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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only The role of endometrial sampling before Hysterectomy in premenopausal women with abnormal uterine bleeding(MDPI, 2024) Kuru, Oguzhan; Erkan, Ipek Betul Ozcivit; Saricoban, Cansu Turker; Akgor, Utku; Ilvan, Sennur; Department of Computer Engineering; İnan, Neslihan Gökmen; Department of Computer Engineering; College of EngineeringBackground/Objectives: An endometrial sampling is recommended for patients experiencing abnormal uterine bleeding above the age of 40 or 45. Valid risk prediction models are needed to accurately assess the risk of endometrial cancer and avoid an unnecessary endometrial biopsy in premenopausal women. We aimed to assess the necessity and usefulness of preoperative endometrial sampling by evaluating premenopausal women who underwent hysterectomy for abnormal uterine bleeding after preoperative endometrial sampling at our clinic. Methods: A retrospective analysis was conducted on 339 patients who underwent preoperative endometrial sampling and subsequently underwent hysterectomy due to abnormal uterine bleeding. Detailed gynecologic examinations, patient histories, and reports of endometrial sampling and hysterectomy were recorded. Cohen's Kappa (kappa) statistic was utilized to evaluate the concordance between histopathological results from an endometrial biopsy and hysterectomy. Results: The mean age of the cohort was 47 +/- 4 years. Endometrial biopsies predominantly revealed benign findings, with 137 (40.4%) cases showing proliferative endometrium and 2 (0.6%) cases showing endometrial cancer. Following hysterectomy, final pathology indicated proliferative endometrium in 208 (61.4%) cases, with 7 (2.1%) cases showing endometrioid cancer. There was a statistically significant but low level of concordance between histopathological reports of endometrial biopsy and hysterectomy results (Kappa = 0.108; p < 0.001). Significant differences were observed only in the body mass index of patients based on hysterectomy results (p = 0.004). When demographic characteristics were compared with cancer incidence, smoking status and preoperative endometrial biopsy findings showed statistically significant differences (p = 0.042 and p = 0.010, respectively). Conclusions: The concordance between the pathological findings of a preoperative endometrial biopsy and hysterectomy is low. Body mass index is an important differentiating factor between benign histopathologic findings of endometrium and endometrial neoplasia. Moreover, adenomyosis was found to be associated with endometrial cancer cases. The current approach to premenopausal women with abnormal uterine bleeding, which includes a routine endometrial biopsy, warrants re-evaluation by international societies and experts.Publication Metadata only Factors affecting Turkish medical students' pursuit of a career in neurosurgery: a single center survey study(Elsevier Inc., 2024) Çalış, Fatih; Şimşek, Abdullah Talha; Topyalın, Nur; Adam, Baha E.; Elias, Çimen; Aksu, Muhammed Emin; Aladdam, Mohammed; Gültekin, Güliz; Sorkun, Muhammet Hüseyin; Tez, Müjgan; Balak, Naci; Department of Computer Engineering; İnan, Neslihan Gökmen; Department of Computer Engineering; College of EngineeringBackground: Statistics show that over the past 2 decades, even in high-income countries, fewer and fewer students have listed neurosurgery as their top career option. Literature on medical students' pursuit of neurosurgical careers in middle- and low-income countries are scarce. The aim of this research, conducted in Turkey with a middle-income economy, was to contribute insights relevant to medical education and neurosurgery across the world. Methods: A survey was conducted with a target sample of fourth-year (167 students), fifth-year (169 students), and sixth-year (140 students) medical students (476 in total) from the Medical School at Istanbul Medeniyet University in Turkey. The response rates of the fourth-, fifth-, and sixth-year students were 62% (104/167), 53% (90/169), and 50% (70/140), respectively (in total, 266, including 147 female and 119 male). Results: In terms of the genuine intention, only 2.5% of men and 2.7% of women were committed to specializing in neurosurgery. This study further revealed that possible reasons for these students' low motivation to specialize in neurosurgery were their beliefs that in neurosurgery, the physical and psychological demands were high, and the night shifts were intense, meaning they would not have a social life or spare time for their hobbies; that morbidity/mortality were high; and that financial incentives were insufficient, especially in public institutions. Conclusion: Turkish medical students did not rank neurosurgery at the top of their career choices. Possible reasons for this are socioeconomic factors and the inadequate introduction of neurosurgery to medical students. © 2024 Elsevier Inc.Publication Metadata only Large language models as a rapid and objective tool for pathology report data extraction(Federation Turkish Pathology Soc., 2024) Department of Computer Engineering; Bolat, Beyza; Eren, Özgür Can; Dur Karasayar, Ayşe Hümeyra; Meriçöz, Çisel Aydın; Demir, Çiğdem Gündüz; Kulaç, İbrahim; Department of Computer Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Health Sciences; College of EngineeringMedical institutions continuously create a substantial amount of data that is used for scientific research. One of the departments with a great amount of archived data is the pathology department. Pathology archives hold the potential to create a case series of valuable rare entities or large cohorts of common entities. The major problem in creation of these databases is data extraction which is still commonly done manually and is highly laborious and error prone. For these reasons, we offer using large language models to overcome these challenges. Ten pathology reports of selected resection specimens were retrieved from electronic archives of Ko & ccedil; University Hospital for the initial set. These reports were de-identified and uploaded to ChatGPT and Google Bard. Both algorithms were asked to turn the reports in a synoptic report format that is easy to export to a data editor such as Microsoft Excel or Google Sheets. Both programs created tables with Google Bard facilitating the creation of a spreadsheet from the data automatically. In conclusion, we propose the use of AI-assisted data extraction for academic research purposes, as it may enhance efficiency and precision compared to manual data entry.Publication Metadata only An evaluation of DNA methylation levels and sleep in relation to hot flashes: a cross-sectional study(MDPI, 2024) Ozcivit Erkan, Ipek Betul; Seyisoglu, Hasan Hakan; Senel, Gulcin Benbir; Karadeniz, Derya; Ozdemir, Filiz; Kalayci, Aysel; Seven, Mehmet; Department of Computer Engineering; İnan, Neslihan Gökmen; Department of Computer Engineering; College of EngineeringObjectives: We aimed to evaluate the DNA methylation levels in perimenopausal and postmenopausal women, measured through Long Interspersed Element-1 (LINE-1) and Alu, and the sleep parameters in relation to the presence of hot flashes (HFs). Methods: This cross-sectional study included 30 peri- or postmenopausal women aged between 45 and 55. The menopausal status was determined according to STRAW + 10 criteria and all participants had a low cardiovascular disease (CVD) risk profile determined by Framingham risk score. The sample was divided into two groups based on the presence or absence of HFs documented in their medical history during their initial visit: Group 1 (n = 15) with HFs present and Group 2 (n = 15) with HFs absent. The patients had polysomnography test and HFs were recorded both by sternal skin conductance and self-report overnight. Genomic DNA was extracted from the women's blood and methylation status was analyzed by fluorescence-based real-time quantitative PCR. The quantified value of DNA methylation of a target gene was normalized by beta-actin. The primary outcome was the variation in methylation levels of LINE-1 and Alu and sleep parameters according to the presence of HFs. Results: LINE-1 and Alu methylation levels were higher in Group 1 (HFs present), although statistically non-significant. LINE-1 methylation levels were negatively correlated with age. Sleep efficiency was statistically significantly lower for women in Group 1 (HFs present) (74.66% +/- 11.16% vs. 82.63% +/- 7.31%;p = 0.03). The ratio of duration of awakening to total sleep time was statistically significantly higher in Group 1 (HFs present) (22.38% +/- 9.99% vs. 15.07% +/- 6.93, p = 0.03). Objectively recorded hot flashes were significantly higher in Group 1 (4.00 +/- 3.21 vs. 1.47 +/- 1.46, p = 0.03). None of the cases in Group 2 self-reported HF despite objectively recorded HFs during the polysomnography. The rate of hot flash associated with awakening was 41.4% in the whole sample. Conclusions: Women with a history of hot flashes exhibited lower sleep efficiency and higher awakening rates. Although a history of experiencing hot flashes was associated with higher LINE-1 and Alu methylation levels, no statistical significance was found. Further studies are needed to clarify this association. This study was funded by the Scientific Research Projects Coordination Unit of Istanbul University-Cerrahpasa. Project number: TTU-2021-35629.Publication Metadata only Could DTI unlock the mystery of subjective tinnitus: it’s time for parameters that go a little out of the routine(Springer, 2024) Yilmaz, Eren; Yildirim, Duzgun; Sanli, Deniz Esin Tekcan; Elpen, Pinar; Tuzuner, Filiz Gosterisli; Sirin, Ahmet; Yagimli, Mustafa; Tozan, Hakan; Sanli, Ahmet Necati; Kandemirli, Sedat Giray; Department of Computer Engineering; İnan, Neslihan Gökmen; Department of Computer Engineering; College of EngineeringIn this study, it was aimed to assess the microstructural changes in the main central auditory pathway in cases with subjective tinnitus. In total, 101 subjects (52 cases with bilateral subjective non-pulsatile tinnitus and 49 healthy cases as the control group) were included in the study. Participants underwent pure tone audiogram and Diffusion Tensor Imaging-Magnetic Resonance Imaging (DTI-MRI) examination with a 3 Tesla MRI device. The number of tracts, tract length, volume, and quantitative anisotropy (QA) and normalized quantitative anisotropy’ (nQA) values were calculated by plotting cochleocortical pathways from the cochlear nerve to ipsilateral and contralateral Heschl’s gyrus (HG). In pure tone audiometry, the control group had lower hearing thresholds than cases with tinnitus. Fibres and nQA values from the right cochlear nerve to the right HG were significantly lower in the tinnitus group than in the control group. Cochlear nuclei voxel counts were significantly decreased in the tinnitus group. Both cochlear nucleus volumes were higher in the tinnitus group than in the control group. nQA values in both cochlear nuclei were decreased in the tinnitus group. This study showed that the most commonly affected part in subjective non-pulsatile tinnitus cases is the cochlear nucleus. Therefore, the cochlear nucleus should be evaluated more carefully in cases presenting with subjective tinnitus.Publication Metadata only HyperE2VID: improving event-based video reconstruction via hypernetworks(IEEE-Inst Electrical Electronics Engineers Inc, 2024) Ercan, Burak; Eker, Onur; Sağlam, Canberk; Erdem, Erkut; Department of Computer Engineering; Erdem, Aykut; Department of Computer Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); College of Engineering;Event-based cameras are becoming increasingly popular for their ability to capture high-speed motion with low latency and high dynamic range. However, generating videos from events remains challenging due to the highly sparse and varying nature of event data. To address this, in this study, we propose HyperE2VID, a dynamic neural network architecture for event-based video reconstruction. Our approach uses hypernetworks to generate per-pixel adaptive filters guided by a context fusion module that combines information from event voxel grids and previously reconstructed intensity images. We also employ a curriculum learning strategy to train the network more robustly. Our comprehensive experimental evaluations across various benchmark datasets reveal that HyperE2VID not only surpasses current state-of-the-art methods in terms of reconstruction quality but also achieves this with fewer parameters, reduced computational requirements, and accelerated inference times.Publication Metadata only Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes(Elsevier, 2012) Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; N/A; Keskin, Özlem; Gürsoy, Attila; Özbabacan, Saliha Ece Acuner; Faculty Member; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26605; 8745; 264351Apoptosis is a matter of life and death for cells and both inhibited and enhanced apoptosis may be involved in the pathogenesis of human diseases. The structures of protein-protein complexes in the apoptosis signaling pathway are important as the structural pathway helps in understanding the mechanism of the regulation and information transfer, and in identifying targets for drug design. Here, we aim to predict the structures toward a more informative pathway than currently available. Based on the 3D structures of complexes in the target pathway and a protein-protein interaction modeling tool which allows accurate and proteome-scale applications, we modeled the structures of 29 interactions, 21 of which were previously unknown. Next, 27 interactions which were not listed in the KEGG apoptosis pathway were predicted and subsequently validated by the experimental data in the literature. Additional interactions are also predicted. The multi-partner hub proteins are analyzed and interactions that can and cannot co-exist are identified. Overall, our results enrich the understanding of the pathway with interactions and provide structural details for the human apoptosis pathway. They also illustrate that computational modeling of protein-protein interactions on a large scale can help validate experimental data and provide accurate, structural atom-level detail of signaling pathways in the human cell.Publication Metadata only Dynamic QoS/QoE-aware reliable service composition framework for edge intelligence(Springer, 2022) Otoum, Safa; N/A; Department of Computer Engineering; Hayyolalam, Vahideh; Özkasap, Öznur; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 113507Edge intelligence has become popular recently since it brings smartness and copes with some shortcomings of conventional technologies such as cloud computing, Internet of Things (IoT), and centralized AI adoptions. However, although utilizing edge intelligence contributes to providing smart systems such as automated driving systems, smart cities, and connected healthcare systems, it is not free from limitations. There exist various challenges in integrating AI and edge computing, one of which is addressed in this paper. Our main focus is to handle the adoption of AI methods on resource-constrained edge devices. In this regard, we introduce the concept of Edge devices as a Service (EdaaS) and propose a quality of service (QoS) and quality of experience (QoE)-aware dynamic and reliable framework for AI subtasks composition. The proposed framework is evaluated utilizing three well-known meta-heuristics in terms of various metrics for a connected healthcare application scenario. The experimental results confirm the applicability of the proposed framework. Moreover, the results reveal that black widow optimization (BWO) can handle the issue more efficiently compared to particle swarm optimization (PSO) and simulated annealing (SA). The overall efficiency of BWO over PSO is 95%, and BWO outperforms SA with 100% efficiency. It means that BWO prevails SA and PSO in all and 95% of the experiments, respectively.Publication Metadata only Hot spots in protein-protein interfaces: towards drug discovery(Elsevier, 2014) N/A; N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Çukuroğlu, Engin; Engin, Hatice Billur; Gürsoy, Attila; Keskin, Özlem; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; N/A; College of Engineering; College of Engineering; N/A; N/A; 8745; 26605Identification of drug-like small molecules that alter protein-protein interactions might be a key step in drug discovery. However, it is very challenging to find such molecules that target interface regions in protein complexes. Recent findings indicate that such molecules usually target specifically energetically favored residues (hot spots) in protein protein interfaces. These residues contribute to the stability of protein-protein complexes. Computational prediction of hot spots on bound and unbound structures might be useful to find druggable sites on target interfaces. We review the recent advances in computational hot spot prediction methods in the first part of the review and then provide examples on how hot spots might be crucial in drug design. (C) 2014 Published by Elsevier Ltd.Publication Metadata only Structural cooperativity in histone H3 tail modifications(Wiley, 2011) N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Şanlı, Deniz; Keskin, Özlem; Gürsoy, Attila; Erman, Burak; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 26605; 8745; 179997Post-translational modifications of histone H3 tails have crucial roles in regulation of cellular processes. There is cross-regulation between the modifications of K4, K9, and K14 residues. The modifications on these residues drastically promote or inhibit each other. In this work, we studied the structural changes of the histone H3 tail originating from the three most important modifications; tri-methylation of K4 and K9, and acetylation of K14. We performed extensive molecular dynamics simulations of four types of H3 tails: (i) the unmodified H3 tail having no chemical modification on the residues, (ii) the tri-methylated lysine 4 and lysine 9 H3 tail (K4me3K9me3), (iii) the tri-methylated lysine 4 and acetylated lysine 14 H3 tail (K4me3K14ace), and (iv) tri-methylated lysine 9 and acetylated lysine 14 H3 tail (K9me3K14ace). Here, we report the effects of K4, K9, and K14 modifications on the backbone torsion angles and relate these changes to the recognition and binding of histone modifying enzymes. According to the Ramachandran plot analysis; (i) the dihedral angles of K4 residue are significantly affected by the addition of three methyl groups on this residue regardless of the second modification, (ii) the dihedral angle values of K9 residue are similarly altered majorly by the tri-methylation of K4 residue, (iii) different combinations of modifications (tri-methylation of K4 and K9, and acetylation of K14) have different influences on phi and psi values of K14 residue. Finally, we discuss the consequences of these results on the binding modes and specificity of the histone modifying enzymes such as DIM-5, GCN5, and JMJD2A.