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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access What is the current role and what are the prospects of the robotic approach in liver surgery?(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Sijberden, J.P.; Hilal, M.A.; Bozkurt, Emre; Koç University HospitalRobotic liver surgery is being applied with increasing frequency. Comparable, and in specific settings superior, perioperative outcomes compared to laparoscopic liver surgery have been reported. In its current form, the most commonly mentioned advantage of robotic surgery is improved dexterity. Important obstacles to its wider implementation in daily clinical practice are the associated costs, technical difficulties, and a scarce amount of evidence. Robotic liver surgery will likely continue to evolve in parallel with technological developments that enhance the robots' abilities. In parallel with the historical development of minimally invasive surgery, the laparoscopic and robotic approaches are now frequently utilized to perform major abdominal surgical procedures. Nevertheless, the role of the robotic approach in liver surgery is still controversial, and a standardized, safe technique has not been defined yet. This review aims to summarize the currently available evidence and prospects of robotic liver surgery. Minimally invasive liver surgery has been extensively associated with benefits, in terms of less blood loss, and lower complication rates, including liver-specific complications such as clinically relevant bile leakage and post hepatectomy liver failure, when compared to open liver surgery. Furthermore, comparable R0 resection rates to open liver surgery have been reported, thus, demonstrating the safety and oncological efficiency of the minimally invasive approach. However, whether robotic liver surgery has merits over laparoscopic liver surgery is still a matter of debate. In the current literature, robotic liver surgery has mainly been associated with non-inferior outcomes compared to laparoscopy, although it is suggested that the robotic approach has a shorter learning curve, lower conversion rates, and less intraoperative blood loss. Robotic surgical systems offer a more realistic image with integrated 3D systems. In addition, the improved dexterity offered by robotic surgical systems can lead to improved intra and postoperative outcomes. In the future, integrated and improved haptic feedback mechanisms, artificial intelligence, and the introduction of more liver-specific dissectors will likely be implemented, further enhancing the robots' abilities.Publication Open Access Evolutionary multiobjective feature selection for sentiment analysis(Institute of Electrical and Electronics Engineers (IEEE), 2021) Pelin Angın; Deniz, Ayça; Department of International Relations; Angın, Merih; Faculty Member; Department of International Relations; College of Administrative Sciences and Economics; 308500Sentiment analysis is one of the prominent research areas in data mining and knowledge discovery, which has proven to be an effective technique for monitoring public opinion. The big data era with a high volume of data generated by a variety of sources has provided enhanced opportunities for utilizing sentiment analysis in various domains. In order to take best advantage of the high volume of data for accurate sentiment analysis, it is essential to clean the data before the analysis, as irrelevant or redundant data will hinder extracting valuable information. In this paper, we propose a hybrid feature selection algorithm to improve the performance of sentiment analysis tasks. Our proposed sentiment analysis approach builds a binary classification model based on two feature selection techniques: an entropy-based metric and an evolutionary algorithm. We have performed comprehensive experiments in two different domains using a benchmark dataset, Stanford Sentiment Treebank, and a real-world dataset we have created based on World Health Organization (WHO) public speeches regarding COVID-19. The proposed feature selection model is shown to achieve significant performance improvements in both datasets, increasing classification accuracy for all utilized machine learning and text representation technique combinations. Moreover, it achieves over 70% reduction in feature size, which provides efficiency in computation time and space.Publication Open Access Comparative spectroscopic investigation of Tm3+: tellurite glasses for 2-mu m lasing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2018) Kurt, Adnan; Speghini, Adolfo; Bettinelli, Marco; Department of Electrical and Electronics Engineering; Department of Physics; Çankaya, Hüseyin; Görgülü, Adil Tolga; Sennaroğlu, Alphan; Researcher; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; College of Sciences; N/A; N/A; 23851We performed a comparative spectroscopic analysis on three novel Tm3+: tellurite-based glasses with the following compositions Tm2O3: TeO2-ZnO (TeZnTm), Tm2O3: TeO2-Nb2O5 (TeNbTm), and Tm3+: TeO2-K2O-Nb2O5 (TeNbKTm), primarily for 2-mu m laser applications. Tellurite glasses were prepared at different doping concentrations in order to investigate the effect of Tm3+ ion concentration as well as host composition on the stimulated emission cross sections and the luminescence quantum efficiencies. By performing Judd-Ofelt analysis, we determined the average radiative lifetimes of the H-3(4) level to be 2.55 +/- 0.07 ms, 2.76 +/- 0.03 ms and 2.57 +/- 0.20 ms for the TeZnTm, TeNbTm and TeNbKTm samples, respectively. We clearly observed the effect of the cross-relaxation, which becomes significant at higher Tm2O3 concentrations, leading to the quenching of 1460-nm emission and enhancement of 1860-nm emission. Furthermore, with increasing Tm2O3 concentrations, we observed a decrease in the fluorescence lifetimes as a result of the onset of non-radiative decay. For the H-3(4) level, the highest obtained quantum efficiency was 32% for the samples with the lowest Tm2O3 ion concentration. For the 1860-nm emission band, the average emission cross section was determined to measure around 6.33 +/- 0.34 x 10(-21) cm(2), revealing the potential of thulium-doped tellurite gain media for 2-mu m laser applications in bulk and fiber configurations.Publication Open Access Thrombolysis in Myocardial Infarction Risk Index predicts one-year mortality in patients with heart failure: an analysis of the SELFIE-TR study(Karger Publishers, 2022) Güvenç, Rengin Çetin; Güvenç, Tolga Sinan; Çavusoğlu, Yüksel; Yılmaz, Mehmet Birhan; Ural, Dilek; Faculty Member; School of Medicine; 1057Objective: predicting outcomes is an essential part of evaluation in patients with heart failure (HF). While there are multiple individual laboratory and imaging variables, as well as risk scores available for this purpose, they are seldom useful during the initial evaluation. In this analysis, we aimed to understand predictive usefulness of Thrombosis in Myocardial Infarction Risk Index (TIMI-RI), a simple index that is calculated at bedside using three commonly available variables, using data from a multicenter HF registry. Subjects and Methods: a total of 728 patients from 23 centers were included to this analysis. Data on hospitalizations and mortality were collected by direct interviews, phone calls and electronic databases. TIMI-RI was calculated as defined before. Patients were divided into three equal tertiles to perform analyses. Results: rehospitalization for HF was significantly higher in patients within the 3rd tertile, and 33.5% of patients within the 3rd tertile were dead within one-year follow up as compared to 14.5% of patients within the 1st tertile and 15.6% patients within the 2nd tertile (p<0.001, log-rank p<0.001 for pairwise comparisons on survival analysis). A TIMI-RI higher than 33 had a negative predictive value of 84.8% and a positive predictive value of 33.8% for prediction of one-year mortality. This predictive usefulness was independent of other demographic, examination and clinical variables (OR:1.74, 95%CI:1.05-2.86, p=0.036). Conclusion: TIMI-RI is a simple index that predicts one-year mortality in patients with HF, and it could be useful for rapid evaluation and triage of HF patients at the time of initial contact.Publication Open Access Autophagy and cancer dormancy(Frontiers, 2021) Akçay, Arzu; Akkoç, Yunus; Peker, Nesibe; Gözüaçık, Devrim; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; N/A; 40248Metastasis and relapse account for the great majority of cancer-related deaths. Most metastatic lesions are micro metastases that have the capacity to remain in a non-dividing state called "dormancy" for months or even years. Commonly used anticancer drugs generally target actively dividing cancer cells. Therefore, cancer cells that remain in a dormant state evade conventional therapies and contribute to cancer recurrence. Cellular and molecular mechanisms of cancer dormancy are not fully understood. Recent studies indicate that a major cellular stress response mechanism, autophagy, plays an important role in the adaptation, survival and reactivation of dormant cells. In this review article, we will summarize accumulating knowledge about cellular and molecular mechanisms of cancer dormancy, and discuss the role and importance of autophagy in this context.Publication Open Access The structural basis of Akt PH domain interaction with calmodulin(Elsevier, 2021) Jang, Hyunbum; Nussinov, Ruth; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Weako, Jackson; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745Akt plays a key role in the Ras/PI3K/Akt/mTOR signaling pathway. In breast cancer, Akt translocation to the plasma membrane is enabled by the interaction of its pleckstrin homology domain (PHD) with calmodulin (CaM). At the membrane, the conformational change promoted by PIP3 releases CaM and facilitates Thr308 and Ser473 phosphorylation and activation. Here, using modeling and molecular dynamics simulations, we aim to figure out how CaM interacts with Akt's PHD at the atomic level. Our simulations show that CaM-PHD interaction is thermodynamically stable and involves a beta-strand rather than an alpha-helix, in agreement with NMR data, and that electrostatic and hydrophobic interactions are critical. The PHD interacts with CaM lobes; however, multiple modes are possible. IP4, the polar head of PIP3, weakens the CaM-PHD interaction, implicating the release mechanism at the plasma membrane. Recently, we unraveled the mechanism of PI3K alpha activation at the atomistic level and the structural basis for Ras role in the activation. Here, our atomistic structural data clarify the mechanism of how CaM interacts, delivers, and releases Akt-the next node in the Ras/PI3K pathway-at the plasma membrane.Publication Open Access REM-predominant obstructive sleep apnea in patients with coronary artery disease(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Newitt, Jennifer; Strollo, Patrick J., Jr.; Balcan, Mehmet Baran; Çelik, Yeliz; Peker, Yüksel; Researcher; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Koç University Hospital; N/A; N/A; 234103Obstructive sleep apnea (OSA) is common in adults with coronary artery disease (CAD). OSA that occurs predominantly during rapid-eye movement (REM) sleep has been identified as a specific phenotype (REM-predominant OSA) in sleep clinic cohorts. We aimed to examine the association of REM-predominant OSA with excessive sleepiness, functional outcomes, mood, and quality of life in a CAD cohort, of whom 286 OSA patients with total sleep time >= 240 min, and REM sleep >= 30 min, were included. REM-predominant OSA was defined as a REM-apnea-hypopnea-index (AHI) /non-REM (NREM) AHI >= 2. In all, 73 (25.5%) had REM-predominant OSA. They were more likely to be female (26.0% vs. 9.9%; p = 0.001), and more obese (42.5% vs. 24.4%; p = 0.003) but had less severe OSA in terms of AHI (median 22.6/h vs. 36.6/h; p < 0.001) compared to the patients with non-stage specific OSA. In adjusted logistic regression models, female sex (odds ratio [OR] 4.64, 95% confidence interval [CI] 1.85-11.64), body-mass-index (BMI; OR 1.17; 95% CI 1.07-1.28) and AHI (OR 0.93, 95% CI 0.91-0.95) were associated with REM-predominant OSA. In univariate linear regression models, there was a dose-response relationship between REM-AHI and Zung Self-rated Depression Scale but not excessive sleepiness, functional outcomes, and anxiety scores. Among the Short Form-36 subdomains, Vitality, Mental Health, and Mental Component Summary (MCS) scores were inversely correlated with REM-AHI. In multivariate linear models, only MCS remained significantly associated with REM-AHI after adjustment for age, BMI, and sex (beta-coefficient -2.20, %95 CI [-0.56, -0.03]; p = 0.028). To conclude, female sex and BMI were related to REM-predominant OSA in this revascularized cohort. MCS was inversely associated with REM-AHI in the multivariate model.Publication Open Access Low complexity adaptation for reconfigurable intelligent surface-based MIMO systems(Institute of Electrical and Electronics Engineers (IEEE), 2020) Yiğit, Zehra; Altunbaş, İbrahim; Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 149116Reconfigurable intelligent surface (RIS)-based transmission technology offers a promising solution to enhance wireless communication performance cost-effectively through properly adjusting the parameters of a large number of passive reflecting elements. This letter proposes a cosine similarity theorem-based low-complexity algorithm for adapting the phase shifts of an RIS that assists a multiple-input multiple-output (MIMO) transmission system. A semi-analytical probabilistic approach is developed to derive the theoretical average bit error probability (ABEP) of the system. Furthermore, the validity of the theoretical analysis is supported through extensive computer simulations.Publication Open Access Increased hemoglobin oxygen affinity with 5-hydroxymethylfurfural supports cardiac function during severe hypoxia(Frontiers, 2019) Lucas, Alfredo; Ao-ieong, Eilleen S. Y.; Williams, Alexander T.; Jani, Vivek P.; Muller, Cynthia R; Cabrales, Pedro; N/A; Yalçın, Özlem; Researcher; School of Medicine; 218440Acclimatization to hypoxia or high altitude involves physiological adaptation processes, to influence oxygen (O2) transport and utilization. Several natural products, including aromatic aldehydes and isothiocyanates stabilize the R-state of hemoglobin (Hb), increasing Hb-O2 affinity and Hb-O2 saturation. These products are a counter intuitive therapeutic strategy to increase O2 delivery during hypoxia. 5-Hydroxymethylfurfural (5-HMF) is well known Amadori compound formed during the Maillard reaction (the non-enzymatic browning and caramelization of carbohydrate-containing foods after thermal treatment), with well documented effects in Hb-O2 affinity. This study explores the therapeutic potential of 5-HMF on left ventricular (LV) cardiac function (LVCF) during hypoxia. Anesthetized Golden Syrian hamsters received 5-HMF i.v., at 100 mg/kg and were subjected to stepwise increased hypoxia (15, 10, and 5%) every 30 min. LVCF was assessed using a closed chest method with a miniaturized conductance catheter via continuous LV pressure-volume (PV) measurements. Heart hypoxic areas were studied using pimonidazole staining. 5-HMF improved cardiac indices, including stroke volume (SV), cardiac output (CO), ejection fraction (EF), and stroke work (SW) compared to the vehicle group. At 5% O2, SV, CO, EF, and SW were increased by 53, 42, 33, and 51% with 5-HMF relative to vehicle. Heart chronotropic activity was not statistically changed, suggesting that differences in LV-CF during hypoxia by 5-HMF were driven by volume dependent effects. Analysis of coronary blood flow and cardiac muscle metabolism suggest no direct pharmacological effects from 5-HMF, therefore these results can be attributed to 5-HMF-dependent increase in Hb-O2 affinity. These studies establish that naturally occurring aromatic aldehydes, such as 5-HMF, produce modification of hemoglobin oxygen affinity with promising therapeutic potential to increase O2 delivery during hypoxic hypoxia.Publication Open Access Fear of happiness among college students: the role of gender, childhood psychological trauma, and dissociation(Medknow Publications, 2019) Türk, Tuğba; Öztürk, Erdinç; N/A; Şar, Vedat; Faculty Member; School of Medicine; 8542Aims: this study aimed to evaluate the fear of happiness among college students and its relationship to gender, childhood psychological trauma, and dissociation. Setting and Design: College students were addressed as study population, and a relational screening method was implemented. Materials and Methods: among 184 participants, 93 (50.5%) were women. The Fear of Happiness Scale (FHS), the Childhood Trauma Questionnaire (CTQ), and the Dissociative Experiences Scale (DES) were administered to all participants. Statistical Analysis Used: MannuWhitney-U and Student's t-tests were implemented for comparison of groups. Pearson correlation and stepwise multiple regression analyses were conducted to identify associations between variables. Results: there were no differences on DES, FHS, and CTQ total scores between genders. DES was associated with CTQ total scores in both genders. Women had higher scores than men on childhood emotional abuse and fear of "cheerfulness ends up with bad faith." Compared to nonmembers, female dissociative taxon members had higher scores on all childhood trauma types except sexual abuse, and on all types of fear of happiness except "good fortune ends up with disaster" which was the only type of fear significantly elevated among male dissociative taxon members. A stepwise regression analysis revealed that depersonalization, childhood emotional neglect, and physical abuse predicted fear of happiness among women which was predicted by absorption among men. Conclusions: there is a relationship between childhood psychological trauma, dissociation, and fear of happiness. Women seem to be more vulnerable in this path of obsessional thinking which affects different realms in male and female genders.