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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Item Metadata only Silicon nanowires driving miniaturization of microelectromechanical systems physical sensors: a review(Wiley-V C H Verlag Gmbh, 2023) 0000-0002-2712-1908; 0000-0003-2063-1566; 0000-0002-7702-0566; 0000-0001-5931-8134; N/A; N/A; N/A; Department of Mechanical Engineering; Karimzadehkhouei, Mehrdad; Ali, Basit; Ghourichaei, Masoud Jedari; Alaca, Burhanettin Erdem; Researcher; PhD Student; PhD Student; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 115108The miniaturization of microelectromechanical systems (MEMS) physical sensors is driven by global connectivity needs and is closely linked to emerging digital technologies and the Internet of Things. Strong technical advantages of miniaturization such as improved sensitivity, functionality, and power consumption are accompanied by significant economic benefits due to semiconductor manufacturing. Hence, the trend to produce smaller sensors and their driving force resemble very much those of the miniaturization of integrated circuits (ICs) as described by Moore's law. In this respect, with its IC-, and MEMS-compatibility, and scalability, the silicon nanowire is frequently employed in frontier research as the sensor building block replacing conventional sensors. The integration of the silicon nanowire with MEMS has thus generated a multiscale hybrid architecture, where the silicon nanowire serves as the piezoresistive transducer and MEMS provide an interface with external forces, such as inertial or magnetic. This approach has been reported for almost all physical sensor types over the last decade. These sensors are reviewed here with detailed classification. In each case, associated technological challenges and comparisons with conventional counterparts are provided. Future directions and opportunities are highlighted.Item Metadata only Dynamics of medical screening: a simulation model of PSA screening for early detection of prostate cancer(MDPI, 2023) 0000-0002-2319-0818; Department of Business Administration; Karanfil, Özge; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Administrative Sciences and Economics; 294019In this study, we present a novel simulation model and case study to explore the long-term dynamics of early detection of disease, also known as routine population screening. We introduce a realistic and portable modeling framework that can be used for most cases of cancer, including a natural disease history and a realistic yet generic structure that allows keeping track of critical stocks that have been generally overlooked in previous modeling studies. Our model is specific to prostate-specific antigen (PSA) screening for prostate cancer (PCa), including the natural progression of the disease, respective changes in population size and composition, clinical detection, adoption of the PSA screening test by medical professionals, and the dissemination of the screening test. The key outcome measures for the model are selected to show the fundamental tradeoff between the main harms and benefits of screening, with the main harms including (i) overdiagnosis, (ii) unnecessary biopsies, and (iii) false positives. The focus of this study is on building the most reliable and flexible model structure for medical screening and keeping track of its main harms and benefits. We show the importance of some metrics which are not readily measured or considered by existing medical literature and modeling studies. While the model is not primarily designed for making inferences about optimal screening policies or scenarios, we aim to inform modelers and policymakers about potential levers in the system and provide a reliable model structure for medical screening that may complement other modeling studies designed for cancer interventions. Our simulation model can offer a formal means to improve the development and implementation of evidence-based screening, and its future iterations can be employed to design policy recommendations to address important policy areas, such as the increasing pool of cancer survivors or healthcare spending in the U.S.Item Metadata only Optimization of gelatin methacryloyl hydrogel properties through an artificial neural network model(Amer Chemical Soc, 2023) 0000-0003-3004-7742; 0000-0001-9092-2698; 0009-0001-5439-0804; N/A; Department of Chemical and Biological Engineering; N/A; Karaoğlu, İsmail Can; Kızılel, Seda; Kebabcı, Aybaran Olca; PhD Student; Faculty Member; Master Student; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; 28376; N/AGelatin methacryloyl (GelMA) hydrogels are promising materials for tissue engineering applications due to their biocompatibility and tunable properties. However, the time-consuming process of preparing GelMA hydrogels with desirable properties for specific biomedical applications limits their clinical use. Visible-light-induced cross-linking is a well-known method for the preparation of GelMA hydrogels; however, a comprehensive investigation on the influence of critical parameters such as Eosin Y (EY), triethanolamine (TEA), and N-vinyl-2-pyrrolidone (NVP) concentrations on the stiffness and gelation time has yet to be performed. In this study, we systematically investigated the effect of these critical parameters on the stiffness and gelation time of GelMA hydrogels. We developed an artificial neural network (ANN) model with three input variables, EY, TEA, and NVP concentrations, and two output variables, Young's modulus and gelation time, derived from our experimental design. Through the alteration of individual chemical concentrations, [EY] between 0.005 and 0.5 mM and [TEA] and [NVP] between 10 and 1000 mM, we studied the impact of these alterations on the real-time values of stiffness and gelation time. Furthermore, we demonstrated the validity of the ANN model in predicting the properties of GelMA hydrogels. We also studied cell survival to establish nontoxic concentration ranges for each component, enabling safer use of GelMA hydrogels in relevant biomedical applications. Our results showed that the ANN model can accurately predict the properties of GelMA hydrogels, allowing for the synthesis of hydrogels with desirable stiffness for various biomedical applications. In conclusion, our study provides a comprehensive library that characterizes the stiffness and gelation time and demonstrates the potential of the ANN model to predict these properties of GelMA hydrogels depending on the critical parameters. The ANN models developed here can facilitate the optimization of GelMA hydrogels with the most efficient mechanical properties that resemble a native extracellular matrix and better address the need in the in vivo microenvironment. The approach of this study is to bring research about the synthesis of GelMA hydrogels to a new level where the synthesis of these hydrogels can be standardized with minimum cost and effort.Item Metadata only A new multi-picture architecture for learned video deinterlacing and demosaicing with parallel deformable convolution and self-attention blocks(Elsevier Ltd, 2024) 0000-0003-1465-8121; 0000-0001-6840-5766; Department of Electrical and Electronics Engineering; N/A; Tekalp, Ahmet Murat; Ji, Ronglei; Faculty Member; PhD Student; College of Engineering; Graduate School of Sciences and Engineering; 26207; N/ADespite the fact real-world video deinterlacing and demosaicing are well-suited to supervised learning from synthetically degraded data because the degradation models are known and fixed, learned video deinterlacing and demosaicing have received much less attention compared to denoising and super-resolution tasks. We propose a new multi-picture architecture for video deinterlacing or demosaicing by aligning multiple supporting pictures with missing data to a reference picture to be reconstructed, benefiting from both local and global spatio-temporal correlations in the feature space using modified deformable convolution blocks and a novel residual efficient top-k self-attention (kSA) block, respectively. Separate reconstruction blocks are used to estimate different types of missing data. Our extensive experimental results, on synthetic or real-world datasets, demonstrate that the proposed novel architecture provides superior results that significantly exceed the state-of-the-art for both tasks in terms of PSNR, SSIM, and perceptual quality. Ablation studies are provided to justify and show the benefit of each novel modification made to the deformable convolution and residual efficient kSA blocks. Code is available: https://github.com/KUIS-AI-Tekalp-Research-Group/Video-Deinterlacing. © 2023Item Metadata only Enantiomer detection via quantum otto cycle(Amer Physical Soc, 2023) 0000-0002-9134-3951; 0000-0001-7517-453X; N/A; Department of Physics; N/A; N/A; Müstecaplıoğlu, Özgür Esat; Izadyari, Mohsen; Naseem, Muhammad Tahir; Faculty Member; PhD Student; PhD Student; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 1674; N/A; N/AEnantiomers are chiral molecules that exist in right-handed and left-handed conformations. Optical techniques of enantiomers' detection are widely employed to discriminate between left- and right-handed molecules. However, identical spectra of enantiomers make enantiomer detection a very challenging task. Here, we investigate the possibility of exploiting thermodynamic processes for enantiomer detection. In particular, we employ a quantum Otto cycle in which a chiral molecule described by a three-level system with cyclic optical transitions is considered a working medium. Each energy transition of the three-level system is coupled with an external laser drive. We find that the left- and right-handed enantiomers operate as a quantum heat engine and a thermal accelerator, respectively, when the overall phase is the control parameter. In addition, both enantiomers act as heat engines by keeping the overall phase constant and using the laser drives' detuning as the control parameter during the cycle. However, the molecules can still be distinguished because both cases' extracted work and efficiency are quantitatively very different. Accordingly, the left- and right-handed molecules can be distinguished by evaluating the work distribution in the Otto cycle.Item Metadata only Miniaturized wireless sensor enables real-time monitoring of food spoilage(Nature Portfolio, 2023) 0000-0002-7756-4192; 0000-0001-9133-3377; 0000-0003-4700-7050; 0000-0001-7747-2389; 0000-0003-1595-431X; 0000-0003-0545-7504; 0000-0002-9777-6619; Cakir, Cengiz; Koydemir, Hatice Ceylan; Department of Chemistry; Department of Chemistry; Department of Mechanical Engineering; Department of Mechanical Engineering; N/A; N/A; Department of Mechanical Engineering; Yılgör, İskender; Yılgör, Emel; İstif, Emin; Mirzajani, Hadi; Dağ, Çağdaş; Mirlou, Fariborz; Beker, Levent; Faculty Member; Researcher; Researcher; Researcher; Faculty Member; PhD Student; Faculty Member; Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; 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); College of Sciences; College of Sciences; College of Engineering; College of Engineering; N/A; Graduate School of Sciences and Engineering; College of Engineering; 24181; N/A; 354990; N/A; N/A; N/A; 308798Food spoilage results in food waste and food-borne diseases. Yet, standard laboratory tests to determine spoilage (mainly volatile biogenic amines) are not performed regularly by supply chain personnel or end customers. Here we developed a poly(styrene-co-maleic anhydride)-based, miniature (2 x 2 cm(2)) sensor for on-demand spoilage analysis via mobile phones. To demonstrate a real-life application, the wireless sensor was embedded into packaged chicken and beef; consecutive readings from meat samples using the sensor under various storage conditions enabled the monitoring of spoilage. While samples stored at room temperature showed an almost 700% change in sensor response on the third day, those stored in the freezer resulted in an insignificant change in sensor output. The proposed low-cost, miniature wireless sensor nodes can be integrated into packaged foods, helping consumers and suppliers detect spoilage of protein-rich foods on demand, and ultimately preventing food waste and food-borne diseases. Standard tests to determine food spoilage are costly and time consuming. A poly(styrene-co-maleic anhydride)-based sensor offers a low-cost alternative that can be linked to mobile phones for real-time spoilage analysis. The device was tested on chicken and beef samples under various storage conditions.Item Metadata only Extracting quantum-geometric effects from Ginzburg-Landau theory in a multiband Hubbard model(Amer Physical Soc, 2023) 0000-0003-0704-1318; Department of Physics; Işkın, Menderes; Faculty Member; College of Sciences; 29659We first apply the functional-integral approach to a multiband Hubbard model near the critical pairing temperature and derive a generic effective action that is quartic in the fluctuations of the pairing order parameter. Then we consider time-reversal-symmetric systems with uniform (i.e., at both low momentum and low frequency) pairing fluctuations in a unit cell and derive the corresponding time-dependent Ginzburg-Landau (TDGL) equation. In addition to the conventional intraband contribution that depends on the derivatives of the Bloch bands, we show that the kinetic coefficients of the TDGL equation have a geometric contribution that is controlled by both the quantum-metric tensor of the underlying Bloch states and their band-resolved quantum-metric tensors. Furthermore, we show that thermodynamic properties such as the London penetration depth, Ginzburg-Landau (GL) coherence length, GL parameter, and upper critical magnetic field have an explicit dependence on quantum geometry.Item Metadata only Associations between sleep characteristics and glycemic variability in youth with type 1 diabetes(Elsevier, 2023) 0000-0002-2614-0832; 0000-0003-3781-3892; 0000-0001-6312-6004; 0000-0002-8889-6811; 0000-0002-7855-1297; 0000-0003-3919-7763; 0000-0003-1633-9570; Boran, Perran; Baris, Hatice Ezgi; Us, Mahmut Caner; Aygun, Burcu; Haliloglu, BelmaBereket, Abdullah; N/A; N/A; N/A; N/A; Department of Computer Engineering; N/A; N/A; İpar, Necla; Gökçe, Tuğba; Can, Ecem; Eviz, Elif; İnan, Neslihan Gökmen; Mutlu, Rahime Gül Yeşiltepe; Hatun, Şükrü; Doctor; Doctor; Nurse; Researcher; Teaching Faculty; Faculty Member; Faculty Member; N/A; N/A; N/A; School of Medicine; College of Engineering; School of Medicine; School of Medicine; Koç University Hospital; N/A; N/A; N/A; 327618; 285581; 153511; 153504Objective: This study aimed to determine sleep characteristics and their associations with glycemic variability in youth with type 1 diabetes (T1D).Material and methods: This cross-sectional study conducted at two pediatric diabetes centers in Istanbul, Turkey, included 84 children with T1D (mean age 10.5 years). Sleep characteristics and glycemic variability were determined by actigraphy, DSM-5 Level 2-Sleep Disturbance Scale Short Form and continuous glucose monitoring. Circadian preference was evaluated by the Children's Chronotype Questionnaire. Sleep disturbances were assessed by the. The sleep quality was determined by actigraphyderived sleep measures. Results: Eighty-eight percent of participants had insufficient age-appropriate total sleep time (TST) (<9 h for 6-13-year-olds and <8 h for 14-17-year-olds). Chronotype was classified as intermediate in 50%, evening in 45.2%, and morning in 4.8%. A higher chronotype score indicating a stronger eveningness preference was associated with more time spent in hypoglycemia (f3= 0.433, p = 0.002). On nights when participants had lower sleep efficiency and longer sleep onset latency, they had significantly higher overnight glycemic variability (f3 = -0.343, p = 0.016, f3 = 0.129, p = 0.017, respectively). Prolonged nocturnal wake duration was significantly associated with more time spent in daytime hypoglycemia (f3 = 0.037, p = 0.046) and higher overnight glycemic variability (J index, f3 = 0.300, p = 0.015). The associations between TST and glycemic variability indices were not significant.Conclusions: Sleep quality rather than TST was significantly associated with glycemic variability in children with T1D. Eveningness preference might contribute to an increased risk of hypoglycemia. Addressing sleep patterns and chronotypes can be crucial in management plans for youth with T1D.& COPY; 2023 Elsevier B.V. All rights reserved.Item Metadata only Self-Q-switched and widely tunable continuous-wave operation of a Tm3+: Lu2O3 ceramic laser near 2 μm(Elsevier, 2023) 0000-0003-4391-0189; 0000-0003-1164-1973; 0000-0003-3446-2062; N/A; Department of Physics; Department of Chemistry; Department of Physics; N/A; Sennaroğlu, Alphan; Aydemir, Umut; Morova, Yağız; içli, Suat; Faculty Member; Faculty Member; Researcher; PhD Student; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; 23851; 58403; N/A; N/AWe report, for the first time to our knowledge, self-Q-switched (SQS) operation of a Tm3+:Lu2O3 ceramic laser near 2 mu m based on the 3F4 -> 3H6 optical transition. By careful optimization of cavity focusing, SQS operation could be achieved at several curved mirror separations without any external modulator and the laser delivered 9.7-mu s pulses at the wavelength of 2091 nm with a pulse repetition rate of 26 kHz. In the experiments, a tight-focusing resonator design was further employed to achieve low-threshold continuous-wave (CW) operation of the laser with lasing threshold pump powers as low as 33 mW. With an incident pump power of 590 mW at 776 nm, a maximum output power of 164 mW was obtained at 2097 nm with a slope efficiency of 30% with respect to the incident pump power. The tuning range of the CW Tm3+:Lu2O3 ceramic laser could be extended up to the wavelength of 2235 nm.Item Metadata only Chloride intracellular channel protein-1 (CLIC1) antibody in multiple sclerosis patients with predominant optic nerve and spinal cord involvement(Elsevier Sci Ltd, 2023) 0000-0002-0860-8964; Karaaslan, Zerrin; Sengul-Yediel, Busra; Yuceer-Korkmaz, Hande; Sanlia, Elif; Gezen-Ak, Duygu; Dursun, Erdinc; Timirci-Kahraman, Ozlem; Baykal, Ahmet Tarik; Yilmaz, Vuslat; Turkoglu, Recai; Kurtuncu, Murat; Gunduz, Tuncay; Gursoy-Ozdemir, Yasemin; Tuzun, Erdem; Kucukali, Cem Ismail; N/A; Özdemir, Yasemin Gürsoy; Faculty Member; School of Medicine; 170592Introduction: Antibodies to cell surface proteins of astrocytes have been described in chronic inflammatory demyelinating disorders (CIDD) of the central nervous system including multiple sclerosis (MS) and neuro-myelitis optica spectrum disorder (NMOSD). Our aim was to identify novel anti-astrocyte autoantibodies in relapsing remitting MS (RRMS) patients presenting predominantly with spinal cord and optic nerve attacks (MS-SCON).Methods: Sera of 29 MS-SCON patients and 36 healthy controls were screened with indirect immunofluorescence to identify IgG reacting with human astrocyte cultures. Putative target autoantigens were investigated with immunoprecipitation (IP) and liquid chromatography-mass/mass spectrometry (LC-MS/MS) studies using cultured human astrocytes. Validation of LC-MS/MS results was carried out by IP and ELISA.Results: Antibodies to astrocytic cell surface antigens were detected in 5 MS-SCON patients by immunocyto-chemistry. LC-MS/MS analysis identified chloride intracellular channel protein-1 (CLIC1) as the single common membrane antigen in 2 patients with MS-SCON. IP experiments performed with the commercial CLIC1 antibody confirmed CLIC1-antibody. Home made ELISA using recombinant CLIC1 protein as the target antigen identified CLIC1 antibodies in 9/29 MS-SCON and 3/15 relapsing inflammatory optic neuritis (RION) patients but in none of the 30 NMOSD patients, 36 RRMS patients with only one or no myelitis/optic neuritis attacks and 36 healthy controls. Patients with CLIC1-antibodies showed trends towards exhibiting reduced disability scores.Conclusion: CLIC1-antibody was identified for the first time in MS and RION patients, confirming once again anti-astrocytic autoimmunity in CIDD. CLIC1-antibody may potentially be utilized as a diagnostic biomarker for differentiation of MS from NMOSD.