Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Improved Colorectal Gland Segmentation in Histopathology Images with Adaptive Resizer-Enhanced U-Net Models(Springer Science and Business Media Deutschland GmbH, 2026) Gümüş, Abdurrahman; Gumus, A.; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyUtilizing low-resolution images for computer vision tasks such as classification and segmentation can sometimes hinder the model’s ability to accurately learn essential features. While using high-resolution images and designing compatible models might seem like viable solutions, they are not always feasible due to energy efficiency and graphical computation constraints. Downsizing images for model training and application is an effective approach for improving computational efficiency and optimizing model performance.The bilinear resizing method, commonly employed for this purpose, inherently causes information loss due to its numerical approach, which relies solely on the four nearest pixel values to compute each target pixel. This limitation becomes more pronounced with high-resolution images, where the down sampling process intensifies the loss of critical information. However, recent advancements have introduced adaptive resizer modules, which dynamically adjust image dimensions to better preserve essential features before processing by deep learning models. In this study, an adaptive resizer-based segmentation framework is proposed for the gland segmentation task, which is crucial for accurate disease diagnosis, particularly in cancer analysis. Three distinct encoder-decoder architecture segmentation models are assessed for image segmentation using the Colorectal Adenocarcinoma Gland (CRAG) gland segmentation database. Each architecture was tested separately, employing six different backbone encoders that were pretrained on the ImageNet dataset. The comparative analysis showed that the adaptive resizer improved segmentation performance, increasing the Intersection over Union (IoU) metric by an average of 5.6%. This enhancement raised the lowest IoU from 62% to 70% and the highest to 78%. The code is available on GitHub at https://github.com/miralab-ai/adaptive-resizer-segmentation. © The Author(s) 2026.Article On the Strengths and Weaknesses of Virtual Reality in Distance Estimation in AEC Domain: A Meta-Analysis of Literature 2014–2024(Springer Science and Business Media Deutschland GmbH, 2026) Kasalı, Altuğ; Doğan, Fehmi; Çevik, A.; Kasali, A.; 02.02. Department of Architecture; 02. Faculty of Architecture; 01. Izmir Institute of TechnologyVirtual reality (VR) became the most used extended reality system in architecture, engineering, and construction domains. It offers advantages through its immersive and interactive interface. There is, however, a need to investigate both its strengths and weaknesses especially in relation to the claim that it is a close surrogate for real-world performances. This study reports the findings of a meta-analysis on distance estimation (DE) in VR. Distance estimation, essential for spatial perception, remains to be a problem in VR even with advanced head-mounted displays. The study questions whether VR can match the real-world performance in DE to highlight its shortcomings as well as its potentials. The meta-analysis includes 77 pieces of data from 29 studies and investigates whether DE accuracy has improved and how DE interacts with task type, task environment, and target range. The results indicate VR is still underperforming in DE, head-mounted display’s weight is the significant factor, and task type and task environment significantly interact with DE. We conclude VR needs to be specifically tailored regarding the needs of practitioners in architecture and engineering industry and that it is not yet a substitute for real-world performances. © The Author(s) 2025.Article Future Circular Collider Feasibility Study Report: Volume 3 Civil Engineering, Implementation and Sustainability(Springer Science and Business Media Deutschland GmbH, 2025) Benedikt, M.; Zimmermann, F.; Auchmann, B.; Bartmann, W.; Burnet, J.P.; Carli, C.; Zykova, M.; 01. Izmir Institute of TechnologyVolume 3 of the FCC Feasibility Report presents studies related to civil engineering, the development of a project implementation scenario, and environmental and sustainability aspects. The report details the iterative improvements made to the civil engineering concepts since 2018, taking into account subsurface conditions, accelerator and experiment requirements, and territorial considerations. It outlines a technically feasible and economically viable civil engineering configuration that serves as the baseline for detailed subsurface investigations, construction design, cost estimation, and project implementation planning. Additionally, the report highlights ongoing subsurface investigations in key areas to support the development of an improved 3D subsurface model of the region. The report describes the development of the project scenario based on the ‘avoid-reduce-compensate’ iterative optimisation approach. The reference scenario balances optimal physics performance with territorial compatibility, implementation risks, and costs. Environmental field investigations covering almost 600 hectares of terrain—including numerous urban, economic, social, and technical aspects—confirmed the project’s technical feasibility and contributed to the preparation of essential input documents for the formal project authorisation phase. The summary also highlights the initiation of public dialogue as part of the authorisation process. The results of a comprehensive socio-economic impact assessment, which included significant environmental effects, are presented. Even under the most conservative and stringent conditions, a positive benefit-cost ratio for the FCC-ee is obtained. Finally, the report provides a summary of the studies conducted to document the current state of the environment. © 2025 Elsevier B.V., All rights reserved.Article Passive Matrix Schottky Barrier 2d Photodiode Array on Graphene/Soi Platform(Springer Science and Business Media Deutschland GmbH, 2025) Çelebi, Cem; Ünverdi, Ö.; Çelebi, C.; 04.05. Department of Pyhsics; 04. Faculty of Science; 01. Izmir Institute of TechnologyWe fabricated 4 × 4 pixel two-dimensional (2D) photodiode array (PDA) out of monolayer graphene and n-type silicon (n-Si) electrodes on a silicon-on-insulator (SOI) substrate. Our device design is based on passive matrix sensor array architecture consisting of individual graphene and silicon electrodes aligned perpendicular to each other. I-V measurements conducted at room temperature to reveal the electronic characteristics of graphene and Si junction in the device structure. The spectral responsivity, respond speed and the optical crosstalk of each G/Si pixels in the array have been determined by wavelength resolved and time dependent photocurrent spectroscopy measurements. Micro-Raman mapping measurements were conducted to examine the surface coverage of graphene electrode on each pixel. The results of Micro-Raman mapping measurements were correlated with the corresponding photocurrent data acquired under light illumination. We believe that this work constitutes a significant potential in integrating variety of 2D materials and SOI technology into next generation image sensing and multiple pixel light detection applications. © The Author(s) 2025.Article Effect of Degassing on Scaling in Hypersaline System: Tuzla Geothermal Field, Turkey(Springer Science and Business Media Deutschland GmbH, 2025) Tonkul, Serhat; Demir, Mustafa Muammer; Baba, Alper; Demir, M.M.; Regenspurg, S.; Kieling, K.; 03.06. Department of Energy Systems Engineering; 03.03. Department of Civil Engineering; 03.09. Department of Materials Science and Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyA serious issue with geothermal power plants is the loss of production and decline in power plant efficiency. Scaling, also known as mineral precipitation, is one of the frequently-observed issue that causes this loss and decreasing efficiency. It is heavily observed in the production wells when the geothermal fluid rises from the depths due to a change in the fluid’s physical and chemical properties. Scaling issue in geothermal power plants result in significant output losses and lower plant effectiveness. In rare instances, it might even result in the power plant being shut down. The chemistry of the geothermal fluid, non-condensable gases, pH, temperature and pressure changes in the process from production to reinjection, power plant type and design, and sometimes the materials used can also play an active role in the scaling that will occur in a geothermal system. ICP–MS was used to evaluate the chemical properties of the fluids. On the other hand, XRD, XRF and SEM were used to investigate the chemical and mineralogical compositions of the scale samples in analytical methods. For the numerical approach, PhreeqC and GWELL codes were used to follow the chemical reactivity of the geothermal fluid in Tuzla production well. The novelty of this study is to determine potential degassing point and to characterize the mineralogical assemblage formed in the well because of the fluid composition, temperature and pressure variations. During production, geothermal fluids degas in the wellbore. This causes a drastic modification of the chemistry of the Tuzla fluids. This is why it is focused the calculations on the nature of the minerals that are able to precipitate inside the well. According to simulation results, the degassing point is estimated to be about 105 m depth, consistent with the field observations. If a small quantity of precipitated minerals is predicted before the boiling point, degassing significantly changes the fluid chemistry, and the model predicts the deposition of calcite along with smaller elements including galena, barite, and quartz. The simulation results are consistent with the mineral composition of scaling collected in the well. © The Author(s) 2024.Article Citation - WoS: 1Citation - Scopus: 2Year-To Differentiation of Black Tea Through Spectroscopic and Chemometric Analysis(Springer Science and Business Media Deutschland GmbH, 2025) Özen, Fatma Banu; Çavdaroğlu, Çağrı; Donmez, O.; Serpen, A.; Ozen, B.; 03.08. Department of Food Engineering; 01. Izmir Institute of Technology; 03. Faculty of EngineeringThe compositions of food products such as tea can vary significantly from one harvest year to another, primarily due to factors such as shifting climatic conditions, and plant periodicity. These fluctuations in composition can significantly affect the overall product quality. Spectral methods combined with chemometric techniques can provide efficient tools to monitor and assess these variations. In this study, 205 black tea samples from two consecutive harvest years were analyzed using mid-infrared, UV–visible, and fluorescence spectroscopy. Mid-infrared spectra were collected for both infused and powdered samples, while only the infused samples were used for the other spectroscopic methods. The study used partial least-square discriminant (PLS-DA) and orthogonal partial least-square discriminant analyses (OPLS-DA) to differentiate samples by harvest year. These models, applied after various data transformations, achieved high correct classification rates. Mid-infrared spectroscopic data yielded rates of 93.33% and 90.33% for powdered and infused samples, respectively. Fluorescence and UV–visible spectra also showed excellent prediction accuracy, with success rates of 98.3% and 100%. The results indicate that these spectroscopic methods, combined with chemometric differentiation, are valuable tools for monitoring year-to-year changes in black tea. © The Author(s) 2024.Article Citation - Scopus: 16Measurement of Prompt Open-Charm Production Cross Sections in Proton-Proton Collisions at √s = 13 Tev(Springer Science and Business Media Deutschland GmbH, 2021) Tumasyan,A.; Adam,W.; Ambrogi,F.; Bergauer,T.; Dragicevic,M.; Erö,J.; Spiridonov,A.; 01. Izmir Institute of TechnologyThe production cross sections for prompt open-charm mesons in proton-proton collisions at a center-of-mass energy of 13 TeV are reported. The measurement is performed using a data sample collected by the CMS experiment corresponding to an integrated luminosity of 29 nb−1. The differential production cross sections of the D∗±, D±, and D0(D ¯) mesons are presented in ranges of transverse momentum and pseudorapidity 4 < pT< 100 GeV and |η| < 2.1, respectively. The results are compared to several theoretical calculations and to previous measurements. [Figure not available: see fulltext.] © 2021, The Author(s).Article Citation - WoS: 24Citation - Scopus: 25Search for Supersymmetry in Pp Collisions at √s = 13 TeV in the Single-Lepton Final State Using the Sum of Masses of Large-Radius Jets(Springer Science and Business Media Deutschland GmbH, 2016) Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Woods, N.; 01. Izmir Institute of TechnologyResults are reported from a search for supersymmetric particles in protonproton collisions in the final state with a single, high transverse momentum lepton; multiple jets, including at least one b-tagged jet; and large missing transverse momentum. The data sample corresponds to an integrated luminosity of 2: 3 fb(-1) at root s = 13TeV, recorded by the CMS experiment at the LHC. The search focuses on processes leading to high jet multiplicities, such as gluino pair production with (g) over tilde -> t (t) over bar(chi) over tilde (0)(1) . The quantity M-J, defined as the sum of the masses of the large-radius jets in the event, is used in conjunction with other kinematic variables to provide discrimination between signal and background and as a key part of the background estimation method. The observed event yields in the signal regions in data are consistent with those expected for standard model backgrounds, estimated from control regions in data. Exclusion limits are obtained for a simplified model corresponding to gluino pair production with three-body decays into top quarks and neutralinos. Gluinos with a mass below 1600 GeV are excluded at a 95% confidence level for scenarios with low (chi) over tilde (0)(1) mass, and neutralinos with a mass below 800 GeV are excluded for a gluino mass of about 1300 GeV. For models with two-body gluino decays producing on-shell top squarks, the excluded region is only weakly sensitive to the top squark mass.Article Citation - WoS: 1Citation - Scopus: 1Enhancing the Sustainable Protein Extraction Process From Black Cumin Seed Cake Press for Eco-Friendly Protein Supplements(Springer Science and Business Media Deutschland GmbH, 2025) Uzuner, Sibel; Uzuner, Sibel; Uzuner, S.; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyFinding new protein sources is essential to meet the global population’s needs. Nigella sativa (black cumin) seeds and the residual cake left after oil cold pressing contain valuable nutritional compounds, including proteins, phenolics, essential amino acids, and various bioactive compounds. In the literature, the structural characteristics and functional properties of proteins from black cumin seeds have been extensively studied. However, there are limited reports on the use of emerging extraction technologies for extracting soluble proteins from black cumin seed cake press (BCSCP). Therefore, two distinct extraction techniques—microwave (MW) and ultrasonication (US)—were assessed for their effectiveness in extracting soluble proteins from BCSCP. The aim of this study was to investigate the effects of various operational conditions on protein extraction yield and functional properties of proteins extracted from BCSCP. The maximum protein yield (27.04%) was achieved using a 10% solid/liquid ratio (SLR) at 33 °C for a 30-min extraction time with the US extraction technique. After ultrafiltration, the protein yield increased to 33.83%, showcasing the predominance of sarcosine (17.18 g/100 g), glutamine (11.63 g/100 g), and proline (33.46 g/100 g) amino acids. The water-holding capacity (WHC), oil-holding capacity (OHC), foam capacity (FC), and foam stability (FS) of the BCSCP isolate were found to be 5.4 ± 0.3 g/g, 9.4 ± 0.0 g/g, 43.6 ± 6.4%, and 39.0 ± 4.7%, respectively. The study revealed that US is a suitable extraction process for obtaining soluble proteins from BCSCP with favorable functional properties. Further studies are needed to evaluate the bioavailability and health impacts of bioactive peptides in order to develop food applications. © The Author(s) 2024.Conference Object Citation - WoS: 1Citation - Scopus: 1Gpprmon: Gpu Runtime Memory Performance and Power Monitoring Tool(Springer Science and Business Media Deutschland GmbH, 2024) Öz, Işıl; Öz,I.; 01. Izmir Institute of Technology; 03.04. Department of Computer Engineering; 03. Faculty of EngineeringGraphics Processing Units (GPUs) perform highly efficient parallel execution for high-performance computation and embedded system domains. While performance concerns drive the main optimization efforts, power issues become important for energy-efficient GPU executions. While performance profilers and architectural simulators offer statistics about the target execution, they either present only performance metrics in a coarse kernel function level or lack visualization support that enables performance bottleneck analysis or performance-power consumption comparison. Evaluating both performance and power consumption dynamically at runtime and across GPU memory components enables a comprehensive tradeoff analysis for GPU architects and software developers. This paper presents a novel memory performance and power monitoring tool for GPU programs, GPPRMon, which performs a systematic metric collection and offers useful visualization views to track power and performance optimizations. Our simulation-based framework dynamically collects microarchitectural metrics by monitoring individual instructions and reports achieved performance and power consumption information at runtime. Our visualization interface presents spatial and temporal views of the execution. While the first demonstrates the performance and power metrics across GPU memory components, the latter shows the corresponding information at the instruction granularity in a timeline. Our case study reveals the potential usages of our tool in bottleneck identification and power consumption for a memory-intensive graph workload. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.