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.
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 - Scopus: 1
Alzheimer Disease Associated Loci: APOE Single Nucleotide Polymorphisms in Marmara Region
(MDPI, 2024) Ismail, Aya Badeea; Dundar, Mehmet Sait; Erguzeloglu, Cemre Ornek; Ergoren, Mahmut Cerkez; Alemdar, Adem; Sag, Sebnem Ozemri; Temel, Sehime Gulsun; 01. Abdullah Gül University
Alzheimer's disease (AD) is a major global health challenge, especially among individuals aged 65 or older. According to population health studies, Turkey has the highest AD prevalence in the Middle East and Europe. To accurately determine the frequencies of common and rare APOE single nucleotide polymorphisms (SNPs) in the Turkish population residing in the Marmara Region, we conducted a retrospective study analyzing APOE variants in 588 individuals referred to the Bursa Uludag University Genetic Diseases Evaluation Center. Molecular genotyping, clinical exome sequencing, bioinformatics analysis, and statistical evaluation were employed to identify APOE polymorphisms and assess their distribution. The study revealed the frequencies of APOE alleles as follows: epsilon 4 at 9.94%, epsilon 2 at 9.18%, and epsilon 3 at 80.68%. The gender-based analysis in our study uncovered a tendency for females to exhibit a higher prevalence of mutant genotypes across various SNPs. The most prevalent haplotype observed was epsilon 3/epsilon 3, while rare APOE SNPs were also identified. These findings align with global observations, underscoring the significance of genetic diversity and gender-specific characteristics in comprehending health disparities and formulating preventive strategies.
Citation - WoS: 4
Citation - Scopus: 5
Analysis of Coronary Angiography Related Psychophysiological Responses
(BMC, 2011) Okkesim, Sukru; Kara, Sadik; Kaya, Mehmet G.; Asyali, Musa H.; 01. Abdullah Gül University
Background: Coronary angiography is an important tool in diagnosis of cardiovascular diseases. However, it is the administration is relatively stressful and emotionally traumatic for the subjects. The aim of this study is to evaluate psychophysiological responses induced by the coronary angiography instead of subjective methods such as a questionnaire. We have also evaluated the influence of the tranquilizer on the psychophysiological responses. Methods: Electrocardiography (ECG), Blood Volume Pulse (BVP), and Galvanic Skin Response (GSR) of 34 patients who underwent coronary angiography operation were recorded. Recordings were done at three phases: "1 hour before," "during," and "1 hour after" the coronary angiography test. Total of 5 features obtained from the physiological signals were compared across these three phases. Sixteen of the patients were administered 5 mg of a tranquilizer (Diazepam) before the operation and remaining 18 were not. Results: Our results indicate that there is a strong correlation between features (LF/HF, Bk, DN1/DN2, skin conductance level and seg_mean) in terms of reflecting psychophysiological responses. However only DN1/DN2 feature has statistically significant differences between angiography phases (for diazepam: p = 0.0201, for non_diazepam p = 0.0224). We also note that there are statistically significant differences between the diazepam and non-diazepam groups for seg_mean features in "before", "during" and "after" phases (p = 0.0156, 0.0282, and 0.0443, respectively). Conclusions: The most intense sympathetic activity is observed in the "during" angiography phase for both of the groups. The obtained features can be used in some clinical studies where generation of the customized/individual diagnoses styles and quantitative evaluation of psychophysiological responses is necessary.
Citation - WoS: 10
Citation - Scopus: 11
Analyzing the Genetic Diversity and Biotechnological Potential of Leuconostoc Pseudomesenteroides by Comparative Genomics
(Frontiers Media S.A., 2023) Gumustop, Ismail; Ortakci, Fatih; 01. Abdullah Gül University
Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species' genetic diversity and biotechnological potential. A mere similar to 12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.
Citation - WoS: 50
Citation - Scopus: 62
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
(MDPI, 2021) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.
Citation - WoS: 7
Citation - Scopus: 7
Assessment of Bohme Abrasion Value of Natural Stones Through Artificial Neural Networks (ANN)
(MDPI, 2022) Strzalkowski, Pawel; Koken, Ekin; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
This present study explored the Bohme abrasion value (BAV) of natural stones through artificial neural networks (ANNs). For this purpose, a detailed literature survey was conducted to collect quantitative data on the BAV of different natural stones from Turkey. As a result of the ANN analyses, several predictive models (M1-M13) were established by using the rock properties, such as the dry density (rho(d)), water absorption by weight (w(a)), Shore hardness value (SHV), pulse wave velocity (V-p), and uniaxial compressive strength (UCS) of rocks. The performance of the established predictive models was evaluated by using several statistical indicators, and the performance analyses indicated that four of the established models (M1, M5, M10, and M11) could be reliably used to estimate the BAV of natural stones. In addition, explicit mathematical formulations of the proposed ANN models were also introduced in this study to let users implement them more efficiently. In this context, the present study is believed to provide practical and straightforward information on the BAV of natural stones and can be declared a case study on how to model the BAV as a function of different rock properties.
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: 1
Benefiting From Both Ethanol Oxidation and Bidentate Thiol Groups of DHLA Ligands Under Photoirradiation for Synthesis of Au Nanoparticles With Their Catalytic and Peroxidase Like Activity
(Amer Chemical Soc, 2025) Temur, Nimet; Dadi, Seyma; Dogan, Ayse Nur; Nisari, Mustafa; Avan, Ilker; Ocsoy, Ismail; 01. Abdullah Gül University
In this work, we rationally synthesized quite stable gold nanoparticles (AuNPs) using dihydrolipoic acid (DHLA) and DHLA-aspartame (DHLA-Asptm) as both reducing and stabilizing agents in a mixture of water/ethanol at RT under photoirradiation in 10 min. The novelty of this work is that benefiting from both the oxidation of ethanol to ethanal and having the bidentate thiol groups of DHLA, stable DHLA@AuNPs and DHLA-Asptm@AuNPs were successfully and rapidly formed without additional reducing reagents. We systematically examined the formation of DHLA@AuNPs and DHLA-Asptm@AuNPs under different pH values and reaction temperatures. Furthermore, the salt tolerance of DHLA@AuNPs and DHLA-Asptm@AuNPs was tested in a series of sodium chloride solutions. We showed the catalytic and peroxidase-like activities of DHLA@AuNPs against 4-nitrophenol and 3,3 ',5,5 '-tetramethylbenzidine. The AuNPs were characterized by UV-vis spectrophotometry, scanning transmission electron microscopy, zeta potential, and dynamic light scattering.
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: 5
Citation - Scopus: 6
BRCA Variations Risk Assessment in Breast Cancers Using Different Artificial Intelligence Models
(MDPI, 2021) Senturk, Niyazi; Tuncel, Gulten; Dogan, Berkcan; Aliyeva, Lamiya; Dundar, Mehmet Sait; Ozemri Sag, Sebnem; Ergoren, Mahmut Cerkez; 01. Abdullah Gül University
Artificial intelligence provides modelling on machines by simulating the human brain using learning and decision-making abilities. Early diagnosis is highly effective in reducing mortality in cancer. This study aimed to combine cancer-associated risk factors including genetic variations and design an artificial intelligence system for risk assessment. Data from a total of 268 breast cancer patients have been analysed for 16 different risk factors including genetic variant classifications. In total, 61 BRCA1, 128 BRCA2 and 11 both BRCA1 and BRCA2 genes associated breast cancer patients' data were used to train the system using Mamdani's Fuzzy Inference Method and Feed-Forward Neural Network Method as the model softwares on MATLAB. Sixteen different tests were performed on twelve different subjects who had not been introduced to the system before. The rates for neural network were 99.9% for training success, 99.6% for validation success and 99.7% for test success. Despite neural network's overall success was slightly higher than fuzzy logic accuracy, the results from developed systems were similar (99.9% and 95.5%, respectively). The developed models make predictions from a wider perspective using more risk factors including genetic variation data compared with similar studies in the literature. Overall, this artificial intelligence models present promising results for BRCA variations' risk assessment in breast cancers as well as a unique tool for personalized medicine software.
Burg-Aided 2D MIMO Array Extrapolation for Improved Spatial Resolution
(MDPI, 2025) Bekar, Muge; Bekar, Ali; Pirkani, Anum; Baker, Christopher John; Gashinova, Marina; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
In this paper, the extrapolation of a 2D multiple-input multiple-output (MIMO) array is proposed using the Burg algorithm to achieve higher angular resolution beyond that of the corresponding 2D MIMO virtual array. The main advantage of such an approach is that it allows us to dramatically decrease both the physical size and the number of antenna elements of the MIMO array. The performance and limitations of the Burg algorithm are examined through both simulation and experimentation at 77 GHz. The experimental methodology used to acquire 3D data of range, azimuth and elevation information with the 1D MIMO off-the-shelf radar is described. Using this method, the performance of the proposed array can be tested experimentally, especially at frequencies where it is desired to assess the antenna response prior to fabricating the antenna.
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 - WoS: 5
Citation - Scopus: 6
Capturing B Type Acute Lymphoblastic Leukemia Cells Using Two Types of Antibodies
(Wiley, 2019) Icoz, Kutay; Gercek, Tayyibe; Murat, Ayseguel; Ozcan, Servet; Unal, Ekrem; 01. Abdullah Gül University
One way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. (c) 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019
Citation - WoS: 2
Citation - Scopus: 2
Cation Exchange Mediated Synthesis of Bright Au@ZnTe Core-Shell Nanocrystals
(IOP Publishing Ltd, 2021) Sadeghi, Sadra; Melikov, Rustamzhon; Sahin, Mehmet; Nizamoglu, Sedat; 01. Abdullah Gül University; 02.02. Endüstri Mühendisliği; 02. Mühendislik Fakültesi
The synthesis of heterostructured core-shell nanocrystals has attracted significant attention due to their wide range of applications in energy, medicine and environment. To further extend the possible nanostructures, non-epitaxial growth is introduced to form heterostructures with large lattice mismatches, which cannot be achieved by classical epitaxial growth techniques. Here, we report the synthetic procedure of Au@ZnTe core-shell nanostructures by cation exchange reaction for the first time. For that, bimetallic Au@Ag heterostructures were synthesized by using PDDA as stabilizer and shape-controller. Then, by addition of Te and Zn precursors in a step-wise reaction, the zinc and silver cation exchange was performed and Au@ZnTe nanocrystals were obtained. Structural and optical characterization confirmed the formation of the Au@ZnTe nanocrystals. The optimization of the synthesis led to the bright nanocrystals with a photoluminescence quantum yield up to 27%. The non-toxic, versatile synthetic route, and bright emission of the synthesized Au@ZnTe nanocrystals offer significant potential for future bio-imaging and optoelectronic applications.
Citation - WoS: 2
Citation - Scopus: 2
CC2D1A Causes Ciliopathy, Intellectual Disability, Heterotaxy, Renal Dysplasia, and Abnormal CSF Flow
(Life Science Alliance Llc, 2024) Kim, Angelina Haesoo; Sakin, Irmak; Viviano, Stephen; Tuncel, Gulten; Aguilera, Stephanie Marie; Goles, Gizem; Deniz, Engin; 01. Abdullah Gül University
Intellectual and developmental disabilities result from abnormal nervous system development. Over a 1,000 genes have been associated with intellectual and developmental disabilities, driving continued efforts toward dissecting variant functionality to enhance our understanding of the disease mechanism. This report identified two novel variants in CC2D1A in a cohort of four patients from two unrelated families. We used multiple model systems for functional analysis, including Xenopus, Drosophila, and patient-derived fibroblasts. Our experiments revealed that cc2d1a is expressed explicitly in a spectrum of ciliated tissues, including the left-right organizer, epidermis, pronephric duct, nephrostomes, and ventricular zone of the brain. In line with this expression pattern, loss of cc2d1a led to cardiac heterotaxy, cystic kidneys, and abnormal CSF circulation via defective ciliogenesis. Interestingly, when we analyzed brain development, mutant tadpoles showed abnormal CSF circulation only in the midbrain region, suggesting abnormal local CSF flow. Furthermore, our analysis of the patient-derived fibroblasts confirmed defective ciliogenesis, further supporting our observations. In summary, we revealed novel insight into the role of CC2D1A by establishing its new critical role in ciliogenesis and CSF circulation.
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 - WoS: 417
Citation - Scopus: 462
Cell Proliferation and Cytotoxicity Assays
(Bentham Science Publ Ltd, 2016) Adan, Aysun; Kiraz, Yagmur; Baran, Yusuf; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve Genetik
Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.
Citation - WoS: 24
Citation - Scopus: 24
Circular RNA-MicroRNA Interaction Predictions in SARS-CoV Infection
(Walter de Gruyter Gmbh, 2021) Demirci, Yilmaz Mehmet; Demirci, Muserref Duygu Sacar; 01. Abdullah Gül University; 02.01. Mühendislik Bilimleri; 02. Mühendislik Fakültesi; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
Different types of noncoding RNAs like MicroRNAs (miRNAs) and circular RNAs (circRNAs) have been shown to take part in various cellular processes including post-transcriptional gene regulation during infection. MiRNAs are expressed by more than 200 organisms ranging from viruses to higher eukaryotes. Since miRNAs seem to be involved in host-pathogen interactions, many studies attempted to identify whether human miRNAs could target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNAs as an antiviral defence mechanism. In this work, a machine learning based miRNA analysis work flow was developed to predict differential expression patterns of human miRNAs during SARS-CoV-2 infection. In order to obtain the graphical representation of miRNA hairpins, 36 features were defined based on the secondary structures. Moreover, potential targeting interactions between human circRNAs and miRNAs as well as human miRNAs and viral mRNAs were investigated.

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