WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 5Citation - Scopus: 5Π-Conjugated Donor-Acceptor Small Molecule Thin-Films on Gold Electrodes for Reducing the Metal Work-Function(Elsevier Science SA, 2016-10) Azum, Naved; Taib, Layla Ahmad; Al Angari, Yasser Mohammed; Asiri, Abdullah M.; Denti, Mitchel; Zhao, Wei; Facchetti, AntonioThis paper reports the design, facile synthesis and purification of four pi-conjugated donor-acceptor small molecules comprising heteroaromatic units, DA-1-DA-4, for surface and electronic structure modification of gold thin film. These molecules were characterized by H-1/C-13 nuclear magnetic resonance spectroscopy, cyclic voltammetry, UV-Vis spectroscopy, and single-crystal X-ray diffraction. Morphologically smooth thin-films (similar to 5 nm) of DA-1-DA-4 were deposited onto Au thin films via thermal evaporation and characterized by atomic force microscopy, theta-2 theta X-ray diffraction and ultraviolet photoelectron spectroscopy. The work functions of the small molecule coated Au electrodes are shifted to lower energies by similar to 0.1-03 eV, compared to that of the bare Au film measured as a reference. The vapor-deposition of structurally,simple small molecules developed here shows great promise as a facile approach to reduce gold work function for electron injection/extraction between organic semiconductors and Au contacts in various opto-electronic devices. (C) 2016 Elsevier B.V. All tights reserved.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: 5Workplace Diversity and Intercultural Communication: A Phenomenological Study(Taylor & Francis As, 2017-01-01) Evans, Adam; Suklun, HarikaFor decades, the United States has seen an increasing number of immigrants, which has led to a significant increase in cultural diversity in the United States. This phenomenological study examines the contextual history of professional non-native English-speaking women in the United States to form a basis of comparison with native English speakers. It attempts to compare their lived communicative experiences with those of non-native English speakers in the workplace. In this study, 16 professional, native English-speaking women currently working in the US were interviewed. Participants in this study were asked to describe professional and intercultural experiences through interactions with non-native English-speaking coworkers, any expectations of the interactions or violations of those expectations, and any miscommunications that may have occurred. Many native English speakers positively reflected upon these intercultural interactions and shared examples of their vocal adjustments and challenges of verbal and intercultural communication. To overcome these challenges, professional native English speakers described trying to slow speech or asking confirming questions such as Do you understand? to mitigate verbal conflicts and miscommunication. Based on the trends within the responses, however, there is a potential for unintentional and often offensive consequences to occur. Several coping mechanisms were found to be considered rude or off-putting by non-native speakers, while the intent of a more direct message was often misinterpreted by native English speakers. In addition, it seems that native English speakers often may have good intentions in their actions but do not have the skillset to better facilitate communication with non-native English speakers.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: 1Citation - Scopus: 1Why Are Faculty Unfavorably Disposed to MOOCs? – A Sharing of Views by Chinese Hospitality Educators(Routledge Journals, Taylor & Francis Ltd, 2021-08-12) Zhang, Xin; Koseoglu, Mehmet Ali; King, Brian; Aladag, Omer FarukThis study explores the negative disposition of many hospitality higher education faculty toward MOOCs, an increasingly prominent delivery mode in pedagogical discourse which potentially enriches student learning. Such enrichment is particularly welcome in the case of hospitality because of its diverse stakeholders and student learning needs. The researchers conducted an in-depth and qualitative exploration with faculty members in mainland China. They combined the Diffusion of Innovation (DOI) approach and theory of motivation to propose five dimensions that account for groupings of resistance to deploying MOOCs. These are attributes and complexities, perceived incompatibility, unsuitability for trial, and lack of observational capacity. The study contributes to knowledge by examining the perspectives of faculty who have the capacity to constrain the deployment of MOOCs. The authors suggest that faculty members should be encouraged to embrace MOOCs as an innovative medium for learning and teaching.Article Citation - WoS: 1Citation - Scopus: 2WSA-Supplements and Proper Classes(MDPI, 2022-08-17) Demirci, Yilmaz Mehmet; Turkmen, ErgulIn this paper, we introduce the concept of wsa-supplements and investigate the objects of the class of short exact sequences determined by wsa-supplement submodules, where a submodule U of a module M is called a wsa-supplement in M if there is a submodule V of M with U + V = M and U boolean AND V is weakly semiartinian. We prove that a module M is weakly semiartinian if and only if every submodule of M is a wsa-supplement in M. We introduce CC-rings as a generalization of C-rings and show that a ring is a right CC-ring if and only if every singular right module has a crumbling submodule. The class of all short exact sequences determined by wsa-supplement submodules is shown to be a proper class which is both injectively and co-injectively generated. We investigate the homological objects of this proper class along with its relation to CC-rings.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: 25Citation - Scopus: 33Volume Fraction, Thickness, and Permeability of the Sealing Layer in Microbial Self-Healing Concrete Containing Biogranules(Frontiers Media S.A., 2018-11-23) Ersan, Yusuf Cagatay; Palin, Damian; Tasdemir, Sena Busra Yengec; Tasdemir, Kasim; Jonkers, Henk M.; Boon, Nico; De Belie, Nele; Yengec Tasdemir, Sena BusraAutonomous repair systems in construction materials have become a promising alternative to current unsustainable and labor-intensive maintenance methods. Biomineralization is a popular route that has been applied to enhance the self-healing capacity of concrete. Various axenic microbial cultures were coupled with protective carriers, and their combination appears to be useful for the development of healing agents for realizing self-healing concrete. The advantageous traits of non-axenic cultures, such as economic feasibility, self-protection, and high specific activity have been neglected so far, and thus the number of studies investigating their performance as healing agents is scarce. Here we present the self-healing performance of a mortar containing a healing agent consisting of non-axenic biogranules with a denitrifying core. Mortar specimens with a defined crack width of 400 mu m were used in the experiments and treated with tap water for 28 days. Self-healing was quantified in terms of the crack volume reduction, the thickness of the sealing layer along the crack depth and water permeability under 0.1 bar pressure. Complete visual crack closure was achieved in the bio-based specimens in 28 days, the thickness of the calcite layer was recorded as 10 mm and the healed crack volume was detected as 6%. Upon self-sealing of the specimens, the water permeability decreased by 83%. Overall, non-axenic biogranules with a denitrifying core shows great potential for development of self-healing bioconcrete.