Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Doctoral Thesis A reliable and secure communication design for underwater sensor networks concerning energy efficiency(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) UYAN, Osman Gökhan; Güngör, Vehbi ÇağrıUnderwater Acoustic Sensor Networks (UASNs) recently attract scientists because of its wide range of applications and emerging technology. A design challenge in UASN's is the limited network lifetime and poor reliability caused by limited battery supply of sensors and harsh channel conditions in underwater environment. Moreover, sensors might transmit sensitive data that must be disguised against eavesdropping attacks. To maintain a reliability level, packet-duplication and multi-path routing method are suggested, which renders eavesdropping attacks easier. For data security, cryptographic encryption is the most acclaimed method. However, encryption needs extra computations, which consume extra energy and cause a decrease in the network lifetime. As a countermeasure along with encryption against silent listening, fragmenting data and transmitting in pieces over different paths has been proposed. To address these challenges, an optimization framework has been developed to analyze the effects of multi-path routing, packet duplication, encryption, and data fragmentation on network lifetime. However, the solution time of the proposed optimization model is quite high, and sometimes it cannot come up with feasible solutions. To this end, in this study, different regression and neural network methods have been proposed to predict the energy consumptions of underwater nodes as supplementary methods to optimization models. Performance evaluations show that the proposed methods yield remarkably accurate predictions and can be used for energy consumption prediction in UASNs.Article Citation - WoS: 21Citation - Scopus: 25miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023-01-12) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, MalikDuring recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .Conference Object Citation - Scopus: 2miRcorrNetPro: Unraveling Algorithmic Insights Through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis(Institute of Electrical and Electronics Engineers Inc., 2023-12-05) Ünlü Yazici, Miray; Yousef, Malik; Marron, J. S.; Bakir-Güngör, Burcu; Yazici, Miray UnluHigh throughput -omics technologies facilitate the investigation of regulatory mechanisms of complex diseases. Along this line, scientists develop promising tools and methods to extend our understanding at the molecular and functional levels. To this end, miRcorrNet tool performs integrative analysis of MicroRNA (miRNA) and gene expression profiles via machine learning (ML) approach to identify significant miRNA groups and their associated target genes. In this study, we propose miRcorrNetPro tool, which extends miRcorrNet by tracking group scoring, ranking and other information through the cross-validation iterations. Heatmap visualizations enable deep novel insights into the collective behavior of clusters of groups in cellular signaling and hence facilitate detection of potential biomarkers for the disease under investigation. Although miRcorrNetPro is designed as a generic tool, here we present our findings and potential miRNA biomarkers for Breast Cancer (BRCA). The miRcorrNetPro tool and all other supplementary files are available at https://github.com/Miray-Unlu/miRcorrNetPro. © 2024 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1eTNT: Enhanced Textnettopics With Filtered LDA Topics and Sequential Forward / Backward Topic Scoring Approaches(Science and Information Organization, 2024) Voskergian, Daniel; Jayousi, Rashid; Bakir-Güngör, BurcuTextNetTopics is a novel text classification-based topic modelling approach that focuses on topic selection rather than individual word selection to train a machine learning algorithm. However, one key limitation of TextNetTopics is its scoring component, which evaluates each topic in isolation and ranks them accordingly, ignoring the potential relationships between topics. In addition, the chosen topics may contain redundant or irrelevant features, potentially increasing the feature set size and introducing noise that can degrade the overall model performance. To address these limitations and improve the classification performance, this study introduces an enhancement to TextNetTopics. eTNT 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. Moreover, it incorporates a filtering component that aims to enhance topics' quality and discriminative power by removing non-informative features from each topic using Random Forest feature importance values. These integrations aim to streamline the topic selection process and enhance classifier efficiency for text classification. The results obtained from the WOS-5736, LitCovid, and MultiLabel datasets provide valuable insights into the superior effectiveness of eTNT compared to its counterpart, TextNetTopics. © 2024 Elsevier B.V., All rights reserved.Article Citation - Scopus: 6Wind Turbine Inspection With Drone: Advantages and Disadvantages(Erol Kurt, 2023-03-31) Tanrıverdi, Harun; Karakuş, Güzide; Ulukan, AhmetThe facilities on wind energy generation are increasingly finding usage areas in line with the ecologically friendly energy generation approach. One of the important activities of wind power generation facilities, which have high investment cost, low operating cost and low environmental impact is the maintenance and repair of wind turbines. A preventive maintenance approach is dominant to reduce maintenance times and eliminate lost time in wind turbines. Damage inspection of turbines has been evolved from tower crane access, rope access, camera viewing, and other applications to image with manual drones over the years. However, when these methods are evaluated within the framework of criteria such as cost, performance, occupational safety and data reliability, they are still insufficient and the need for inspection with autonomous drones arises. The advantages and disadvantages of autonomous drones used in the determination of damage in wind turbines are analyzed and the results are considered to contribute to the practitioners operating in the sector and academicians working in the field. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 33Citation - Scopus: 37Wind Farm Site Selection Using GIS-Based Multicriteria Analysis With Life Cycle Assessment Integration(Springer Heidelberg, 2024-01-19) Demir, Abdullah; Dincer, Ali Ersin; Ciftci, Cihan; Gulcimen, Sedat; Uzal, Nigmet; Yilmaz, KutayThe sustainability of wind power plants depends on the selection of suitable installation locations, which should consider not only economic and technical factors including manufacturing and raw materials, but also issues pertaining to the environment. In the present study, a novel methodology is proposed to determine the suitable locations for wind turbine farms by analyzing from the environmental perspective. In the methodology, the life cycle assessment (LCA) of wind turbines is incorporated into the decision process. The criteria are ranked using analytical hierarchy process (AHP). The study area is chosen as the western region of Turkiye. The obtained suitability map reveals that wind speed is not the sole criterion for selecting a site for wind turbine farms; other factors, such as bird migration paths, distance from urban areas and land use, are also crucial. The results also reveal that constructing wind power plants in the vicinity of Izmir, canakkale, Istanbul, and Balikesir in Turkiye can lead to a reduction in emissions. Izmir and its surrounding area show the best environmental performance with the lowest CO2 per kilowatt-hour (7.14 g CO2 eq/kWh), to install a wind turbine due to its proximity to the harbor and steel factory across the study area. canakkale and the northwest region of Turkiye, despite having high wind speeds, are less environmentally favorable than Izmir, Balikesir, and Istanbul. The findings of LCA reveal that the nacelle and rotor components of the wind turbine contribute significantly (43-97%) to the environmental impact categories studied, while the tower component (0-36%) also has an impact.Article Citation - WoS: 7Citation - Scopus: 8Whether and When Did Bitcoin Sentiment Matter for Investors? Before and During the COVID-19 Pandemic(Springer, 2023-12-21) Aysan, Ahmet Faruk; Mugaloglu, Erhan; Polat, Ali Yavuz; Tekin, HasanUsing a wavelet coherence approach, this study investigates the relationship between Bitcoin return and Bitcoin-specific sentiment from January 1, 2016 to June 30, 2021, covering the COVID-19 pandemic period. The results reveal that before the pandemic, sentiment positively drove prices, especially for relatively higher frequencies (2-18 weeks). During the pandemic, the relationship was still positive, but interestingly, the lead-lag relationship disappeared. Employing partial wavelet tools, we factor out the number of COVID-19 cases and deaths and the Equity Market Volatility Infectious Disease Tracker index to observe the direct relationship between a change in sentiment and return. Our results robustly reveal that, before the pandemic, sentiment had a positive effect on return. Although positive coherence still existed during the pandemic, the lead-lag relationship disappeared again. Thus, the causal relationship that states that sentiment leads to return can only be integrated into short-term trading strategies (up to six weeks frequency).Article Citation - WoS: 6Citation - Scopus: 6WDR31 Displays Functional Redundancy With GTpase-Activating Proteins (GAPs) ELMOD and RP2 in Regulating Ift Complex and Recruiting the BBsome to Cilium(Life Science Alliance Llc, 2023-05-19) Cevik, Sebiha; Peng, Xiaoyu; Beyer, Tina; Pir, Mustafa S.; Yenisert, Ferhan; Woerz, Franziska; Kaplan, Oktay, IThe correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caeno-rhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumu-lations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into the cilia and exit from the cilia are impacted. Furthermore, anterograde IFT in the middle segment travels at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into the cilia of wdr-31;rpi-2;elmd-1, possibly because of IFT de-fects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.Article Citation - WoS: 7Citation - Scopus: 7Villages in the City - Urban Planning for Neighbourhood Love(Wiley, 2024-03-17) Kourtit, Karima; Nijkamp, Peter; Turk, Umut; Wahlstrom, MiaThe city comprises of a wide variety of heterogeneous territorial units (e.g. districts or neighbourhoods). In many - especially larger - cities, social capital assets (like community bonds) are mirrored at the level of neighbourhoods which form the home for many sociocultural communities or distinct socio-economic classes. We postulate in this study that the big city is essentially an 'archipelago' made up of 'urban villages'. We analyse the residents' perceived attractiveness regarding their daily local neighbourhood by introducing the concept of 'village love' (or 'neighbourhood love'), inspired by the recent literature on 'city love' (comprising 'body', 'soul' and 'community' constituents of urban life). Based on an extensive and detailed multi-annual database for all neighbourhoods in Rotterdam, the present paper seeks to identify the background factors shaping 'village love' in the city, with particular attention to the citizens' subjective appreciation for and access to a great variety of (physical and immaterial) urban amenities shaping the place-based satisfaction of residents. The theoretical framing of our research resembles the basics of traditional central place theory here transmitted to the urban space in which local proximity to amenities plays a key role. A wide array of relevant amenities impacting on the place-specific well-being feelings ('village love') of residents in various neighbourhoods in the city of Rotterdam is distinguished using inter alia-rich multi-annual survey data. This approach is empirically tested and verified by means of LISA statistics and advanced spatial econometric dependence models ('urbanometrics'). The findings confirm the usefulness of a central place interpretation of 'urban village love' in the city. 'Villages in the City - Urban Planning for Neighbourhood Love': This study advocates that cities are composed of interconnected 'urban villages', each with its own social capital and community bonds. Using extensive data from Rotterdam, we investigate the factors influencing residents' perceived attractiveness and satisfaction with their local neighbourhoods. Our analysis highlights the importance of access to diverse amenities in shaping residents' sense of 'village love'. Through spatial econometric models, the study confirms the central place interpretation of 'urban village love' in the city, shaping future urban planning strategies for fostering vibrant and cohesive communities.imageArticle Citation - WoS: 8Citation - Scopus: 8Very High Early Strength Calcium Aluminate Based Binary and Ternary Cementitious Systems: Properties, Hydration and Microstructure(Taylor & Francis Ltd, 2023-06-16) Saydan, Murat; Keskin, Ulku Sultan; Uzal, BurakCalcium aluminate cement (CAC) is a cement type that has superior properties such as rapid strength gain, high resistance to high temperatures and harmful chemicals. However, the result of the using of CACs in the production of structural elements occur strength decreases at later ages as a result of a series of chemical reactions called 'conversion reactions' seen in these cements. In this study, the hydration kinetics and the crystalline and amorphous structures formed as a result of hydration were investigated in CAC containing different amounts and types of main oxides-based binary and ternary systems. Considering the results obtained, the main hydration product seen in these specimens was ettringite. Unlike many studies in the literature, metastable structures which cause conversion reactions, such as CAH(10), C(2)AH(8), have not been observed. Instead of conversion of the phases, ettringite needles were became thin and elongate which causes the paste structure porous and thus causing expansion and strength reduction at the later stages of hydration in some mixtures produce high amounts of ettringite. On the other hand, it is understood that the formation of stratlingite was limited strength decreases in systems where high silica fume is used.