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Publication Open Access A preliminary study of tracking B-cell kinetics in patients with lung transplantation by monitoring kappa-deleting recombination excision circles(BAYCINAR MEDICAL PUBL-BAYCINAR TIBBI YAYINCILIK, 2022) Akbulut, Zeynep; Akdeniz, Tuba; Vayvada, Mustafa; Kalamanoğlu, Merih; Yeğinsu, Ali; Yanıkkaya Demirel, Gülderen; Kutlu, Cemal Asım; Maltepe University; Yeditepe University; Bahcesehir University; Istanbul Yeni Yuzyil University; Yeditepe University; Bahcesehir UniversityBackground: This study aims to evaluate humoral immune system response by measuring copy numbers of kappa-deleting recombination excision circles (KREC) gene segment from B lymphocytes in patients with lung transplantation. Methods: Between September 2015 and November 2016, a total of 11 patients (8 males, 3 females, mean age: 45.4 +/- 12.0 years, range, 23 to 59 years) who underwent lung transplantation with different primary indications were included. The copy numbers of KREC gene segment were quantified using real-time polymerase chain reaction method in peripheral blood samples collected pre- and post-transplantation. The samples of the patients were compared with the KREC levels in deoxyribonucleic acid extracted from blood samples of healthy children. Results: There was no significant change in KREC levels between pre- and post-operation (p=0.594 and p=0.657), although the median values indicated that the highest increase in the KREC levels (7x10(5)-12x10(5) , 85-170) was on Day 7 of transplantation. There was a positive correlation between the KREC levels (mL in blood) and lymphocytes at 24 h after transplantation (p=0.043) and between KREC copies per 10(6) of blood and age on Day 7. Conclusion: Our preliminary results suggest that KREC levels as an indicator of B lymphocyte production are elevated after lung transplantation. A prognostic algorithm by tracking B cell kinetics after post-transplantation for long-term follow-up can be developed following the confirmation of these preliminary results with more patient samples.Publication Open Access A mentorship model for teacher education: Young STEM researchers and practitioners program(MEHMET TEKEREK, 2022) Yabas, Defne; Bozoğlu, Hayriye Sinem; Bahçeşehir ÜniversitesiThe current research is about the impact of the young STEM researchers and practitioners program implemented within the STEM: Integrated teaching project. The aim of the program is to incorporate STEM integrated teaching knowledge in the teacher preparation period. In this phenomenological study, we explored five pre-school teachers' program experiences and their STEM conceptions. Data were collected with semi-structured interviews, including questions about the impact and elements of the program and participants' STEM conceptions. Content analysis showed that awareness for STEM education, development of integrated teaching knowledge, and program elements were the emergent themes about the program experience. Teacher candidates responded to the models that include real-world problems and engineering as contexts as most desirable when shown STEM education models to understand their STEM conceptions. The young STEM researchers and practitioners program can be evaluated as a developing model to be incorporated into teacher education programs. Further research can explore how pre-service teachers form their STEM conceptions and develop their integrated teaching knowledge.Publication Open Access Fizyoterapi ve Rehabilitasyon Öğrencilerinin Öğrenme Stili Tercihlerine Göre Akademik Başarı, Akademik Öz Güven ve Eğitim Ortamı Algısının Karşılaştırılması(2025) Açar, Görkem; Delibay, Aylin Aydoğdu; Kiloatar, Hümeyra; Turan, Onur; Bahçeşehir Üniversitesi; Kütahya Sağlık Bilimleri Üniversitesi; İstanbul Atlas ÜniversitesiBu çalışmanın amacı lisans düzeyindeki fizyoterapi ve rehabilitasyon öğrencilerinin farklı öğrenme stili tercihlerine göre akademik başarılarını, akademik özgüvenlerini ve öğrenme çevrelerini incelemekti. Çalışmaya lisans düzeyindeki 180 fizyoterapi ve rehabilitasyon öğrencisi dahil edilmiştir. Bireylerin öğrenme stili tercihleri Kolb Öğrenme Stili Envanteri-3 ile, öğrenme çevreleri Dundee Mevcut Eğitim Ortamı Değerlendirme Ölçeği (DREEM) ile, özgüvenleri ise Akademik Özgüven Ölçeği (AÖÖ) ile değerlendirilmiştir. Bireylerin akademik başarıları Genel Akademik Not Ortalamaları aracılığıyla değerlendirilmiştir. Farklı öğrenme stillerini tercih eden bireylerin Akademik Özgüven Ölçeği ile ölçülen akademik özgüvenleri benzerdi (p>0,05). Farklı öğrenme stillerini tercih eden bireylerin DREEM anketiyle ölçülen öğrenme çevresi algıları istatistiksel olarak farklıydı (p<0,05). Özümseyen öğrenme stilini tercih eden öğrencilerinin DREEM puanı ayrıştıran ve yerleştiren öğrenme stilini tercih eden bireylere göre daha düşük bulundu (p<0,05). Farklı öğrenme stillerini tercih eden bireylerin akademik başarıları istatistiksel olarak farklı bulundu (p<0,05). Değiştiren ve ayrıştıran öğrenme stillerine sahip öğrenciler arasında (χ² = 16.36, p = 0.0025), ayrıca yerleştiren ve ayrıştıran öğrenme stillerine sahip öğrenciler arasında (χ² = 16.37, p = 0.0025) istatistiksel olarak anlamlı farklılıklar bulunmuştur. Bu çalışma, fizyoterapi ve rehabilitasyon öğrencilerinde öğrenme stili tercihlerinin akademik başarı ve öğrenme ortamı algısı üzerinde anlamlı bir etkisi olduğunu ortaya koymuştur. Özümseyen öğrenme stiline sahip öğrencilerin eğitim ortamına yönelik memnuniyet düzeylerinin daha düşük olduğu, ayrıştırıcı öğrenme stiline sahip öğrencilerin ise akademik başarılarının daha düşük olduğu bulunmuştur. Buna karşılık, akademik özgüven düzeyleri öğrenme stilleri arasında anlamlı bir farklılık göstermemiştir. Bu bulgular, farklı öğrenme stillerine uygun eğitim stratejilerinin geliştirilmesinin, fizyoterapi ve rehabilitasyon eğitiminde öğrenci memnuniyetini ve akademik başarıyı artırabileceğini göstermektedir.Publication Open Access Assessment of Vascular Patency and Inflammation with Intravascular Optical Coherence Tomography in Patients with Superficial Femoral Artery Disease Treated with Zilver PTX Stents(Elsevier Inc. usjcs@elsevier.com, 2020) Hoyt, Taylor; Feldman, Marc David; Okutucu, Sercan; Lendel, Vasili; Marmagkiolis, Konstantinos; McIntosh, Victoria; Ates, Ismail; Kose, Gulcan; Mego, David M.; Paixao, Andre R.M.; Hoyt, Taylor, The University of Texas Health Science Center at San Antonio, San Antonio, United States; Feldman, Marc David, The University of Texas Health Science Center at San Antonio, San Antonio, United States; Okutucu, Sercan, Ankara Numune Hospital, Ankara, Turkey; Lendel, Vasili, Arkansas Heart Hospital, Little Rock, United States; Marmagkiolis, Konstantinos, Florida Hospital, Orlando, United States; McIntosh, Victoria, Arkansas Heart Hospital, Little Rock, United States; Ates, Ismail, School of Medicine, Bahçeşehir Üniversitesi, Istanbul, Turkey; Kose, Gulcan, School of Medicine, Bahçeşehir Üniversitesi, Istanbul, Turkey; Mego, David M., Arkansas Heart Hospital, Little Rock, United States; Paixao, Andre R.M., Arkansas Heart Hospital, Little Rock, United StatesPurpose: Zilver PTX nitinol self-expanding drug-eluting stent with paclitaxel coating is effective for treatment of superficial femoral artery (SFA) disease. However, as with any stent, it induces a measure of vascular inflammatory response. The current clinical trial (NCT02734836) aimed to assess vascular patency, remodeling, and inflammatory markers with intravascular optical coherence tomography (OCT) in patients with SFA disease treated with Zilver PTX stents. Methods: Serial OCT examinations were performed in 13 patients at baseline and 12-month follow-up. Variables evaluated included neointimal area, luminal narrowing, thrombus area, stent expansion as well as measures of inflammation including, peri-strut low-intensity area (PLIA), macrophage arc, neovascularization, stent strut apposition and coverage. Results: Percentage of malapposed struts decreased from 10.3 ± 7.9% post-intervention to 1.1 ± 2.2% at 12-month follow-up, but one patient showed late-acquired stent malapposition (LASM). The percent of uncovered struts at follow-up was 3.0 ± 4.5%. Average expansion of stent cross-sectional area from baseline to follow-up was 35 ± 19%. The average neointimal area was 7.8 ± 3.8 mm2. Maximal luminal narrowing was 61.1 ± 25.0%, and average luminal narrowing was 35.4 ± 18.2%. Average peri-strut low-intensity area (PLIA) per strut was 0.017 ± 0.018 mm2. Average number of neovessels per mm of stent was 0.138 ± 0.181. Average macrophage angle per frame at follow-up was 7 ± 11°. Average thrombus area at follow-up was 0.0093 ± 0.0184 mm2. Conclusion: At 12-month follow-up, OCT analysis of Zilver PTX stent shows outward remodeling and minimal neointimal growth, but evidence of inflammation including PLIA, neovessels, thrombus and macrophages. Thirteen patients with PAD had paclitaxel-coated stents implanted in their SFAs and were then imaged with OCT at baseline and 12-month follow-up. OCT proxy metrics of inflammation were quantified. © 2020 Elsevier B.V., All rights reserved.Publication Open Access Legume genomics and transcriptomics: From classic breeding to modern technologies(Elsevier B.V., 2020) Afzal, Muhammad Zohaib; Alghamdi, Salem Safer; Migdadi, Hussein M.; Khan, Muhammad Altaf; Nurmansyah, undefined; Mirza, Shaher Bano; El-Harty, Ehab H.; Afzal, Muhammad Zohaib, Plant Production Department, King Saud University, Riyadh, Saudi Arabia; Alghamdi, Salem Safer, Plant Production Department, King Saud University, Riyadh, Saudi Arabia; Migdadi, Hussein M., Plant Production Department, King Saud University, Riyadh, Saudi Arabia; Khan, Muhammad Altaf, Plant Production Department, King Saud University, Riyadh, Saudi Arabia; Nurmansyah, undefined, Plant Production Department, King Saud University, Riyadh, Saudi Arabia; Mirza, Shaher Bano, Department of Biophysics, Bahçeşehir Üniversitesi, Istanbul, Turkey, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan; El-Harty, Ehab H., Plant Production Department, King Saud University, Riyadh, Saudi ArabiaLegumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers, genotyping, high density genetic linkage maps, quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs), and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production. © 2019 Elsevier B.V., All rights reserved.Publication Open Access Fabrication and characterizations of Al nanoparticles doped ZnO nanostructures-based integrated electrochemical biosensor(Elsevier Editora Ltda, 2020) Gherab, Kichou N.; Ai-Douri, Y.; Hashim, U.; Ameri, M.; Bouhemadou, Abdelmadjid; Mujasam Batoo, Khalid Mujasam; Adil, Syed F.; Khan, Mujeeb; Raslan, Emad H.; Gherab, Kichou N., Universiti Malaysia Perlis, Arau, Malaysia; Ai-Douri, Y., Cihan University– Sulaymania, Sulaymaniyah, Iraq, Nanotechnology and Catalysis Research Center (NANOCAT), Universiti Malaya, Kuala Lumpur, Malaysia, Department of Mechanical Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Hashim, U., Universiti Malaysia Perlis, Arau, Malaysia; Ameri, M., Laboratoire Physico-Chimie des Matériaux Avancés (LPCMA), Université Djillali Liabes de Sidi Bel Abbes, Sidi Bel Abbes, Algeria; Bouhemadou, Abdelmadjid, Laboratory for Developing New Materials and Their Characterizations, Université Ferhat Abbas Sétif 1, Setif, Algeria; Mujasam Batoo, Khalid Mujasam, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia; Adil, Syed F., Department of Chemistry, King Saud University, Riyadh, Saudi Arabia; Khan, Mujeeb, Department of Chemistry, King Saud University, Riyadh, Saudi Arabia; Raslan, Emad H., Department of Physics, King Saud University, Riyadh, Saudi ArabiaThe benefits of the electrical-based biosensor include cheap production and fast response time of detecting diseases. An interdigitated electrode (IDE) is fabricated using silver (Ag) as a metal contact that is deposited on aliminium (Al) nanoparticles doped with both zinc oxide (ZnO) and Silicon (Si) forming AZO/Si nanostructures by vacuum coater in a thermal evaporator. The electrical properties are studied as a function of frequency and voltage using I-V characteristics. Sol-gel method under annealing temperature, 500 ◦C is utilized to generate Al nanoparticles doped ZnO nanostructures. UV-vis spectrophotometer, Atomic Force Microscopy (AFM), Scanning Electron Microscopy (SEM) and X-ray diffractometer (XRD) are used for analyzing optical, topographical, morphological and structural studies of AZO nanostructure, respectively. Specific empirical models of optical dielectric constant, bulk modulus and refractive index are also verified. © 2020 Elsevier B.V., All rights reserved.Publication Open Access A two-level facility location and sizing problem for maximal coverage(Elsevier Ltd, 2020) Karatas, Mumtaz; Dasci, Abdullah; Karatas, Mumtaz, Department of Industrial Engineering, Milli Savunma Üniversitesi, Istanbul, Turkey, Department of Industrial Engineering, Bahçeşehir Üniversitesi, Istanbul, Turkey; Dasci, Abdullah, School of Business, Sabancı Üniversitesi, Tuzla, TurkeyThis paper presents a two-stage hierarchical location problem for systems where the lower level facilities act as the first points contact for the customers while the upper level facilities act as suppliers of the lower level facilities that either serve them or provide advanced services to customers. Furthermore, more recent and realistic coverage constructs such as gradual and cooperative covering are included in our setting. Although our problem can be applicable in various settings, the most fitting application is in wireless telecommunication networks to determine the location of base stations and mobile switching centers. We have developed two competing formulations for the problem, each of which involve nonlinear components that are difficult to deal with. We then develop their respective linearizations and tested their performances. These formulations are solved by commercial optimizers for a set of reasonably large problem instances and it is found that majority of the problems can be solved within a maximum of 10% optimality gap within a short time. © 2019 Elsevier B.V., All rights reserved.Publication Open Access Effects of PEGylated Fe–Fe3O4 core-shell nanoparticles on NIH3T3 and A549 cell lines(Elsevier Ltd, 2020) Domac, Begum Hira; AlKhatib, Sara; Zirhli, Onur; Gunduz Akdogan, Nilay Gunduz; Öçal Dirican, Ş. C.; Bulut, Gulay; Akdogan, O. A.B.; Domac, Begum Hira, Mechatronics Engineering Department Besiktas, Bahçeşehir Üniversitesi, Istanbul, Turkey; AlKhatib, Sara, Bioengineering Program, Bahçeşehir Üniversitesi, Istanbul, Turkey; Zirhli, Onur, Mechatronics Engineering Department Besiktas, Bahçeşehir Üniversitesi, Istanbul, Turkey, Faculty of Engineering and Natural Sciences, Sabancı Üniversitesi, Tuzla, Turkey; Gunduz Akdogan, Nilay Gunduz, Faculty of Engineering, Pîrî Reis Üniversitesi, Istanbul, Turkey; Öçal Dirican, Ş. C., Biology Graduate Program, Ankara Üniversitesi, Ankara, Turkey; Bulut, Gulay, Department of Molecular Biology and Genetics, Bahçeşehir Üniversitesi, Istanbul, Turkey; Akdogan, O. A.B., Mechatronics Engineering Department Besiktas, Bahçeşehir Üniversitesi, Istanbul, TurkeyMagnetic nanoparticles are key components in many fields of science and industry. Especially in cancer diagnosis and therapy, they are involved in targeted drug delivery and hyperthermia applications due to their ability to be controlled remotely. In this study, a PEG-coated Fe/Fe3O4 core-shell nanoparticle with an average size of 20 nm and 13 nm and high room temperature coercivity (350 Oe) has been successfully synthesized. These nanoparticles were further tested for their effect on cellular toxicity (IC50) and proliferation by WST assay. In addition, their potential as anti-cancer agents were assessed using scratch assay in NIH3T3 mouse embryonic fibroblast and A549 non-small cell lung cancer cell lines. In previous reports, the IC50 values of the magnetite nanoparticles are reported at concentrations of 100 μg/ml and higher. In this study, IC50 value is observed to be at 1 μg/ml, which is significantly lower when compared to similar studies. In scratch assay, the Fe/Fe3O4 core-shell nanoparticle showed a higher inhibitory potential on cell motility in A549 lung cancer cells in comparison to the NIH3T3 cells mouse embryonic fibroblasts. This could be due to the accelerated release of free Fe ion from the Fe core, resulting in cell death. Consequently, data obtained from this study suggest that the synthesized nanoparticles can be a potential drug candidate with anti-cancer activity for chemotherapeutic treatment., Drug delivery, Biophysics, Magnetism, Nanoparticle synthesis, Nanotechnology, Chemotherapy, Fe–Fe3O4 nanoparticles, Targeted drug delivery. © 2019 Elsevier B.V., All rights reserved.Publication Open Access Evaluation of monocyte to high-density lipoprotein ratio, lymphocytes, monocytes, and platelets in psoriasis(Elsevier Espana S.L., 2020) Aktaş Karabay, Ezgi; Demir, Damla; Aksu Çerman, Asli; Aktaş Karabay, Ezgi, Department of Dermatology and Venereology, Bahçeşehir Üniversitesi, Istanbul, Turkey; Demir, Damla, Department of Dermatology and Venereology, University of Health Sciences, Istanbul, Turkey; Aksu Çerman, Asli, Department of Dermatology and Venereology, University of Health Sciences, Istanbul, TurkeyBackground: Psoriasis is a chronic immune-mediated inflammatory skin disease that is associated with cardiovascular comorbidities. Objectives: The objective of this retrospective study is to assess the C-reactive protein, monocyte-to-high-density-lipoprotein ratio, neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio as inflammatory markers in patients with psoriasis and to search for a relationship between these parameters and psoriasis severity, as defined by the psoriasis area and severity index. Methods: There were 94 patients with psoriasis and 118 healthy controls enrolled in the study. The C-reactive protein, monocyte-to-high-density-lipoprotein ratio, neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio values of two groups were retrospectively evaluated. Results: Statistically significant differences were observed in terms of C-reactive protein, monocyte-to-high-density-lipoprotein ratio, neutrophil-to-lymphocyte ratio and monocyte-to-lymphocyte ratio between the patient and control groups (p = 0.001, p = 0.003, p = 0.038, and p = 0.007, respectively). Positive correlations were found between the psoriasis area and severity index and the values of C-reactive protein, monocyte-to-high-density-lipoprotein ratio, neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio (r: 0.381, p < 0.01, r: 0.203, p < 0.05, r: 0.268, p < 0.01, r: 0.374, p < 0.01, r: 0.294, p < 0.01, respectively). Study limitations: The small sample size and the retrospective design of the study are limitations. Conclusion: Elevated C-reactive protein, monocyte-to-high-density-lipoprotein ratio, neutrophil-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio were significantly associated with psoriasis. A positive correlation between C-reactive protein and monocyte-to-high-density-lipoprotein ratio leads to the suggestion that monocyte-to-high-density-lipoprotein ratio might be a reliable parameter in psoriasis during the follow-up. The relationship between the diasease and inflammatory parameters might provide early detection of cardiovascular morbidities in psoriasis patients. © 2020 Elsevier B.V., All rights reserved.Publication Open Access Presepsin levels in experimental sepsis and massive bowel resection models in rats(International Institute of Anticancer Research, 2020) Demirel, Ozlem Unay; Iǧnak, Seyda; Oruǧ, Taner; Yüksel, Meral; Demirel, Ozlem Unay, Department of Biochemistry, Bahçeşehir Üniversitesi, Istanbul, Turkey; Iǧnak, Seyda, Department of Biology, Bahçeşehir Üniversitesi, Istanbul, Turkey; Oruǧ, Taner, Department of Surgery, Medicana International Istanbul, Beylikduzu, Turkey; Yüksel, Meral, Department of Medical Laboratory Techniques, Marmara Üniversitesi, Istanbul, TurkeyBackground/Aim: Presepsin is a useful biomarker for diagnosing sepsis. This study aimed to investigate the relationship between oxidative stress and presepsin levels in animal models. Materials and Methods: Sprague-Dawley rats were used for cecal ligation and puncture (CLP) and to generate massive bowel resection (MBR) models. Trunk blood was collected for analysis of presepsin. Liver and intestinal tissue samples were taken to determine oxidative stress parameters. Results: Presepsin levels in MBR and CLP sepsis models were higher than those in control groups. Reactive oxygen and nitrogen species (RONS) and malondialdehyde levels were increased in the liver and small intestine of rats in both models, whereas glutathione levels were decreased. Conclusion: Presepsin levels and RONS may be released by the same mechanism which is closely associated with the progression of sepsis and inflammation in both CLP and MBR models. © 2021 Elsevier B.V., All rights reserved.