Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 4Citation - Scopus: 5Diffusion-Based Data Augmentation Methodology for Improved Performance in Ocular Disease Diagnosis Using Retinography Images(Springer Heidelberg, 2024) Aktas, Burak; Düzyel, Okan; Ates, Doga Deniz; Gümüş, Abdurrahman; Duzyel, Okan; Gumus, Abdurrahman; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyDeep learning models, integral components of contemporary technological landscapes, exhibit enhanced learning capabilities with larger datasets. Traditional data augmentation techniques, while effective in generating new data, have limitations, especially in fields like ocular disease diagnosis. In response, alternative augmentation approaches, including the utilization of generative AI, have emerged. In our study, we employed a diffusion-based model (Stable Diffusion) to synthesize data by faithfully recreating crucial vascular structures in the retina, vital for detecting eye diseases by using the Ocular Disease Intelligent Recognition dataset. Our goal was to augment retinography images for ocular disease diagnosis using diffusion-based models, optimizing the outputs of the fine-tuned Stable Diffusion model, and ensuring the generated data closely resembles real-world scenarios. This strategic approach resulted in improved performance in classification models and augmentation outperformed traditional methods, exhibiting high precision rates ranging from 85% to 76.2% and recall values of 86%, and 75% for 5 classes. Beyond performance enhancement, we demonstrated that the inclusion of synthetic data, coupled with data reduction using the t-SNE method, effectively addressed dataset imbalance. As a result of synthetic data addition, notable increases of 3.4% in the precision metric and 12.8% in the recall metric were observed in the 7-class case. Strategically synthesizing data addressed underrepresented classes, creating a balanced dataset for comprehensive model learning. Surpassing performance improvements, this approach underscores synthetic data's ability to overcome the limitations of traditional methods, particularly in sensitive medical domains like ocular disease diagnosis, ensuring accurate classification. The codes of the study will be shared on GitHub in a way that benefits everyone interested: https://github.com/miralab-ai/generative-data-augmentation.Article Citation - WoS: 1Citation - Scopus: 1Abnormally Accumulated Gm2 Ganglioside Contributes To Skeletal Deformity in Tay-Sachs Mice(Springer Heidelberg, 2024) Demir, Secil Akyildiz; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyTay-Sachs Disease is a rare lysosomal storage disorder caused by mutations in the HEXA gene, responsible for the degradation of ganglioside GM2. In addition to progressive neurodegeneration, Tay-Sachs patients display bone anomalies, including kyphosis. Tay-Sachs disease mouse model (Hexa-/-Neu3-/-) shows both neuropathological and clinical abnormalities of the infantile-onset disease phenotype. In this study, we investigated the effects of GM2 accumulation on bone remodeling activity. Here, we evaluated the bone phenotype of 5-month-old Hexa-/-Neu3-/- mice with age-matched control groups using gene expression analysis, bone plasma biomarker analysis, and micro-computed tomography. We demonstrated lower plasma alkaline phosphatase activity and calcium levels with increased tartrate-resistant acid phosphatase levels, indicating reduced bone remodeling activity in mice. Consistently, gene expression analysis confirmed osteoblast reduction and osteoclast induction in the femur of mice. Micro-computed tomography and analysis show reduced trabecular bone volume, mineral density, number, and thickness in Hexa-/-Neu3-/- mice. In conclusion, we demonstrated that abnormal GM2 ganglioside accumulation significantly triggers skeletal abnormality in Tay-Sachs mice. We suggest that further investigation of the molecular basis of bone structure anomalies is necessary to elucidate new therapeutic targets that prevent the progression of bone symptoms and improve the life standards of Tay-Sachs patients.Article Citation - WoS: 3Citation - Scopus: 2Development of Transition Metal Oxide Platforms for Aptasensing of Psa in Cell Cultures(Springer Heidelberg, 2024) Kirlangic, Irem Aydin; Uner, Goklem; Kara, Pinar; Kirmizibayrak, Petek Ballar; Ertas, Fatma Nil; 01. Izmir Institute of TechnologyIn this study, a novel aptasensor based on a transition metal oxide-modified pencil graphite electrode (PGE) was developed for the diagnosis of early-stage prostate cancer (PCa) via monitoring the prostate-specific antigen (PSA), which is the main biomarker for PCa. Single-use PGEs modified with pulsed deposited manganese oxide (MnOx) film were used to attach the amino-terminated aptamer specific to the PSA via carbodiimide chemistry. The designed aptasensor was placed in an electrochemical cell containing ferri/ferrocyanide ions as a redox probe to measure the charge transfer resistances (Rct) of the electrode surface by electrochemical impedance spectroscopy (EIS) to follow the response of each modification step. The effect of the medium pH on the ionic structure of the aptamer molecule according to its pI value and, thus, the reversing of the direction of the response (Delta Rct) by the pH change was also discussed. The level of PSA secreted from PCa cells was investigated using impedimetric transduction. The specificity of the aptasensor was validated through selectivity studies against non-specific tumor markers like VEGF and different cancer cell lines including breast cancer and androgen-insensitive prostate cancer. The developed system showcases a label-free, fast, specific, and cost-effective approach for PSA detection, highlighting the importance of medium pH and the electrostatic environment on the aptamer's response. Our work emphasizes the potential for such aptasensors in clinical diagnostics and paves the way for further exploration into using transition metal oxides in biosensing applications.Article A Methodology Providing New Insights Into the Flow Patterns of Karst Aquifers: an Example From Sw Türkiye(Springer Heidelberg, 2024) Maramathas, Athanasios; Baba, Alper; Katsanou, Konstantina; Sagir, Cagdas; Baba, Alper; Lambrakis, Nikolaos; 03.03. Department of Civil Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThis paper presents a new and innovative methodology for the investigation of karst systems using spring discharge. The behaviour of springs in phase space is investigated by plotting the measurements of spring discharge versus the measurements of the water level at the spring's outlet. Such a diagram reveals new features of the function of the karst system and the discharge pattern of the spring that are not captured by common research methods. The application of this method to the Azmak Spring in southwestern T & uuml;rkiye revealed the existence of five distinct discharge subsystems that operate alternately and never simultaneously. They have a specific connection between them, while the transition from one to another is not random but follows a pattern. An attempt was made to interpret these features using concepts from percolation theory.Article Citation - WoS: 1Citation - Scopus: 1Calcite Precipitation on Excavated Andesite Surfaces From the Archaeological Sites of Aigai and Assos (turkey)(Springer Heidelberg, 2024) Kaplan, Caglayan Deniz; Böke, Hasan; Boke, Hasan; 02.01. Department of Conservation and Restoration of Cultural Heritage; 02. Faculty of Architecture; 01. Izmir Institute of TechnologyThe conservation interventions of crusts or patinas formed on the surfaces of stone monuments should be evaluated within a comprehensive approach in archaeological excavations, taking into account their material characteristics. In this study, the mineralogical, chemical and microstructural characteristics of whitish crusts formed on the surfaces of buried and later excavated andesite surfaces at the archaeological sites of Aigai and Assos (Turkey) were investigated by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), X-ray fluorescence (XRF) and scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS) analyses in order to establish a conservation approach at the archaeological sites. The whitish crusts formed on the excavated andesite surfaces are mainly composed of calcite with freshwater diatom species. Calcite is most likely formed by the alteration of plagioclase by carbon dioxide in the soil during the burial of the andesites. In the soil, CO2 reacts with plagioclase to produce kaolinite and calcite which are precipitated on the andesite surfaces after excavation. The presence of freshwater diatom species in the whitish crusts may indicate that the andesite remains were buried in the waterlogged soil for many years and later excavated. Therefore, whitish crusts should not be cleaned from the andesite surfaces, as they are a sign of the burial history of the monuments and a protective layer against weathering.Article Citation - WoS: 4Citation - Scopus: 4The Future of Regional Inequalities: an Arima Forecast(Springer Heidelberg, 2024) Duran, Hasan Engin; Duran, Hasan Engin; 02.03. Department of City and Regional Planning; 02. Faculty of Architecture; 01. Izmir Institute of TechnologyThe existing stream of empirical literature on regional inequalities has always adopted a retrospective look by analyzing the past evolution. We depart from the main stream by adopting a future perspective: Will regional inequalities shrink over time? How will the shape of income distribution evolve? Will spatial dependency increase? In the current paper, we forecast the long-term trajectory of per capita real personal income for U.S. states using the ARIMA model. We estimate the future of disparity level (for 2050 and 2090), the shape and spatial pattern of income distribution, convergence trend and spatial dependence by the help of inequality indexes (Atkinson, Coefficient of Variation, Theil) Kernel probability density distributions, explorative maps and Moran's I test. The dataset includes 48 coterminous U.S. states over the period 1929-2022. A set of important results appeared to emerge as an outcome of the empirical analyses: First, income disparities are expected to increase over the long-term period that implies a divergence pattern. Second, the forecasted shape of the income distribution is bi-modal and polarized, therefore, pointing to a widening of the inequalities. Third, the geography of the prosperity is projected to change in a way that the geographical position of high and low-income areas will change. Fourth, spatial dependence in per capita income is expected to fade away in the future. From a political stand point, additional resources should be devoted to the states that are expected to become backward (for some states in Northeast and Southwest) in order to maintain territorial cohesion.Article Citation - WoS: 13Citation - Scopus: 17Convenient Site Selection of a Floating Pv Power Plant in Türkiye by Using Gis-Fuzzy Analytical Hierarchy Process(Springer Heidelberg, 2024) Karipoğlu, Fatih; Koca, Kemal; Ilbahar, Esra; 03.06. Department of Energy Systems Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyFloating photovoltaics (FPVs) are appearing as a promising and an alternative renewable energy opinion in which PV panels are mounted on floating platforms in order to produce electricity from renewable energy on water such as seas, dams, rivers, oceans, canals, fish farms, and reservoirs. So far, such studies related to the body knowledge on financial, technical, and environmental aspects of installation of FPV have not been performed in Turkey while expanding steadily in other countries. In this study, suitable site selection for installation of FPV power plants on three lakes in Turkey was studied by performing geographic information system (GIS) and the fuzzy analytic hierarchy process (FAHP) as multi-criteria decision-making (MCDM) method. This detailed study revealed that the criterion of global horizontal irradiance (GHI) was determined as the most crucial criterion for the installation of FPV on Beysehir Lake, Lake of Tuz, and Van Lake. Additionally, it was clearly seen that the Beysehir Lake had the highest value approximately 52% among other lakes for installation, that is why Beysehir Lake is selected as the best option for installation of an FPV system with this multi-criteria approach.Article Citation - WoS: 4Citation - Scopus: 6A Sustainable Clean Energy Source for Mitigating Co<sub>2</Sub> Emissions: Numerical Simulation of Hamit Granitoid, Central Anatolian Massif(Springer Heidelberg, 2024) Ayzit, Tolga; Chandrasekharam, Dornadula; Singh, Mrityunjay; Baba, Alper; Chandrasekharam, Dornadula; Baba, Alper; 03.03. Department of Civil Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyT & uuml;rkiye relies on coal-fired power plants for approximately 18 GW of annual electricity generation, with significantly higher CO2 emissions compared to geothermal power plants. On the other hand, geothermal energy resources, such as Enhanced Geothermal Systems (EGS) and hydrothermal systems, offer low CO2 emissions and baseload power, making them attractive clean energy sources. Radiogenic granitoid, with high heat generation capacity, is a potential and cleaner energy source using EGS. The Anatolian plateau hosts numerous tectonic zones with plutonic rocks containing high concentrations of radioactive elements, such as the Central Anatolian Massif. This study evaluates the power generation capacity of the Hamit granitoid (HG) and presents a thermo-hydraulic-mechanical (THM) model for a closed-loop geothermal well for harnessing heat from this granitoid. A sensitivity analysis based on fluid injection rates and wellbore length emphasizes the importance of fluid resident time for effective heat extraction. Closed-loop systems pose fewer geomechanical risks than fractured systems and can be developed through site selection, system design, and monitoring. Geothermal wellbore casing material must withstand high temperatures, corrosive environments, and should have low thermal conductivity. The HG exhibits the highest heat generation capacity among Anatolian granitoid intrusions and offers potential for sustainable energy development through EGS, thereby reducing CO2 emissions.Article Citation - WoS: 3Citation - Scopus: 4Enhancing Biogas Production From Chicken Manure Through Vacuum Stripping of Digestate(Springer Heidelberg, 2023) Sengur, Ozlem; Bayrakdar, Alper; Bayrakdar, Alper; Calli, Baris; 03.07. Department of Environmental Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe vacuum stripping's combined ammonia removal and disintegration effect on chicken manure digestate was evaluated for the first time at different pH values (8.5, 9.5, and 10.5) and temperatures (30, 50, and 70 degrees C). In this way, the potential increase in biogas production by recirculating the vacuum-stripped digestate to the anaerobic digester was determined. Experimental results showed that increasing pH and temperature significantly increase TAN removal, but pH is more effective. A significant portion of the ammonia was removed in the first 30 min. Therefore, a second set of stripping tests was performed for 30 min and at 70 degrees C and pH 10.5. After 30-min tests, a biomethane potential (BMP) assay was performed using the vacuum-stripped digestate to determine how vacuum stripping affects biomethane production. Despite having the lowest disintegration efficiency, the highest biomethane potential (56.2 +/- 29.7 mL CH4/gVS) was obtained with the digestate, which was subjected to vacuum stripping at 70 celcius without pH adjustment, and 48.7% more methane was produced than the control set. The lower residual biomethane potential in vacuum-stripped digestate at pH 9.5 and 10.5 was attributed to Na+ inhibition resulting from high NaOH consumption for pH adjustment.Article Citation - WoS: 5Citation - Scopus: 5The Potential of Walnut Shells for Production of Oligosaccharides by Liquid Hot Water Treatment(Springer Heidelberg, 2023) Surek, Ece; Büyükkileci, Ali Oğuz; Buyukkileci, Ali Oguz; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyWalnut shell (WS), which is discarded in a large amount, is usually utilized for heating purposes; therefore, obtaining fuctional products can add value to this waste biomass. In this study, xylan was determined as the dominant carbohydrate (18.6% of dry weight) in WS. The potential applicability of liquid hot water (LHW) treatment to WS was investigated in order to solubilize hemicellulose and hydrolyze it into oligomers such as xylooligosaccharide (XOS) as a prebiotic oligosaccharide and recover solid and liquid fractions, which can be raw materials for other value-added products. LHW was applied at different temperatures (170-210 degrees C) for various times (15-120 min), and their effect was combined calculating severity factor (log R-o = 3.39-4.74). The solubilization of biomass was increased (up to 60.9%) with severity. Under optimum conditions (log R-o of 3.95, 190 degrees C-15 min), 81.5% of xylan was hydrolyzed and recovered as mainly XOS (69.8% of xylan), and also xylose and arabinose. The total oligosaccharide (XOS, arabino, gluco- and galacto-oligosaccharides) and monosaccharide (mainly xylose) concentration were 14.3 and 2 g/L, respectively, and by-products did not exceed 1.6 g/L. Moreover, 2.5 mg GAE/mL of total phenolics were obtained at those conditions, whereas that was raised to 3.4 mg GAE/mL at harsher conditions. This study presented that LHW treatment was an eco-friendly alternative method for valorization of WS through production of a liquid with high value-added compounds such as oligosaccharides and solid rich in cellulose and lignin.