WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 4Citation - Scopus: 4Novel Electrospun-Based Extractive Probes for Rapid Determination of Clinically Important Compounds in Human Plasma(Elsevier B.V., 2024) Eroğlu, Ahmet Emin; Eroğlu,A.E.; Salih,B.; Boyaci,E.; 01. Izmir Institute of Technology; 04.01. Department of Chemistry; 04. Faculty of ScienceBackground: Coated blade spray (CBS) represents an innovative approach that utilizes solid-phase microextraction principles for sampling and sample preparation. When combined with ambient mass spectrometry (MS), it can also serve as an electrospray ionization source. Therefore, it became a promising tool in analytical applications as it can significantly reduce the analysis time. However, the current CBS coatings are based on the immobilization of extractive particles in bulk polymeric glue, which constrains the diffusion of the analytes to reach the extractive phase; therefore, the full reward of the system cannot be taken at pre-equilibrium. This has sparked the notion of developing new CBS probes that exhibit enhanced kinetics. Results: With this aim, to generate a new extractive phase with improved extraction kinetics, poly(divinylbenzene) (PDVB) nanoparticles were synthesized by mini-emulsion polymerization and then immobilized into sub-micrometer (in diameter) sized polyacrylonitrile fibers which were obtained by electrospinning method. Following the optimization and characterization studies, the electrospun-coated blades were used to determine cholesterol, testosterone, and progesterone in plasma spots using the CBS-MS approach. For testosterone and progesterone, 10 ng mL−1 limits of quantification could be obtained, which was 200 ng mL−1 for cholesterol in spot-sized samples without including any pre-treatment steps to samples prior to extraction. Significance: The comparison of the initial kinetics for dip-coated and electrospun-coated CBS probes proved that the electrospinning process could enhance the extraction kinetics; therefore, it can be used for more sensitive analyses. The total analysis time with this method, from sample preparation to instrumental analysis, takes only 7 min, which suggests that the new probes are promising for fast diagnostic applications. © 2024 Elsevier B.V.Article Citation - WoS: 8Citation - Scopus: 7Delignification of Corncob by Choline Chloride-Urea Deep Eutectic Solvent for Enzymatic Production of Xylooligosaccharides(Elsevier B.V., 2024) Büyükkileci, Ali Oğuz; Buyukkileci,A.O.; 01. Izmir Institute of Technology; 03.08. Department of Food Engineering; 03. Faculty of EngineeringDeep eutectic solvent (DES) pretreatment was applied to corncob to obtain xylooligosaccharides (XOS) by enzymatic hydrolysis using xylanase. Based on the XOS titers in the hydrolysate, urea was the most effective among the hydrogen bond donors tested to couple choline chloride (ChCl). DES pretreatment at 130 °C for two hours with ChCl-Urea (molar ratio of 1:2) containing 40 % water, decreased lignin fraction from 12.8 % to 6.9 %, while 79 % of the xylan was retained in the pretreated corncob. The highest XOS production was obtained using 400 U/g xylanase at 60 °C, which yielded 12.0 g/L XOS with a low degree of polymerization (LDP-XOS). The total XOS yield based on the raw corncob was calculated as 14.4 %, 90 % of which was LDP-XOS. The cellulose-rich residual biomass could be hydrolyzed enzymatically to glucose with 65 % cellulose digestibility. The discarded biomass after hydrolyzes was 21.7 % of the raw material. The results showed that DES was a promising pretreatment for enhancing enzymatic XOS production. © 2024 Elsevier B.V.Article Citation - WoS: 13Citation - Scopus: 12Dunaliella Salina Microalgae Aqueous Extract-Based Magnetic Nanoparticles (fe3o4-Nps): Green Synthesis, Characterization and in Vitro Anticancer Investigations(Elsevier B.V., 2024) Mohammadpourfard, Mousa; Hamishehkar,H.; Mohammadpourfard,M.; 01. Izmir Institute of Technology; 03.06. Department of Energy Systems Engineering; 03. Faculty of EngineeringIn the current study, a facile, rapid, and eco-friendly method was provided for green synthesizing of magnetic Fe3O4-NPs with enhanced stability and biocompatibility using different weight concentrations (1 %, 3 %, and 5 %) of aqueous extract of Dunaliella salina (D. salina) microalgae. The properties of the green-synthesized magnetic nanoparticles (GMNPs-ex1%, GMNPs-ex3%, and GMNPs-ex5%) were compared with chemically-synthesized ones (CMNPs) via XRD, TEM, FESEM, VSM, DLS, ZP, FTIR, hemolysis, cell viability, DAPI staining, and apoptosis analyses. TEM imaging revealed mean sizes of 11.21 ± 2.63 nm and 14.08 ± 3.24 nm for GMNPs-ex5% and CMNPs, respectively, with better dispersity for GMNPs-ex5%, as confirmed with their polydispersity index (PDI = 0.24 for GMNPs-ex5% and 0.58 for CMNPs). These sizes were consistent with the crystallite size of pure magnetite phase nanoparticles obtained from XRD. FESEM images confirmed spherical shape for the majority of nanoparticles. FTIR spectra confirmed the involvement of functional groups from the extract in GMNPs, contributing to their stability (ZP of GMNPs-ex5% = −34 mV). The saturation magnetization decreased with increasing the extract ratio (from 62.41 to 8.94 emu/g), attributed to the non-magnetic nature of the extract coating. GMNPs-ex5% exhibited a negligible hemolysis rate (< 2 %) compared to CMNPs. Furthermore, IC50 values of GMNPs and extract against HFF-2 and A549 cells were higher than those of CMNPs, indicating the biocompatibility of green-synthesized nanoparticles. In the DAPI staining method, GMNPs-ex5%, similar to the extract, caused less DNA damage to HFF-2 cells. Additionally, the apoptosis assay using annexin V/PI staining kit indicated that green-synthesized nanoparticles induced lower apoptosis in normal cells. Overall, this study highlights the potential of green-synthesized Fe3O4-NPs for various biomedical applications, showcasing their enhanced properties and biocompatibility compared to conventionally synthesized counterparts. © 2024 Elsevier B.V.Article Effects of Edge Addition or Removal on the Nullity of a Graph(Elsevier B.V., 2024) Batal, Ahmet; 01. Izmir Institute of Technology; 04.02. Department of Mathematics; 04. Faculty of ScienceLights Out is a game which can be played on any graph G. Initially we have a configuration which assigns one of the two states on or off to each vertex. The aim of the game is to turn all vertices to off state for an initial configuration by activating some vertices where each activation switches the state of the vertex and all of its neighbors. If the aim of the game can be accomplished for all initial configurations then G is called always solvable. We call the dimension of the kernel of the closed neighborhood matrix of the graph over the field Z2, nullity of G. It turns out that G is always solvable if and only if its nullity is zero. Moreover, the number of solutions of a given configuration is also determined by the nullity. We investigate the problem of how nullity changes when an edge is added to or removed from a graph. As a result we show that for every graph with positive nullity there exists an edge whose removal decreases the nullity. Conversely, we show that for every always solvable graph which is not an even graph with odd order, there exists an edge whose addition increases the nullity. We also show that if an always solvable graph is not even, then there is an edge whose removal increases the nullity. © 2024Article Citation - WoS: 10Citation - Scopus: 11Arabinoxylan-Based Psyllium Seed Hydrocolloid: Single-Step Aqueous Extraction and Use in Tissue Engineering(Elsevier B.V., 2024) Yildirim-Semerci,Ö.; Bilginer-Kartal,R.; Arslan-Yildiz,A.; 01. Izmir Institute of TechnologyBiomacromolecules derived from natural sources offer superior biocompatibility, biodegradability, and water-holding capacity, which make them promising scaffolds for tissue engineering. Psyllium seed has gained attention in biomedical applications recently due to its gel-forming ability, which is provided by its polysaccharide-rich content consisting mostly of arabinoxylan. This study focuses on the extraction and gelation of Psyllium seed hydrocolloid (PSH) in a single-step water-based protocol, and scaffold fabrication using freeze-drying method. After characterization of the scaffold, including morphological, mechanical, swelling, and protein adsorption analyses, 3D cell culture studies were done using NIH-3 T3 fibroblast cells on PSH scaffold, and cell viability was assessed using Live/Dead and Alamar Blue assays. Starting from day 1, high cell viability was obtained, and it reached 90 % at the end of 15-day culture period. Cellular morphology on PSH scaffold was monitored via SEM analysis; cellular aggregates then spheroid formation were observed throughout the study. Collagen Type-I and F-actin expressions were followed by immunostaining revealing a 9- and 10-fold increase during long-term culture. Overall, a single-step and non-toxic protocol was developed for extraction and gelation of PSH. Obtained results unveiled that PSH scaffold provided a favorable 3D microenvironment for cells, holding promise for further tissue engineering applications. © 2024 Elsevier B.V.Article Citation - WoS: 3Citation - Scopus: 3Macroporous Polymer-Derived Ceramics Produced by Standard and Additive Manufacturing Methods: How the Shaping Technique Can Affect Their High Temperature Thermal Behavior(Elsevier B.V., 2024) Ahmetoğlu, Çekdar Vakıf; Kulkarni,A.; Semerci,T.; Vakifahmetoglu,C.; Pelanconi,M.; Bottacin,S.; Sorarù,G.D.; 01. Izmir Institute of Technology; 03.09. Department of Materials Science and Engineering; 03. Faculty of EngineeringThis work proposes the processing of porous ceramic lattices via three polymer-derived ceramic routes, namely powder bed fusion and infiltration, fused filament fabrication and replica, and a direct replica of a foamed polymer. A common feature in the processing of these lattices is the use of the same polysilazane as the preceramic source for the Si-C-N-O network that builds up during ceramization. We adopted rotated cube, honeycomb and randomized cellular geometries as a matter of comparison for thermal exchange when an air flow is forced through the structures up to 1050 °C. The three procedural pathways are discussed in their limitations regarding geometry, polymer-to-ceramic conversion, high-temperature heat exchange performance and durability. In this regard, while rotated cube geometry results in the best thermal exchange and highest pressure drop, we show a correlation between chemical composition and high temperature oxidation of the Si-C-N-O network, possibly attributed to the selection of the processing routes. © 2024 The AuthorsArticle Citation - WoS: 4Citation - Scopus: 4Automating Modern Code Review Processes With Code Similarity Measurement(Elsevier B.V., 2024) Kartal,Y.; Akdeniz,E.K.; Özkan,K.; 01. Izmir Institute of TechnologyContext: Modern code review is a critical component in software development processes, as it ensures security, detects errors early and improves code quality. However, manual reviews can be time-consuming and unreliable. Automated code review can address these issues. Although deep-learning methods have been used to recommend code review comments, they are expensive to train and employ. Instead, information retrieval (IR)-based methods for automatic code review are showing promising results in efficiency, effectiveness, and flexibility. Objective: Our main objective is to determine the optimal combination of the vectorization method and similarity to measure what gives the best results in an automatic code review, thereby improving the performance of IR-based methods. Method: Specifically, we investigate different vectorization methods (Word2Vec, Doc2Vec, Code2Vec, and Transformer) that differ from previous research (TF-IDF and Bag-of-Words), and similarity measures (Cosine, Euclidean, and Manhattan) to capture the semantic similarities between code texts. We evaluate the performance of these methods using standard metrics, such as Blue, Meteor, and Rouge-L, and include the run-time of the models in our results. Results: Our results demonstrate that the Transformer model outperforms the state-of-the-art method in all standard metrics and similarity measurements, achieving a 19.1% improvement in providing exact matches and a 6.2% improvement in recommending reviews closer to human reviews. Conclusion: Our findings suggest that the Transformer model is a highly effective and efficient approach for recommending code review comments that closely resemble those written by humans, providing valuable insight for developing more efficient and effective automated code review systems. © 2024 Elsevier B.V.Article Citation - WoS: 3Citation - Scopus: 4Caffeic Acid Phenethyl Ester (cape) Chitosan Capped Zno Nanoparticles: Preparation, Characterization, and Its Potential for the Treatment of Prostate Cancer(Elsevier B.V., 2024) Güler, Günnur; Yıldırım,Y.; Göker,E.; Güler,G.; Saltan,F.; Acar,R.; Medine,E.İ.; 01. Izmir Institute of Technology; 04.05. Department of Pyhsics; 04. Faculty of ScienceThe synthesis of zinc oxide nanoparticles/chitosan (ZnONPs/CS) formulation loaded with Caffeic acid phenethyl ester (CAPE) was performed to evaluate its prostate cancer treatment efficiency within the scope of this research. It has been hypothesized that a dual active materials delivery system containing ZnO and CAPE loaded Chitosan (CS) nanoparticles has better bioavailability compared to single one against to cancer cells. ZnONPs were synthesized between 45 and 60 nm particle sizes and then they were capped with CS biodegradable polymer prior to load with CAPE bioactive molecule. ZnONPs/CS-CAPE system was characterized by using Fourier Transform Infrared (FTIR) for structural elucidation, Scanning Electron Microscope (SEM) for particle size determination, High Performance Liquid Chromatography (HPLC) system for determination of CAPE amount. 131I CAPE and 131I ZnONPs/CS-CAPE labeled by the Iodogen method with 131I were used in-vitro cell culture experiments. Cell viabilities (%) of CAPE and ZnONPs/CS-CAPE were examined using Cell Counting Kit-8 assay on PC-3 (human adenocarcinoma prostate), LnCaP (human carcinoma prostate), and RWPE-1 (human normal prostate). IC50 values of ZnONPs /CS -CAPE on all cells were found 2-fold lower than neat CAPE. Based on the FTIR data, the most significant spectral changes (lipid, protein, nucleic acids, glycogen) were monitored for the PC-3 and LnCaP cancer cells incubated with ZnONPs/CS-CAPE samples while being exposed to neat CAPE molecules caused small cellular changes when compared to RWPE-1 healthy cell lines. © 2024Review Citation - WoS: 5Citation - Scopus: 5Development and Functionalization of Electrospun Fiber Coated Thin Film Microextraction Devices for Rapid Mass Spectrometric Determination of Biologically Important Polar Molecules(Elsevier B.V., 2024) Eroğlu, Ahmet Emin; Salih,B.; Eroğlu,A.E.; Boyaci,E.; 01. Izmir Institute of Technology; 04.01. Department of Chemistry; 04. Faculty of ScienceRapid diagnosis of diseases is one of the challenging areas in clinical research. From the analytical chemist's perspective, the main challenges are isolating the compounds from the bio-specimen and lengthy analysis times. In this regard, solid phase microextraction offers a platform to address the abovementioned challenges. Moreover, its sharp tip-thin film geometry, known as coated blade spray (CBS), can enhance the extraction and act as an ionization source in direct mass spectrometric analysis. In this study, a new CBS device specifically designed for polar analytes was prepared and optimized to determine urinary metabolites. For this purpose, polyacrylonitrile (PAN) was selected as a base polymer as it can be electrospun to form a nanofibrous structure, and it can be modified with weak ion exchange moieties to interact with polar analytes. Following the electrospinning of PAN, hydrolysis was optimized, and conditions leading to sufficient extraction enhancement without dissolving the polymer were obtained when probes were treated with 5.0 M of NaOH for 2.5 h. Using the coated blades prepared as explained, the evaluation of various extraction conditions showed that 5 min is sufficient for equilibrium extraction. In addition, the solution's ionic strength and pH significantly affect the extraction. Optimum sorption was obtained at no salt added and pH 7.0 conditions. The CBS-MS optimization showed that 10.0 µL of ACN/MeOH/H2O (40:40:20, v/v/v) with formic acid kept for 15 seconds on the blade before voltage application leads to the highest signal. The limits of quantification of the analytes are between 50 and 100 ng/mL. © 2024 Elsevier B.V.Article Citation - WoS: 2Citation - Scopus: 2Small Angle X-Ray Scattering Analysis of Thermophilic Cytochrome P450 Cyp119 and the Effects of the N-Terminal Histidine Tag(Elsevier B.V., 2024) Sürmeli, Nur Başak; Sakallı,T.; Liu,G.; Sayers,Z.; Surmeli,N.B.; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringCombining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution. © 2024 Elsevier B.V.