PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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Citation - WoS: 6
Citation - Scopus: 6
Absorption Enhancement by Semi-Cylindrical Structures for an Organic Solar Cell Application
(Optical Soc Amer, 2020) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
Organic solar cells are attractive for various applications with their flexibility and low-cost manufacturability. In order to increase their attractiveness in practice, it is essential to improve their energy conversion efficiency. In this work, semi-cylindrical-shell-shaped structures are proposed as one of the approaches, aiming at absorption enhancement in an organic solar cell. Poly(3-hexylthiophene-2,5-diyl) blended with indene-C60 bisadduct (P3HT:ICBA) is considered as the active layer. Light coupling to the guided modes and a geometrical advantage are attributed to this absorption enhancement. Finite-difference time-domain methods and finite element analysis are used to examine the absorption spectra for two types of devices, i.e., a debossed type and an embossed type. It is shown that absorption enhancement increases as the radius of the cylinder increases, but reaches a saturation at about 4-mu m radius. The average absorption enhancement with an active layer thickness of 200 nm and radius of 4 mu m, and for incidence angles between 0 degrees and 70 degrees, is found as 51%-52% for TE-polarized input and as 30%-33% for TM-polarized input when compared to a flat structure. Another merit of the proposed structures is that the range of incidence angles where the integrated absorption is at the level of the normal incidence is significantly broadened, reaching 70 degrees-80 degrees. This feature can be highly useful especially when organic solar cells are to be placed around a round object. The study results also exhibit that the proposed devices bear broadband absorption characteristics. (C) 2020 Optical Society of America
Citation - WoS: 34
Citation - Scopus: 38
Advances in Micelle-Based Drug Delivery: Cross-Linked Systems
(Bentham Science Publ Ltd, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
There are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.
Aerial Swarms: Recent Applications and Challenges
(Springer, 2021) Mohamed Abdelkader; Samet Güler; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Güler, Samet; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
Purpose of review: Currently, there is a large body of research on multi-agent systems addressing their different system theoretic aspects. Aerial swarms as one type of multi-agent robotic systems have recently gained huge interest due to their potential applications. However, aerial robot groups are complex multi-disciplinary systems and usually research works focus on specific system aspects for particular applications. The purpose of this review is to provide an overview of the main motivating applications that drive the majority of research works in this field, and summarize fundamental and common algorithmic components required for their development._x000D_ _x000D_ Recent findings: Most system demonstrations of current aerial swarms are based on simulations, some have shown experiments using few 10 s of robots in controlled indoor environment, and limited number of works have reported outdoor experiments with small number of autonomous aerial vehicles. This indicates scalability issues of current swarm systems in real world environments. This is mainly due to the limited confidence on the individual robot's localization, swarm-level relative localization, and the rate of exchanged information between the robots that is required for planning safe coordinated motions._x000D_ _x000D_ Summary: This paper summarizes the main motivating aerial swarm applications and the associated research works. In addition, the main research findings of the core elements of any aerial swarm system, state estimation and mission planning, are also presented. Finally, this paper presents a proposed abstraction of an aerial swarm system architecture that can help developers understand the main required modules of such systems.
Citation - WoS: 3
Citation - Scopus: 3
Alantolactone Ameliorates Graft Versus Host Disease in Mice
(Elsevier, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Serife; Cakir, Mustafa; Unal, Ekrem; 01. Abdullah Gül University
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naive (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2-18 (n = 4) and non-GVHD patients between ages 2-50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naive phenotype (CD62L+ CD44-). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Citation - WoS: 1
Analysis of the in Vitro Nanoparticle-Cell Interactions via a Smoothing-Splines Mixed-Effects Model
(Taylor & Francis Ltd, 2016) Dogruoz, Elifnur; Dayanik, Savas; Budak, Gurer; Sabuncuoglu, Ihsan; 01. Abdullah Gül University
A mixed-effects statistical model has been developed to understand the nanoparticle (NP)-cell interactions and predict the rate of cellular uptake of NPs. NP-cell interactions are crucial for targeted drug delivery systems, cell-level diagnosis, and cancer treatment. The cellular uptake of NPs depends on the size, charge, chemical structure, and concentration of NPs, and the incubation time. The vast number of combinations of these variable values disallows a comprehensive experimental study of NP-cell interactions. A mathematical model can, however, generalize the findings from a limited number of carefully designed experiments and can be used for the simulation of NP uptake rates, to design, plan, and compare alternative treatment options. We propose a mathematical model based on the data obtained from in vitro interactions of NP-healthy cells, through experiments conducted at the Nanomedicine and Advanced Technologies Research Center in Turkey. The proposed model predicts the cellular uptake rate of silica, polymethyl methacrylate, and polylactic acid NPs, given the incubation time, size, charge and concentration of NPs. This study implements the mixed-model methodology in the field of nanomedicine for the first time, and is the first mathematical model that predicts the rate of cellular uptake of NPs based on sound statistical principles. Our model provides a cost-effective tool for researchers developing targeted drug delivery systems.
Citation - WoS: 389
Citation - Scopus: 417
Analyzing the Environmental Kuznets Curve for the EU Countries: The Role of Ecological Footprint
(Springer Heidelberg, 2018) Destek, Mehmet Akif; Ulucak, Recep; Dogan, Eyup; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
A great majority of the environmental Kuznets curve (EKC) literature use CO2 emissions to proxy for environmental degradation. However, this is an important shortage in application of the EKC concept because environmental degradation cannot be captured by CO2 emissions only. By using a broader proxy, ecological footprint, this study aims to investigate the presence of environmental Kuznets curve hypothesis for the EU countries. The annual data from 1980 to 2013 is examined with second generation panel data methodologies which take into account the cross-sectional dependence among countries. The results show that there is U-shaped relationship between the real income and ecological footprint. In addition, non-renewable energy increases the environmental degradation while renewable energy and trade openness decrease the environmental degradation in the EU countries. Policy implications are further discussed.
Citation - WoS: 127
Citation - Scopus: 141
Analyzing the Nexus Between Energy Transition, Environment and ICT: A Step Towards COP26 Targets
(Academic Press Ltd- Elsevier Science Ltd, 2023) Tzeremes, Panayiotis; Dogan, Eyup; Alavijeh, Nooshin Karimi; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
In line with the Sustainable Development Goals and the recent COP26 summit, energy transition, low carbon emissions and technology have become extremely important subjects in the agenda of governments and poli-cymakers. The present study thus discusses the nexus between energy transition, economic growth, CO2 emis-sions and information and communications technology (ICT) in BRICS countries applying the novel GMM-PVAR method proposed on the annual data for the period 2000-2017. This method is strong to the issue of endogeneity which is commonly faced in the context of panel data analysis but mostly ignored in the literature. The findings of this research demonstrate that carbon emissions have a positive and significant effect on energy transition; similarly, raising economic growth augments the consumption of energy transition. Furthermore, ICT is found to be a significant choice in the development of energy transition and the solution of environmental challenges. Overall, technological factors in addition to economic and environmental factors also have great roles in the development of renewable energy and energy transition. Thus, results from this study call for government supports to develop ICT across the BRICS countries.
Citation - WoS: 9
Citation - Scopus: 10
An Answer to Colon Cancer Treatment by Mesenchymal Stem Cell Originated from Adipose Tissue
(Mashhad Univ Med Sciences, 2018) Iplik, Elif Sinem; Ertugrul, Baris; Kozanoglu, Ilknur; Baran, Yusuf; Cakmakoglu, Bedia; 01. Abdullah Gül University
Objective(s): Colon cancer is risen up with its complex mechanism that directly impacts on its treatment as well as its common prevalence. Mesenchymal stem cells (MSCs) have been considered as a therapeutic candidate for conventional disease including cancer. In this research, we have focused on apoptotic effects of adipose tissue-derived MSCs in colon cancer. Materials and Methods: MSCs were obtained from adipose tissue and characterized by Flowcytometer using suitable antibodies. MSCs, HT-29, HCT-116, RKO and healthy cell line MRC5 were cultured by different seeding procedure. After cell viability assay, changes in caspase 3 enzyme activity and the level of phosphatidylserine were measured. Results: For cell viability assay, a 48 hr incubation period was chosen to seed all cells together. There was a 1.36-fold decrease in caspase 3 enzyme activity by co-treatment of RKO and MSCs in addition to 2.02-fold decrease in HT-29 and MSCs co-treatment, and 1.103-fold increase in HCT-116 and MSCs. The results demonstrated that HCT-116 led to the highest rate of apoptotic cell death (7.5%) compared with other cells. Conclusion: We suggest that MSCs might remain a new treatment option for cancer by its differentiation and repair capacity.
Citation - Scopus: 4
Barriers to Strategy Implementation in Turkey’s Healthcare Industry: Hospital Manager Perspectives
(Informa UK Ltd, 2022) Ocak, Saffet; Aladag, Omer Faruk; Köseoglu, Mehmet Ali; King, Brian E.M.; 01. Abdullah Gül University
Although strategy implementation has profound implications for delivering efficient service, it has been largely neglected in the healthcare management literature. This study explores the barriers to effective implementation of strategic plans in healthcare organizations. To achieve this end, empirical data were collected from 185 hospital managers in Turkey using a survey-based methodology. A descriptive analysis was undertaken of the survey responses to determine the most important barriers to strategy implementation. The most significant barriers undermining strategy implementation efforts were found to be: low employee motivation, an exclusive focus on financial performance and lack of consensus among decision makers. © 2023 Elsevier B.V., All rights reserved.
Citation - WoS: 105
Citation - Scopus: 113
Bodipy-Based Semiconducting Materials for Organic Bulk Heterojunction Photovoltaics and Thin-Film Transistors
(Wiley-VCH Verlag GmbH, 2019) Ho, Dongil; Ozdemir, Resul; Kim, Hyungsug; Earmme, Taeshik; Usta, Hakan; Kim, Choongik; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
The rapid emergence of organic (opto)electronics as a promising alternative to conventional (opto)electronics has been achieved through the design and development of novel pi-conjugated systems. Among various semiconducting structural platforms, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) pi-systems have recently attracted attention for use in organic thin-films transistors (OTFTs) and organic photovoltaics (OPVs). This Review article provides an overview of the developments in the past 10 years on the structural design and synthesis of BODIPY-based organic semiconductors and their application in OTFT/OPV devices. The findings summarized and discussed here include the most recent breakthroughs in BODIPYs with record-high charge carrier mobilities and power conversion efficiencies (PCEs). The most up-to-date design rationales and discussions providing a strong understanding of structure-property-function relationships in BODIPY-based semiconductors are presented. Thus, this review is expected to inspire new research for future materials developments/applications in this family of molecules.
Citation - WoS: 43
Citation - Scopus: 44
Boronic Acid Moiety as Functional Defect in UiO-66 and Its Effect on Hydrogen Uptake Capacity and Selective Co2 Adsorption: a Comparative Study
(Amer Chemical Soc, 2018) Erkartal, Mustafa; Sen, Unal; 01. Abdullah Gül University
Herein, we use linker fragmentation approach to introduce boronic acid moieties as functional defects into Zr-based metal organic frameworks (MOFs, UiO-66). Our findings show that the amount of permanently incorporated boronic acid containing ligand is directly dependent on the synthesis method. The accessible boronic acid moieties in the pore surfaces significantly improve the hydrogen uptake values, which are 3.10 and 3.44 wt % at 21 bar, 77 K for dimethylformamide (DMF)/H2O and DMF/HCI synthesis methods, respectively. Also, CO2 selectivity of the resulting MOFs over N-2 and CH4 significantly increases due to the quadrupolar interaction between active surfaces and CO2 molecules. To the best of our knowledge, both hydrogen storage and selectivity of CO2 for UiO-66 are the highest reported values in the literature to date. Furthermore, another striking result that emerged from the high-pressure hydrogen uptake isotherms is the direct correlation between the defects and hysteric adsorption behavior, which may result in the shift from rigidity to flexibility of the framework due to the uncoordinated sites.
Citation - Scopus: 5
Building a Challenging Medical Dataset for Comparative Evaluation of Classifier Capabilities
(Elsevier Ltd, 2024) Bozkurt, Berat; Coskun, Kerem; Bakal, Gokhan; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Since the 2000s, digitalization has been a crucial transformation in our lives. Nevertheless, digitalization brings a bulk of unstructured textual data to be processed, including articles, clinical records, web pages, and shared social media posts. As a critical analysis, the classification task classifies the given textual entities into correct categories. Categorizing documents from different domains is straightforward since the instances are unlikely to contain similar contexts. However, document classification in a single domain is more complicated due to sharing the same context. Thus, we aim to classify medical articles about four common cancer types (Leukemia, Non-Hodgkin Lymphoma, Bladder Cancer, and Thyroid Cancer) by constructing machine learning and deep learning models. We used 383,914 medical articles about four common cancer types collected by the PubMed API. To build classification models, we split the dataset into 70% as training, 20% as testing, and 10% as validation. We built widely used machine-learning (Logistic Regression, XGBoost, CatBoost, and Random Forest Classifiers) and modern deep-learning (convolutional neural networks - CNN, long short-term memory - LSTM, and gated recurrent unit - GRU) models. We computed the average classification performances (precision, recall, F-score) to evaluate the models over ten distinct dataset splits. The best-performing deep learning model(s) yielded a superior F1 score of 98%. However, traditional machine learning models also achieved reasonably high F1 scores, 95% for the worst-performing case. Ultimately, we constructed multiple models to classify articles, which compose a hard-to-classify dataset in the medical domain. © 2024 Elsevier B.V., All rights reserved.
Citation - WoS: 2
Citation - Scopus: 3
Can Mesenchymal Stem/Stromal Cells and Their Secretomes Combat Bacterial Persisters
(Springer, 2023) Bicer, Mesude; Fidan, Ozkan; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
The increasing number of life-threatening infections caused by persister bacteria is associated with various issues, including antimicrobial resistance and biofilm formation. Infections due to persister cells are often difficult to suppress without the use of last-resort antibiotics. Throughout the world, bacterial persistence and resistance create an unmet clinical demand for the exploration of newly introduced therapeutic approaches. Mesenchymal stem / stromal cells (MSCs) have an antimicrobial activity to protect against bacterial infections, including those caused by bacterial persisters. MSCs have substantial potential to secrete antimicrobial peptides (AMPs), including cathelicidin, beta-defensins, lipocalin-2, hepcidin, indoleamine 2,3-dioxygenase (IDO), cysteine proteases, and inducible nitric oxide synthases (iNOS). MSCs possess the potential to contribute to innate immunity by regulating the immune response. Recently, MSCs and their secreted components have been reported to improve antimicrobial activity. Bactericidal activity by MSCs and their secretomes has been shown to be mediated in part by the secretion of AMPs. Even though they were discovered more than 80 years ago, therapeutic options for persisters are restricted, and there is an urgent need for alternative treatment regimens. Hence, this review intends to critically assess the current literature on the effects of MSCs and their secretomes on persister bacteria. MSCs and their secretome-based therapies could be preferred as an up-and-coming approach to reinforce the antimicrobial efficiency in persister infections.
Citation - Scopus: 4
CCPred: Global and Population-Specific Colorectal Cancer Prediction and Metagenomic Biomarker Identification at Different Molecular Levels Using Machine Learning Techniques
(Elsevier Ltd, 2024) Bakir-Güngör, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, Malik; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2′ 3′ cyclic 3′ phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED. © 2024 Elsevier B.V., All rights reserved.
Citation - WoS: 51
Citation - Scopus: 52
CdSe/ZnS Quantum Dot Films for High Performance Flexible Lighting and Display Applications
(IOP Publishing Ltd, 2016) Altintas, Yemliha; Genc, Sinan; Talpur, Mohammad Younis; Mutlugun, Evren; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
Colloidal quantum dots have attracted significant interest in recent years for lighting and display applications and have recently appeared in high-end market products. The integration of quantum dots with light emitting diodes has made them promising candidates for superior lighting applications with tunable optical characteristics. In this work we propose and demonstrate high quality colloidal quantum dots in their novel free-standing film forms to allow high quality white light generation to address flexible lighting and display applications. High quality quantum dots have been characterized using transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, steady state and time resolved photoluminescence and dynamic light scattering methods. The engineering of colloidal quantum dot composition and its optical properties in stand-alone film form has led to the experimentally high NTSC color gamut of 122.5 (CIE-1931) for display applications, color rendering index of 88.6, luminous efficacy of optical radiation value of 290 lm/W-opt and color temperature of 2763 K for lighting applications.
Citation - Scopus: 7
Cerium 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 University
In 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.
Citation - WoS: 1
Citation - Scopus: 1
Cinnamomum Zeylanicum Extract Incorporated Electrospun Poly(Lactic Acid)/ Gelatin Membrane as a New Wound Dressing
(Elsevier, 2025) Tarhan, Seray Zora; Pepe, Nihan Aktas; Sen, Alaattin; Isoglu, Ismail Alper; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
In this study, we fabricated poly(lactic acid)/gelatin electrospun membranes containing various concentrations of Cinnamomum zeylanicum extract and evaluated them as a novel wound dressing. The electrospun membranes were chemically, morphologically, and mechanically characterized, and the results were discussed in comparison with the literature. Electrospun membranes' biodegradability, swelling, and release properties were evaluated, with the CE7.5 membrane having values of 29.60 f 7.20 and 542.1 f 48.3 % and 66.9 %, respectively. Antibacterial activity was observed in CE7.5 and CE10 membranes against E. coli and S. aureus strains. At the highest concentration (CE10), 111.7 f 5.6 % and 96 f 12.375 % cell viability were detected in fibroblasts and differentiated LPS-induced THP-1 cells. Cell viability was further evaluated by Annexin-V/PI staining, revealing that 97.95 f 1.63 % of the cells remained viable in the CE7.5-treated membranes, while only 1.85 f 1.49 % of necrotic cells were detected in the treated cell population. Fibroblasts treated with the CE7.5 membrane showed a 42 % improvement in wound closure compared to non-treated cells. The anti-inflammatory properties of the electrospun membranes were also investigated. Treatment with the conditioned CE7.5 membrane downregulated Tba1 and tau proteins by 45.1 and 51.055 %, respectively. This study concluded that the newly developed Cinnamomum zeylanicum extract incorporated poly(lactic acid)/gelatin electrospun membranes could be a promising wound dressing material.
Citation - WoS: 933
Citation - Scopus: 963
Co2 Emissions, Real Output, Energy Consumption, Trade, Urbanization and Financial Development: Testing the EKC Hypothesis for the USA
(Springer Heidelberg, 2016) Dogan, Eyup; Turkekul, Berna; 01. Abdullah Gül University; 03.02. Ekonomi; 03. Yönetim Bilimleri Fakültesi
This study aims to investigate the relationship between carbon dioxide (CO2) emissions, energy consumption, real output (GDP), the square of real output (GDP(2)), trade openness, urbanization, and financial development in the USA for the period 1960-2010. The bounds testing for cointegration indicates that the analyzed variables are cointegrated. In the long run, energy consumption and urbanization increase environmental degradation while financial development has no effect on it, and trade leads to environmental improvements. In addition, this study does not support the validity of the environmental Kuznets curve (EKC) hypothesis for the USA because real output leads to environmental improvements while GDP(2) increases the levels of gas emissions. The results from the Granger causality test show that there is bidirectional causality between CO2 and GDP, CO2 and energy consumption, CO2 and urbanization, GDP and urbanization, and GDP and trade openness while no causality is determined between CO2 and trade openness, and gas emissions and financial development. In addition, we have enough evidence to support one-way causality running from GDP to energy consumption, from financial development to output, and from urbanization to financial development. In light of the long-run estimates and the Granger causality analysis, the US government should take into account the importance of trade openness, urbanization, and financial development in controlling for the levels of GDP and pollution. Moreover, it should be noted that the development of efficient energy policies likely contributes to lower CO2 emissions without harming real output.
A Comprehensive MicroRNA-seq Transcriptomic Analysis of Tay-Sachs Disease Mice Revealed Distinct miRNA Profiles in Neuroglial Cells
(Springernature, 2025) Kaya, Beyza; Orhan, Mehmet Emin; Yanbul, Selman; Demirci, Muserref Duygu Sacar; Demir, Secil Akyildiz; Seyrantepe, Volkan; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
Tay-Sachs disease (TSD) is a rare lysosomal storage disorder marked by the progressive buildup of GM2 in the central nervous system (CNS). This condition arises from mutations in the HEXA gene, which encodes the alpha subunit of the enzyme beta-hexosaminidase A. A newly developed mouse model for early-onset TSD (Hexa-/-Neu3-/-) exhibited signs of neurodegeneration and neuroinflammation, evidenced by elevated levels of pro-inflammatory cytokines and chemokines, as well as significant astrogliosis and microgliosis. Identifying disease-specific MicroRNAs (miRNAs) may aid the development of targeted therapies. Although previous small-scale studies have investigated miRNA expression in some regions of GM2 gangliosidosis mouse models, thorough profiling of miRNAs in this innovative TSD model remains to be done. In this study, we employed next-generation sequencing to analyze the complete miRNA profile of neuroglial cells from Hexa-/-Neu3-/- mice. By comparing KEGG and Reactome pathways associated with neurodegeneration, neuroinflammation, and sphingolipid metabolism in Hexa-/-Neu3-/- neuroglial cells, we discovered new MicroRNAs and their targets related to the pathophysiology of GM2 gangliosidosis. For the first time, our findings showed that miR-708-5p, miR-672-5p, miR-204-5p, miR-335-5p, and miR-296-3p were upregulated, while miR-10 b-5p, miR-615-3p, miR-196a-5p, miR-214-5p, and miR-199a-5p were downregulated in Hexa-/-Neu3-/- neuroglial cells in comparison to age-matched wild-type (WT). These specific changes in miRNA expression deepen our understanding of the disease's neuropathological characteristics in Hexa-/-Neu3-/- mice. Our study suggests that miRNA-based therapeutic strategies may improve clinical outcomes for TSD patients.
Citation - Scopus: 4
Computational Detection of Pre-MicroRNAs
(Humana Press Inc., 2022) Saçar Demirci, Müşerref Duygu; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
MicroRNA (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.

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