benign histology in almost 1/4 of the cases. After a median followup of 33 months, all of our patients were alive. Only one patient (5.8%) experienced local recurrence. Conclusions. NSS is a feasible and safe option for large (>7 cm) renal masses. It may be considered not only for imperative conditions but also for highly selected cases with a normal contralateral kidney.
Language	English
Publishing date	2013-04-04
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2612998-X
ISSN	2090-5793 ; 2090-5785
ISSN (online)	2090-5793
ISSN	2090-5785
DOI	10.1155/2013/691080
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