PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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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: .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: 13Citation - Scopus: 14Unravelling the Moderating Roles of Environmental Regulations on the Impact of Foreign Direct Investment on Environmental Sustainability(Academic Press Ltd- Elsevier Science Ltd, 2025-02) Ehigiamusoe, Kizito Uyi; Chen, Danqing; Dogan, Eyup; Binsaeed, Rima H.In the era of economic globalization, China attracts significant foreign direct investment (FDI) to accelerate economic prosperity. FDI inflows could have ramifications on environmental degradation (ED) despite the enactment of different environmental regulations (ERs) such as market-incentive, command-and-control as well as informal regulations. Though some studies have shown that FDI and ED have significant relationship, the moderating roles of different ERs on the environmental impact of FDI has not been empirically unraveled. This study fills this research gap by analyzing the direct impact of FDI on ED (i.e., carbon dioxide emissions, ecological footprint) using the provincial panel data. Second, it unravels the moderating roles of different ERs on the environmental impact of FDI in the provinces and regions. The results indicate that FDI directly mitigates ED, verifying the pollution halo hypothesis while ERs directly alleviate ED in China. However, the interaction between FDI and ERs do not alleviate ED in China albeit regional heterogeneity exist. The economic implication is that FDI is not a channel through which ERs enhance environmental sustainability in China. This study recommends some policy options arising from the findings.Article Citation - WoS: 11Citation - Scopus: 10UV Light Promoted Dihydrolipoic Acid and Its Alanine Derivative Directed Rapid Synthesis of Stable Gold Nanoparticles and Their Catalytic Activity(Nature Portfolio, 2024-10-21) Temur, Nimet; Dadi, Seyma; Nisari, Mustafa; Ucuncuoglu, Neslihan; Avan, Ilker; Ocsoy, IsmailIn general, colloidal gold nanoparticles (AuNPs) have been synthesized in heated or boiling water containing HAuCl4 precursor with sodium citrate as reducing stabilizing reagent. Although temperature plays a driving for synthesis of AuNPs, elevated temperature in thermal reduction method causes aggregation of the AuNPs. The preferential, rapid and strong binding of dihydro-lipoic acid and its derivatives on surface of AuNPs via thiol - Au chemistry promote the production of very stable AuNPs. In this study, we have developed citric acid (CA), dihydrolipoic acid (DHLA) and DHLA-Alanine (DHLA-Ala) directed rapid synthesis of ultra-stable AuNPs, DHLA@AuNPs and DHLA-Ala@AuNPs, under the UV (311 nm) irradiation at room temperature (RT: 25 degrees C) in around 10 min (min). CA is used as a potential reducing agent to expedite both reduction of Au3+ ion and AuNP formation, DHLA and DHLA-Ala act as stabilizing agents by replacing CA molecules on surface of AuNPs in order to produce quite stable AuNP. It is worthy to mention that reduction of Au3+ ion, formation and surface stabilization of AuNPs are consequently occurred in one step. We also investigated how experimental parameters including reaction time and temperature, pH of reaction solution, affect formation of the AuNPs. The effects of salt concentration and storage temperature were studied to show stability of the AuNPs. The synthesized DHLA@AuNPs and DHLA-Alanine@AuNPs were characterized via UV-Vis spectrophotometer (UV-Vis), scanning transmission electron microscope (STEM), dynamic light scattering (DLS) and Zeta potential (ZT) devices. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) was efficiently catalyzed by the AuNPs in the presence of sodium borohydride in aqueous solution.Article Citation - WoS: 13Citation - Scopus: 13Tuning the Shades of Red Emission in InP/ZnSe Nanocrystals With Narrow Full Width for Fabrication of Light-Emitting Diodes(Amer Chemical Soc, 2023-10-13) Soheyli, Ehsan; Bicer, Aysenur; Ozel, Sultan Suleyman; Tiras, Kevser Sahin; Mutlugun, Evren; Sahin Tiras, KevserWhile Cd-based luminescent nanocrystals (NCs) are the most mature NCs for fabricating efficient red light-emitting diodes (LEDs), their toxicity related limitation is inevitable, making it necessary to find a promising alternative. From this point of view, multishell-coated, red-emissive InP-based NCs are excellent luminescent nanomaterials for use as an emissive layer in electroluminescent (EL) devices. However, due to the presence of oxidation states, they suffer from a wide emission spectrum, which limits their performance. This study uses tris-(dimethyl-amino)-phosphine (3DMA-P) as a low-cost aminophosphine precursor and a double HF treatment to suggest an upscaled, cost-effective, and one-pot hot-injection synthesis of purely red-emissive InP-based NCs. The InP core structures were coated with thick layers of ZnSe and ZnS shells to prevent charge delocalization and to create a narrow size distribution. The purified NCs showed an intense emission signal as narrow as 43 nm across the entire red wavelength range (626-670 nm) with an emission quantum efficiency of 74% at 632 nm. The purified samples also showed an emission quantum efficiency of 60% for far-red wavelengths of 670 nm with a narrow full width of 50 nm. The samples showed a relatively long average emission lifetime of 50-70 ns with a biexponential decay profile. To demonstrate the practical ability of the prepared NCs in optoelectronics, we fabricated a red-emissive InP-based LEDs. The best-performing device showed an external quantum efficiency (EQE) of 1.16%, a luminance of 1039 cd m(-2), and a current efficiency of 0.88 cd A(-1).Article Citation - WoS: 5Citation - Scopus: 6Transfer Learning for P300 Brain-Computer Interfaces by Joint Alignment of Feature Vectors(IEEE-Inst Electrical Electronics Engineers Inc, 2023-10) Altindis, Fatih; Banerjee, Antara; Phlypo, Ronald; Yilmaz, Bulent; Congedo, MarcoThis article presents a new transfer learning method named group learning, that jointly aligns multiple domains (many-to-many) and an extension named fast alignment that aligns any further domain to previously aligned group of domains (many-to-one). The proposed group alignment algorithm (GALIA) is evaluated on brain-computer interface (BCI) data and optimal hyper-parameter values of the algorithm are studied for classification performance and computational cost. Six publicly available P300 databases comprising 333 sessions from 177 subjects are used. As compared to the conventional subject-specific train/test pipeline, both group learning and fast alignment significantly improve the classification accuracy except for the database with clinical subjects (average improvement: 2.12 +/- 1.88%). GALIA utilizes cyclic approximate joint diagonalization (AJD) to find a set of linear transformations, one for each domain, jointly aligning the feature vectors of all domains. Group learning achieves a many-to-many transfer learning without compromising the classification performance on non-clinical BCI data. Fast alignment further extends the group learning for any unseen domains, allowing a many-to-one transfer learning with the same properties. The former method creates a single machine learning model using data from previous subjects and/or sessions, whereas the latter exploits the trained model for an unseen domain requiring no further training of the classifier.Article Citation - WoS: 36Citation - Scopus: 35Trail Promotes the Polarization of Human Macrophages Toward a Proinflammatory M1 Phenotype and Is Associated With Increased Survival in Cancer Patients With High Tumor Macrophage Content(Frontiers Media S.A., 2023-09-21) Gunalp, Sinem; Helvaci, Derya Goksu; Oner, Aysenur; Bursali, Ahmet; Conforte, Alessandra; Guener, Hueseyin; Sag, Duygu; Güner, HüseyinBackgroundTNF-related apoptosis-inducing ligand (TRAIL) is a member of the TNF superfamily that can either induce cell death or activate survival pathways after binding to death receptors (DRs) DR4 or DR5. TRAIL is investigated as a therapeutic agent in clinical trials due to its selective toxicity to transformed cells. Macrophages can be polarized into pro-inflammatory/tumor-fighting M1 macrophages or anti-inflammatory/tumor-supportive M2 macrophages and an imbalance between M1 and M2 macrophages can promote diseases. Therefore, identifying modulators that regulate macrophage polarization is important to design effective macrophage-targeted immunotherapies. The impact of TRAIL on macrophage polarization is not known.MethodsPrimary human monocyte-derived macrophages were pre-treated with either TRAIL or with DR4 or DR5-specific ligands and then polarized into M1, M2a, or M2c phenotypes in vitro. The expression of M1 and M2 markers in macrophage subtypes was analyzed by RNA sequencing, qPCR, ELISA, and flow cytometry. Furthermore, the cytotoxicity of the macrophages against U937 AML tumor targets was assessed by flow cytometry. TCGA datasets were also analyzed to correlate TRAIL with M1/M2 markers, and the overall survival of cancer patients.ResultsTRAIL increased the expression of M1 markers at both mRNA and protein levels while decreasing the expression of M2 markers at the mRNA level in human macrophages. TRAIL also shifted M2 macrophages towards an M1 phenotype. Our data showed that both DR4 and DR5 death receptors play a role in macrophage polarization. Furthermore, TRAIL enhanced the cytotoxicity of macrophages against the AML cancer cells in vitro. Finally, TRAIL expression was positively correlated with increased expression of M1 markers in the tumors from ovarian and sarcoma cancer patients and longer overall survival in cases with high, but not low, tumor macrophage content.ConclusionsTRAIL promotes the polarization of human macrophages toward a proinflammatory M1 phenotype via both DR4 and DR5. Our study defines TRAIL as a new regulator of macrophage polarization and suggests that targeting DRs can enhance the anti-tumorigenic response of macrophages in the tumor microenvironment by increasing M1 polarization.Article Topological Feature Generation for Link Prediction in Biological Networks(PeerJ Inc, 2023-05-09) Temiz, Mustafa; Bakir-Gungor, Burcu; Sahan, Pinar Guner; Coskun, Mustafa; Güner Şahan, PınarGraph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions in a graph with low-dimensional vectors, which facilitates research to predict potential interactions in networks. However, most graph embedding methods suffer from high computational costs in the form of high computational complexity of the embedding methods and learning times of the classifier, as well as the high dimensionality of complex biological networks. To address these challenges, in this study, we use the Chopper algorithm as an alternative approach to graph embedding, which accelerates the iterative processes and thus reduces the running time of the iterative algorithms for three different (nervous system, blood, heart) undirected protein-protein interaction (PPI) networks. Due to the high dimensionality of the matrix obtained after the embedding process, the data are transformed into a smaller representation by applying feature regularization techniques. We evaluated the performance of the proposed method by comparing it with state-of-the-art methods. Extensive experiments demonstrate that the proposed approach reduces the learning time of the classifier and performs better in link prediction. We have also shown that the proposed embedding method is faster than state-of-the-art methods on three different PPI datasets.Article Citation - WoS: 1Citation - Scopus: 2Tomatidine, a Steroidal Alkaloid, Synergizes With Cisplatin to Inhibit Cell Viability and Induce Cell Death Selectively on FLT3-ITD+ Acute Myeloid Leukemia Cells(Humana Press inc, 2024-07-11) Ayvaz, Havva Berre; Yenigul, Munevver; Akcok, Emel Basak Gencer; Gencer Akçok, Emel BaşakBackgroundAcute Myeloid Leukemia (AML) is a hematological cancer that frequently presents with a range of side effects and drug resistance during anticancer drug treatment. The current study aims to achieve increased efficacy by combining lower doses of cisplatin with increasing concentrations of tomatidine in AML cells to increase efficacy.MethodsAnti-proliferative effects of single and combination of cisplatin and tomatidine were assessed via MTT cell viability assay. The Annexin V/Propidium Iodide Double Staining method was used to measure the apoptotic effects of combined tomatidine and cisplatin treatment. Then, Western Blot analysis was performed to measure Poly (ADP-ribose) polymerase (PARP) and Caspase-3 protein expression levels.ResultsCisplatin treatment with lower concentrations displayed high cytotoxic effects on AML cells, compared with tomatidine. The combination of the Inhibitory Concentration (IC) 20 value of cisplatin and increasing doses of tomatidine exhibited a significant decrease in cell viability relative to single treatments. The combination index analysis revealed a mild synergistic effect of cisplatin IC20 and varying tomatidine doses. The apoptosis induced when cisplatin was combined with 500 mu M tomatidine by almost 20%, while the percentage of apoptosis in combination with 1 mM tomatidine was measured by 50% for both cell lines. The upregulation of proapoptotic cleaved-PARP (3.2 and 1.08-fold for THP-1 and MOLM-13, respectively) and downregulation in Caspase-3 (0.23 and 0.13-fold for THP-1 and MOLM-13, respectively) was detected.ConclusionsTogether, the study indicated that when tomatidine combined with cisplatin on AML cell lines, a combinatorial anti-proliferative and apoptotic effect is observed. The combination of cisplatin with tomatidine may be a promising approach.Article Theoretical Investigation of Steric Effects on the S1 Potential Energy Surface of O-Carborane Derivatives(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Alkan, FahriTDDFT scan calculations were performed for s-carborane-anthracene derivatives (o-CB-X-Ant where X=-H,-CH3,-C2H5 and tert-butyl or-tBu) in order to understand the interplay between the steric effects, S1 potential energy surface (PES) and photophysical properties. The results show that all systems exhibit three local minima on the S1 PES, which correspond to the emissive LE and TICT state, along with the nonemissive CT state respectively. In the case of the unsubstituted system (o-CB-H-Ant), and-CH3 and-C2H5 substituted cases, S1 PES is predicted to be quite flat for certain conformations indicating that it is possible for these systems to reach the nonemissive CT state without a large energy penalty. In comparison, conformational pathways for the nonemissive CT state are predicted to be energetically unfavorable for o-CB-tBu-Ant as a result of both steric and electronic effects. These results provide a mechanism for the enhanced emission of cr-CB-fluorophore molecules with bulky ligands.