WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

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Citation - Scopus: 1
AlN Piezoelectric Quad-Actuators for 2D Optical Micro Scanning
(Taylor & Francis Ltd, 2022) Hah, Dooyoung
Piezoelectric actuation has been one of the frequent choices for optical micro scanning. In most of the cases, lead zirconate titanate (PZT) has been used as the piezoelectric material. However, PZT has a potential issue in biomedical applications due to the content of lead. For this, AlN can be used as an alternative. The main drawback of AlN is its low piezoelectric coefficients. In order to overcome such a drawback, this paper presents a novel actuator configuration, designed for a quasi-static operation mode. Quad-actuators and meander-shaped hinges are the essence of the proposed actuator configuration. Numerical simulation study is carried out to prove the concept of the device. The study also shows that the proposed scanner can have the optical scan angle of 9 degree at a quasi-static mode. Two different scan modes, a raster-like mode and a Lissajous mode are tested, demonstrating the two-dimensional scanning capability of the device.
Citation - WoS: 2
Citation - Scopus: 2
Analysis of the Motion of a Rigid Rod on a Circular Surface Using Interpolated Variational Iteration Method
(Yildiz Technical Univ, 2022) Coskun, Safa Bozkurt; Senturk, Erman; Atay, Mehmet Tarik
In this paper, interpolated variational iteration method (IVIM) is applied to investigate the vibration period and steady-state response for the motion of rigid rod rocking back and forth on a circular surface without slipping. The problem can be considered as a strongly nonlinear oscillator. In this solution procedure, analytical variational iteration technique is utilized by evaluating the integrals numerically. The approximate analytical results produced by the presented method are compared with the other existing solutions available in the literature. The advantage of using numerical evaluation of integrals, the method becomes fast convergent and a highly accurate solution can be obtained within seconds. The authors believe that the presented technique has potentially wide application in the other nonlinear oscillation problems.
Apatinib Sensitizes Human Breast Cancer Cells Against Navitoclax and Venetoclax Despite Up-Regulated Bcl-2 and Mcl-1 Gene Expressions
(Kare Publ, 2021) Kavakcioglu Yardimci, Berna; Ozgun Acar, Ozden; Semiz, Asli; Sen, Alaattin
OBJECTIVE Defects in apoptotic cell death which restrict the success of conventional cytotoxic therapies have pivotal roles in a number of pathological conditions including cancer. However, a novel drug class targeting pro-survival Bcl-2 protein family members has been developed with the understanding of the structures and interactions of Bcl-2 proteins. Within this new class, Bcl-2/Bcl-xL inhibitor Navitoclax and Bcl-2 specific inhibitor Venetoclax have been shown to demonstrate strong anticancer activities on several types of cancers. But their low affinity to other anti-apoptotic proteins limits their clinical usage. Here, we investigated the cytotoxic and apoptotic effects of Navitoclax/Venetoclax and their combinations with specific tyrosine kinase inhibitor Apatinib on estrogen receptor (ER)-positive MCF-7 and ER-negative MDA-MB-231 breast cancer cell lines. METHODS MTT assay was used for the evaluation of the inhibition of cancer cell proliferation. ELISA test and Quantitative real-time PCR assay was performed to determine the role of caspase-3, Bak, Bax, Bcl-2, Bcl-xL and Mcl-1 proteins in the inhibition of cell proliferation triggered by the tested agents. RESULTS We found that aggressive MDA-MB-231 cell line was more sensitive to all tested agents. Apatinib significantly enhanced Navitoclax/Venetoclax mediated inhibition of cell viability in both cancer cell lines despite up-regulation in the expression levels of Bcl-2 and Mcl-1 genes. We further demonstrated significant Bak/Bax and caspase-3 expression in less aggressive MCF-7 cells. CONCLUSION Our findings have impacts on Navitoclax/Venetoclax plus Apatinib based therapy for breast adenocarcinoma. On the other hand, further studies should be conducted to elucidate the mechanisms underlying synergistic effects of Navitoclax/Venetoclax plus Apatinib combinations.
Citation - WoS: 3
Citation - Scopus: 3
Artificial Cells: A Potentially Groundbreaking Field of Research and Therapy
(Sciendo, 2024) Dundar, Mehmet Sait; Yildirim, A. Baki; Yildirim, Duygu T.; Akalin, Hilal; Dundar, Munis
Artificial cells are synthetic constructs that mimic the architecture and functions of biological cells. Artificial cells are designed to replicate the fundamental principles of biological systems while also have the ability to exhibit novel features and functionalities that have not been achieved before. Mainly, Artificial cells are made up of a basic structure like a cell membrane, nucleus, cytoplasm and cellular organelles. Nanotechnology has been used to make substances that possess accurate performance in these structures. There are many roles that artificial cells can play such as drug delivery, bio-sensors, medical applications and energy storage. An additional prominent facet of this technology is interaction with biological systems. The possibility of synthetic cells being compatible with living organisms opens up the potential for interfering with specific biological activities. This element is one of the key areas of research in medicine, aimed at developing novel therapies and comprehending life processes. Nevertheless, artificial cell technology is not exempt from ethical and safety concerns. The interplay between these structures and biological systems may give rise to questions regarding their controllability and safety. Hence, the pursuit of artificial cell research seeks to reconcile ethical and safety concerns with the potential advantages of this technology.
Citation - WoS: 1
Citation - Scopus: 3
Biosynthesis of Novel Naphthoquinone Derivatives in the Commonly-Used Chassis Cells Saccharomyces Cerevisiae and Escherichia Coli
(Pleiades Publishing inc, 2021) Wu, W.; Wang, S.; Zhang, H.; Guo, W.; Lu, H.; Xu, H.; Sun, L.
Naphthoquinones harboring 1,4-naphthoquinone pharmacophore are considered as privileged structures in medicinal chemistry. In pharmaceutical industry and fundamental research, polyketide naphthoquinones were widely produced by heterologous expression of polyketide synthases in microbial chassis cells, such as Saccharomyces cerevisiae and Escherichia coli. Nevertheless, these cell factories still remain, to a great degree, black boxes that often exceed engineers' expectations. In this work, the biotransformation of juglone or 1,4-naphthoquinone was conducted to generate novel derivatives and it was revealed that these two naphthoquinones can indeed be modified by the chassis cells. Seventeen derivatives, including 6 novel compounds, were isolated and their structural characterizations indicated the attachment of certain metabolites of chassis cells to naphthoquinones. Some of these biosynthesized derivatives were reported as potent antimicrobial agents with reduced cytotoxic activities. Additionally, molecular docking as simple and quick in silico approach was performed to screen the biosynthesized compounds for their potential antiviral activity. It was found that compound 11 and 17 showed the most promising binding affinities against Nsp9 of SARS-CoV-2, demonstrating their potential antiviral activities. Overall, this work provides a new approach to generate novel molecules in the commonly used chassis cells, which would expand the chemical diversity for the drug development pipeline. It also reveals a novel insight into the potential of the catalytic power of the most widely used chassis cells.
Citation - WoS: 12
Citation - Scopus: 15
CO2 Emissions, Real GDP, Renewable Energy and Tourism: Evidence From Panel of the Most-Visited Countries
(Cesky Statistical office, 2017) Dogan, Eyup
Previous studies on the energy-environment-growth literature overlook the investigation of the most-visited countries. Since these countries do not only belong to the largest economies and the top carbon dioxide (CO2) emitters in the world but are also listed in renewable energy country attractiveness index, this study analyzes the impacts of real GDP, renewable energy and tourism on the level of CO2 emissions for the top 10 most-visited countries. Applying several panel econometric approaches, we find out that renewable energy mitigates the pollution whereas real GDP and tourism contribute to the level of emissions. Thus, regulatory policies are necessary to increase the awareness of sustainable tourism. In addition, the use of renewable energy and the adoption of clean technologies in tourism sector as well as in producing goods and services play a significant role in CO2 mitigation.
Colorectal Cancer Prediction via Applying Recursive Cluster Elimination With Intra-Cluster Feature Elimination on Metagenomic Pathway Data
(Springer International Publishing AG, 2024) Temiz, Mustafa; Kuzudisli, Cihan; Yousef, Malik; Bakir-Gungor, Burcu
Advances in next-generation sequencing and in "-omics" technologies enable the characterization of the human gut microbiome. Colorectal cancer (CRC), the third most common cancer worldwide, is caused by genetic mutations, environmental influences, and abnormalities in the gut microbiota. The aim of this study is to identify pathways that influence host metabolism in CRC patients. The CRC-related metagenomic dataset used in this study contains the relative abundance values of 551 pathways calculated for 1262 samples. Here, two different approaches based on the feature grouping reduce the number of features by considering relevant features as groups, eliminate irrelevant features, and perform classification. The recursive cluster elimination with intra-cluster feature elimination (RCE-IFE) approach achieves anAUCof 0.72 using an average of 66.2 features on CRC-associated metagenomics dataset. In these experiments, P163-PWY: L-lysine fermentation to acetate and butanoate and PWY-6151: S-adenosyl-L-methionine cycle I pathways are identified as potential biomarkers associated with CRC. These experiments also reduce the number of features reported by both approaches in P163-PWY: L-lysine fermentation to acetate and butanoate and PWY-6151: Sadenosyl-L-methionine cycle I pathways reported by both approaches are considered possible CRC-related biomarkers. This study contributes to the molecular diagnosis and treatment of colorectal cancer by revealing the pathways associated with CRC. Our results are promising for the study of the gut microbiota and its role in CRC.
Citation - WoS: 3
Combined Effect of Midostaurin and Sphingosine Kinase-1 Inhibitor on FMS-Like Tyrosine Kinase 3 (FLT3) Wild Type Acute Myeloid Leukemia Cells
(Walter de Gruyter Gmbh, 2022) Sahin, Hande Nur; Adan, Aysun
Objectives Therapeutic potential of clinically approved FLT3 inhibitor midostaurin has been neglected in wild-type FLT3 positive acute myeloid leukemia (AML). Sphingosine kinase-1 (SK-1) having anti-proliferative functions is studied in various cancers, but not in FLT3 wild-type AML. We aimed to develop new therapeutic strategies to combat FLT3 wild-type AML by combining midostaurin with SK-1 inhibitor (SKI II) in THP1 cells. Methods The anti-proliferative effects of midostaurin, SKI II and in combination on THP1 cells were determined by MTT assay. The combination indexes were calculated using calcusyn software. SK-1 expression and PARP cleavage were checked by western blot. Cell cycle distributions (PI staining) and apoptosis (annexin-V/PI dual staining) were assessed by flow cytometry for each agent alone and in combinations. Results Midostaurin decreased SK-1 protein level. Midostaurin, SKI II and certain combinations decreased cell viability in a dose dependent manner. The combined anti-leukemic effects of the aforementioned drug combination afforded additive effect. Co-administration induced both necrosis and apoptosis via phosphatidylserine externalization, PARP cleavage and cell cycle arrest at G0/G1 and S phases. Conclusions Targeting sphingosine kinase-1 together with FLT3 inhibition could be a novel mechanism to increase limited clinic response to midostaurin in wild-type FLT3 overexpressing AML after further pre-clinical studies.
Citation - WoS: 2
Comparison of Deep Learning and Conventional Machine Learning Methods for Classification of Colon Polyp Types
(Sciendo, 2021) Dogan, Refika Sultan; Yilmaz, Bulent
Determination of polyp types requires tissue biopsy during colonoscopy and then histopathological examination of the microscopic images which tremendously time-consuming and costly. The first aim of this study was to design a computer-aided diagnosis system to classify polyp types using colonoscopy images (optical biopsy) without the need for tissue biopsy. For this purpose, two different approaches were designed based on conventional machine learning (ML) and deep learning. Firstly, classification was performed using random forest approach by means of the features obtained from the histogram of gradients descriptor. Secondly, simple convolutional neural networks (CNN) based architecture was built to train with the colonoscopy images containing colon polyps. The performances of these approaches on two (adenoma & serrated vs. hyperplastic) or three (adenoma vs. hyperplastic vs. serrated) category classifications were investigated. Furthermore, the effect of imaging modality on the classification was also examined using white-light and narrow band imaging systems. The performance of these approaches was compared with the results obtained by 3 novice and 4 expert doctors. Two-category classification results showed that conventional ML approach achieved significantly better than the simple CNN based approach did in both narrow band and white-light imaging modalities. The accuracy reached almost 95% for white-light imaging. This performance surpassed the correct classification rate of all 7 doctors. Additionally, the second task (three-category) results indicated that the simple CNN architecture outperformed both conventional ML based approaches and the doctors. This study shows the feasibility of using conventional machine learning or deep learning based approaches in automatic classification of colon types on colonoscopy images.
Citation - WoS: 11
Citation - Scopus: 15
A Comparison of Proactive and Reactive Environmental Strategies in Green Product Innovation
(Inderscience Publishers, 2019) Genç, Ebru; Di Benedetto, C. Anthony
Companies are exposed to different kinds of pressures to respond to environmental sustainability issues. It is critical to understand how firms integrate environmental issues into their corporate agendas and how these integration strategies affect corporate performance. This paper investigates factors that motivate firms to adopt environmental marketing strategies and their relative impact on green product innovation performance. A comprehensive conceptual framework is developed and tested that portrays the antecedents and consequences of environmental marketing strategy (EMS). The results show that developing environmental strategies that exceed regulations (proactive strategies) leads to better new product performance than those that only adhere to regulations (reactive strategies). In addition, we find that commitment from top management becomes critical only for proactive strategies, not for reactive strategies. Finally, with regard to the consequences, we show that environmental marketing strategies lead to new product advantage and, ultimately, improved sustainable new product performance. © 2021 Elsevier B.V., All rights reserved.
Citation - WoS: 30
Citation - Scopus: 30
Compatibility of Superplasticizers With Limestone-Metakaolin Blended Cementitious System
(Springer, 2015) Zaribaf, Behnaz H.; Uzal, Burak; Kurtis, Kimberley
This study investigates the performance of polycarboxylate ether (PCE), polymelamine sulfonate (PMS), sodium lignosulfonate and naphthalene formaldehyde condensate (PNS) superplasticizers (SPs) with ASTM C595 Type IL cement (with up to 15% calcium carbonate) combined with 10 and 30 % metakaolin (MK) substitutions by mass. The required dosage of each SP for 10 % and 30 % MK substitutions were determined based on mini slump test to establish equivalent paste flow. At these dosage rates, the effects of SPs on setting time, hydration kinetics, and strength development were measured. Life cycle assessment (LCA) was carried out on different cement compositions used in this study to evaluate the greenhouse gas emissions and embodied energy of limestone-metakaolin blended cement with SP addition. While MK substitution decreases the workability of samples and shortens the setting time, this study shows that adequate dosages of a compatible type of SP can be used to compensate for these effects. Of the SPs examined, PCE and PMS are found to be more compatible, compared to PNS and sodium lignosulfonate, with limestone-metakaolin blended cements.
Comprehensive Prediction of FBN1 Targeting Mirnas: A Systems Biology Approach for Marfan Syndrome
(Galenos Publishing House, 2025) Orhan, M.E.; Demirci, Y.M.; Saçar Demirci, M.D.S.
Objective: Marfan syndrome (MFS) is a genetic connective tissue disorder primarily caused by mutations in the FBN1 gene. Emerging evidence highlights the regulatory role of microRNAs (miRNAs) in modulating gene expression in MFS, but a systematic investigation into miRNAs targeting FBN1 is lacking. This study aimed to comprehensively identify miRNAs interacting with the FBN1 transcript to reveal potential molecular regulators and therapeutic targets. Methods: Human miRNA sequences were retrieved from miRBase (Release 22.1), and the canonical FBN1 transcript (RefSeq: NM_000138.5) was used for target prediction. Computational interaction analysis was conducted using the psRNATarget server with stringent parameters to detect potential miRNA binding sites. Expression profiles and disease associations of the top candidate miRNAs were further investigated through database integration and literature review. Results: Out of 2656 human mature miRNAs analyzed, 251 were predicted to bind FBN1, with the hsa-miR-181 family exhibiting the highest number of predicted interactions. Evidence from the literature highlighted dysregulation of hsa-miR-181 expression in MFS patients, suggesting a functional role in disease pathophysiology. Conclusion: This study identifies key members of the hsa-miR-181 family as post-transcriptional regulators of FBN1, offering new insights into miRNA-driven mechanisms in MFS. These findings support the potential of RNA-based diagnostics and therapeutic strategies targeting miRNA-FBN1 interactions. ©Copyright 2025 The Author.
Citation - WoS: 19
Citation - Scopus: 26
Computational Prediction of Functional MicroRNA-mRNA Interactions
(Humana Press Inc, 2019) Demirci, Muserref Duygu Sacar; Yousef, Malik; Allmer, Jens
Proteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is driven by miRNAs acting as recognition sequences for their target mRNAs within a larger regulatory machinery. A miRNA can have many target mRNAs and an mRNA can be targeted by many miRNAs which makes it difficult to experimentally discover all miRNA-mRNA interactions. Therefore, computational methods have been developed for miRNA detection and miRNA target prediction. An abundance of available computational tools makes selection difficult. Additionally, interactions are not currently the focus of investigation although they more accurately define the regulation than pre-miRNA detection or target prediction could perform alone. We define an interaction including the miRNA source and the mRNA target. We present computational methods allowing the investigation of these interactions as well as how they can be used to extend regulatory pathways. Finally, we present a list of points that should be taken into account when investigating miRNA-mRNA interactions. In the future, this may lead to better understanding of functional interactions which may pave the way for disease marker discovery and design of miRNA-based drugs.
Citation - Scopus: 1
Correlation of PAPP-A Values With Maternal Characteristics, Biochemical and Ultrasonographic Markers of Pregnancy
(Marmara Univ, Fac Medicine, 2021) Kaymakcalan, Hande; Uzut, Ommu Gulsum; Harkonen, Juho; Bakir Gungor, Burcu
Objective: Our aim is to investigate whether there is a correlation of pregnancy-associated plasma protein A (PAPP-A) values with other variables in pregnancy and maternal characteristics. Materials and Methods: We retrospectively analyzed the relation between the PAPP-A levels, demographics, biochemical and ultrasonographic markers of the first trimester screening of 11,842 pregnant women seen at a tertiary hospital between November 2002 and November 2008. Results: A significant difference between PAPP-A values of the diabetic and non-diabetic pregnant women were observed (p=0.0005, Mann-Whitney U test). In terms of weight, crown-rump length, Beta-hCG values, significant differences were observed between low and medium level PAPP-A subgroups and between low and high level PAPP-A subgroups. PAPP-A levels were found to differ significantly between the pregnant women of Caucasian origin and other racial origins. Conclusions: Pregnant women with different ethnic and medical backgrounds have different PAPP-A values and other markers of the aneuploidy screening. 'lb make patient specific risk predictions, understanding these interactions and differences is important. Future studies are needed to understand the pathopyhsiology behind these differences.
Cytotoxic and Cytostatic Effects of Targeting mTOR and Hedgehog Pathways in Acute Myeloid Leukemia
(Istanbul Univ, 2022) Cicek, Enes; Kucuktas, Fulya Mina; Yenigul, Munevver; Akcok, Emel Basak Gencer
Objectives: Acute myeloid leukemia (AML) is a highly aggressive heterogeneous hematopoietic malignancy characterized by a rapid and abnormal proliferation of immature myeloid leukemia cells in the bone marrow and peripheral blood. Aberrant alterations in signal transduction pathways are strongly associated with the progression of AML. This study aimed to investigate cell viability and the cell cycle in AML cells by targeting the Hedgehog and mTOR signaling pathways with rapamycin and GANT61. Materials and Method: The antiproliferative effect of rapamycin and GANT61 was assessed by the MTT cell viability assay in two AML cell lines: CMK and MOLM-13. The effect of the inhibitors on cell-cycle distribution was determined using propidium iodide staining and measured with flow cytometry. Results: Rapamycin, an mTOR inhibitor, and GANT61, a Gli-1 inhibitor, decreased the cell proliferation of CMK and MOLM-13 cells. The IC20 values, which is the drug concentration that inhibits cell growth by 20%, were combined and administered to the cells. The results show the drugs to have a combinatorial inhibitory effect on CMK cells but not on MOLM-13 cells. In addition, the combination of drugs arrested the cells during the G0/G1 phase. Conclusion: This study suggests a novel combination therapy approach for AML via mTOR and Hedgehog signaling pathway inhibition using rapamycin and GANT61, respectively. It also suggest further studies be performed to reveal the mechanism of action.
Developing a Label Propagation Approach for Cancer Subtype Classification Problem
(Tubitak Scientific & Technological Research Council Turkey, 2022) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa
Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.
Development of Resistant Starch Type-5 and Its Utilization in Cookie-Preparation
(North University Center Baia Mare, 2025) Oskaybas-Emlek, Betul; Ozbey, Ayse; Kahraman, Kevser
The objective of this study was the production of resistant starch type-5 (RS-5), its characterization, and utilization in cookie making. In first part of the study, the effects of starch-fatty acid complex formation (RS-5) between tapioca starch and lauric acid on the structure, digestibility, thermal and morphological properties of tapioca starch were investigated. X-ray diffraction revealed that the RS-5 had a V-type crystalline pattern. FT-IR analysis showed that a distinctive peak at 2846 cm-1 was only observed in RS-5. The resistant starch (RS) content of native starch increased from 22.76% to 28.02% with RS-5 formation. In the second part of the study, the RS-5 was added as a replacement for wheat flour with 10%, 20%, and 30% compared to control sample made with 100% wheat flour in cookie-making. The effects of RS-5 replacement of cookie samples on some physicochemical, estimated glycemic index (eGI) value, physical, and hardness properties were determined. Compared to control cookie, the cookie samples included RS-5 had lower hardness value, higher spread ratio. The eGI value of cookie samples was slightly decreased with the replacement with RS-5. The results demonstrated that the RS-5 has good potential for developing softer cookie with no adverse impact on eGI value.
Citation - WoS: 4
Citation - Scopus: 4
Differential in Vitro Anti-Leukemic Activity of Resveratrol Combined With Serine Palmitoyltransferase Inhibitor Myriocin in FMS-Like Tyrosine Kinase 3-Internal Tandem Duplication (FLT3-LTD) Carrying AML Cells
(Springer, 2022) Ersoz, Nur Sebnem; Adan, Aysun
Treatment of FMS-like tyrosine kinase 3 (FLT3)-internal tandem duplication (ITD) AML is restricted due to toxicity, drug resistance and relapse eventhough targeted therapies are clinically available. Resveratrol with its multi-targeted nature is a promising chemopreventive remaining limitedly studied in FLT3-ITD AML regarding to ceramide metabolism. Here, its cytotoxic, cytostatic and apoptotic effects are investigated in combination with serine palmitoyltransferase (SPT), the first enzyme of de novo pathway of ceramide production, inhibitor myriocin on MOLM-13 and MV4-11 cells. We assessed dose-dependent cell viability, flow cytometric cell death and cell cycle profiles of resveratrol in combination with myriocin by MTT assay, annexin-V/PI staining and PI staining respectively. Resveratrol's dose-dependent effect on SPT protein expression was also checked by western blot. Resveratrol decreased cell viability in a dose- dependent manner whereas myriocin did not affect cell proliferation effectively in both cell lines after 48h treatments. Although resveratrol induced both apoptosis and a significant S phase arrest in MV4-11 cells, it triggered apoptosis and non-significant S phase accumulation in MOLM-13 cells. Co-administrations reduced cell viability. Increased cytotoxic effect of co-treatments was further proved mechanistically through induction of apoptosis via phosphatidylserine relocalization. The cell cycle alteration in co-treatment was significant with an S phase arrest in MV4-11 cells, however, it was not effective on cell cycle progression of MOLM-13 cells. Resveratrol also increased SPT expression. Overall, modulation of SPT together with resveratrol might be the possible explanation for resveratrol's action. It could be an integrative medicine for FLT3-ITD AML after investigating its detailed mechanism of action in relation to de novo pathway of ceramide production.
Citation - WoS: 2
Citation - Scopus: 2
Diffuse-Layer Surface Potentials of Colemanites Mined in Turkey
(Oficyna Wydawnicza Politechniki Wrocławskiej, 2022) Arslan, Dilek Senol; Drelich, Jaroslaw W.
Colemanite crystal specimens were handpicked at Kestelek, Emet (Hisarcik, Espey), Bigadic mines in Turkey for characterization of their composition and surface potential. X-ray diffraction analysis revealed no differences in mineralogical makeup of the crystals, but elemental analysis indicated differences in the type of trace (<0.1 wt%) elements. Zeta potential measurements showed small differences in zeta potential values, with isoelectric points (iep) varying from about pH = 9.6 to pH = 10.2. However, no correlation was found between iep and the type of trace elements. Additionally, atomic force microscopy (AFM) was employed to measure the colloidal interactions between a silicon nitride (Si3N4) cantilever tip and colemanite crystal surfaces in 1 wt% colemanite-saturated aqueous solutions at three different pHs (8.4, 9.4 and 11). The Derjaguin-Landau-Verwey-Overbeek theory (DLVO) was applied to examine the AFM tip interactions with colemanite surfaces in an aqueous solution of colemanite saturated solutions. The results revealed attractive forces at pH = 8.4 and 9.4 and repulsive forces at pH = 11, confirming the location of an isoelectric point for colemanite specimens somewhere between pH = 9.5 and pH = 10.1. Theoretical analysis of the force curves using the DLVO theory allowed for assessment of both surface charge density and surface potential for colemanite specimens used in this study.
Citation - WoS: 6
Citation - Scopus: 7
Dimensionality Reduction for Protein Secondary Structure and Solvent Accesibility Prediction
(World Scientific Publ Co Pte Ltd, 2018) Aydin, Zafer; Kaynar, Oguz; Gormez, Yasin
Secondary structure and solvent accessibility prediction provide valuable information for estimating the three dimensional structure of a protein. As new feature extraction methods are developed the dimensionality of the input feature space increases steadily. Reducing the number of dimensions provides several advantages such as faster model training, faster prediction and noise elimination. In this work, several dimensionality reduction techniques have been employed including various feature selection methods, autoencoders and PCA for protein secondary structure and solvent accessibility prediction. The reduced feature set is used to train a support vector machine at the second stage of a hybrid classifier. Cross-validation experiments on two difficult benchmarks demonstrate that the dimension of the input space can be reduced substantially while maintaining the prediction accuracy. This will enable the incorporation of additional informative features derived for predicting the structural properties of proteins without reducing the accuracy due to overfitting.

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