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  1. Article ; Online: Targeting the PANoptosome with miRNA Loaded Mesenchymal Stem Cell Derived Extracellular Vesicles; a New Path to Fight Against the Covid-19?

    Çetin, Zafer

    Stem cell reviews and reports

    2021  Volume 17, Issue 3, Page(s) 1074–1077

    MeSH term(s) COVID-19 ; Caspase 8 ; Cell Death ; Extracellular Vesicles ; Humans ; Inflammasomes ; Mesenchymal Stem Cells ; MicroRNAs/genetics ; NLR Family, Pyrin Domain-Containing 3 Protein ; Pyroptosis ; Receptor-Interacting Protein Serine-Threonine Kinases ; SARS-CoV-2
    Chemical Substances Inflammasomes ; MicroRNAs ; NLR Family, Pyrin Domain-Containing 3 Protein ; RIPK3 protein, human (EC 2.7.11.1) ; Receptor-Interacting Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Caspase 8 (EC 3.4.22.-)
    Language English
    Publishing date 2021-04-13
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2495577-2
    ISSN 2629-3277 ; 1558-6804 ; 1550-8943
    ISSN (online) 2629-3277 ; 1558-6804
    ISSN 1550-8943
    DOI 10.1007/s12015-021-10166-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Identifying the tumor location-associated candidate genes in development of new drugs for colorectal cancer using machine-learning-based approach.

    Bayrak, Tuncay / Çetin, Zafer / Saygılı, E İlker / Ogul, Hasan

    Medical & biological engineering & computing

    2022  Volume 60, Issue 10, Page(s) 2877–2897

    Abstract: Numerous studies have been conducted to elucidate the relation of tumor proximity to cancer prognosis and treatment efficacy in colorectal cancer. However, the molecular pathways and prognoses of left- and right-sided colorectal cancers are different, ... ...

    Abstract Numerous studies have been conducted to elucidate the relation of tumor proximity to cancer prognosis and treatment efficacy in colorectal cancer. However, the molecular pathways and prognoses of left- and right-sided colorectal cancers are different, and this difference has not been fully investigated at the genomic level. In this study, a set of data science approaches, including six feature selection methods and three classification models, were used in predicting tumor location from gene expression profiles. Specificity, sensitivity, accuracy, and Mathew's correlation coefficient (MCC) evaluation metrics were used to evaluate the classification ability. Gene ontology enrichment analysis was applied by the Gene Ontology PANTHER Classification System. For the most significant 50 genes, protein-protein interactions and drug-gene interactions were analyzed using the GeneMANIA, CytoScape, CytoHubba, MCODE, and DGIdb databases. The highest classification accuracy (90%) is achieved with the most significant 200 genes when the ensemble-decision tree classification model is used with the ReliefF feature selection method. Molecular pathways and drug interactions are investigated for the most significant 50 genes. It is concluded that a machine-learning-based approach could be useful to discover the significant genes that may have an important role in the development of new therapies and drugs for colorectal cancer.
    MeSH term(s) Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Gene Ontology ; Humans ; Machine Learning
    Language English
    Publishing date 2022-08-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 282327-5
    ISSN 1741-0444 ; 0025-696X ; 0140-0118
    ISSN (online) 1741-0444
    ISSN 0025-696X ; 0140-0118
    DOI 10.1007/s11517-022-02641-w
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  3. Article ; Online: Modeling the Evaporation of Drying Sessile Droplets with Buoyancy Driven Internal Convection

    Akdag Osman / Akkus Yigit / Çetin Barbaros / Dursunkaya Zafer

    E3S Web of Conferences, Vol 321, p

    2021  Volume 04013

    Abstract: Droplet evaporation is a fundamental phenomenon encountered in diverse applications such as inkjet printing, DNA mapping, film coating, and electronics cooling. Modeling the evaporation process of a sessile droplet is complicated because of the coupling ... ...

    Abstract Droplet evaporation is a fundamental phenomenon encountered in diverse applications such as inkjet printing, DNA mapping, film coating, and electronics cooling. Modeling the evaporation process of a sessile droplet is complicated because of the coupling of several physical phenomena occurring in different phases and various magnitudes such as the buoyant convection of the liquid in millimeter size droplets and that of the surrounding air/water vapor mixture, in the order of meters. In this study, the theoretical framework presented previously for the steadily fed droplets [Int J Therm Sci, 158 (2020) 106529] is extended to resolve the evaporation of drying droplets with a pinned contact line. Based on the quasi-steady-state assumption, buoyant convection inside the droplet and diffusive-convective transport of vapor in the gas domain are modeled. As a test case, drying process of a water droplet with a 68° initial contact angle on a heated substrate is simulated and the predictions of the model are interpreted.
    Keywords droplet evaporation ; evaporation modeling ; computational fluid dynamics ; Environmental sciences ; GE1-350
    Subject code 660
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Performance of a flat grooved heat pipe with a localized heat load

    Sezmen Ramazan Aykut / Çetin Barbaros / Dursunkaya Zafer

    E3S Web of Conferences, Vol 321, p

    2021  Volume 04010

    Abstract: Heat pipes are phase change heat transfer devices used in wide range of heat transport applications due to their high thermal transport capacities with low temperature differences. Heat pipes are especially preferred for electronic cooling applications ... ...

    Abstract Heat pipes are phase change heat transfer devices used in wide range of heat transport applications due to their high thermal transport capacities with low temperature differences. Heat pipes are especially preferred for electronic cooling applications and aerospace avionics to satisfy high heat transfer rate requirements. In this study, heat transfer and phase change mechanisms of working fluid are investigated and modeled using a 3-D thermal resistance network for multichannel flat grooved heat pipes. First, heat transfer and fluid flow are modeled in half of a single grooved structure due to symmetry, and is subjected to uniform heat flux. Radius of meniscus curvature and temperature distribution along the groove are calculated. Results are compared with experiments in the literature and show good agreement. The validated heat transfer and fluid flow models are extended to a multichannel model to observe performance of grooved heat pipes with localized heat sources, not covering the entire width, a vital feature for realistic simulation of operational devices. Predictions of the temperature distribution along the multichannel of the heat pipe are provided and the effect of the distribution of heat sources on the heat pipe is discussed.
    Keywords Environmental sciences ; GE1-350
    Subject code 621
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Crosstalk between CML cells with HUVECS and BMSCs through CML derived exosomes.

    Cetin, Zafer / Ilker Saygili, Eyup / Yilmaz, Mehmet

    Frontiers in bioscience (Landmark edition)

    2021  Volume 26, Issue 3, Page(s) 444–467

    Abstract: Chronic Myeloid Leukemia (CML) is a myeloproliferative neoplasm characterized by presence of the BCR-ABL fusion gene which encodes the constitutively active BCR-ABL chimeric protein. Imatinib is first FDA approved first-line BCR-ABL targeting drug for ... ...

    Abstract Chronic Myeloid Leukemia (CML) is a myeloproliferative neoplasm characterized by presence of the BCR-ABL fusion gene which encodes the constitutively active BCR-ABL chimeric protein. Imatinib is first FDA approved first-line BCR-ABL targeting drug for the treatment of newly diagnosed CML cases. Nowadays there are recently developed and more efficient TKIs in the market. Despite the improvements in the CML therapy by using tyrosine kinase inhibitors (TKIs) primary/secondary resistance or progression from chronic to accelerated and blastic phase may be developed in some cases. Underlying mechanisms of TKI resistance and disease progression may results from BCR/ABL dependent or independent alterations. Recently it was revealed that tumor microenvironment is very important for cancer cell growth, survival, proliferation, hemostasis, invasion and metastasis. Exosomes derived from tumor cells contain many important signaling molecules and transfer these molecules in the neighbouring cells. In the bone marrow matrix CML cells, CML leukemic stem cells,cells, bone marrow mesenchymal stromal cells can communicate with each other through exosomes. In this review we focused on biological and clinical importance of CML derived exosomes and we will summarize the recent studies in this field.
    MeSH term(s) Cell Proliferation ; Cell Survival ; Exosomes/metabolism ; Hematopoietic Stem Cells/cytology ; Human Umbilical Vein Endothelial Cells ; Humans ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
    Language English
    Publishing date 2021-01-01
    Publishing country Singapore
    Document type Journal Article ; Review
    ZDB-ID 2704569-9
    ISSN 2768-6698 ; 1093-9946
    ISSN (online) 2768-6698
    ISSN 1093-9946
    DOI 10.2741/4901
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Announcing the New Website of Balkan Medical Journal

    Zafer Koçak / Çetin Hakan Karadağ

    Balkan Medical Journal, Vol 34, Iss 5, Pp 384-

    2017  Volume 384

    Keywords Medicine ; R
    Language English
    Publishing date 2017-10-01T00:00:00Z
    Publisher Galenos Publishing House
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Announcing the New Website of Balkan Medical Journal.

    Koçak, Zafer / Karadağ, Çetin Hakan

    Balkan medical journal

    2017  Volume 34, Issue 5, Page(s) 384

    Language English
    Publishing date 2017-09-29
    Publishing country Turkey
    Document type Journal Article
    ZDB-ID 2612982-6
    ISSN 2146-3131 ; 2146-3123
    ISSN (online) 2146-3131
    ISSN 2146-3123
    DOI 10.4274/balkanmedj.2017.5.0002
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  8. Article ; Online: Possible Role of Endocannabinoids in Olfactory and Taste Dysfunctions in COVID-19 Patients and Volumetric Changes in the Brain

    Ergül, Zafer / Kaptan, Zülal / Kars, Ayhan / Biçer, Gülşah / Kılınç, Çetin / Petekkaya, Emine / Çöplü, Nilay

    Chem. Percept.. 2022 Oct., v. 15, no. 2 p.135-144

    2022  

    Abstract: INTRODUCTION: COVID-19 infection develops neurologic symptoms such as smell and taste loss. We aimed to determine the volumetric changes in the brain and correlation of possible related biochemical parameters and endocannabinoid levels after COVID-19 ... ...

    Abstract INTRODUCTION: COVID-19 infection develops neurologic symptoms such as smell and taste loss. We aimed to determine the volumetric changes in the brain and correlation of possible related biochemical parameters and endocannabinoid levels after COVID-19 recovery. METHODS: Brain magnetic resonance images of recovered COVID-19 patients and healthy volunteers, whose olfactory and gustatory scores were obtained through a questionnaire, were taken, and the volumes of the brain regions associated with taste and smell were measured by automatic and semiautomatic methods. Endocannabinoids (EC), which are critical in the olfactory system, and vitamin B12, zinc, iron, ferritin, thyroid-stimulating hormone (TSH), and thyroxine (T4) levels, which are reported to have possible roles in olfactory disorders, were measured in peripheral blood. RESULTS: Taste and smell disorder scores and EC levels were found to be higher in recovered COVID-19 patients compared to controls. EC levels were negatively correlated with bilateral entorhinal cortex (ENT) volumes in the COVID-19 group. Subgenual anterior cingulate cortex volumes showed correlations with gustatory complaints and ferritin in recovered COVID-19 patients. CONCLUSIONS: The critical finding of our study is the high EC levels and negative correlation between EC levels and left ENT volumes in recovered COVID-19 patients. IMPLICATIONS: It is possible that ECs are potential neuromodulators in many conditions leading to olfactory disorders, including COVID-19.
    Keywords COVID-19 infection ; blood ; brain ; cannabinoids ; cortex ; ferritin ; iron ; magnetism ; neurotransmitters ; questionnaires ; smell ; taste ; thyroxine ; vitamin B12 ; zinc
    Language English
    Dates of publication 2022-10
    Size p. 135-144.
    Publishing place Springer US
    Document type Article ; Online
    ZDB-ID 2424048-5
    ISSN 1936-5810 ; 1936-5802
    ISSN (online) 1936-5810
    ISSN 1936-5802
    DOI 10.1007/s12078-022-09301-1
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: Possible Role of Endocannabinoids in Olfactory and Taste Dysfunctions in COVID-19 Patients and Volumetric Changes in the Brain.

    Ergül, Zafer / Kaptan, Zülal / Kars, Ayhan / Biçer, Gülşah / Kılınç, Çetin / Petekkaya, Emine / Çöplü, Nilay

    Chemosensory perception

    2022  , Page(s) 1–10

    Abstract: Introduction: COVID-19 infection develops neurologic symptoms such as smell and taste loss. We aimed to determine the volumetric changes in the brain and correlation of possible related biochemical parameters and endocannabinoid levels after COVID-19 ... ...

    Abstract Introduction: COVID-19 infection develops neurologic symptoms such as smell and taste loss. We aimed to determine the volumetric changes in the brain and correlation of possible related biochemical parameters and endocannabinoid levels after COVID-19 recovery.
    Methods: Brain magnetic resonance images of recovered COVID-19 patients and healthy volunteers, whose olfactory and gustatory scores were obtained through a questionnaire, were taken, and the volumes of the brain regions associated with taste and smell were measured by automatic and semiautomatic methods. Endocannabinoids (EC), which are critical in the olfactory system, and vitamin B12, zinc, iron, ferritin, thyroid-stimulating hormone (TSH), and thyroxine (T4) levels, which are reported to have possible roles in olfactory disorders, were measured in peripheral blood.
    Results: Taste and smell disorder scores and EC levels were found to be higher in recovered COVID-19 patients compared to controls. EC levels were negatively correlated with bilateral entorhinal cortex (ENT) volumes in the COVID-19 group. Subgenual anterior cingulate cortex volumes showed correlations with gustatory complaints and ferritin in recovered COVID-19 patients.
    Conclusions: The critical finding of our study is the high EC levels and negative correlation between EC levels and left ENT volumes in recovered COVID-19 patients.
    Implications: It is possible that ECs are potential neuromodulators in many conditions leading to olfactory disorders, including COVID-19.
    Language English
    Publishing date 2022-10-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2424048-5
    ISSN 1936-5810 ; 1936-5802
    ISSN (online) 1936-5810
    ISSN 1936-5802
    DOI 10.1007/s12078-022-09301-1
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  10. Article ; Online: Preclinical Experimental Applications of miRNA Loaded BMSC Extracellular Vesicles.

    Cetin, Zafer / Saygili, Eyup I / Görgisen, Gokhan / Sokullu, Emel

    Stem cell reviews and reports

    2021  Volume 17, Issue 2, Page(s) 471–501

    Abstract: Bone marrow mesenchymal stem cells have been investigated for many years, especially for tissue regeneration, and have inherent limitations. One of the rapidly developing fields in the scientific world in recent years is extracellular vesicles. ... ...

    Abstract Bone marrow mesenchymal stem cells have been investigated for many years, especially for tissue regeneration, and have inherent limitations. One of the rapidly developing fields in the scientific world in recent years is extracellular vesicles. Especially, bone marrow mesenchymal stem cell originated extracellular vesicles are known to have positive contributions in tissue regeneration, and these extracellular vesicles have also been used as gene transfer systems for cellular therapy. Through gene expression analysis and bioinformatics tools, it is possible to determine which genes have changed in the targeted tissue or cell and which miRNAs that can correct this gene expression disorder. This approach connecting the stem cell, extracellular vesicles, epigenetics regulation and bioinformatics fields is one of the promising areas for the treatment of diseases in the future. With this review, it is aimed to present the studies carried out for the use of bone marrow stem cell-derived extracellular vesicles loaded with targeted miRNAs in different in vivo and in vitro human disease models and to discuss recent developments in this field.
    MeSH term(s) Animals ; Bone Marrow ; Epigenomics ; Extracellular Vesicles ; Humans ; Mesenchymal Stem Cells ; MicroRNAs/genetics
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2021-01-04
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2495577-2
    ISSN 2629-3277 ; 1558-6804 ; 1550-8943
    ISSN (online) 2629-3277 ; 1558-6804
    ISSN 1550-8943
    DOI 10.1007/s12015-020-10082-x
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