PubMed İndeksli Yayınlar Koleksiyonu

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

Browse

Now showing 1 - 20 of 108

3Mont: A Multi-Omics Integrative Tool for Breast Cancer Subtype Stratification
(Public Library Science, 2025) Unlu Yazici, Miray; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
Breast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular sub-types, Hormone Receptor negative (HR-) BRCA cases, especially Basal-like BRCA sub-types, lack estrogen and progesterone hormone receptors and they exhibit a higher tumor growth rate compared to HR+ cases. Improving survival time and predicting prognosis for distinct molecular profiles is substantial. In this study, we propose a novel approach called 3-Multi-Omics Network and Integration Tool (3Mont), which integrates various -omics data by applying a grouping function, detecting pro-groups, and assigning scores to each pro-group using Feature importance scoring (FIS) component. Following that, machine learning (ML) models are constructed based on the prominent pro-groups, which enable the extraction of promising biomarkers for distinguishing BRCA sub-types. Our tool allows users to analyze the collective behavior of features in each pro-group (biological groups) utilizing ML algorithms. In addition, by constructing the pro-groups and equalizing the feature numbers in each pro-group using the FIS component, this process achieves a significant 20% speedup over the 3Mint tool. Contrary to conventional methods, 3Mont generates networks that illustrate the interplay of the prominent biomarkers of different -omics data. Accordingly, exploring the concerted actions of features in pro-groups facilitates understanding the dynamics of the biomarkers within the generated networks and developing effective strategies for better cancer sub-type stratification. The 3Mont tool, along with all supporting materials, can be found at https://github.com/malikyousef/3Mont.git.
Citation - WoS: 12
Citation - Scopus: 14
4D-QSAR Investigation and Pharmacophore Identification of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Electron Conformational-Genetic Algorithm Method
(Taylor & Francis Ltd, 2016) Ozalp, A.; Yavuz, S. C.; Sabanci, N.; Copur, F.; Kokbudak, Z.; Saripinar, E.; 01. Abdullah Gül University
In this paper, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational-genetic algorithm (EC-GA) method as 4D-QSAR analysis. Using the data obtained from quantum chemical calculations at PM3/HF level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as the template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal the electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, the nonlinear least square regression method and genetic algorithm were performed. For four types of activity including the GI(50), TGI, LC50 and IC50 of the pyrrolo[2,1-c][1,4] benzodiazepine series, the r(train)(2), r(test)(2) and q(2) values were 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, 0.600; and 0.776, 0.722, 0.687, respectively.
Aguhyper: A Hyperledger-Based Electronic Health Record Management Framework
(PeerJ Inc, 2024) Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off -chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper ' s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identi fi ed in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper ' s implementation con fi gurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes signi fi cantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the fi eld.
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: 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 - 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 - 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: 2
Citation - Scopus: 2
Biochemical, Pharmacological, and Toxicological Attributes of Caper (Capparis Ovata) Flowering Buds and Berries Pickles
(Wiley, 2022) Ozgun-Acar, Ozden; Celik-Turgut, Gurbet; Guner, Huseyin; Sezer, Serdar; Sen, Alaattin; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve Genetik
Capparis ovata is a natural plant that grows widely in Turkey and its flowering buds and berry pickle are used in traditional medicine. Thus, the current study was expanded to evaluate the biochemical, pharmacological, and toxicological aspects of the Capparis ovata water extract (COWE). To determine the biochemical properties of COWE, mineral and fatty acid content, elemental analysis, flavonoid/phenolic content, radical-scavenging capacity, and pesticide analysis were performed. Furthermore, to find out whether it had anti-inflammatory properties, reverse transcription-polymerase chain reaction (RT-PCR) and nuclear factor kappa B (NF-kappa B) luciferase activity tests were conducted. Whole-genome transcriptomic profiling was carried out at a dose level of 500 mg/kg COWE to understand its pharmacological effect. Transaminases in serum were tested, and quantitative polymerase chain reaction (qPCR) was done using a custom design array that included the stress and molecular toxicology pathway to establish its toxicological qualities. As a result of the evaluations, it was observed that COWE has a high mineral and unsaturated fatty acid content, flavonoid/phenolic content, and radical-scavenging ability. It significantly inhibited NF-kappa B transcriptional activity as well as inflammatory cytokine expression in T-lymphoblast cells. Whole-genome transcriptomic profiling depicted that COWE modulates immune responses by upregulating natural killer cell activation, cellular response to type I interferon, B-cell proliferation and differentiation, and Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathways. Molecular Toxicology Pathfinder RT2 Profiler PCR array analysis revealed that COWE at or lower dose of 500 mg/kg/day did not cause a comparatively adverse effect. According to the findings, COWE is a rich source of nutrients and can be used as an adjunct therapy for various inflammatory diseases.
Citation - WoS: 17
Citation - Scopus: 27
Blockchain for Genomics and Healthcare: A Literature Review, Current Status, Classification and Open Issues
(PeerJ Inc, 2021) Dedeturk, Beyhan Adanur; Soran, Ahmet; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
The tremendous boost in the next generation sequencing technologies and in the "omics"technologies resulted in the generation of hundreds of gigabytes of data per day. Nowadays, via integrating -omics data with other data types, such as imaging and electronic health record (EHR) data, panomics studies attempt to identify novel and potentially actionable biomarkers for personalized medicine applications. In this respect, for the accurate analysis of -omics data and EHR, there is a need to establish secure and robust pipelines that take the ethical aspects into consideration, regulate privacy and ownership issues, and data sharing. These days, blockchain technology has picked up significant attention in diverse fields, including genomics, since it offers a new solution for these problems from a different perspective. Blockchain is an immutable transaction ledger, which offers secure and distributed system without a central authority. Within the system, each transaction can be expressed with cryptographically signed blocks, and the verification of transactions is performed by the users of the network. In this review, firstly, we aim to highlight the challenges of EHR and genomic data sharing. Secondly, we attempt to answer "Why"or "Why not"the blockchain technology is suitable for genomics and healthcare applications in detail. Thirdly, we elucidate the general blockchain structure based on the Ethereum, which is a more suitable technology for the genomic data sharing platforms. Fourthly, we review current blockchain-based EHR and genomic data sharing platforms, evaluate the advantages and disadvantages of these applications, and classify these applications using different metrics. Finally, we conclude by discussing the open issues and introducing our suggestion on the topic. In summary, to facilitate the diagnosis, monitoring and therapy of diseases with the effective analysis of -omics data with other available data types, through this review, we put forward the possible implications of the blockchain technology to life sciences and healthcare.
Citation - WoS: 6
Citation - Scopus: 7
BLSTM Based Night-Time Wildfire Detection From Video
(Public Library Science, 2022) Agirman, Ahmet K.; Tasdemir, Kasim; 01. Abdullah Gül University
Distinguishing fire from non-fire objects in night videos is problematic if only spatial features are to be used. Those features are highly disrupted under low-lit environments because of several factors, such as the dynamic range limitations of the cameras. This makes the analysis of temporal behavior of night-time fire indispensable for classification. To this end, a BLSTM based night-time wildfire event detection from a video algorithm is proposed. It is shown in the experiments that the proposed algorithm attains 95.15% of accuracy when tested against a wide variety of actual recordings of night-time wildfire incidents and 23.7 ms per frame detection time. Moreover, to pave the way for more targeted solutions to this challenging problem, experiment-based thorough investigations of possible sources of incorrect predictions and discussion of the unique nature of night-time wildfire videos are presented in the paper.
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: 53
Citation - Scopus: 55
Bond Energies of ThO+ and ThC+: A Guided Ion Beam and Quantum Chemical Investigation of the Reactions of Thorium Cation With O2 and CO
(AIP Publishing, 2016) Cox, Richard M.; Citir, Murat; Armentrout, P. B.; Battey, Samuel R.; Peterson, Kirk A.; 01. Abdullah Gül University
Kinetic energy dependent reactions of Th+ with O-2 and CO are studied using a guided ion beam tandem mass spectrometer. The formation of ThO+ in the reaction of Th+ with O-2 is observed to be exothermic and barrierless with a reaction efficiency at low energies of k/k(LGS) = 1.21 +/- 0.24 similar to the efficiency observed in ion cyclotron resonance experiments. Formation of ThO+ and ThC+ in the reaction of Th+ with CO is endothermic in both cases. The kinetic energy dependent cross sections for formation of these product ions were evaluated to determine 0 K bond dissociation energies (BDEs) of D-0(Th+-O) = 8.57 +/- 0.14 eV and D-0(Th+-C) = 4.82 +/- 0.29 eV. The present value of D-0(Th+-O) is within experimental uncertainty of previously reported experimental values, whereas this is the first report of D-0(Th+-C). Both BDEs are observed to be larger than those of their transition metal congeners, TiL+, ZrL+, and HfL+ (L = O and C), believed to be a result of lanthanide contraction. Additionally, the reactions were explored by quantum chemical calculations, including a full Feller-Peterson-Dixon composite approach with correlation contributions up to coupled-cluster singles and doubles with iterative triples and quadruples (CCSDTQ) for ThC, ThC+, ThO, and ThO+, as well as more approximate CCSD with perturbative (triples) [CCSD(T)] calculations where a semi-empirical model was used to estimate spin-orbit energy contributions. Finally, the ThO+ BDE is compared to other actinide (An) oxide cation BDEs and a simple model utilizing An(+) promotion energies to the reactive state is used to estimate AnO(+) and AnC(+) BDEs. For AnO(+), this model yields predictions that are typically within experimental uncertainty and performs better than density functional theory calculations presented previously. Published by AIP Publishing.
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: 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: 11
Citation - Scopus: 10
Clinical and Molecular Evaluation of MEFV Gene Variants in the Turkish Population: A Study by the National Genetics Consortium
(Springer Heidelberg, 2022) Dundar, Munis; Fahrioglu, Umut; Yildiz, Saliha Handan; Bakir-Gungor, Burcu; Temel, Sehime Gulsun; Akin, Haluk; Erdem, Levent; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

Browse

Browsing PubMed İndeksli Yayınlar Koleksiyonu by WoS Q "Q2"