WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Development of Resistant Starch Type-5 and Its Utilization in Cookie-Preparation(North University Center Baia Mare, 2025-11-30) Oskaybas-Emlek, Betul; Ozbey, Ayse; Kahraman, KevserThe objective of this study was the production of resistant starch type-5 (RS-5), its characterization, and utilization in cookie making. In first part of the study, the effects of starch-fatty acid complex formation (RS-5) between tapioca starch and lauric acid on the structure, digestibility, thermal and morphological properties of tapioca starch were investigated. X-ray diffraction revealed that the RS-5 had a V-type crystalline pattern. FT-IR analysis showed that a distinctive peak at 2846 cm-1 was only observed in RS-5. The resistant starch (RS) content of native starch increased from 22.76% to 28.02% with RS-5 formation. In the second part of the study, the RS-5 was added as a replacement for wheat flour with 10%, 20%, and 30% compared to control sample made with 100% wheat flour in cookie-making. The effects of RS-5 replacement of cookie samples on some physicochemical, estimated glycemic index (eGI) value, physical, and hardness properties were determined. Compared to control cookie, the cookie samples included RS-5 had lower hardness value, higher spread ratio. The eGI value of cookie samples was slightly decreased with the replacement with RS-5. The results demonstrated that the RS-5 has good potential for developing softer cookie with no adverse impact on eGI value.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 Developing a Label Propagation Approach for Cancer Subtype Classification Problem(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, MustafaCancer 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.Editorial What Does the Water Inside the Brain Tell Us? Diffusion Tensor Imaging(Sciendo, 2018-10-01) Acer, Niyazi; Dundar, Mehmet Sait; Bastepe-Gray, SerapThe brain consist of about 75 percent water. Diffusion tensor imaging (DTI) is an advanced magnetic resonance (MR) technique imaging that has been developed for diagnostic and research in medicine. It can be use DTI tractography to better understand degenerating axons of white matter lesions in some neurological diseases such as MS, AD, trauma, cerebral ischemia, epilepsy, brain tumors and metabolic disorders.Article Target Attractor Formed via Fractional Feedback Control(Yildiz Technical Univ, 2021) Borisenok, SergeyWe discuss here the stabilization problem for an ordinary differential equation (ODE) dynamical model. To make such a control, one can form a Kolesnikov's subset attracting the phase trajectories to its neighborhood in the phase space via defining the appropriate feedback signal. Kolesnikov's target attractor algorithm provides the exponential convergence, but at the same time it demands the permanent power supply pumping the energy to the system even if the control goal is achieved. To decrease the power cost of Kolesnikov's control, we re-formulate the feedback in the form of Caputo's fractional derivative. In this case the solution to the ODE together with the feedback control signal could be found with the Rida-Arafa method based on the generalized Mittag-Leffler function. We prove that for the certain constraints over the initial condition and the target stabilization level, the integer-dimensional Kolesnikov algorithm can be replaced with the fractional target attractor feedback to provide the minimal power cost.Conference Object Citation - WoS: 17Citation - Scopus: 21Sol-Gel Applications for Ceramic Membrane Preparation(Amer Inst Physics, 2017) Erdem, I.Ceramic membranes possessing superior properties compared to polymeric membranes are more durable under severe working conditions and therefore their service life is longer. The ceramic membranes are composed of some layers. The support is the layer composed of coarser ceramic structure and responsible for mechanical durability under filtration pressure and it is prepared by consolidation of ceramic powders. The top layer is composed of a finer ceramic micro-structure mainly responsible for the separation of components present in the fluid to be filtered and sol-gel method is a versatile tool to prepare such a tailor-made ceramic filtration structure with finer pores. Depending on the type of filtration (e.g. micro-filtration, ultra-filtration, nano-filtration) aiming separation of components with different sizes, sols with different particulate sizes should be prepared and consolidated with varying precursors and preparation conditions. The coating of sol on the support layer and heat treatment application to have a stable ceramic micro-structure are also important steps determining the final properties of the top layer. Sol-gel method with various controllable parameters (e.g. precursor type, sol formation kinetics, heat treatment conditions) is a practical tool for the preparation of top layers of ceramic composite membranes with desired physicochemical properties.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: 4Citation - Scopus: 5Recovery of Manganese From Spent Batteries Using Activated Carbon Powder as Reductant in Sulfuric Acid Solution(Asian Journal of Chemistry, 2013) Kursunoglu, Sait; Kaya, MuammerRecovery of manganese from spent batteries was investigated using activated carbon powder as a reducing agent in sulfuric acid solution. The effects of four different leaching parameters (sulfuric acid concentration, amount of activated carbon powder, temperature and time) on the leaching of manganese from spent batteries were investigated using central composite design technique. The maximum manganese recovery conditions were determined as 1 M of sulfuric acid concentration, 3 g of activated carbon powder, 80 degrees C of temperature and 3 h of leaching time. Under these conditions, the recovery of manganese was 86.39 % and pH value of the solution was 0.77. According to the reductive acid leaching results, an empirical second order equation for manganese recovery based on four investigated parameters was calculated. The observed values of manganese recoveries using model equation were found to be in a good agreement with the predicted values (R-2 = 0.92).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: 1Citation - Scopus: 2Protocol for Determining the Average Speed and Frequency of Kinesin and Dynein-Driven Intraflagellar Transport (IFT) in C. Elegans(Elsevier, 2022-09) Turan, Merve G.; Kantarci, Hanife; Temtek, Sadiye D.; Cakici, Onur; Cevik, Sebiha; Kaplan, Oktay, IHere, we present a protocol to image a fluorescent-labeled intraflagellar trans-port (IFT) component in Caenorhabditis elegans with fluorescence microscopy, including steps of sample preparations, in vivo live-cell imaging, and post -micro-scopy analysis with kymographs. This protocol breaks down all processes into three categories: (1) pre-imaging preparations, (2) preparations for the time of image acquisition, and (3) post-imaging analyses. The protocol can be applied to determine the speed and frequency of moving particles. For complete details on the use and execution of this protocol, please refer to Cevik et al. (2021).