TR-Dizin İndeksli Yayınlar Koleksiyonu
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Article Deprem Anında ve Sonrasında Dönüşebilen Tasarım Önerileri: Günlük Kullanımdan Hayat Kurtaran Birimlere(Afet ve Acil Durum Yonetimi Baskanligi (AFAD), 2025-12-30) Özmen, Nihan Muş; Kurtuluş, Vacide BetülDepremler, yıkılan binalar ve devrilen eşyalar nedeniyle meydana gelen yaralanmalarla insan hayatını ciddi şekilde tehdit etmektedir. Bu çalışma, mobilyalara kendini kurtarma alanları entegre ederek ezilme yaralanmalarını önlemeyi ve deprem sonrası barınma ihtiyaçlarını karşılamayı amaçlayan tasarım önerileri sunmaktır. 2022 Güz döneminde Abdullah Gül Üniversitesi Deneysel Tasarım Stüdyosu kapsamında yürütülen çalışma, tanınmış bir mobilya tasarım firmasıyla iş birliği içinde gerçekleştirilmiştir. Öğrenciler hem günlük yaşamda işlevsel hem de afet anlarında acil barınma alanı olarak kullanılabilecek çift amaçlı mobilya tasarımları geliştirmiştir. Projeler, deprem sırasında ve sonrasında kullanılmak üzere iki ana kategoriye ayrılmış; yaşam ve çalışma mekânlarında, dönüşebilir mobilya tasarımlarına odaklanmıştır. Bulgular, işlevsel ve uyarlanabilir tasarımlar yoluyla risk azaltma ve deprem sonrası uyum konularında yenilikçi yaklaşımları ortaya koymaktadır.Article Citation - Scopus: 5University Librarians’ Perceptions Of Artificial Intelligence, Its Application Areas İn Libraries, And The Future(University and Research Librarians Association (UNAK), 2024-12-26) Cuhadar, S.; Mert, S.; Gezer, Ç.; Helvacioğlu, E.; Arus, O.; Aslan, Ö.; Atli, S.; Gurdal, Gultekin; Erken, MehmetToday, libraries are among the institutions affected by changing technology and innovations. The popularization of artificial intelligence (AI) technologies has also begun to transform library services. In this research, a survey was conducted to determine the adjustments that university libraries in Turkey have made and plan to make during the development process of AI technologies and applications, and to identify the services they have developed specific to the relevant period. The survey was carried out with the participation of 111 university library managers from 208 university libraries in Turkey. Through the analysis of the data, the status, knowledge, and awareness levels of university libraries regarding AI technologies and applications were determined, and measures and recommendations were presented to improve deficiencies and weaknesses. This research is the first and most comprehensive study conducted in Turkey by obtaining opinions and suggestions from university library managers on artificial intelligence. The research findings revealed that university libraries use AI applications such as ChatGPT, Gemini, and Grammarly to a certain extent; however, they have needs in developing institutional policies, enhancing personnel competencies, and planning related to AI. © 2024 University and Research Librarians Association (UNAK). All rights reserved.Article Developing a Label Propagation Approach for Cancer Subtype Classification Problem(TUBITAK, 2021) Güner, P.; Bakir-Güngör, B.; Coşkun, M.; Şahan, Pınar GünerCancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. © 2022 Elsevier B.V., All rights reserved.Article Citation - WoS: 1Comprehensive Prediction of FBN1 Targeting Mirnas: A Systems Biology Approach for Marfan Syndrome(Galenos Publishing House, 2025-09-22) Orhan, M.E.; Demirci, Y.M.; Saçar Demirci, M.D.S.; Demirci, Muserref Duygu SacarObjective: Marfan syndrome (MFS) is a genetic connective tissue disorder primarily caused by mutations in the FBN1 gene. Emerging evidence highlights the regulatory role of microRNAs (miRNAs) in modulating gene expression in MFS, but a systematic investigation into miRNAs targeting FBN1 is lacking. This study aimed to comprehensively identify miRNAs interacting with the FBN1 transcript to reveal potential molecular regulators and therapeutic targets. Methods: Human miRNA sequences were retrieved from miRBase (Release 22.1), and the canonical FBN1 transcript (RefSeq: NM_000138.5) was used for target prediction. Computational interaction analysis was conducted using the psRNATarget server with stringent parameters to detect potential miRNA binding sites. Expression profiles and disease associations of the top candidate miRNAs were further investigated through database integration and literature review. Results: Out of 2656 human mature miRNAs analyzed, 251 were predicted to bind FBN1, with the hsa-miR-181 family exhibiting the highest number of predicted interactions. Evidence from the literature highlighted dysregulation of hsa-miR-181 expression in MFS patients, suggesting a functional role in disease pathophysiology. Conclusion: This study identifies key members of the hsa-miR-181 family as post-transcriptional regulators of FBN1, offering new insights into miRNA-driven mechanisms in MFS. These findings support the potential of RNA-based diagnostics and therapeutic strategies targeting miRNA-FBN1 interactions. ©Copyright 2025 The Author.Article Citation - Scopus: 1Kayseri İlindeki Bazı Tarihi Eserlerde Bozunma Etkilerinin Tahribatsız Deney Yöntemleriyle Değerlendirilmesi(TMMOB Chamber of Geological Engineers, 2025-06-11) Akin, Mutluhan; Akin, Muge; Akgül, Muhammed Kamilİç Anadolu’da önemli bir yerleşim merkezi olan Kayseri, farklı dönemlerden günümüze kadar gelen birçok tarihi esere ev sahipliği yapmaktadır. İlin farklı bölgelerinde özellikle yoğun yerleşimin bulunduğu alanlarda, Selçuklu Dönemi’ne ait 12. ve 14. yüzyıllar arası yapılmış çok sayıda cami, kümbet ve medrese türü tarihi esere rastlamak mümkündür. Kültürel miras niteliğindeki bu eserler çoğunlukla yakın çevrede yoğun olarak bulunan farklı renk ve dokudaki ignimbirit türü kaya malzemesi kullanılarak inşa edilmişlerdir. Genel olarak düşük dayanıma sahip ve su etkilerine karşı hassas olan bu ignimbiritler zaman içerisinde atmosferik etkenler, hava kirliği, vandalizm vb. gibi olaylar sonucunda bozunmakta ve ilksel özelliklerini kaybetmektedirler. Bu çalışmada Kayseri il merkezindeki Roma ve Selçuklu dönemlerine ait tarihi eserler ile bu eserlerde zaman içinde meydana gelen bozunma etkileri incelenmiştir. Bozunma etkilerinin gözlemsel olarak incelenmesinin yanı sıra, eserlere herhangi bir zararı bulunmayan tahribatsız deney yöntemlerinden İğne Penetrometresi, Schmidt Çekici ve P-dalga hızı deneylerinden faydalanılmıştır. Bunun yanı sıra, bozunmuş ignimbirit bloklarına ait yerinde deneylerle belirlenen değerler, aynı malzemeye ait taze örneklerin fiziko-mekanik özellikleri ile karşılaştırılmıştır. Yapılan değerlendirmeler sonucunda tarihi eserlerin taban bölümlerinde özellikle kılcallık sebebiyle pullanma ve kavlaklanma türü bozunmaların geliştiği ve ignimbiritlerin bu bölümlerde dayanımlarını önemli ölçüde kaybettiği tespit edilmiştir. İncelenen kümbetlerin bazılarına uygulanan iyileştirme çalışmalarında ise kümbetlerin çevresinde bulunan yüzey suyu drenajlarının yeterli ölçüde yapılamadığı ve yağmur ile biriken suların tarihi eserlerin daha fazla bozunmasına sebep olduğu saptanmıştır. Kültürel miras olarak değerlendirilen bu tarihi yapıların korunup gelecek nesillere aktarılması amacıyla, ignimbirit yapılarının yüzeysularına karşı duyarlılığı dikkate alınarak tarihi kümbetlerin çevresinde su drenajı iyileştirme çalışmaları yapılması önerilmektedir.Article Citation - Scopus: 2Zeolite Synthesis by Alkali Fusion Method Using Two Different Fly Ashes Derived From Turkish Thermal Power Plants(Chamber of Mining Engineers of Turkey, 2020-03-01) Top, S.; Vapur, HüseyinIn this study, Faujasite (Na-LSX) (3.5(Ca0.3)3.5(Na0.6)3.5(Mg0.1)Al7Si17O48 32(H2O)) type zeolites and Ca-Filipsite (CaK0.6Na0.4Si5.2Al2.8O16 6(H2O)) type zeolites were produced from Sugözü Thermal Power Plant and Çatalaǧzi Thermal Power Plant fly ashes by alkali fusion method followed by water leaching, respectively. In these methods, fly ashes and sodium hydroxide (NaOH) were mixed in certain proportions and sintered at 600°C in ash furnace. Then, zeolites were obtained from the ground materials after water leaching and solid/liquid separation, respectively. Cation Exchange Capacity (CEC), X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM), Fourier-Transform Infrared Spectroscopy (FTIR), X-Ray Fluorescence (XRF) and Atomic Absorption Spectrometer (AAS) analyses were used to characterize the synthesized zeolites. The zeolites synthesized with Sugözü fly ashes in a ratio of 1:2 had 136.93 meq/100 g CEC, whereas the CEC of synthesized zeolite from Çatalaǧzi fly ashes was found to be 247.88 meq/100 g. As a result, zeolites, which can be used as wastewater treatment agent, energy storage material, catalyst and separator, were synthesized by using 2 different Class F fly ash. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 6Citation - Scopus: 6Sex Effect on the Correlation of Immunoglobulin G Glycosylation With Rheumatoid Arthritis Disease Activity(Tubitak Scientific & Technological Research Council Turkey, 2020-12-14) Ercan, AltanRheumatoid arthritis (RA) is a chronic autoimmune disease which affects females more than males with a presence of autoantibodies. Immunoglobulin G (IgG) produced by adaptive arm has 2 functional domains, Fc and Fab. The Fc domain binds Fc gamma receptors and C1q proteins of the innate arm. Therefore, the IgG Fc domain serves as a bridge between the innate and adaptive arms and is regulated by an evolutionarily conserved N-glycosylation with variable structures. These glycans are classified as agalactosylated G0, monogalactosylated G1, and digalactosylated G2, which are further modified by core-fucosylation (F) and bisecting N-acetylglucosamine (B) moieties such as G0F and G0FB. Interestingly, proinflammatory G0F is shown to be regulated by estrogen in vivo. Here, it is hypothesized that the regulation of G0F by estrogen contributes to sex dichotomy in RA by setting up the level of IgG-dependent inflammation and therefore, RA disease activity (Das28-CRP3). To investigate this hypothesis, IgG glycosylation was characterized in serum samples from active RA patients (n = 232) and healthy controls (n = 232) by serum N-glycan analysis using the high performance liquid chromatography. According to the results, the IgG Fc glycan phenotype originates predominantly from the structure of G0F, and both G0F and G0FB correlate with Das28-CRP3 in females, but not in males. In conclusion, IgG G0F-dependent inflammation differs in males and females, and these differences point to the differential regulation of inflammation by sex hormone estrogen via IgG glycosylation.Article Citation - WoS: 1Citation - Scopus: 1RPI-1 (Human DCDC2) Displays Functional Redundancy With Nephronophthisis 4 in Regulating Cilia Biogenesis in C. Elegans(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Kaplan, Oktay I.Projecting from most cell surfaces, cilia serve as important hubs for sensory and signaling processes and have been linked to a variety of human disorders, including Bardet-Biedl Syndrome (BBS), Meckel-Gruber Syndrome (MKS), Nephronophthisis (NPHP), and Joubert Syndrome, and these diseases are collectively known as a ciliopathy. DCDC2 is a ciliopathy protein that localizes to cilia; nevertheless, our understanding of the role of DCDC2 in cilia is still limited. We employed C. elegans to investigate the function of C. elegans RPI-1, a Caenorhabditis elegans ortholog of human DCDC2, in cilia and found that C. elegans RPI-1 localizes to the entire ciliary axoneme, but is not present in the transition zone and basal body. We generated a null mutant of C. elegans rpi-1, and our analysis with a range of fluorescence-based ciliary markers revealed that DCDC2 and nephronophthisis 4 (NPHP-4/NPHP4) display functional redundant roles in regulating cilia length and cilia positions. Taken together, our analysis discovered a novel genetic interaction between two ciliopathy disease genes (RPI-1/DCDC2 and NPHP-4/NPHP4) in C. elegans.Article Citation - WoS: 3Citation - Scopus: 3MicroRNA Prediction Based on 3D Graphical Representation of RNA Secondary Structures(Tubitak Scientific & Technological Research Council Turkey, 2019-08-05) Sacar Demirci, Muserref Duygu; Demirci, Müşerref Duygu SaçarMicroRNAs (miRNAs) are posttranscriptional regulators of gene expression. While a miRNA can target hundreds of messenger RNA (mRNAs), an mRNA can be targeted by different miRNAs, not to mention that a single miRNA might have various binding sites in an mRNA sequence. Therefore, it is quite involved to investigate miRNAs experimentally. Thus, machine learning (ML) is frequently used to overcome such challenges. The key parts of a ML analysis largely depend on the quality of input data and the capacity of the features describing the data. Previously, more than 1000 features were suggested for miRNAs. Here, it is shown that using 36 features representing the RNA secondary structure and its dynamic 3D graphical representation provides up to 98% accuracy values. In this study, a new approach for ML-based miRNA prediction is proposed. Thousands of models are generated through classification of known human miRNAs and pseudohairpins with 3 classifiers: decision tree, naive Bayes, and random forest. Although the method is based on human data, the best model was able to correctly assign 96% of nonhuman hairpins from MirGeneDB, suggesting that this approach might be useful for the analysis of miRNAs from other species.Article Citation - Scopus: 2Impact of High Speed Railway Systems on Inter-Regional Trips and Accessibility in Turkey(Istanbul Teknik Universitesi, Faculty of Architecture itudergisi@itu.edu.tr, 2020) Baş, Ahmet; Yüzer, Mehmet AliHigh-speed trains are faster, safer, more comfortable than road transport for trips of 250–1000 kilometers. Accordingly, a significant increase has been observed in inter-city railway transport following the construction of high-speed railway (HSR) connections. The present study shows the effects of HSR on accessibility and potential savings in time when compared to other transportation modes. The time saved by HSR systems has been shown to change purpose trip. The level of accessibility provided by the HSR between Konya–Ankara–Istanbul link is compared with the accessibility of other travel modes through an investigation of the weighted average travel times and an analysis of costs. Furthermore, data gathered from a field study carried out among users of the Konya-Ankara HSR link is used to identify the distribution of travel choices among different transportation modes, based on such social and economic indicators as income, car ownership and employment status. It is found that HSR service increases accessibility between cities, and changes travel demands and purpose, in favor of railways, and that economic factors such as income and car ownership are important in the use of HSR services. Finally, this research identifies social and cultural activities as a new reason for travel, in which users diversify their travel destinations because of the time savings offered by HSR systems. © 2020 Elsevier B.V., All rights reserved.