Scopus İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395

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An effective colorectal polyp classification for histopathological images based on supervised contrastive learning
(Elsevier, 2024) Yengec-Tasdemir,Sena Busra; Aydin,Zafer; Akay,Ebru; Doğan,Serkan; Yilmaz,Bulent; 0000-0001-7686-6298; AGÜ, Fen Bilimleri Enstitüsü, Elektrik ve Bilgisayar Mühendisliği Ana Bilim Dalı; Aydın, Zafer; Yilmaz, Bulent
Early detection of colon adenomatous polyps is pivotal in reducing colon cancer risk. In this context, accurately distinguishing between adenomatous polyp subtypes, especially tubular and tubulovillous, from hyperplastic variants is crucial. This study introduces a cutting-edge computer-aided diagnosis system optimized for this task. Our system employs advanced Supervised Contrastive learning to ensure precise classification of colon histopathology images. Significantly, we have integrated the Big Transfer model, which has gained prominence for its exemplary adaptability to visual tasks in medical imaging. Our novel approach discerns between in-class and out-of-class images, thereby elevating its discriminatory power for polyp subtypes. We validated our system using two datasets: a specially curated one and the publicly accessible UniToPatho dataset. The results reveal that our model markedly surpasses traditional deep convolutional neural networks, registering classification accuracies of 87.1% and 70.3% for the custom and UniToPatho datasets, respectively. Such results emphasize the transformative potential of our model in polyp classification endeavors
Matching variants for functional characterization of genetic variants
(Oxford University Press, 2023) Cevik,Sabiha; Zhao,Pei; Zorluer,Atiyye; Pir, Mustafa S.; Bian, Wenyin; Kaplan, Oktay I.; 0000-0002-0935-1929; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Cevik, Sabiha; Zorluer, Atiye; Pir, Mustafa S.
Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.
Integrating Biological Domain Knowledge with Machine Learning for Identifying Colorectal-Cancer-Associated Microbial Enzymes in Metagenomic Data
(MDPI, 2025) Bakir-Gungor, Burcu; Ersoz, Nur Sebnem; Yousef, Malik; 0000-0002-2272-6270; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Bakir-Gungor, Burcu; Ersoz, Nur Sebnem
Advances in metagenomics have revolutionized our ability to elucidate links between the microbiome and human diseases. Colorectal cancer (CRC), a leading cause of cancer-related mortality worldwide, has been associated with dysbiosis of the gut microbiome. This study aims to develop a method for identifying CRC-associated microbial enzymes by incorporating biological domain knowledge into the feature selection process. Conventional feature selection techniques often evaluate features individually and fail to leverage biological knowledge during metagenomic data analysis. To address this gap, we propose the enzyme commission (EC)-nomenclature-based Grouping-Scoring-Modeling (G-S-M) method, which integrates biological domain knowledge into feature grouping and selection. The proposed method was tested on a CRC-associated metagenomic dataset collected from eight different countries. Community-level relative abundance values of enzymes were considered as features and grouped based on their EC categories to provide biologically informed groupings. Our findings in randomized 10-fold cross-validation experiments imply that glycosidases, CoA-transferases, hydro-lyases, oligo-1,6-glucosidase, crotonobetainyl-CoA hydratase, and citrate CoA-transferase enzymes can be associated with CRC development as part of different molecular pathways. These enzymes are mostly synthesized by Eschericia coli, Salmonella enterica, Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, and Clostridioides dificile. Comparative evaluation experiments showed that the proposed model consistently outperforms traditional feature selection methods paired with various classifiers.
Axial free vibration analysis of a tapered nanorod using Adomian decomposition method
(TECHNO-PRESS, 2025) Coskun, Safa B.; Kara, Ozge; Atay, Mehmet T.; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Atay, Mehmet T.
This study aimed to conduct an analysis of the axial free vibration of tapered nanorods based on nonlocal elasticity theory. The small-scale effect on the free axial vibration of a tapered nanorod was studied employing the Adomian decomposition method (ADM) and the finite difference method (FDM) as a checking tool where a contradiction existed between the results of this study and available results in one highly cited work in the literature, which was used for comparison purposes in this work. Different boundary conditions for the nanorod were considered: fixed-fixed nanorod, fixed-free nanorod, and fixed-linear spring nanorod. The governing equation of the problem is a variable coefficient differential equation for which analytical solutions are strictly limited. For this type of problem, analytical approximate methods are effective, and there are many studies available in the literature on the application of these methods to solve linear/nonlinear ordinary/partial differential equations. ADM is one of the methods and was successfully used in this study to analyze the free vibration of nanorods. The results obtained in this study have shown that the presented technique is so powerful and has potential for applications in nanomechanics based on nonlocal elasticity theory.
Horseradish peroxidase (HRP) nanoflowers-mediated polymerization of vinyl monomers
(SPRINGER NATURE LINK, 2024) Ozaydin, Gulbahar; Mirioglu, Muge; Kaplan, Naime; Dadi, Seyma; Ocsoy, Ismail; Gokturk, Ersen; 0000-0001-6280-3966; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Dadi, Seyma
The effects of flower-shaped hybrid nano biocatalyst (hFe-NFs) from coordination between horseradish peroxidase (HRP) enzyme and Fe2+ ions on the free-radical polymerization reactions of three different vinyl monomers (styrene, methylmethacrylate and acrylamide) were investigated. Polymerizations of styrene and methylmethacrylate (MMA) were performed under emulsion conditions using three different surfactants in the presence of acetylacetone (AcAc) and hydrogen peroxide (H2O2) initiator. Polymerization of water soluble acrylamide was accomplished under surfactant-free media. According to the obtained outcomes, hFe-NFs exhibited higher catalytic activity towards polymerization of vinyl monomers compared to the free-HRP enzyme in terms of yields and the number average molecular weights (Mn) of the synthesized polymers. hFe-NFs also demonstrated very high thermal stability. While optimum polymerization of styrene was achieved at room temperature (RT), the highest polymerization yields for acrylamide and MMA were respectively accomplished at 70 and 60 degrees C in which free-HRP enzyme loses its catalytic activity. Preparation of the flower-shaped hFe-NFs, therefore, enables inexpensive and stable catalyst system for free-radical polymerization of vinyl monomers compared to free-HRP enzyme. Increasing catalytic activity and stability of hFe-NFs at higher reaction temperatures are very crucial for utilization of these types of catalysts in both scientific and industrial purposes.
Electrochemical and Optical Multi-Detection of Escherichia coli Through Magneto-Optic Nanoparticles: A Pencil-on-Paper Biosensor
(MDPI, 2024) Soysaldi, Furkan; Ekici, Derya Dincyurek; Soylu, Mehmet cagri; Mutlugun, Evren; 0000-0003-1120-5557; 0000-0001-5807-9944; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Ekici, Derya Dincyurek; Mutlugun, Evren
Escherichia coli (E. coli) detection suffers from slow analysis time and high costs, along with the need for specificity. While state-of-the-art electrochemical biosensors are cost-efficient and easy to implement, their sensitivity and analysis time still require improvement. In this work, we present a paper-based electrochemical biosensor utilizing magnetic core-shell Fe2O3@CdSe/ZnS quantum dots (MQDs) to achieve fast detection, low cost, and high sensitivity. Using electrochemical impedance spectroscopy (EIS) as the detection technique, the biosensor achieved a limit of detection of 2.7 x 10(2) CFU/mL for E. coli bacteria across a concentration range of 10(2)-10(8) CFU/mL, with a relative standard deviation (RSD) of 3.5781%. From an optical perspective, as E. coli concentration increased steadily from 10(4) to 10(7) CFU/mL, quantum dot fluorescence showed over 60% lifetime quenching. This hybrid biosensor thus provides rapid, highly sensitive E. coli detection with a fast analysis time of 30 min. This study, which combines the detection advantages of electrochemical and optical biosensor systems in a graphite-based paper sensor for the first time, has the potential to meet the needs of point-of-care applications. It is thought that future studies that will aim to examine the performance of the production-optimized, portable, graphite-based sensor system on real food samples, environmental samples, and especially medical clinical samples will be promising.
Discovery of a C-S lyase inhibitor for the prevention of human body malodor formation: tannic acid inhibits the thioalcohol production in Staphylococcus hominis
(SPRINGER NATURE LINK, 2025) Fidan, Ozkan; Karipcin, Ayse Doga; Kose, Ayse Hamide; Anaz, Ayse; Demirsoy, Beyza Nur; Arslansoy, Nuriye; Sun, Lei; Mujwar, Somdutt; 0000-0001-5312-4742; 0009-0005-7132-842X; 0009-0008-5514-8711; 0000-0003-4037-5475; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Fidan, Ozkan; Karipcin, Ayse Doga; Kose, Ayse Hamide; Anaz, Ayse; Demirsoy, Beyza Nur; Arslansoy, Nuriye
Human body odor is a result of the bacterial biotransformation of odorless precursor molecules secreted by the underarm sweat glands. In the human axilla, Staphylococcus hominis is the predominant bacterial species responsible for the biotransformation process of the odorless precursor molecule into the malodorous 3M3SH by two enzymes, a dipeptidase and a specific C-S lyase. The current solutions for malodor, such as deodorants and antiperspirants are known to block the apocrine glands or disrupt the skin microbiota. Additionally, these chemicals endanger both the environment and human health, and their long-term use can influence the function of sweat glands. Therefore, there is a need for the development of alternative, environmentally friendly, and natural solutions for the prevention of human body malodor. In this study, a library of secondary metabolites from various plants was screened to inhibit the C-S lyase, which metabolizes the odorless precursor sweat molecules, through molecular docking and molecular dynamics (MD) simulation. In silico studies revealed that tannic acid had the strongest affinity towards C-S lyase and was stably maintained in the binding pocket of the enzyme during 100-ns MD simulation. We found in the in vitro biotransformation assays that 1 mM tannic acid not only exhibited a significant reduction in malodor formation but also had quite low growth inhibition in S. hominis, indicating the minimum inhibitory effect of tannic acid on the skin microflora. This study paved the way for the development of a promising natural C-S lyase inhibitor to eliminate human body odor and can be used as a natural deodorizing molecule after further in vivo analysis.
TextNetTopics-SFTS-SBTS: TextNetTopics Scoring Approaches Based Sequential Forward and Backward
(Springer Science and Business Media Deutschland GmbH, 2024) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, Malik; 0009-0005-7544-9210; 0000-0002-2272-6270; 0000-0001-8780-6303; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Bakir-Gungor, Burcu
TextNetTopics is a text classification-based topic modeling approach that performs topic selection rather than word selection to train a machine learning algorithm. However, one main limitation of TextNetTopics is that its scoring component (the S component) assesses each topic independently and ranks them accordingly, neglecting the potential relationship between topics. In order to address this limitation and improve the classification performance, this study introduces an enhancement to TextNetTopics. TextNetTopics-SFTS-SBTS integrates two novel scoring approaches: Sequential Forward Topic Scoring (SFTS) and Sequential Backward Topic Scoring (SBTS), which consider topic interactions by assessing sets of topics simultaneously. This integration aims to streamline the topic selection process and enhance classifier efficiency for text classification. The results obtained across three datasets offer valuable insights into the context-dependent effectiveness of the new scoring mechanisms across diverse datasets and varying numbers of topics involved in the analysis.
Classification of Breast Cancer Molecular Subtypes with Grouping-Scoring-Modeling Approach that Incorporates Disease-Disease Association Information
(IEEE Xplore, 2024) Qumsiyeh, Emma; Bakir-Gungor, Burcu; Yousef, Malik; 0000-0002-2272-6270; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bakir-Gungor, Burcu
This study uses modern sequencing technology and large biological databases to investigate the molecular intricacies of complicated diseases like cancer. Using gene expression databases and biomarkers, the research aims to improve breast cancer molecular subtype identification for better patient outcomes. Using BRCA LumAB_ Her2Basal dataset, this study compares an integrative machine learning-based strategy (GediNET) to traditional feature selection approaches across machine learning classifiers. GediNET excels at uncovering crucial disease-disease connections and potential biomarkers using the Grouping-Scoring-Modeling (GSM) approach, which favors gene groupings above individual genes. Our comparative analysis highlights GediNET's exceptional performance, notably in terms of accuracy and Area Under the Curve metrics, underscoring its effectiveness in uncovering the genetic intricacies of breast cancer. GediNET's promise to improve disease classification and biomarker identification by improving biological mechanism understanding goes beyond exceeding traditional approaches. The work shows that GediNET's integrative method can promote bioinformatics research by identifying the most informative genes associated with certain diseases, enabling focused and customized medicine.
N-Type Molecular Thermoelectrics Based on Solution-Doped Indenofluorene-Dimalononitrile: Simultaneous Enhancement of Doping Level and Molecular Order
(WILEY- Advanced, 2025) Wang, Suhao; Wei, Huan; Rillaerts, Antoine; Deneme, Ibrahim; Depriester, Michael; Manikandan, Suraj; Andreasen, Jens Wenzel; Daoudi, Abdelylah; Peralta, Sebastien; Longuemart, Stephane; Usta, Hakan; Cornil, Jerome; Hu, Yuanyuan; Pisula, Wojciech; 0000-0001-9415-0242; 0000-0002-0618-1979; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Usta, Hakan; Deneme, Ibrahim
The development of n-type organic thermoelectric materials, especially π-conjugated small molecules, lags far behind their p-type counterparts, due primarily to the scarcity of efficient electron-transporting molecules and the typically low electron affinities of n-type conjugated molecules that leads to inefficient n-doping. Herein, the n-doping of two functionalized (carbonyl vs dicyanovinylene) indenofluorene-based conjugated small molecules, 2,8-bis(5-(2-octyldodecyl)thien-2-yl)indeno[1,2-b]fluorene-6,12-dione (TIFDKT) and 2,2′-(2,8-bis(3-alkylthiophen-2-yl)indeno[1,2-b]fluorene-6,12-diylidene)dimalononitrile (TIFDMT) are demonstrated, with n-type dopant N-DMBI. While TIFDKT shows decent miscibility with N-DMBI, it can be hardly n-doped owing to its insufficiently low LUMO. On the other hand, TIFDMT, despite a poorer miscibility with N-DMBI, can be efficiently n-doped, reaching a respectable electrical conductivity of 0.16 S cm−1. Electron paramagnetic resonance measurements confirm the efficient n-doping of TIFDMT. Based on density functional theory (DFT) calculations, the LUMO frontier orbital energy of TIFDMT is much lower, and its wave function is more delocalized compared to TIFDKT. Additionally, the polarons are more delocalized in the n-doped TIFDMT. Remarkably, as indicated by the grazing-incidence wide-angle X-ray scattering (GIWAXS), the molecular order for TIFDMT thin-film is enhanced by n-doping, leading to more favorable packing with edge-on orientation and shorter π-π stacking distances (from 3.61 to 3.36 Å). This induces more efficient charge transport in the doped state. Upon optimization, a decent thermoelectric power factor of 0.25 µWm−1K−2 is achieved for n-doped TIFDMT. This work reveals the effect of carbonyl vs dicyanovinylene on the n-doping efficiency, microstructure evolution upon doping and thermoelectric performance, offering a stepping stone for the future design of efficient n-type thermoelectric molecules.
Molecular Separation by Using Active and Passive Microfluidic chip Designs: A Comprehensive Review
(WILEY Advanced, 2024) Ebrahimi, Aliakbar; Icoz, Kutay; Didarian, Reza; Shih, Chih-Hsin; Tarim, E. Alperay; Nasseri, Behzad; Akpek, Ali; Cecen, Berivan; Bal-Ozturk, Ayca; Gulec, Kadri; Li, Yi-Chen Ethan; Shih, Steven; Tarim, Burcu Sirma; Tekin, H. Cumhur; Alarcin, Emine; Tayybi-Azar, Mehdi; Ghorbanpoor, Hamed; Ozel, Ceren; Sariboyaci, Ayla Eker; Guzel, Fatma Dogan; Bassous, Nicole; Shin, Su Ryon; Avci, Huseyin; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Icoz, Kutay
Separation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. “Lab-on-a-chip” systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, “lab-on-a-chip” methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques.
Effect of bio-mimicked surface texturing on the shear strength of additively manufactured metal single-lap joints: An innovative approach
(PERGAMON-ELSEVIER SCIENCE LTD, 2025) Atahan, M. Gokhan; Maskery, Ian; Ashcroft, Ian; Apalak, M. Kemal; Pappas, Athanasios; 0000-0002-8180-5876; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Atahan, M. Gokhan
In this paper, we investigate the mechanical performance of metal single-lap joints featuring bio-mimicking surface textures. The inspiration for the surface textures was the foot and toe of the gecko, a creature whose ability to climb smooth shear surfaces is attributed to the mesoand micro-structures of its feet. Three surface textures were investigated: a hexagonal texture based on the central region of the foot, a lamellae-like texture based on the toe, and a mixed texture of both. Metal adherends with these textures were produced using the laser powder bed fusion (LPBF) additive manufacturing method. Finite element analysis was performed to examine the influence of surface texture on stress distribution in the adhesive layer, while mechanical testing was used to determine joint strength and failure mode. Compared to the as- printed surface texture, bio-mimicking surface textures improved the wettability of the bonding surfaces, and significantly improved the lap shear strength of the joints. Mechanical interlocking due to surface texture was more effective than the increase in bonding surface area in enhancing joint strength. The bio-mimicking textures improved the damage tolerance capacity of the joints by reducing local stress concentrations at the overlap edges of the adhesive layer and ensured that the adhesive failure type was mixed mode due to the mechanical interlocking effect. The presented novel bio-mimicked surface texture method offers promising results for both industrial applications and scientific studies.
Macronutrients in diets differentially affect gastrointestinal cytokine and tight junction protein levels
(UNIV PUTRA MALAYSIA PRESS, 2025) Ulutas, M. S.; Cebeci, A.; 0000-0002-2044-726X; 0000-0002-6158-8798; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Cebeci, A.
Western diet is known to result in intestinal inflammation and loss of barrier function. In the present work, we investigated whether other macronutrients contribute to inflammation and destabilising barrier function in mice, without using any inflammatory agents, to see the sole effects of dietary intervention. The present work was designed to determine the direct effects of diet on the intestinal barrier function and inflammation, using eight diets that differed on carbohydrate, fat, and fibre ratios for 17 weeks. At the end of the study, a distinct difference in mRNA expressions of cytokines and tight junction proteins was observed between intestinal and colon samples. Small intestinal cytokine expressions showed no difference among different diets, and tight junction protein expressions were only significant for occludin and ZO-1 in high carbohydrate diets. Colon samples had significantly different TNFα and IL-6 expressions among diets, especially in high carbohydrate diets. Tight junction protein expressions also differed significantly among diets, and low carbohydrate zero fibre diet had the lowest expression levels compared to the rest of diets. The present work reveals that not only western diet, but also diets high in carbohydrate negatively affect intestinal health, resulting in significant changes in inflammation markers. The role of carbohydrate and fiber contents are also observed in regulating tight junction protein expression. Based on these findings, adjusting macronutrient ratios can be used as a potential approach to help manage intestinal inflammation, though further research is needed.
CompreCity: Accelerating the Traveling Salesman Problem on GPU with data compression
(ELSEVIER, 2025) Yalcin, Salih; Usul, Hamdi Burak; Yalcin, Gulay; 0000-0001-6476-4542; 0000-0003-3929-8126; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Yalcin, Salih; Yalcin, Gulay
Traveling Salesman Problem (TSP) is one of the significant problems in computer science which tries to find the shortest path for a salesman who needs to visit a set of cities and it is involved in many computing problems such as networks, genome analysis, logistics etc. Using parallel executing paradigms, especially GPUs, is appealing in order to reduce the problem solving time of TSP. One of the main issues in GPUs is to have limited GPU memory which would not be enough for the entire data. Therefore, transferring data from the host device would reduce the performance in execution time. In this study, we applied three data compression methodologies to represent cities in the TSP such as (1) Using Greatest Common Divisor (2) Shift Cities to the Origin (3) Splitting Surface to Grids. Therefore, we include more cities in GPU memory and reduce the number of data transfers from the host device. We implement our methodology in Iterated Local Search (ILS) algorithm with 2-opt and The Lin-Kernighan-Helsgaun (LKH) Algorithm. We show that our implementation presents more than 25% performance improvement for both algorithms.
Stress and damage distribution analysis of steel reinforced geopolymer concrete beams: Finite element method and experimental comparison under varying design parameters
(ELSEVIER, 2025) Ozbayrak, Ahmet; Kucukgoncu, Hurmet; Aslanbay, Huseyin Hilmi; Aslanbay, Yuksel Gul; 0000-0001-5148-8753; AGÜ, Mühendislik Fakültesi, İnşaat Mühendisliği Bölümü; Kucukgoncu, Hurmet
Geopolymer concrete (GPC) is a sustainable and eco-friendly alternative to ordinary Portland cement-based concrete (OPC). However, its application in reinforced concrete structures remains limited due to insufficient research on structural performance. This study examines the effects of tensile reinforcement ratio, sodium silicate/sodium hydroxide ratio, and curing method on GPCreinforced concrete (GPC-RC) beams. Experimental and numerical bending tests were performed on GPC and OPC beams with similar tensile reinforcement and strength properties. Load- displacement and moment-curvature relationships were obtained and compared, while stress and stiffness behaviors were analyzed numerically. The results show that curing methods and reinforcement ratios significantly influence GPC beam behavior. In GPC samples, numerical and experimental displacement and load values differed by approximately 10 % at both yield and ultimate points. For OPC, these differences were 35 % and 14 % at the yield point and 17 % and 25 % at the ultimate point. GPC exhibited distinct stress and damage distribution characteristics compared to OPC. The finite element models were statistically validated, confirming their consistency with experimental results. These findings contribute to the understanding of GPC's structural behavior and provide guidance for its design and optimization in reinforced concrete applications.
Did Liberal Lockdown Policies Change Spatial Behaviour in Sweden? Mapping Daily Mobilities in Stockholm Using Mobile Phone Data During COVID-19
(SPRINGER Nature Link, 2024) Shuttleworth, Ian; Toger, Marina; Turk, Umut; Osth, John; 0000-0002-8440-7048; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Türk, Umut
Sweden had the most liberal lockdown policies in Europe during the Covid-19 pandemic. Relying on individual responsibility and behavioural nudges, their effectiveness was questioned from the perspective of others who responded with legal restrictions on behaviour. In this study, using mobile phone data, we therefore examine daily spatial mobilities in Stockholm to understand how they changed during the pandemic from their pre-pandemic baseline given this background. The analysis demonstrates: that mobilities did indeed change but with some variations according to (a) the residential social composition of places and (b) their locations within the city; that the changes were long lasting; and that the average fall in spatial mobility across the whole was not caused by everybody moving less but instead by more people joining the group of those who stayed close to home. It showed, furthermore, that there were seasonal differences in spatial behaviour as well as those associated with major religious or national festivals. The analysis indicates the value of mobile phone data for spatially fine-grained mobility research but also shows its weaknesses, namely the lack of personal information on important covariates such as age, gender, and education.
Exploring CsPbX3 (X = Cl, Br, I) Perovskite Nanocrystals in Amorphous Oxide Glasses: Innovations in Fabrication and Applications
(WILEY Online Library, 2024) Samiei, Sadaf; Soheyli, Ehsan; Vighnesh, Kunnathodi; Nabiyouni, Gholamreza; Rogach, Andrey L.; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Soheyli, Ehsan
Metal halide perovskites with excellent optical and electronic properties have become a trending material in the current research. However, their limited stability under ambient conditions degrades quality and threatens their potential commercialization as optoelectronic devices. Various approaches are adopted to improve the stability of perovskite nanocrystals (PeNC) while maintaining their advantageous optical properties, particularly strong luminescence. Among different possible improvement strategies, encapsulation of PeNCs within the amorphous glass matrices of inorganic oxides has drawn widespread attention because it ensures high resistance against chemical corrosion and high temperature, thus enhancing their chemical, thermal, and mechanical stability with improved light-emission characteristics. In this article, two types of materials, namely all-inorganic metal halide PeNCs and amorphous oxide glasses are briefly introduced, and then the methods are reviewed to fabricate and improve the quality of PeNC@glass composites. These methods are classified into three universal categories: compositional modification, structural modification, and dual encapsulation. In the final part of this review paper, examples of applications of PeNCs@glass composites in light-emitting devices and displays, data storage and anti-counterfeiting, lasing, photodetectors and X-ray detectors, photocatalysis, optical filters, solar concentrators, and batteries are provided.
A functional barley-based fermented soup (tarhana) with high β-glucan content
(SPRINGER, 2025) Koksel, Hamit; Ozkan, Kubra; Tekin-Cakmak, Zeynep Hazal; Karasu, Salih; Kahraman, Kevser; Oruc, Sena; Sagdic, Osman; Sestili, Francesco; 0000-0002-2786-3944; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Kahraman, Kevser
This study investigates the impact of using different flours, including high beta-glucan barley, on the nutritional properties of tarhana. Mineral composition, phenolic content, and antioxidant capacity of tarhana powder samples produced using flours of high beta-glucan hull-less barley (cv. Chifaa; ChF), hull-less barley cv. Yalin (YF), bread wheat cv. Tosunbey (white flour: TWF1 and whole wheat flour: TWF2). Furthermore, in vitro glycemic index (GI), pasting properties, and RVA soup index of their soups were investigated. Tarhana made with Chifaa barley flour (Tar-ChF) exhibited significantly higher levels of key minerals (K, Mg, Ca), beta-glucan and total phenolic content compared to those made with other flours (Tar YF, Tar TWF1, and Tar TWF2). Barley tarhana samples also showed greater antioxidant activity of bound phenolic fractions and lower GI values, indicating a healthier profile. The study highlights the potential of high beta-glucan barley flour to enhance tarhana's nutritional benefits without significantly affecting its sensory properties, such as color and viscosity. This research supports the integration of health-promoting ingredients like barley flour into traditional Mediterranean foods to improve their nutritional quality.
Rural Feet Voting of Leisure Explorers
(WILEY Online Library, 2025) Turk, Umut; Toger, Marina; Osth, John; Kourtit, Karima; Nijkamp, Peter; 0000-0002-8440-7048; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Turk, Umut
In the COVID-19 period, spatial leisure behavior, often driven by the desire to escape urban life, reflected health and environmental concerns. This study examines how pandemic-induced spatial motives and changes impacted disparities in leisure mobility, specifically urban-to-rural tourism, in Sweden. Analyzing pre-pandemic, during pandemic, and post-pandemic periods, using anonymized mobile phone and socioeconomic data, the paper explores urban-rural leisure mobility variations. Despite a decline in professional geographical mobility, mainly of people in affluent urban areas, due to remote work, the spatial leisure activities remained rather stable? Our findings, based on a negative binomial regression analysis, reveal also exacerbated socioeconomic segregation in recreational trips. The disruption in mobility accessibility due to COVID-19 appears to amplify existing socioeconomic disparities, notably in urban-to-rural leisure travel. Our research sheds new light on the widening gap in geographical leisure activities, emphasizing the need for equitable access to nonurban destinations.
Ground failures and foundation performances in Adıyaman-Gölbaşı following the 6 February 2023 Kahramanmaraş-Türkiye Earthquake Sequence
(SAGE PUBLICATIONS INC, 2025) Cetin, Kemal Onder; Moug, Diane; Soylemez, Berkan; Ayhan, Bilal Umut; Zarzour, Moutasem; Suhaily, Ahmed Al; Akil, Bulent; Unutmaz, Berna; Firat, Seyhan; Tekin, Erhan; Cakir, Elife; Frost, David; Macedo, Jorge; Bray, Jonathan; Moss, Robb; Bassal, Patrick; Gurbuz, Ayhan; Isik, Nihat Sinan; Akin, Muge; Sahin, Arda; Duman, Emre; 0000-0001-8873-5287; AGÜ, Mühendislik Fakültesi, İnşaat Mühendisliği Bölümü; Akin, Muge
The 6 February 2023 Kahramanmara & scedil;-T & uuml;rkiye earthquake sequence (M7.8 and M7.6) presents an exceptional opportunity to investigate both the effects of local soil conditions on damage patterns under strong shaking conditions and the performance of building foundations in areas that experienced ground failure. The significant ground failure and structural damage in Ad & imath;yaman-G & ouml;lba & scedil;& imath; triggered an intensive series of detailed reconnaissance and field surveys. This article aims to present the resulting database of observations on ground failures, building, and foundation performances. The field reconnaissance of ground failures and their effects on building performances involved aerial and walk-down surveys, including high-quality photographs taken across the town. In addition, data on building damage statistics compiled by the Ministry of Environment, Urbanization, and Climate Change were accessed and analyzed. The subsurface characteristics of the town were characterized using available data from pre-earthquake site investigation campaigns employed for town planning purposes. It is concluded that the ground failures in the town primarily resulted from soil liquefaction and cyclic softening. Most of the poor building and foundation performances and ground failures were documented in the northern part of Atat & uuml;rk Boulevard, closer to the lake of G & ouml;lba & scedil;& imath;, where soil site characteristics were unfavorable. This revealed once again the significant effects of local soil site conditions, particularly soil liquefaction, on the intensified ground failures, foundation, and structural damage levels.

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