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Article AlN Piezoelectric Quad-Actuators for 2D Optical Micro Scanning(Taylor & Francis Ltd, 2022) Hah, Dooyoung; 0000-0002-1290-0597; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiPiezoelectric actuation has been one of the frequent choices for optical micro scanning. In most of the cases, lead zirconate titanate (PZT) has been used as the piezoelectric material. However, PZT has a potential issue in biomedical applications due to the content of lead. For this, AlN can be used as an alternative. The main drawback of AlN is its low piezoelectric coefficients. In order to overcome such a drawback, this paper presents a novel actuator configuration, designed for a quasi-static operation mode. Quad-actuators and meander-shaped hinges are the essence of the proposed actuator configuration. Numerical simulation study is carried out to prove the concept of the device. The study also shows that the proposed scanner can have the optical scan angle of 9 degree at a quasi-static mode. Two different scan modes, a raster-like mode and a Lissajous mode are tested, demonstrating the two-dimensional scanning capability of the device.Article Citation - WoS: 2Citation - Scopus: 2Analysis of the Motion of a Rigid Rod on a Circular Surface Using Interpolated Variational Iteration Method(Yildiz Technical Univ, 2022) Coskun, Safa Bozkurt; Senturk, Erman; Atay, Mehmet Tarik; 01. Abdullah Gül University; 02.01. Mühendislik Bilimleri; 02. Mühendislik FakültesiIn this paper, interpolated variational iteration method (IVIM) is applied to investigate the vibration period and steady-state response for the motion of rigid rod rocking back and forth on a circular surface without slipping. The problem can be considered as a strongly nonlinear oscillator. In this solution procedure, analytical variational iteration technique is utilized by evaluating the integrals numerically. The approximate analytical results produced by the presented method are compared with the other existing solutions available in the literature. The advantage of using numerical evaluation of integrals, the method becomes fast convergent and a highly accurate solution can be obtained within seconds. The authors believe that the presented technique has potentially wide application in the other nonlinear oscillation problems.Book Part Citation - Scopus: 7ANT-M: Design of Passive Lower-Limb Exoskeleton for Weight-Bearing Assistance in Industry(Springer International Publishing, 2019) Guncan, Berkay; Unal, Ramazan; 01. Abdullah Gül UniversityThis study describes the optimized design of a passive lower limb exoskeleton for workers in the industry. The exoskeleton is aimed at helping workers who carry heavy loads, by supporting their posture and reducing stress in their knees which would prevent future injuries. However, most of the previous passive designs are insufficient in a way that they are bulky. Therefore, this study is focused on achieving lightweight passive exoskeleton. Topology optimization has been carried out to reach this goal. The results are validated using finite elements methods, in ANSYS environment. © 2018 Elsevier B.V., All rights reserved.Article Anticancer Effect of Ethanolic Yellow Hawthorn Extract on Chronic Myeloid Leukemia Cells and Acute Myeloid Leukemia Cells(Ondokuz Mayis Universitesi, 2025) Arslan, Ayşe Nur; Akçok, Ismail; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikCancer is a disease characterized by abnormal cell growth and invasion and metastasis of these cells to other tissues or organs of the body. Natural products have been used for centuries as drugs or in drug development, especially for the treatment of cancer. Besides, extracting natural products with several bioactive compounds has a promising effect on cancer treatment. In this study, we aimed to investigate the anticancer effect of the ethanolic extract of yellow hawthorn fruits on K562 (Chronic Myeloid Leukemia) and MOLM-13 (Acute Myeloid Leukemia) cell lines. The antiproliferative effect of the ethanolic extract of yellow hawthorn fruits was investigated in time-and dose-dependent manners. The Annexin-V/Propidium Iodide (PI) double staining was used to examine the apoptosis. Furthermore, cell cycle analysis is conducted by PI staining. The cell viability of K562 and MOLM-13 cell lines was significantly reduced by the ethanolic extract of yellow hawthorn fruits with IC50 values of 9144 µg/mL and 3515 µg/mL in 48-hour incubation time, respectively. Moreover, the results showed that the ethanolic extract of yellow hawthorn fruits caused an increased apoptosis by 12.7-and 8.87-fold changes in K562 and MOLM-13 cell lines compared to control groups, respectively. Ethanolic extract of yellow hawthorn fruit has reduced cell proliferation, induced apoptosis and arrested the cell cycle at G0/G1 phase by 71% in MOLM-13 and at G2/M phase by 80.3% and G0/G1 phase by 38.2 % in K562 cells. Further studies should be conducted to elucidate the mechanism of the effect of yellow hawthorn fruit on these cancer cells. © 2025 Elsevier B.V., All rights reserved.Article Apatinib Sensitizes Human Breast Cancer Cells Against Navitoclax and Venetoclax Despite Up-Regulated Bcl-2 and Mcl-1 Gene Expressions(Kare Publ, 2021) Kavakcioglu Yardimci, Berna; Ozgun Acar, Ozden; Semiz, Asli; Sen, Alaattin; 01. Abdullah Gül UniversityOBJECTIVE Defects in apoptotic cell death which restrict the success of conventional cytotoxic therapies have pivotal roles in a number of pathological conditions including cancer. However, a novel drug class targeting pro-survival Bcl-2 protein family members has been developed with the understanding of the structures and interactions of Bcl-2 proteins. Within this new class, Bcl-2/Bcl-xL inhibitor Navitoclax and Bcl-2 specific inhibitor Venetoclax have been shown to demonstrate strong anticancer activities on several types of cancers. But their low affinity to other anti-apoptotic proteins limits their clinical usage. Here, we investigated the cytotoxic and apoptotic effects of Navitoclax/Venetoclax and their combinations with specific tyrosine kinase inhibitor Apatinib on estrogen receptor (ER)-positive MCF-7 and ER-negative MDA-MB-231 breast cancer cell lines. METHODS MTT assay was used for the evaluation of the inhibition of cancer cell proliferation. ELISA test and Quantitative real-time PCR assay was performed to determine the role of caspase-3, Bak, Bax, Bcl-2, Bcl-xL and Mcl-1 proteins in the inhibition of cell proliferation triggered by the tested agents. RESULTS We found that aggressive MDA-MB-231 cell line was more sensitive to all tested agents. Apatinib significantly enhanced Navitoclax/Venetoclax mediated inhibition of cell viability in both cancer cell lines despite up-regulation in the expression levels of Bcl-2 and Mcl-1 genes. We further demonstrated significant Bak/Bax and caspase-3 expression in less aggressive MCF-7 cells. CONCLUSION Our findings have impacts on Navitoclax/Venetoclax plus Apatinib based therapy for breast adenocarcinoma. On the other hand, further studies should be conducted to elucidate the mechanisms underlying synergistic effects of Navitoclax/Venetoclax plus Apatinib combinations.Article Atatürk’ün Esir Aldığı Yunan General Nikolaos Trikupis ve Talas Üsera Garnizonu(Sabit Dokuyan, 2023) Karataş, Murat; Metin, Mehmet; 01. Abdullah Gül University; 10. RektörlükAfter the First World War, especially with the support of England, the Greek army invaded Anatolian lands on the way to realize Megali Idea (Greater Greece). The regular army of the Turkish Grand National Assembly established on the Western Front dealt the final blow to the Greek army with The Great Offensive and the Battle of the Commander –in-Chief. In addition to the Greek soldiers captured in the wars before this victory, many Greek soldiers, as well as the commander –in-chief of the Greek army, General Trikupis, and her entourage were also captured after the said victory. As the number of prisoners increased rapidly after The Great Offensive and the Battle of the Commander –in-Chief, the captive officers were transferred to Afyon, Kırşehir and Kayseri. Other military and civilian prisoners were transferred to different parts of Anatolia. Greek prisoners of war were kept in the prisoner garrisons until the implementation of the document on the mutual release of prisoners signed between the states of Turkey and Greece at the Lausanne Peace Conference. Only Greek Officers remained in Talas Prisoner Garrison, one of these prisoner garrisons. The Talas Prisoner Garrison was inspected twice by international Committee of the Red Cross. The delegation prepared reports on the condition of the prisoners and the garrison. In this study, the captivity of General Trikupis on the battlefield, the Talas Prisoner Garrison and situation of the captive Greek officers staying here, the aid of the Red Crescent Society to the prisoners will be emphasized. The Study was planned to be prepared by making use archival resources, memoirs, newspapers and copyright-reviewed works. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 1Citation - Scopus: 3Biosynthesis of Novel Naphthoquinone Derivatives in the Commonly-Used Chassis Cells Saccharomyces Cerevisiae and Escherichia Coli(Pleiades Publishing inc, 2021) Wu, W.; Wang, S.; Zhang, H.; Guo, W.; Lu, H.; Xu, H.; Sun, L.; 01. Abdullah Gül UniversityNaphthoquinones harboring 1,4-naphthoquinone pharmacophore are considered as privileged structures in medicinal chemistry. In pharmaceutical industry and fundamental research, polyketide naphthoquinones were widely produced by heterologous expression of polyketide synthases in microbial chassis cells, such as Saccharomyces cerevisiae and Escherichia coli. Nevertheless, these cell factories still remain, to a great degree, black boxes that often exceed engineers' expectations. In this work, the biotransformation of juglone or 1,4-naphthoquinone was conducted to generate novel derivatives and it was revealed that these two naphthoquinones can indeed be modified by the chassis cells. Seventeen derivatives, including 6 novel compounds, were isolated and their structural characterizations indicated the attachment of certain metabolites of chassis cells to naphthoquinones. Some of these biosynthesized derivatives were reported as potent antimicrobial agents with reduced cytotoxic activities. Additionally, molecular docking as simple and quick in silico approach was performed to screen the biosynthesized compounds for their potential antiviral activity. It was found that compound 11 and 17 showed the most promising binding affinities against Nsp9 of SARS-CoV-2, demonstrating their potential antiviral activities. Overall, this work provides a new approach to generate novel molecules in the commonly used chassis cells, which would expand the chemical diversity for the drug development pipeline. It also reveals a novel insight into the potential of the catalytic power of the most widely used chassis cells.Article Citation - Scopus: 7Cerium Oxide Nanoparticles Biosynthesized Using Fresh Green Walnut Shell in Microwave Environment and Their Anticancer Effect on Breast Cancer Cells(John Wiley and Sons Inc, 2022) Sulak, Mine; Turgut, Gurbet Çelik; Sen, Alaattin; 01. Abdullah Gül UniversityIn this study, cerium oxide nanoparticles (CONPs) were synthesized using fresh green walnut shell extract in microwave environment. The morphology and structure of the CONPs were determined using ultraviolet-visible (UV/VIS), attenuated total reflection-Fourier transform infrared (ATR-FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray (EDX) spectroscopy, and scanning electron microscopy (SEM). Crystal purple staining, Annexin V-FITC detection, RT-PCR, P53, and NF-κB luciferase reporter assays were performed to evaluate the mechanism of action of CONPs in breast cancer cell lines (MCF7). The biosynthesized CONPs showed cytotoxic effects and induced apoptosis in MCF7 cells. Furthermore, CONPs induced P53 expression and suppressed NF-κB gene expression, both of which were confirmed using reporter assays. Based on the present results, it was concluded that CONPs can induce apoptosis by acting on P53 at the transcriptional level and may cause cell death by suppressing NF-κB-mediated transcription. © 2022 Elsevier B.V., All rights reserved.Article Citation - WoS: 12Citation - Scopus: 14CO2 Emissions, Real GDP, Renewable Energy and Tourism: Evidence From Panel of the Most-Visited Countries(Cesky Statistical office, 2017) Dogan, Eyup; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri FakültesiPrevious studies on the energy-environment-growth literature overlook the investigation of the most-visited countries. Since these countries do not only belong to the largest economies and the top carbon dioxide (CO2) emitters in the world but are also listed in renewable energy country attractiveness index, this study analyzes the impacts of real GDP, renewable energy and tourism on the level of CO2 emissions for the top 10 most-visited countries. Applying several panel econometric approaches, we find out that renewable energy mitigates the pollution whereas real GDP and tourism contribute to the level of emissions. Thus, regulatory policies are necessary to increase the awareness of sustainable tourism. In addition, the use of renewable energy and the adoption of clean technologies in tourism sector as well as in producing goods and services play a significant role in CO2 mitigation.Conference Object Citation - Scopus: 2Colibri: An International Blended Learning Experience Based on Real-World Problems(University of Minho, 2016) Pedersen, Jens Myrup; Kuran, Mehmet Şükrü; Frick, Jan; Mank, Lea; 01. Abdullah Gül UniversityColibri is a European project funded by Erasmus+, where seven universities, a governmental organisation and two enterprises work together and explore new and innovative approaches to teaching. As part of the project we offer a joint course during the spring semester which was followed by 30 students in 2015. It contains both course and project activities. In this paper we describe our experiences from the project work, from the initial formulation of the project problems by the companies, over the organisation of the seminars and virtual collaboration phase to the final exams. The whole course was organised as follows: First there was a virtual kick-off meeting for all students and teachers. This was followed by a phase where students studied different modules online. Each student chooses an individual combination of modules that fits his/her background while also supporting the later project work. After the online modules, the students and teachers all meet physically for a week in Istanbul to finalize the modules and begin working on the real life projects provided by the enterprises. Then there was a period of virtual collaboration in the groups followed by the final seminar in Riga where everyone (students, teachers, and company representatives) met to finalize the projects, prepare for presentations/exams, and conduct examinations. Overall, the project was successful and received positive evaluations from the students, particularly regarding the international and interdisciplinary dimensions. On the other hand, we also learned how important it is to facilitate the collaboration, group work, and project planning during the first physical seminar. We found that it is both challenging and important to be very explicit about what exactly is expected from the students, as both students and supervisors have differing understandings of what a project is. Discussing the learning objectives with the students to obtain a common understanding can be a useful tool. © 2017 Elsevier B.V., All rights reserved.Conference Object Colorectal Cancer Prediction via Applying Recursive Cluster Elimination With Intra-Cluster Feature Elimination on Metagenomic Pathway Data(Springer International Publishing AG, 2024) Temiz, Mustafa; Kuzudisli, Cihan; Yousef, Malik; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik FakültesiAdvances in next-generation sequencing and in "-omics" technologies enable the characterization of the human gut microbiome. Colorectal cancer (CRC), the third most common cancer worldwide, is caused by genetic mutations, environmental influences, and abnormalities in the gut microbiota. The aim of this study is to identify pathways that influence host metabolism in CRC patients. The CRC-related metagenomic dataset used in this study contains the relative abundance values of 551 pathways calculated for 1262 samples. Here, two different approaches based on the feature grouping reduce the number of features by considering relevant features as groups, eliminate irrelevant features, and perform classification. The recursive cluster elimination with intra-cluster feature elimination (RCE-IFE) approach achieves anAUCof 0.72 using an average of 66.2 features on CRC-associated metagenomics dataset. In these experiments, P163-PWY: L-lysine fermentation to acetate and butanoate and PWY-6151: S-adenosyl-L-methionine cycle I pathways are identified as potential biomarkers associated with CRC. These experiments also reduce the number of features reported by both approaches in P163-PWY: L-lysine fermentation to acetate and butanoate and PWY-6151: Sadenosyl-L-methionine cycle I pathways reported by both approaches are considered possible CRC-related biomarkers. This study contributes to the molecular diagnosis and treatment of colorectal cancer by revealing the pathways associated with CRC. Our results are promising for the study of the gut microbiota and its role in CRC.Article Citation - WoS: 3Combined Effect of Midostaurin and Sphingosine Kinase-1 Inhibitor on FMS-Like Tyrosine Kinase 3 (FLT3) Wild Type Acute Myeloid Leukemia Cells(Walter de Gruyter Gmbh, 2022) Sahin, Hande Nur; Adan, Aysun; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve GenetikObjectives Therapeutic potential of clinically approved FLT3 inhibitor midostaurin has been neglected in wild-type FLT3 positive acute myeloid leukemia (AML). Sphingosine kinase-1 (SK-1) having anti-proliferative functions is studied in various cancers, but not in FLT3 wild-type AML. We aimed to develop new therapeutic strategies to combat FLT3 wild-type AML by combining midostaurin with SK-1 inhibitor (SKI II) in THP1 cells. Methods The anti-proliferative effects of midostaurin, SKI II and in combination on THP1 cells were determined by MTT assay. The combination indexes were calculated using calcusyn software. SK-1 expression and PARP cleavage were checked by western blot. Cell cycle distributions (PI staining) and apoptosis (annexin-V/PI dual staining) were assessed by flow cytometry for each agent alone and in combinations. Results Midostaurin decreased SK-1 protein level. Midostaurin, SKI II and certain combinations decreased cell viability in a dose dependent manner. The combined anti-leukemic effects of the aforementioned drug combination afforded additive effect. Co-administration induced both necrosis and apoptosis via phosphatidylserine externalization, PARP cleavage and cell cycle arrest at G0/G1 and S phases. Conclusions Targeting sphingosine kinase-1 together with FLT3 inhibition could be a novel mechanism to increase limited clinic response to midostaurin in wild-type FLT3 overexpressing AML after further pre-clinical studies.Article Citation - Scopus: 3Combined Effect of Midostaurin and Sphingosine Kinase-1 İnhibitor on FMS-Like Tyrosine Kinase 3 (FLT3) Wild Type Acute Myeloid Leukemia Cells(De Gruyter Open Ltd, 2022) Şahin, Hande Nur; Adan, Aysun; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve GenetikObjectives: Therapeutic potential of clinically approved FLT3 inhibitor midostaurin has been neglected in wild-type FLT3 positive acute myeloid leukemia (AML). Sphingosine kinase-1 (SK-1) having anti-proliferative functions is studied in various cancers, but not in FLT3 wild-type AML. We aimed to develop new therapeutic strategies to combat FLT3 wild-type AML by combining midostaurin with SK-1 inhibitor (SKI II) in THP1 cells. Methods: The anti-proliferative effects of midostaurin, SKI II and in combination on THP1 cells were determined by MTT assay. The combination indexes were calculated using calcusyn software. SK-1 expression and PARP cleavage were checked by western blot. Cell cycle distributions (PI staining) and apoptosis (annexin-V/PI dual staining) were assessed by flow cytometry for each agent alone and in combinations. Results: Midostaurin decreased SK-1 protein level. Midostaurin, SKI II and certain combinations decreased cell viability in a dose dependent manner. The combined anti-leukemic effects of the aforementioned drug combination afforded additive effect. Co-administration induced both necrosis and apoptosis via phosphatidylserine externalization, PARP cleavage and cell cycle arrest at G0/G1 and S phases. Conclusions: Targeting sphingosine kinase-1 together with FLT3 inhibition could be a novel mechanism to increase limited clinic response to midostaurin in wild-type FLT3 overexpressing AML after further pre-clinical studies. © 2022 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1Comparison of Mechanical and Physical Properties of Screed With and Without Expanded Polystyrene (EPS) Particles(Yildiz Technical University, 2022) Kiliç, Fikret Merih; Yorulmaz, Hediye; Özuzun, Sümeyye; Durak, Uğur; İLkentapar, Serhan; Karahan, Okan; Atis, C. D.; 01. Abdullah Gül University; 02.03. İnşaat Mühendisliği; 02. Mühendislik FakültesiIn this study, in order to observe the mechanical and physical properties of ordinary screed, sandy-lightweight screed and lightweight screed samples, expanded polystyrene (EPS) was used as fine aggregate and lightweight screed systems were produced by replacing sand at 100%, 50% and 0%. Samples of cement dosages of 250, 300, 350 kg/m3 were produced for lightweight screeds, sandy-lightweight screeds and ordinary screeds. Unit weight, water absorption capacity, flexural strength, compressive strength, fire resistance, abrasion and thermal conductivity tests were performed on the produced screed systems. As a result of the research, it was determined that as EPS ratio increases in screed system; unit weights decreased, water absorption rates increased. Besides, the flexural and compressive strengths, fire and abrasion resistance are also decreased. However, it was observed that the thermal conductivity coefficient reduced with the increment of EPS particles in the screed. In normal, sandy-lightweight and lightweight screeds, it was determined that as the cement dosage increased; the unit weights, flexural and compressive strengths, fire and abrasion resistance increased, water absorption capacity and the thermal conductivity coefficient decreased. © 2022 Elsevier B.V., All rights reserved.Conference Object Citation - Scopus: 2Comparison of Secondary Crushing Operations Through Cone and Horizontal Shaft Impact Crushers(International Multidisciplinary Scientific Geoconference, 2020) Köken, E.; Qu, Jili; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik FakültesiIndustrial size reduction processes such as crushing and grinding play vital roles in rock quarrying. The present study states real field data concerning secondary crushing operations through the cone and horizontal shaft impact (HSI) crushers. In this regard, a total of 44 case studies were collected from several rock quarries located in various parts of the world. Based on the field data, crushing performances of the cone and HSI crushers were compared by statistical analyses. The statistical analyses demonstrated that the specific energy consumption of HSI type crushers is relatively higher than those of cone crushers when comparing their production capacities. However, the difference in the specific energy consumption decreases with increasing the Los Angeles abrasion loss (LAA) of rocks. Specifically, the difference closes remarkably up when the LAA approaches 40%. It was also achieved that there is no remarkable superiority over the crushers with a specific energy consumption lower than 0.75 kWh/ton. Furthermore, the maximum feed size for cone and HSI crushers could be estimated at 12% of the mainframe opening and 39% of the rotor diameter, respectively. The ratios statistically found could be declared a start-up. These ratios are, therefore, beneficial for initial sizing related to secondary crushing operations. It was also claimed that for higher achievements in the production capacity (e.g.,> 8000 ton/day), cone crushers could be more feasible for handling rocks whose LAA is lower than 30%. Otherwise, the selection of secondary crushing equipment is associated with rock lithology, its reserve, economic constraints, targets, and marketplaces of rock aggregate manufacturers. © 2021 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 30Citation - Scopus: 30Compatibility of Superplasticizers With Limestone-Metakaolin Blended Cementitious System(Springer, 2015) Zaribaf, Behnaz H.; Uzal, Burak; Kurtis, Kimberley; 01. Abdullah Gül University; 02.03. İnşaat Mühendisliği; 02. Mühendislik FakültesiThis study investigates the performance of polycarboxylate ether (PCE), polymelamine sulfonate (PMS), sodium lignosulfonate and naphthalene formaldehyde condensate (PNS) superplasticizers (SPs) with ASTM C595 Type IL cement (with up to 15% calcium carbonate) combined with 10 and 30 % metakaolin (MK) substitutions by mass. The required dosage of each SP for 10 % and 30 % MK substitutions were determined based on mini slump test to establish equivalent paste flow. At these dosage rates, the effects of SPs on setting time, hydration kinetics, and strength development were measured. Life cycle assessment (LCA) was carried out on different cement compositions used in this study to evaluate the greenhouse gas emissions and embodied energy of limestone-metakaolin blended cement with SP addition. While MK substitution decreases the workability of samples and shortens the setting time, this study shows that adequate dosages of a compatible type of SP can be used to compensate for these effects. Of the SPs examined, PCE and PMS are found to be more compatible, compared to PNS and sodium lignosulfonate, with limestone-metakaolin blended cements.Article Comprehensive Prediction of FBN1 Targeting miRNAs: A Systems Biology Approach for Marfan Syndrome(Galenos Publ House, 2025) Orhan, Mehmet Emin; Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu Sacar; 02.01. Mühendislik Bilimleri; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikObjective: 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.Book Part Citation - Scopus: 4Computational Detection of Pre-MicroRNAs(Humana Press Inc., 2022) Saçar Demirci, Müşerref Duygu; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikMicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs is a vital element for investigating miRNA mediated posttranscriptional gene regulation machineries. Furthermore, experimental methods have challenging inadequacies in their capability to detect rare miRNAs, and are also limited to the state of the organism under examination (e.g., tissue type, developmental stage, stress-disease conditions). These issues have initiated the creation of high-level computational methodologies endeavoring to distinguish potential miRNAs in silico. On the other hand, most of these tools suffer from high numbers of false positives and/or false negatives and as a result they do not provide enough confidence for validating all their predictions experimentally. In this chapter, computational difficulties in detection of pre-miRNAs are discussed and a machine learning based approach that has been designed to address these issues is reviewed. © 2021 Elsevier B.V., All rights reserved.Book Part Citation - WoS: 19Citation - Scopus: 26Computational Prediction of Functional MicroRNA-mRNA Interactions(Humana Press Inc, 2019) Demirci, Muserref Duygu Sacar; Yousef, Malik; Allmer, Jens; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. BiyomühendislikProteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is driven by miRNAs acting as recognition sequences for their target mRNAs within a larger regulatory machinery. A miRNA can have many target mRNAs and an mRNA can be targeted by many miRNAs which makes it difficult to experimentally discover all miRNA-mRNA interactions. Therefore, computational methods have been developed for miRNA detection and miRNA target prediction. An abundance of available computational tools makes selection difficult. Additionally, interactions are not currently the focus of investigation although they more accurately define the regulation than pre-miRNA detection or target prediction could perform alone. We define an interaction including the miRNA source and the mRNA target. We present computational methods allowing the investigation of these interactions as well as how they can be used to extend regulatory pathways. Finally, we present a list of points that should be taken into account when investigating miRNA-mRNA interactions. In the future, this may lead to better understanding of functional interactions which may pave the way for disease marker discovery and design of miRNA-based drugs.Article Citation - Scopus: 1Control Over Performance of Qubit-Based Sensors(Institute for Problems in Mechanical Engineering, Russian Academy of Sciences dvv@msa.ipme.ru, 2018) Borisenok, S.; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik MühendisliğiThe extreme sensitivity of quantum systems towards the external perturbations and in the same time their ability to be strongly coupled to the measured target field makes them to be stable under the environmental noise. A high quality quantum sensor can be engineered even on the platform of a single trapped qubit. There is a variety of optimal and sub-optimal algorithms for effective control over the quantum system states. Here we discuss the opportunity to improve the efficiency of the external field quantum sensor based on a single qubit via its feedback tracking. © 2020 Elsevier B.V., All rights reserved.
