PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
Browse
81 results
Search Results
Article Citation - WoS: 26Citation - Scopus: 33miRmoduleNet: Detecting miRNA-mRNA Regulatory Modules(Frontiers Media S.A., 2022-04-12) Yousef, Malik; Goy, Gokhan; Bakir-Gungor, BurcuIncreasing evidence that MicroRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis.Article Citation - WoS: 20Citation - Scopus: 24miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023-01-12) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, MalikDuring recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .Letter Citation - WoS: 18Yemen's Triple Emergency: Food Crisis Amid a Civil War and COVID-19 Pandemic(Elsevier, 2021-11) Hashim, Hashim Talib; Miranda, Adriana Viola; Babar, Maryam Salma; Essar, Mohammad Yasir; Hussain, Hasham; Ahmad, Shoaib; Basalilah, Ashraf Fhed MohammedYemen has been termed as the world's worst humanitarian crisis by the United Nations. About 20.1 million (more than 50% of population) Yemenis are facing hunger and 10 million are severely food insecure according to reports by the World Food Programme. With the spread of COVID-19, the situation in Yemen has worsened and humanitarian aid from other countries has become the basis of life for hundreds of thousands of Yemenis after the threat of famine. Yemen is practically one of the poorest countries in the world. It has structural vulnerabilities that have developed over a protracted period of conflict and poor governance and more than 50% live in starving, they suffer for getting one meal a day. To prevent a total collapse of Yemen's food crises, the government and the international community should act now more decisively.Article Citation - WoS: 13Citation - Scopus: 13Why Do Muse Stem Cells Present an Enduring Stress Capacity? Hints From a Comparative Proteome Analysis(MDPI, 2021-02-19) Acar, Mustafa B.; Aprile, Domenico; Ayaz-Guner, Serife; Guner, Huseyin; Tez, Coskun; Di Bernardo, Giovanni; Galderisi, UmbertoMuse cells are adult stem cells that are present in the stroma of several organs and possess an enduring capacity to cope with endogenous and exogenous genotoxic stress. In cell therapy, the peculiar biological properties of Muse cells render them a possible natural alternative to mesenchymal stromal cells (MSCs) or to in vitro-generated pluripotent stem cells (iPSCs). Indeed, some studies have proved that Muse cells can survive in adverse microenvironments, such as those present in damaged/injured tissues. We performed an evaluation of Muse cells' proteome under basic conditions and followed oxidative stress treatment in order to identify ontologies, pathways, and networks that can be related to their enduring stress capacity. We executed the same analysis on iPSCs and MSCs, as a comparison. The Muse cells are enriched in several ontologies and pathways, such as endosomal vacuolar trafficking related to stress response, ubiquitin and proteasome degradation, and reactive oxygen scavenging. In Muse cells, the protein-protein interacting network has two key nodes with a high connectivity degree and betweenness: NFKB and CRKL. The protein NFKB is an almost-ubiquitous transcription factor related to many biological processes and can also have a role in protecting cells from apoptosis during exposure to a variety of stressors. CRKL is an adaptor protein and constitutes an integral part of the stress-activated protein kinase (SAPK) pathway. The identified pathways and networks are all involved in the quality control of cell components and may explain the stress resistance of Muse cells.Article Citation - WoS: 6Citation - Scopus: 6WDR31 Displays Functional Redundancy With GTpase-Activating Proteins (GAPs) ELMOD and RP2 in Regulating Ift Complex and Recruiting the BBsome to Cilium(Life Science Alliance Llc, 2023-05-19) Cevik, Sebiha; Peng, Xiaoyu; Beyer, Tina; Pir, Mustafa S.; Yenisert, Ferhan; Woerz, Franziska; Kaplan, Oktay, IThe correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caeno-rhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumu-lations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into the cilia and exit from the cilia are impacted. Furthermore, anterograde IFT in the middle segment travels at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into the cilia of wdr-31;rpi-2;elmd-1, possibly because of IFT de-fects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.Article Citation - WoS: 15Citation - Scopus: 14Understanding Plasmon Coupling in Nanoparticle Dimers Using Molecular Orbitals and Configuration Interaction(Royal Soc Chemistry, 2019) Alkan, Fahri; Aikens, Christine M.We perform a theoretical investigation of the electronic structure and optical properties of atomic nanowire and nanorod dimers using DFT and TDDFT. In both systems at separation distances larger than 0.75 nm, optical spectra show a single feature that resembles the bonding dipole plasmon (BDP) mode. A configuration interaction (CI) analysis shows that the BDP mode arises from constructive coupling of transitions, whereas the destructive coupling does not produce significant oscillator strength for such separation distances. At shorter separation distances, both constructive and destructive coupling produce oscillator strength due to wave-function overlap, which results in multiple features in the calculated spectra. Our analysis shows that a charge-transfer plasmon (CTP) mode arises from destructive coupling of transitions, whereas the BDP results from constructive coupling of the same transitions at shorter separation distances. Furthermore, the coupling elements between these transitions are shown to depend heavily on the amount of exact Hartree-Fock exchange (HFX) in the functional, which affects the splitting of CTP and BDP modes. With 50% HFX or more, the CTP and BDP modes mainly merge into a single feature in the spectra. These findings suggest that the effects of exact exchange must be assessed during the prediction of CTP modes in plasmonic systems.Article Citation - WoS: 19Citation - Scopus: 19Understanding and Tailoring Excited State Properties in Solution-Processable Oligo(p-Phenyleneethynylene)s: Highly Fluorescent Hybridized Local and Charge Transfer Character via Experiment and Theory(Amer Chemical Soc, 2021-10-13) Usta, Hakan; Cosut, Bunyemin; Alkan, FahriRod-shaped oligo(p-phenyleneethynylene) (OPE) offers an attractive p-framework for the development of solution-processable highly fluorescent molecules having tunable hybridized local and charge transfer (HLCT) excited states and (reverse) intersystem crossing ((R)ISC) channels. Herein, an HLCT oligo(p-phenyleneethynylene) library was studied for the first time in the literature in detail systematically via experiment and theory. The design, synthesis, and full characterization of a new highly fluorescent (Phi(PL-solution) similar to 1) sky blue emissive 4',4 ''-((2,5-bis((2-ethylhexyl)oxy)-1,4-phenylene)bis(ethyne-2,1-diyl))bis(N,N-diphenyl-[1,1'-bi-phenyl]-4-amine) (2EHO-TPA-PE) was also reported. The new molecule consists of a D'-Ar-pi-D-pi-Ar-D' molecular architecture with an extended pi-spacer and no acceptor unit, and detailed structural, physicochemical, single-crystal, and optoelectronic characterizations were performed. A high solid-state quantum efficiency (Phi(PL-solution) similar to 0.8) was achieved as a result of suppressed exciton-phonon/vibronic couplings (no pi-pi interactions and multiple (14 per dimeric form) strong C-H center dot center dot center dot pi interactions). Strong solution-phase/solid-state dipole-dependent tunable excited state behavior (local excited (LE) -> HLCT -> charge transfer (CT)) and decay dynamics covering a wide spectral region were demonstrated, and the CT state was observed to be highly fluorescent despite extremely large Stokes shift (similar to 130 nm)/fwhm (similar to 125 nm) and significant charge separation (0.75 charge.nm). Employing the Lippert-Mataga model, along with detailed photophysical studies and TDDFT calculations, key relationships between molecular design-electronic structure-exciton characteristics were elucidated with regards to HLCT and hot exciton channel formations. The interstate coupling between CT and LE states and the interplay of this coupling with respect to medium polarity were explored. A key relationship between excited-state symmetry breaking process and the formation of HLCT state was discussed for TPA-ended rod-shaped OPE p-systems. (R)ISC-related delayed fluorescence (tau similar to 2-6 ns) processes were evident following the prompt decays (similar to 0.4-0.9 ns) both in the solution and in the solid-state. As a unique observation, the delayed fluorescence could be tuned and facilitated via small dielectric changes in the medium. Our results and the molecular engineering perspectives presented in this study may provide unique insights into the structural and electronic factors governing tunable excited state and hot-exciton channel formations in OPEs for (un)conventional solution-processed luminescence applications.Article Citation - WoS: 4Citation - Scopus: 4Transparent Films Made of Highly Scattering Particles(Amer Chemical Soc, 2020-01-13) Erdem, Talha; Yang, Lan; Xu, Peicheng; Altintas, Yemliha; O'Neil, Thomas; Caciagli, Alessio; Eiser, ErikaToday, colloids are widely employed in various products from creams and coatings to electronics. The ability to control their chemical, optical, or electronic features by controlling their size and shape explains why these materials are so widely preferred. Nevertheless, altering some of these properties may also lead to some undesired side effects, one of which is an increase in optical scattering upon concentration. Here, we address this strong scattering issue in films made of binary colloidal suspensions. In particular, we focus on raspberry-type polymeric particles made of a spherical polystyrene core decorated by small hemispherical domains of acrylate with an overall positive charge, which display an unusual stability against aggregation in aqueous solutions. Their solid films display a brilliant red color due to Bragg scattering but appear completely white on account of strong scattering otherwise. To suppress the scattering and induce transparency, we prepared films by hybridizing them with oppositely charged PS particles with a size similar to that of the bumps on the raspberries. We report that the smaller PS particles prevent raspberry particle aggregation in solid films and suppress scattering by decreasing the spatial variation of the refractive index inside the film. We believe that the results presented here provide a simple strategy to suppress strong scattering of larger particles to be used in optical coatings.Article Citation - WoS: 11Citation - Scopus: 12Towards Analysis and Optimization for Contact Zone Temperature Changes and Specific Wear Rate of Metal Matrix Composite Materials Produced From Recycled Waste(MDPI, 2021-09-08) Gunes, Aydin; Salur, Emin; Aslan, Abdullah; Kuntoglu, Mustafa; Giasin, Khaled; Pimenov, Danil Yurievich; Sahin, Omer SinanTribological properties are important to evaluate the in-service conditions of machine elements, especially those which work as tandem parts. Considering their wide range of application areas, metal matrix composites (MMCs) serve as one of the most significant materials equipped with desired mechanical properties such as strength, density, and lightness according to the place of use. Therefore, it is crucial to determine the wear performance of these materials to obtain a longer life and to overcome the possible structural problems which emerge during the production process. In this paper, extensive discussion and evaluation of the tribological performance of newly produced spheroidal graphite cast iron-reinforced (GGG-40) tin bronze (CuSn10) MMCs, including optimization, statistical, graphical, and microstructural analysis for contact zone temperature and specific wear rate, are presented. For this purpose, two levels of production temperature (400 and 450 degrees C), three levels of pressure (480, 640, and 820 MPa), and seven different samples reinforced by several ingredients (from 0 to 40 wt% GGG-40, pure CuSn10, and GGG-40) were investigated. According to the obtained statistical results, the reinforcement ratio is remarkably more effective on contact zone temperature and specific wear rate than temperature and pressure. A pure CuSn10 sample is the most suitable option for contact zone temperature, while pure GGG-40 seems the most suitable material for specific wear rates according to the optimization results. These results reveal the importance of reinforcement for better mechanical properties and tribological performance in measuring the capability of MMCs.Article Citation - WoS: 5Citation - Scopus: 10Three Dimensional Patient-Specific Guides for Guide Pin Positioning in Reverse Shoulder Arthroplasty: An Experimental Study on Different Glenoid Types(Sage Publications Ltd, 2022-01) Sadeghi, Majid Mohammad; Kececi, Emin Faruk; Kapicioglu, Mehmet; Aralasmak, Ayse; Tezgel, Okan; Basaran, Murat Alper; Bilsel, Kerem; Mohammad Sadeghi, MajidIntroduction Incorrect positioning is one of the main factors for glenoid component loosening in reverse shoulder arthroplasty and component placement can be challenging. This study aimed to assess whether Patient-Specific Instrumentation (PSI) provides better guide pin positioning accuracy and is superior to standard guided and freehand instrumentation methods in cases of glenoid bone deformity. Materials and Methods Based on the Walch classification, five different scapula types were acquired by computed tomography (CT). For each type, two different surgeons placed a guide pin into the scapula using three different methods: freehand method, conventional non-patient-specific guide, and PSI guide. Each method was repeated five times by both surgeons. In these experiments, a total of 150 samples of scapula models were used (5 x 2 x 3 x 5 = 150). Post-operative CT scans of the samples with the guide pin were digitally assessed and the accuracy of the pin placement was determined by comparison to the preoperative planning on a three-dimensional (3D) model. Results The PSI method showed accuracies to the preoperative plan of 2.68 (SD 2.10) degrees for version angle (p < .05), 2.59 (SD 2.68) degrees for inclination angle (p < .05), and 1.55 (SD 1.26) mm for entry point offset (p < .05). The mean and standard deviation errors compared to planned values of version angle, inclination angle, and entry point offset were statistically significant for the PSI method for the type C defected glenoid and non-arthritic glenoid. Conclusion Using the PSI guide created by an image processing software tool for guide pin positioning showed advantages in glenoid component positioning over other methods, for defected and intact glenoid types, but correlation with clinical outcomes should be examined.