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: 1Citation - Scopus: 1Application of a Size Measurement Standard for Data Warehouse Projects(Wiley, 2024) Unlu, Hueseyin; Yueruem, Ozan Rasit; Yildiz, Ali; Demirors, OnurMethodologyIn this research, we conducted a case study to establish a foundation for size measurement and effort estimation in DWH projects. We first applied a productivity-based estimation approach using linear regression with the ISBSG repository to assist organizations without historical data. We then evaluated various machine learning algorithms to improve estimation accuracy. Finally, we tested a combined model that integrates both approaches for estimating effort in external projects.ResultsUsing the ISBSG dataset, linear regression models based on productivity achieved a Mean Magnitude of Relative Error (MMRE) of 0.285. Machine learning algorithms improved accuracy by 22.81%, reducing the MMRE to 0.220. The final model, applied to external projects, yielded MRE values between 0.010 and 0.245.ConclusionThe ISBSG repository is a valuable resource for effort estimation in DWH projects. Combining productivity-based estimation with machine learning enhances accuracy and predictive performance, making it a more reliable approach than traditional models.Article Phenotypically Plastic Drug-Resistant Chronic Myeloid Leukaemia Cell Line Displays Enhanced Cellular Dynamics in a Zebrafish Xenograft Model(Wiley, 2024) Baykal, Seda; Yuce, Zeynep; Ozhan, GunesUnderstanding the mechanisms by which cancer cells switch between different adaptive states and evade therapeutic interventions is essential for clinical management. In this study, the in vivo cellular dynamics of a new chronic myeloid leukaemia cell line displaying altered phenotype and resistance to tyrosine kinase inhibitors were investigated in correlation with their parental cells for invasiveness/metastasis, angiogenic potential and population kinetics. We showed that the cells exhibiting drug resistance and plastic phenotype possess an increased capacity for invasion compared to their parental cells, that exposure to imatinib mesylate has the potential to enhance cellular motility and that in a leukaemic cell population, even a minority of plastic cells exhibit improved migratory ability. Furthermore, we show that these plastic cells have angiogenic and extravasation potential. The present study provides significant insights into the cellular dynamics displayed by a TKI-resistant, phenotypically plastic CML cell line, using a zebrafish (Danio rerio) xenograft model.Article Citation - WoS: 4Citation - Scopus: 5Near-Infrared Emissive Super Penetrating Conjugated Polymer Dots for Intratumoral Imaging in 3d Tumor Spheroid Models(Wiley, 2024) Karabacak, Soner; Coban, Basak; Yildiz, Ahu Arslan; Yildiz, Umit HakanThis study describes the formation of single-chain polymer dots (Pdots) via ultrasonic emulsification of nonionic donor-acceptor-donor type (D-A-D) alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (Poly BT) with amphiphilic cetyltrimethylammonium bromide (CTAB). The methodology yields Pdots with a high cationic surface charge (+56.5 mV +/- 9.5) and average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots emit near-infrared (NIR) light at a maximum wavelength of 860 nm owing to their conjugated polymer backbone consisting of D-A-D monomers. Both colloidal and optical properties of these Pdots make them promising fluorescence emissive probes for bioimaging applications. The significant advantage of positively charged Pdots is demonstrated in diffusion-limited mediums such as tissues, utilizing human epithelial breast adenocarcinoma, ATCC HTB-22 (MCF-7), human bone marrow neuroblastoma, ATCC CRL-2266 (SH-SY5Y), and rat adrenal gland pheochromocytoma, CRL-1721 (PC-12) tumor spheroid models. Fluorescence microscopy analysis of tumor spheroids from MCF-7, SH-SY5Y, and PC-12 cell lines reveals the intensity profile of Pdots, confirming extensive penetration into the central regions of the models. Moreover, a comparison with mitochondria staining dye reveals an overlap between the regions stained by Pdots and the dye in all three tumor spheroid models. These results suggest that single-chain D-A-D type Pdots, cationized via CTAB, exhibit long-range mean free path of penetration (approximate to 1 mu m) in dense mediums and tumors. The single chain near infrared (NIR) emissive Pdots with high cationic surface charge enable penetration in dense medium such as tumor spheroids. Both colloidal and optical properties of Pdots make them promising fluorescent probe in bioimaging. imageArticle Citation - WoS: 5Citation - Scopus: 5Stabilisation of Extra Virgin Olive Oil-In Emulsions Prepared by Citrus Pectin Using Green Tea and Grape Seed Phenolic Extracts and Catechin(Wiley, 2024) Buyuk, Miray; Yemenicioglu, AhmetThis study aimed at the solution of stability problems of extra virgin olive oil rich (oil:aqueous phase ratio = 50:50) model oil-in-water emulsions prepared with pectin using green tea (GTE) and grape seed extracts (GSE), and (+)-catechin (CAT). Olive oil-in-water emulsion prepared with pectin at 0.5% (w/v) without phenolics lost 36% of its stability within 1 day. GTE at 1% (w/v) caused a limited increase in emulsion stability while emulsions with GSE at >= 0.25% or CAT at 1% maintained >90% of their stability after 14 days. GSE and CAT reduced the emulsion droplet size (2.6- and 1.9-fold) while GTE increased the emulsion droplet size (1.5-fold). Emulsions with GSE showed the smallest and most densely packed lipid droplets. The highest phenolic content and antioxidant activity in emulsions were obtained with CAT followed by GSE and GTE. This work is significant in that it showed the possibility of using GSE to obtain stable extra virgin olive oil emulsion-based functional foods.Review Citation - WoS: 3Citation - Scopus: 4Long Non-Coding Rna-Mediated Modulation of Endoplasmic Reticulum Stress Under Pathological Conditions(Wiley, 2024) Ciftci, Yusuf Cem; Yurtsever, Yigit; Akgul, BunyaminEndoplasmic reticulum (ER) stress, which ensues from an overwhelming protein folding capacity, activates the unfolded protein response (UPR) in an effort to restore cellular homeostasis. As ER stress is associated with numerous diseases, it is highly important to delineate the molecular mechanisms governing the ER stress to gain insight into the disease pathology. Long non-coding RNAs, transcripts with a length of over 200 nucleotides that do not code for proteins, interact with proteins and nucleic acids, fine-tuning the UPR to restore ER homeostasis via various modes of actions. Dysregulation of specific lncRNAs is implicated in the progression of ER stress-related diseases, presenting these molecules as promising therapeutic targets. The comprehensive analysis underscores the importance of understanding the nuanced interplay between lncRNAs and ER stress for insights into disease mechanisms. Overall, this review consolidates current knowledge, identifies research gaps and offers a roadmap for future investigations into the multifaceted roles of lncRNAs in ER stress and associated diseases to shed light on their pivotal roles in the pathogenesis of related diseases.Article Citation - Scopus: 1Mitigating Thermal Stratification in Lakes/Reservoirs Through Wind-Powered Air Diffusers(Wiley, 2024) Hazar, Oguz; Elci, SebnemThermal stratification can cause various water quality issues in large water bodies. To address this, a new wind-powered artificial mixing system is designed and experimentally tested for various Savonius rotor combinations (three-stage and four-stage rotors). These turbines directly utilize wind energy to draw air into the water column for aeration, bypassing the need for electrical conversion. The rotor performances were tested in terms of power and torque coefficients. Additionally, these rotors were tested for artificial mixing efficiencies in a specially designed water tank that can mimic thermal stratification typically observed in an actual water supply reservoir. Among the rotors, the three-stage rotor with a 60 degrees phase shift was found to exhibit superior power and torque coefficients, achieving a power efficiency value of 0.14. As for the mixing efficiency, the four-stage rotor with a 45 degrees phase shift excelled in mixing efficiency, reaching 95%.Practitioner Points A new wind-powered artificial mixing system is designed and tested for various Savonius rotor combinations. While keeping the total rotor height constant, the three-stage Savonius rotor class shows superior performance against the four-stage Savonius rotor class in terms of power and torque efficiency. Apart from the rotor performance results, the four-stage Savonius rotors show greater artificial mixing efficiency than the three-stage Savonius rotors. Single-pump/diffuser artificial destratification system exhibits better mixing efficiency than multiple-pump/diffuser systems. A new wind-powered artificial mixing system is designed and tested for various Savonius rotor combinations. The three-stage 60 degrees phase shift Savonius rotor demonstrated the best performance of turbine efficiency. The four-stage Savonius rotor with a 45 degrees phase shift connected to a single-pump system achieved the highest destratification efficiency at 95%. imageArticle Citation - WoS: 3Citation - Scopus: 3Liposomal Black Mulberry Extract Loaded-Nanofibers: Preparation, Characterisation, and Bioaccessibility of Phenolics by Simulated <i>in Vitro</I> Digestion Combined With the Caco-2 Cell Model(Wiley, 2024) Caglar, Nagihan Kalintas; Saroglu, Oznur; Karakas, Canan Yagmur; Tasci, Cansu Ozel; Catalkaya, Gizem; Yildirim, Rusen Metin; Karadag, AyseBlack mulberry extract (BME) is rich in phenolics; however, their health benefits are restricted by their instability and poor absorption in the small intestine. Liposomal BME-loaded pullulan/pectin nanofibers were developed to enhance the in vitro bioaccessibility of BME. The liposomes with BME (0.8%, w/v), were produced by the thin-film hydration and ultrasonication method with a size of 76.41 +/- 1.23 nm and encapsulated 79.40 +/- 0.99%.of the BME. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) images showed that the uniform distribution of liposomes within the defect-free fiber structure. Liposomal BME loading elevated the mucoadhesiveness of the nanofibers compared to free BME loading. Liposomal BME-loaded nanofiber demonstrated a nearly two-fold increase in the bioaccessibility of anthocyanins. The cellular release of all four different anthocyanins by Caco-2 cells was significantly higher (3.92%-10.50%) in liposomal BME-loaded nanofiber. Therefore, liposomal nanofibers show great potential as a method for delivering phenolics, specifically anthocyanins.Review Citation - WoS: 6Citation - Scopus: 8Recent Developments Shaping the Future of Antimicrobial Edible Food Packaging: a Review(Wiley, 2024) Yemenicioglu, AhmetThis article aimed at reviewing recent developments shaping the future of antimicrobial edible food packaging. The main issues discussed in the article are (i) factors (e.g. waste valorisation, sustainability, health and environmental concerns, religious concerns, etc.) causing emerging of alternative hydrocolloids extracted from farming/processing wastes of plants, animals, fungi, insects, snails, etc. as antimicrobial edible packaging material; (ii) emerging methods of manufacturing antimicrobial packaging (e.g. extruded and co-extruded antimicrobial casings, antimicrobial electrospun mats, and electrosprayed films, coatings and particles); (iii) emerging concepts in using natural antimicrobials in edible packaging such as using narrow- or broad-spectrum antimicrobials, synergetic mixtures, and controlled release strategies based on nanoencapsulation (e.g. Pickering emulsions, nanoemulsions, inclusion complexes, solid lipid nanoparticles and nanostructured lipid carriers). This review helps discovering the future of active edible packaging that is expected to play a central role in improving food safety and quality, human health and environmentally friendly practices. Factors shaping the future of antimicrobial edible packaging. imageArticle Citation - WoS: 7Citation - Scopus: 7Development of Resin-Based Dental Composites Containing Hydroxyapatite and Zirconia Nanoparticles(Wiley, 2024) Taskiran, Senagul Tunca; Tanoglu, Metin; Cerci, Nazife; Cevahir, Aref; Damar, Ceren Turkdogan; Unver, Elcin; Aktas, Mustafa IlkerIn clinical applications, resin-based dental composites primarily face challenges with fractures and secondary caries. To overcome these issues, the physical characteristics of dental composites, especially mechanical properties, need to be improved. Hydroxyapatite (HA), present in the structure of the teeth, is preferred due to its biological properties, and zirconia (ZrO2) nanoparticles are known to enhance the mechanical properties of this type of composites. The aim of this study is to develop resin-based dental composites containing HA and ZrO2 nanoparticles. The study also aims to explore the synergistic effect of these two nanoparticles on the physical properties of the developed composites. Composites with nine different compositions were prepared by mixing the components with the help of a mortar mill. The flexural and compressive strength, polymerization shrinkage, depth of cure and water sorption, and solubility properties of the prepared composites have been investigated. All composites have been found to meet the requirements of ISO 4049 standard. Among them, composite containing 5 wt. % HA and 1 wt. % ZrO2 (H5Z1) has exhibited the highest flexural strength with an increase of 58% compared to the control sample, and composite containing 3 wt. % HA and 2 wt. % ZrO2 (H3Z2) has exhibited the highest compressive strength with an increase of 22% compared to the control sample. Other physical properties of the composites have been found to be in an acceptable level.Highlights Dental composites with HA and ZrO2 fillers were developed by a mortar mill. Synergistic effect of HA and ZrO2 nanoparticles was investigated. Mechanical properties of dental composites were significantly improved. Physical properties of dental composites were found to be at acceptable levels. Depth of cure decreases with increasing HA and ZrO2 loading. Synthesis of a resin-based dental composites containing HA and ZrO2 nanoparticles by a mortar mill and characterization of microstructural and mechanical properties. imageReview Citation - WoS: 4Citation - Scopus: 4Unraveling the Intriguing Interplay: Exploring the Role of Lncrnas in Caspase-Independent Cell Death(Wiley, 2024) Ciftci, Yusuf Cem; Akgül, Bünyamin; Vatansever, Ipek Erdogan; Akgul, BuenyaminCell death plays a crucial role in various physiological and pathological processes. Until recently, programmed cell death was mainly attributed to caspase-dependent apoptosis. However, emerging evidence suggests that caspase-independent cell death (CICD) mechanisms also contribute significantly to cellular demise. We and others have reported and functionally characterized numerous long noncoding RNAs (lncRNAs) that modulate caspase-dependent apoptotic pathways potentially in a pathway-dependent manner. However, the interplay between lncRNAs and CICD pathways has not been comprehensively documented. One major reason for this is that most CICD pathways have been recently discovered with some being partially characterized at the molecular level. In this review, we discuss the emerging evidence that implicates specific lncRNAs in the regulation and execution of CICD. We summarize the diverse mechanisms through which lncRNAs modulate different forms of CICD, including ferroptosis, necroptosis, cuproptosis, and others. Furthermore, we highlight the intricate regulatory networks involving lncRNAs, protein-coding genes, and signaling pathways that orchestrate CICD in health and disease. Understanding the molecular mechanisms and functional implications of lncRNAs in CICD may unravel novel therapeutic targets and diagnostic tools for various diseases, paving the way for innovative strategies in disease management and personalized medicine.