PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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Activation of methane by Os+: Guided-ion-beam and theoretical studies
(CHEMM, 2013) Armentrout P.B.; Parke, Laura; Hinton, Christopher; Citir, Murat; 0000-0002-7957-110X; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Citir, Murat
Activation of methane by the third-row transition-metal cation Os + is studied experimentally by examining the kinetic energy dependence of reactions of Os+ with CH4 and CD4 using guided-ion-beam tandem mass spectrometry. A flow tube ion source produces Os+ in its electronic ground state and primarily in the ground spin-orbit level. Dehydrogenation to form [Os,C,2 H]++H2 is exothermic, efficient, and the only process observed at low energies for reaction of Os+ with methane, whereas OsH+ dominates the product spectrum at higher energies. The kinetic energy dependences of the cross sections for several endothermic reactions are analyzed to give 0K bond dissociation energies (in eV) of D0(Os+-C)=6.20±0. 21, D0(Os+-CH)=6.77±0.15, and D0(Os +-CH3)=3.00±0.17. Because it is formed exothermically, D0(Os+-CH2) must be greater than 4.71eV, and a speculative interpretation suggests the exothermicity exceeds 0.6eV. Quantum chemical calculations at the B3LYP/def2-TZVPP level show reasonable agreement with the experimental bond energies and with previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surfaces. Notably, the structure of the dehydrogenation product is predicted to be HOsCH+, rather than OsCH2+, in contrast to previous work.
Advances in Micelle-based Drug Delivery: Cross-linked Systems
(BENTHAM SCIENCE PUBL LTDEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer; 0000-0002-6887-6549; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü
There are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.
Aerial Swarms: Recent Applications and Challenges
(Springer, 2021) Mohamed Abdelkader; Samet Güler; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Güler, Samet
Purpose of review: Currently, there is a large body of research on multi-agent systems addressing their different system theoretic aspects. Aerial swarms as one type of multi-agent robotic systems have recently gained huge interest due to their potential applications. However, aerial robot groups are complex multi-disciplinary systems and usually research works focus on specific system aspects for particular applications. The purpose of this review is to provide an overview of the main motivating applications that drive the majority of research works in this field, and summarize fundamental and common algorithmic components required for their development. Recent findings: Most system demonstrations of current aerial swarms are based on simulations, some have shown experiments using few 10 s of robots in controlled indoor environment, and limited number of works have reported outdoor experiments with small number of autonomous aerial vehicles. This indicates scalability issues of current swarm systems in real world environments. This is mainly due to the limited confidence on the individual robot's localization, swarm-level relative localization, and the rate of exchanged information between the robots that is required for planning safe coordinated motions. Summary: This paper summarizes the main motivating aerial swarm applications and the associated research works. In addition, the main research findings of the core elements of any aerial swarm system, state estimation and mission planning, are also presented. Finally, this paper presents a proposed abstraction of an aerial swarm system architecture that can help developers understand the main required modules of such systems.
The Age Structure, Stringency Policy, Income, and Spread of Coronavirus Disease 2019: Evidence From 209 Countries
(FRONTIERS MEDIA SAAVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE CH-1015, SWITZERLAND, 2021) Bilgili, Faik; Dundar, Munis; Kuskaya, Sevda; Lorente, Daniel Balsalobre; Unlu, Fatma; Gencoglu, Pelin; Mugaloglu, Erhan; 0000-0001-5362-6259; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Mugaloglu, Erhan
This article aims at answering the following questions: (1) What is the influence of age structure on the spread of coronavirus disease 2019 (COVID-19)? (2) What can be the impact of stringency policy (policy responses to the coronavirus pandemic) on the spread of COVID-19? (3) What might be the quantitative effect of development levelincome and number of hospital beds on the number of deaths due to the COVID-19 epidemic? By employing the methodologies of generalized linear model, generalized moments method, and quantile regression models, this article reveals that the shares of median age, age 65, and age 70 and older population have significant positive impacts on the spread of COVID-19 and that the share of age 70 and older people in the population has a relatively greater influence on the spread of the pandemic. The second output of this research is the significant impact of stringency policy on diminishing COVID-19 total cases. The third finding of this paper reveals that the number of hospital beds appears to be vital in reducing the total number of COVID-19 deaths, while GDP per capita does not affect much the level of deaths of the COVID-19 pandemic. Finally, this article suggests some governmental health policies to control and decrease the spread of COVID-19.
Aguhyper: a hyperledger-based electronic health record management framework
(PEERJ INC, 2024) Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu; 0000-0003-4983-2417; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off-chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper’s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identified in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper’s implementation configurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes significantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the field.
Air-stable, nanostructured electronic and plasmonic materials from solution-processable, silver nanocrystal building blocks
(American Chemical Society, 2014) Fafarman, Aaron T.; Hong, Sung-Hoon; Oh, Soong Ju; Caglayan, Humeyra; Ye, Xingchen; Diroll, Benjamin T.; Engheta, Nader; Murray, Christopher B.; Kagan, Cherie R.; 0000-0002-0656-614X; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Caglayan, Humeyra
Herein we describe a room-temperature, chemical process to transform silver nanocrystal solids, deposited from colloidal solutions, into highly conductive, corrosion-resistant, optical and electronic materials with nanometer-scale architectures. After assembling the nanocrystal solids, we treated them with a set of simple, compact, organic and inorganic reagents: ammonium thiocyanate, ammonium chloride, potassium hydrogen sulfide, and ethanedithiol. We find that each reagent induces unique changes in the structure and composition of the resulting solid, giving rise to films that vary from insulating to, in the case of thiocyanate, conducting with a remarkably low resistivity of 8.8 × 10-6 ·cm, only 6 times that of bulk silver. We show that thiocyanate mediates the spontaneous sintering of nanocrystals into structures with a roughness of less than 1/10th of the wavelength of visible light. We demonstrate that these solution-processed, low-resistivity, optically smooth films can be patterned, using imprint lithography, into conductive electrodes and plasmonic mesostructures with programmable resonances. We observe that thiocyanate-treated solids exhibit significantly retarded atmospheric corrosion, a feature that dramatically increases the feasibility of employing silver for electrical and plasmonic applications.
Airbnb and COVID-19: SPACE-TIME vulnerability effects in six world-cities
(Elsevier, 2022) Kourtit, Karima; Nijkamp, Peter; Östh, John; Türk, Umut; 0000-0002-8440-7048; 0000-0002-4068-8132; 0000-0002-7171-994X; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü
This study examines the COVID-19 vulnerability and subsequent market dynamics in the volatile hospitality market worldwide, by focusing in particular on individual Airbnb bookings-data for six world-cities in various continents over the period January 2020–August 2021. This research was done by: (i) looking into factual survival rates of Airbnb accommodations in the period concerned; (ii) examining place-based impacts of intracity location on the economic performance of Airbnb facilities; (iii) estimating the price responses to the pandemic by means of a hedonic price model. In our statistical analyses based on large volumes of time- and space-varying data, multilevel logistic regression models are used to trace ‘corona survivability footprints’ and to estimate a hedonic price-elasticity-of-demand model. The results reveal hardships for the Airbnb market as a whole as well as a high volatility in prices in most cities. Our study highlights the vulnerability and ‘corona echoeffects’ on Airbnb markets for specific accommodation segments in several large cities in the world. It adds to the tourism literature by testing the geographic distributional impacts of the corona pandemic on customers’ choices regarding type and intra-urban location of Airbnb accommodations.
Alantolactone ameliorates graft versus host disease in mice
(ELSEVIER, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Şerife; Çakır, Mustafa; Özcan, Alper; Yılmaz, Ebru; Karakukcu, Musa; Donmez-Altuntas, Hamiyet; Yay, Arzu Hanim; Deniz, Kemal; Altay, Derya; Arslan, Duran; Canatan, Halit; Eken, Ahmet; Unal, Ekrem; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Kendirli, Perihan Kader
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naïve (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2–18 (n = 4) and non-GVHD patients between ages 2–50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naïve phenotype (CD62L+ CD44− ). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Alzheimer Disease Associated Loci: APOE Single Nucleotide Polymorphisms in Marmara Region
(MDPI, 2024) Ismail, Aya Badeea; Dundar, Mehmet Sait; Erguzeloglu, Cemre Ornek; Ergoren, Mahmut Cerkez; Alemdar, Adem; Ozemri Sag, Sebnem; Temel, Sehime Gulsun; 0000-0002-0336-4825; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Dundar, Mehmet Sait
Alzheimer’s disease (AD) is a major global health challenge, especially among individuals aged 65 or older. According to population health studies, Turkey has the highest AD prevalence in the Middle East and Europe. To accurately determine the frequencies of common and rare APOE single nucleotide polymorphisms (SNPs) in the Turkish population residing in the Marmara Region, we conducted a retrospective study analyzing APOE variants in 588 individuals referred to the Bursa Uludag University Genetic Diseases Evaluation Center. Molecular genotyping, clinical exome sequencing, bioinformatics analysis, and statistical evaluation were employed to identify APOE polymorphisms and assess their distribution. The study revealed the frequencies of APOE alleles as follows: ε4 at 9.94%, ε2 at 9.18%, and ε3 at 80.68%. The gender-based analysis in our study uncovered a tendency for females to exhibit a higher prevalence of mutant genotypes across various SNPs. The most prevalent haplotype observed was ε3/ε3, while rare APOE SNPs were also identified. These findings align with global observations, underscoring the significance of genetic diversity and gender-specific characteristics in comprehending health disparities and formulating preventive strategies.
Analysis of CO 2 emissions and energy consumption by sources in MENA countries: evidence from quantile regressions
(Springer Nature 2021, 2021) Majed Alharthi; Eyup Dogan; Dilvin Taskin; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Dogan, Eyup
The development of economies and energy usage can significantly impact the carbon dioxide (CO2) emissions in the Middle East and North Africa (MENA) countries. Therefore, this study aims to analyze the factors that determine CO2 emissions in MENA under the environmental Kuznets curve (EKC) framework by applying novel quantile techniques on data for CO2 emissions, real income, renewable and non-renewable energy consumption, and urbanization over the period from 1990 to 2015. The results from the estimations suggest that renewable energy consumption significantly reduces the level of emissions; furthermore, its impact increases with higher quantiles. In addition, non-renewable energy consumption increases CO2 emissions, while its magnitude decreases with higher quantiles. The empirical results also confirm the validity of EKC hypothesis for the panel of MENA economies. Policymakers in the region should implement policies and regulations to promote the adoption and use of renewable energy to mitigate carbon emissions.
Analysis of coronary angiography related psychophysiological responses
(BMC, CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2011) Okkesim, Sukru; Kara, Sadik; Kaya, Mehmet G.; Asyali, Musa H.; AGÜ, Mimarlık Fakültesi, Mimarlık Bölümü;
Background: Coronary angiography is an important tool in diagnosis of cardiovascular diseases. However, it is the administration is relatively stressful and emotionally traumatic for the subjects. The aim of this study is to evaluate psychophysiological responses induced by the coronary angiography instead of subjective methods such as a questionnaire. We have also evaluated the influence of the tranquilizer on the psychophysiological responses. Methods: Electrocardiography (ECG), Blood Volume Pulse (BVP), and Galvanic Skin Response (GSR) of 34 patients who underwent coronary angiography operation were recorded. Recordings were done at three phases: "1 hour before," "during," and "1 hour after" the coronary angiography test. Total of 5 features obtained from the physiological signals were compared across these three phases. Sixteen of the patients were administered 5 mg of a tranquilizer (Diazepam) before the operation and remaining 18 were not. Results: Our results indicate that there is a strong correlation between features (LF/HF, Bk, DN1/DN2, skin conductance level and seg_mean) in terms of reflecting psychophysiological responses. However only DN1/DN2 feature has statistically significant differences between angiography phases (for diazepam: p = 0.0201, for non_diazepam p = 0.0224). We also note that there are statistically significant differences between the diazepam and non-diazepam groups for seg_mean features in "before", "during" and "after" phases (p = 0.0156, 0.0282, and 0.0443, respectively). Conclusions: The most intense sympathetic activity is observed in the "during" angiography phase for both of the groups. The obtained features can be used in some clinical studies where generation of the customized/individual diagnoses styles and quantitative evaluation of psychophysiological responses is necessary.
Analysis of the in vitro nanoparticle-cell interactions via a smoothing-splines mixed-effects model
(TAYLOR & FRANCIS LTD, 2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND, 2016) Dogruoz, Elifnur; Dayanik, Savas; Budak, Gurer; Sabuncuoglu, Ihsan; AGÜ, Mühendislik Fakültesi, Endüstri Mühendisliği Bölümü;
A mixed-effects statistical model has been developed to understand the nanoparticle (NP)-cell interactions and predict the rate of cellular uptake of NPs. NP-cell interactions are crucial for targeted drug delivery systems, cell-level diagnosis, and cancer treatment. The cellular uptake of NPs depends on the size, charge, chemical structure, and concentration of NPs, and the incubation time. The vast number of combinations of these variable values disallows a comprehensive experimental study of NP-cell interactions. A mathematical model can, however, generalize the findings from a limited number of carefully designed experiments and can be used for the simulation of NP uptake rates, to design, plan, and compare alternative treatment options. We propose a mathematical model based on the data obtained from in vitro interactions of NP-healthy cells, through experiments conducted at the Nanomedicine and Advanced Technologies Research Center in Turkey. The proposed model predicts the cellular uptake rate of silica, polymethyl methacrylate, and polylactic acid NPs, given the incubation time, size, charge and concentration of NPs. This study implements the mixed-model methodology in the field of nanomedicine for the first time, and is the first mathematical model that predicts the rate of cellular uptake of NPs based on sound statistical principles. Our model provides a cost-effective tool for researchers developing targeted drug delivery systems.
Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
(Frontiers Media S.A., 2023) Gumustop, Ismail; Ortakci, Fatih; 0000-0003-1319-0854; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Gumustop, Ismail; Ortakci, Fatih
Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species’ genetic diversity and biotechnological potential. A mere ~12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.
Analyzing the nexus between energy transition, environment and ICT: A step towards COP26 targets
(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2023) Tzeremes, Panayiotis; Dogan, Eyup; Alavijeh, Nooshin Karimi; 0000-0003-0476-5177; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Doğan, Eyüp
In line with the Sustainable Development Goals and the recent COP26 summit, energy transition, low carbon emissions and technology have become extremely important subjects in the agenda of governments and poli-cymakers. The present study thus discusses the nexus between energy transition, economic growth, CO2 emis-sions and information and communications technology (ICT) in BRICS countries applying the novel GMM-PVAR method proposed on the annual data for the period 2000-2017. This method is strong to the issue of endogeneity which is commonly faced in the context of panel data analysis but mostly ignored in the literature. The findings of this research demonstrate that carbon emissions have a positive and significant effect on energy transition; similarly, raising economic growth augments the consumption of energy transition. Furthermore, ICT is found to be a significant choice in the development of energy transition and the solution of environmental challenges. Overall, technological factors in addition to economic and environmental factors also have great roles in the development of renewable energy and energy transition. Thus, results from this study call for government supports to develop ICT across the BRICS countries.
Analyzing the nexus of COVID-19 and natural resources and commodities: Evidence from time-varying causality
(ELSEVIER SCI LTD, 2022) Doğan, Eyüp; Majeed, Muhammad Tariq; Luni, Tania; 0000-0001-9374-5025; 0000-0003-0476-5177; 0000-0002-7022-1920; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Doğan, Eyüp
Even though a few studies have focused on natural resources and commodity sectors by considering the pandemic, they have only compared their status in pre-COVID19 to post-COVID19. None of the studies has directly examined the causal relationship between the pandemic, and natural resource index and the primary commodity-related sector indices. This study fills the gap of exploring the dynamic association between them by analyzing the causal relationship between the COVID19, and natural resources index and the primary commodity-related sectors (i.e., agribusiness, energy, and metals & mining) by applying a novel time-varying causality test on daily data from January 23, 2020, to November 12, 2021. The empirical results support the presence of time-varying causality from COVID19 to natural resources, agribusiness, energy and metals & mining. The results obtained from the rolling window algorithm support causal linkages between the variables however at several points it fails to capture the dynamics of linkages between the variables which is captured by the recursive window algorithm. The outcome is robust when the pandemic is proxied by either number of cases or deaths. Similarly, the findings obtained from heteroskedastic-robust specification also validate our findings. Several policy implications are further discussed in the study.
An answer to colon cancer treatment by mesenchymal stem cell originated from adipose tissue
(MASHHAD UNIV MED SCIENCES, VICE-CHANCELLOR FOR RES CTR OFF IJBMS, DANESHGAH ST, PO BOX 9138813944 - 445, MASHHAD, 00000, IRAN, 2018) Iplik, Elif; Ertugrul, Baris; Kozanoglu, İlknur; Baran, Yusuf; Cakmakoglu, Bedia; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü;
Objective(s): Colon cancer is risen up with its complex mechanism that directly impacts on its treatment as well as its common prevalence. Mesenchymal stem cells (MSCs) have been considered as a therapeutic candidate for conventional disease including cancer. In this research, we have focused on apoptotic effects of adipose tissue-derived MSCs in colon cancer. Materials and Methods: MSCs were obtained from adipose tissue and characterized by Flowcytometer using suitable antibodies. MSCs, HT-29, HCT-116, RKO and healthy cell line MRC5 were cultured by different seeding procedure. After cell viability assay, changes in caspase 3 enzyme activity and the level of phosphatidylserine were measured. Results: For cell viability assay, a 48 hr incubation period was chosen to seed all cells together. There was a 1.36-fold decrease in caspase 3 enzyme activity by co-treatment of RKO and MSCs in addition to 2.02-fold decrease in HT-29 and MSCs co-treatment, and 1.103-fold increase in HCT-116 and MSCs. The results demonstrated that HCT-116 led to the highest rate of apoptotic cell death (7.5%) compared with other cells. Conclusion: We suggest that MSCs might remain a new treatment option for cancer by its differentiation and repair capacity.
Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells
(SAGE PUBLICATIONS LTD, 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND, 2016) Kiraz, Yagmur; Neergheen-Bhujun, Vidushi S.; Rummun, Nawraj; Baran, Yusuf; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü;
Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts.
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
(MDPIST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND, 2021) Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, Burcu; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Bakir-Gungor, Burcu
In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is possible to unravel biomarkers by comparing the gene expression levels under different conditions, such as disease vs. control, treated vs. not treated, drug A vs. drug B, etc. This problem refers to a well-studied problem in the machine learning domain, i.e., the feature selection problem. In biological data analysis, most of the computational feature selection methodologies were taken from other fields, without considering the nature of the biological data. Thus, integrative approaches that utilize the biological knowledge while performing feature selection are necessary for this kind of data. The main idea behind the integrative gene selection process is to generate a ranked list of genes considering both the statistical metrics that are applied to the gene expression data, and the biological background information which is provided as external datasets. One of the main goals of this review is to explore the existing methods that integrate different types of information in order to improve the identification of the biomolecular signatures of diseases and the discovery of new potential targets for treatment. These integrative approaches are expected to aid the prediction, diagnosis, and treatment of diseases, as well as to enlighten us on disease state dynamics, mechanisms of their onset and progression. The integration of various types of biological information will necessitate the development of novel techniques for integration and data analysis. Another aim of this review is to boost the bioinformatics community to develop new approaches for searching and determining significant groups/clusters of features based on one or more biological grouping functions.
ARL13B regulates juxtaposed cilia-cilia elongation in BBSome dependent manner in Caenorhabditis elegans
(CELL PRESS, 2025) Turan, Merve Gul; Kantarci, Hanife; Cevik, Sebiha; Kaplan, Oktay I.; 0000-0002-0935-1929; 0000-0002-8733-0920; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; Turan, Merve Gul; Kantarci, Hanife; Cevik, Sebiha; Kaplan, Oktay I.
The interaction of cilia with various cellular compartments, such as axons, has emerged as a new form of cellular communication. Cilia often extend in proximity to cilia from neighboring cells. However, the mechanisms driving this process termed juxtaposed cilia-cilia elongation (JCE) remain unclear. We use fluorescence-based visualization to study the mechanisms of coordinated cilia elongation in sensory neurons of Caenorhabditis elegans. Conducting a selective gene-based screening strategy reveals that ARL-13/ARL13B and MKS-5/RPGRIP1L are essential for JCE. We demonstrate that ARL-13 modulates JCE independently of cilia length. Loss of NPHP-2/inversin along with HDAC-6 enhances the cilia misdirection phenotype of arl-13 mutants, while disruption of the BBSome complex, but not microtubule components, partially suppresses the JCE defects in arl-13 mutants. We further show changes in the phospholipid compositions in arl-13 mutants. We suggest that ARL-13 contributes to JCE, in part, through the modulation of the ciliary membrane.
Arousal state transitions occlude sensory-evoked neurovascular coupling in neonatal mice
(NATURE PORTFOLIO, 2023) Gheres, Kyle W. W.; Unsal, Hayreddin S. S; Han, Xu; Zhang, Qingguang; Turner, Kevin L.; Zhang, Nanyin; Drew, Patrick J.; 0009-0000-6906-2144; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Unsal, Hayreddin S. S
In the adult sensory cortex, increases in neural activity elicited by sensory stimulation usually drive vasodilation mediated by neurovascular coupling. However, whether neurovascular coupling is the same in neonatal animals as adults is controversial, as both canonical and inverted responses have been observed. We investigated the nature of neurovascular coupling in unanesthetized neonatal mice using optical imaging, electrophysiology, and BOLD fMRI. We find in neonatal (postnatal day 15, P15) mice, sensory stimulation induces a small increase in blood volume/BOLD signal, often followed by a large decrease in blood volume. An examination of arousal state of the mice revealed that neonatal mice were asleep a substantial fraction of the time, and that stimulation caused the animal to awaken. As cortical blood volume is much higher during REM and NREM sleep than the awake state, awakening occludes any sensory-evoked neurovascular coupling. When neonatal mice are stimulated during an awake period, they showed relatively normal (but slowed) neurovascular coupling, showing that that the typically observed constriction is due to arousal state changes. These result show that sleep-related vascular changes dominate over any sensory-evoked changes, and hemodynamic measures need to be considered in the context of arousal state changes. A combination of optical imaging, electrophysiology, and BOLD fMRI in unanesthetized neonatal mice reveals that sleep-related vascular changes dominate over sensory-evoked changes.

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