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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Uncovering the penile clock: expression of molecular clock proteins in human penile cavernous tissue(Korean Soc Sexual Medicine and Andrology, 2024) Alkan, Ilter; Bozkurt, Muammer; Canat, Halil Lutfi; N/A; Durkut, Begüm; Uçak, Melike; Özenci, Çiler Çelik; Koç University Research Center for Translational Medicine (KUTTAM); Graduate School of Health Sciences; School of MedicinePurpose: To evaluate the expression of core molecular clock genes/proteins in penile cavernous tissue from healthy male subjects and to determine whether their expression has circadian variation. Materials and Methods: Corpus cavernosum biopsy samples were obtained from 10 healthy males with penile deviation or fracture who underwent surgical intervention during the day and night. The daytime group (n=5) underwent corpus cavernosum tissue sampling during zeitgeber time (ZT) 8-12, while the nighttime group (n=5) underwent sampling during ZT 20-24. The expression and localization of BMAL1, CLOCK, PER1, PER2, PER3, CRY1, and CRY2 proteins were analyzed using immunohistochemistry and quantified using H-score analysis. RT-qPCR analysis was performed to assess the expression of core molecular clock genes in the corpus cavernosum tissue of 5 additional daytime patients. Results: The expression of core molecular clock proteins was detected in vascular endothelial cells (VECs) and smooth muscle cells (SMCs) in corpus cavernosum during daytime and nighttime. BMAL1 exhibited the most significant nuclear expression during daytime in both cell types, whereas its expression decreased significantly at night. In VECs, a significant decrease in the nuclear expression of CRY1 was observed at night. In SMCs, a significant decrease in the cytoplasmic expression of PER3 was observed at night. The expression patterns of the core molecular clock genes were ascertained through a RT-qPCR analysis. Conclusions: Our research provides compelling evidence that core molecular clock genes are distinctly expressed in penile tissue in humans. Furthermore, we observed the expression of molecular clock proteins within the VECs and SMCs of the corpus cavernosum, with BMAL1 being the most prominently expressed. The discovery of core molecular clock genes in penile tissue, as well as proteins within the SMCs and VECs of the corpus cavernosum, introduces the potential significance of the molecular clock mechanism in the physiology of penile erection.Publication Metadata only Exploration of novel 6,8,9-trisubstituted purine analogues: synthesis, in vitro biological evaluation, and their effect on human cancer cells(Tubitak Scientific & Technological Research Council Turkey, 2024) Polat, Muhammed Fatih; Atalay, Rengul; Tuncbilek, Meral; N/A; Şahin, İrem Durmaz; Koç University Research Center for Translational Medicine (KUTTAM); School of MedicineCancer, a leading global cause of mortality, demands continuous advancements in therapeutic strategies. This study focuses on the design and synthesis of a novel series of purine derivatives, specifically 6 -(substituted phenyl piperazine)-8-(4-phenoxyphenyl)9-cyclopentyl purine derivatives (5-11). The motivation behind this endeavor lies in addressing acquired resistance mechanisms in cancer cells, a significant hurdle in current treatment modalities. The synthesis, starting from 4,6-dichloro-5-nitropyrimidine, involves a multi -step process, resulting in seven new purine derivatives. Biological evaluation against human liver, colon, and breast cancer cells (Huh7, HCT116, and MCF7, respectively) was performed using the SRB assay. Among the synthesized analogs, compounds 5 and 6, exhibited notable cytotoxic activity, surpassing clinically used positive controls 5-Fluorouracil and Fludarabine in terms of efficacy. This research underscores the potential of purine derivatives with a phenyl group at the C-8 position as a scaffold for developing compounds with improved anticancer properties. The findings offer insights for future exploration and development of novel agents in cancer pharmaceutical research.Publication Metadata only Fracture toughness of AlTiN coatings investigated by nanoindentation and microcantilever bending(Elsevier Science Sa, 2024) Kaygusuz, Burcin; Karadayi, Ozcan; Kazmanli, Kuersat; Ozerinc, Sezer; N/A; Motallebzadeh, Amir; Koç University Surface Science and Technology Center (KUYTAM); N/AMetal nitride coatings are increasingly used in MEMS applications. The brittle nature of these coatings makes fracture one of the main failure mechanisms during operation. Therefore, quantifying the fracture toughness of nitride coatings in a reliable fashion is important to understand the failure behavior and to optimize device performance and reliability. This study investigated the fracture toughness of AlTiN coatings produced by cathodic arc evaporation, a widely used technique in the industry. Nanoindentation and microcantilever bending-based measurements indicated a fracture toughness of 6.6 and 4.8 MPa & sdot;m1/2, respectively. The lower toughness results of microcantilever bending were attributed to the columnar growth of the coating, which promoted crack propagation perpendicular to the film surface. The results provide useful data toward a better understanding of the fracture of hard coatings and give insight into the advantages and disadvantages of different measurement methods.Publication Metadata only Robust speech recognition using adaptively denoised wavelet coefficients(IEEE, 2004) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; N/A; Tekalp, Ahmet Murat; Erzin, Engin; Akyol, Emrah; Faculty Member; Faculty Member; Master Student; Department of Electrical and Electronics Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26207; 34503; N/AThe existence of additive noise affects the performance of speech recognition in real environments. We propose a new set of feature vectors for robust speech recognition using denoised wavelet coefficients. The use of wavelet coefficients in speech processing is motivated by the ability of the wavelet transform to capture both time and frequency information and the non-stationary behaviour of speech signals. We use one set of noisy data, such as data with car noise, and we use hard thresholding in the best basis for denoising. We use isolated digits as our database in our HMM based speech recognition system. A performance comparison of hard thresholding denoised wavelet coefficients and MFCC feature vectors is presented.Publication Metadata only Exploring users interested in 3D food printing and their attitudes: case of the employees of a kitchen appliance company(Taylor and Francis inc, 2022) N/A; N/A; Department of Sociology; Department of Media and Visual Arts; Kocaman, Yağmur; Mert, Aslı Ermiş; Özcan, Oğuzhan; PhD Student; Faculty Member; Faculty Member; Department of Sociology; Department of Media and Visual Arts; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Social Sciences and Humanities; College of Social Sciences and Humanities; College of Social Sciences and Humanities; N/A; N/A; 125323D Food Printing (3DFP) technology is expected to enter homes in the near future as a kitchen appliance. on the other hand, 3DFP is perceived as a non-domestic technology by potential users and domestic users' attitudes and everyday habits received less attention in previous 3DFP research. Exploring their perspective is needed to reflect their daily kitchen dynamics on the design process and discover possible new benefits situated in the home kitchen. on this basis, this study focuses on finding potential 3DFP users and explores their attitudes towards using 3DFP technology in their home kitchens through a two-stage study: First, we prioritized potential users based on their relationship with food through a questionnaire and found six factors that positively affect their attitude towards 3DFP: cooking every day, ordering food less than once a month, eating out at least a couple of times a month, having a mini oven, A multicooker, or a kettle, liking to try new foods, thinking that cooking is a fun activity. Second, we conducted semi-structured interviews with seven participants to discuss the possible benefits and drawbacks of 3DFP technology for their daily lives in the kitchen. Results revealed two new benefits that 3DFP at home may provide: risk-free cooking and cooking for self-improvement. We discuss the potential implications of these two benefits for design and HCI research focusing on how to facilitate automation and pleasurable aspects of cooking into future 3DFP devices.Publication Metadata only Elucidating the common basis for task-dependent differential manifestations of category advantage: a decision theoretic approach(Wiley, 2022) N/A; Department of Psychology; Department of Psychology; Akbıyık, Seda; Göksun, Tilbe; Balcı, Fuat; Master Student; Faculty Member; Faculty Member; Department of Psychology; N/A; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Social Sciences and Humanities; College of Social Sciences and Humanities; College of Social Sciences and Humanities; N/A; 47278; 51269Cross-category hues are differentiated easier than otherwise equidistant hues that belong to the same linguistic category. This effect is typically manifested through both accuracy and response time gains in tasks with a memory component, whereas only response times are affected when there is no memory component. This raises the question of whether there is a common generative process underlying the differential behavioral manifestations of category advantage in color perception. For instance, within the framework of noisy evidence accumulation models, changes in accuracy can be readily attributed to an increase in the efficacy of perceptual evidence integration (after controlling for threshold setting), whereas changes in response time can also be attributed to shorter nondecisional delays (e.g., due to facilitated signal detection). To address the latent decision processes underlying category advantage across different behavioral demands, we introduce a decision-theoretic perspective (i.e., diffusion decision model) to categorical color perception in three complementary experiments. In Experiment 1, we collected data from a binary color naming task (1) to determine the green-blue boundary in our sample and (2) to trace how parameter estimates of interest in the model output change as a function of color typicality. In Experiments 2 and 3, we used same-different task paradigms (with and without a memory component, respectively) and traced the category advantage in color discrimination in two parameters of the diffusion decision model: nondecision time and drift rate. An increase in drift rate predominantly characterized the category advantage in both tasks. Our results show that improved efficiency in perceptual evidence integration is a common driving force behind different manifestations of category advantage.Publication Metadata only Characterization of finite photonic crystals with defects(Institute of Electrical and Electronics Engineers (IEEE), 2011) N/A; Department of Electrical and Electronics Engineering; Karabulut, Emine Pınar; Aksun, M. İrşadi; Reseacher; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; College of Engineering; N/A; 28358A simple computational approach is proposed to obtain the dispersion characteristics that could be observed outside of general finite-extent photonic crystals with defects. Since introducing and tailoring defects in photonic crystals are crucial for designing practical devices, the proposed method may play an important role in characterization and optimization of such defects. The method uses reflection data, due to an incident plane wave at a given frequency, collected at the front interface of a photonic crystal. It is simple and applicable for general photonic crystals, that is, photonic crystals with any periodicity, 1D, 2D, and 3D, and even with any kind of defects. The validity of the method was tested and verified on 1D and 2D finite photonic crystals, for which the reflection coefficient data at the front interface can be easily obtained by analytical means and numerical simulations, respectively. In addition, different types of defects, like random and periodic defects, were studied and it has been shown that the method is capable of providing information pertinent to the outside world on the defect modes.Publication Metadata only Object placement for high bandwidth memory augmented with high capacity memory(IEEE, 2017) N/A; N/A; Department of Computer Engineering; Laghari, Mohammad; Erten, Didem Unat; Master Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 219274High bandwidth memory (HBM) is a new emerging technology that aims to improve the performance of bandwidth limited applications. Even though it provides high bandwidth, it must be augmented with DRAM to meet the memory capacity requirement of any applications. Due to this limitation, objects in an application should be optimally placed on the heterogeneous memory subsystems. In this study, we propose an object placement algorithm that places program objects to fast or slow memories in case the capacity of fast memory is insufficient to hold all the objects to increase the overall application performance. Our algorithm uses the reference counts and type of references (read or write) to make an initial placement of data. In addition, we perform various memory bandwidth benchmarks to be used in our placement algorithm on Intel Knights Landing (KNL) architecture. Not surprisingly high bandwidth memory sustains higher read bandwidth than write bandwidth, however, placing write-intensive data on HBM results in better overall performance because write-intensive data is punished by the DRAM speed more severely compared to read intensive data. Moreover, our benchmarks demonstrate that if a basic block makes references to both types of memories, it performs worse than if it makes references to only one type of memory in some cases. We test our proposed placement algorithm with 6 applications under various system configurations. By allocating objects according to our placement scheme, we are able to achieve a speedup of up to 2x.Publication Metadata only Effect of preservation period on the viscoelastic material properties of soft tissues with implications for liver transplantation(Asme, 2010) N/A; N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Öcal, Sina; Özcan, Mustafa Umut; Başdoğan, İpek; Başdoğan, Çağatay; Master Student; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 179940; 125489The liver harvested from a donor must be preserved and transported to a suitable recipient immediately for a successful liver transplantation. In this process, the preservation period is the most critical, since it is the longest and most tissue damage occurs during this period due to the reduced blood supply to the harvested liver and the change in its temperature. We investigate the effect of preservation period on the dynamic material properties of bovine liver using a viscoelastic model derived from both impact and ramp and hold experiments. First, we measure the storage and loss moduli of bovine liver as a function of excitation frequency using an impact hammer. Second, its time-dependent relaxation modulus is measured separately through ramp and hold experiments performed by a compression device. Third, a Maxwell solid model that successfully imitates the frequency- and time-dependent dynamic responses of bovine liver is developed to estimate the optimum viscoelastic material coefficients by minimizing the error between the experimental data and the corresponding values generated by the model. Finally, the variation in the viscoelastic material coefficients of bovine liver are investigated as a function of preservation period for the liver samples tested 1 h, 2 h, 4 h, 8 h, 12 h, 24 h, 36 h, and 48 h after harvesting. The results of our experiments performed with three animals show that the liver tissue becomes stiffer and more viscous as it spends more time in the preservation cycle.Publication Metadata only Affect burst detection using multi-modal cues(IEEE, 2015) Department of Computer Engineering; Department of Computer Engineering; N/A; Department of Computer Engineering; N/A; Sezgin, Tevfik Metin; Yemez, Yücel; Türker, Bekir Berker; Erzin, Engin; Marzban, Shabbir; Faculty Member; Faculty Member; PhD Student; Faculty Member; Master Student; Department of Computer Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; 18632; 107907; N/A; 34503; N/ARecently, affect bursts have gained significant importance in the field of emotion recognition since they can serve as prior in recognising underlying affect bursts. In this paper we propose a data driven approach for detecting affect bursts using multimodal streams of input such as audio and facial landmark points. The proposed Gaussian Mixture Model based method learns each modality independently followed by combining the probabilistic outputs to form a decision. This gives us an edge over feature fusion based methods as it allows us to handle events when one of the modalities is too noisy or not available. We demonstrate robustness of the proposed approach on 'Interactive emotional dyadic motion capture database' (IEMOCAP) which contains realistic and natural dyadic conversations. This database is annotated by three annotators to segment and label affect bursts to be used for training and testing purposes. We also present performance comparison between SVM based methods and GMM based methods for the same configuration of experiments.