PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7645

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Citation - WoS: 9
Citation - Scopus: 10
An Answer To Colon Cancer Treatment by Mesenchymal Stem Cell Originated From Adipose Tissue
(Mashhad University of Medical Sciences, 2018-05) İplik, Elif Sinem; ERtuğrul, Barış; Kozanoğlu, İlknur; Baran, Yusuf
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.
Citation - WoS: 5
Citation - Scopus: 7
Arabinoxylan-Based Psyllium Seed Hydrocolloid: Single-Step Aqueous Extraction and Use in Tissue Engineering
(Elsevier B.V., 2024) Yildirim-Semerci,Ö.; Bilginer-Kartal,R.; Arslan-Yildiz,A.
Biomacromolecules derived from natural sources offer superior biocompatibility, biodegradability, and water-holding capacity, which make them promising scaffolds for tissue engineering. Psyllium seed has gained attention in biomedical applications recently due to its gel-forming ability, which is provided by its polysaccharide-rich content consisting mostly of arabinoxylan. This study focuses on the extraction and gelation of Psyllium seed hydrocolloid (PSH) in a single-step water-based protocol, and scaffold fabrication using freeze-drying method. After characterization of the scaffold, including morphological, mechanical, swelling, and protein adsorption analyses, 3D cell culture studies were done using NIH-3 T3 fibroblast cells on PSH scaffold, and cell viability was assessed using Live/Dead and Alamar Blue assays. Starting from day 1, high cell viability was obtained, and it reached 90 % at the end of 15-day culture period. Cellular morphology on PSH scaffold was monitored via SEM analysis; cellular aggregates then spheroid formation were observed throughout the study. Collagen Type-I and F-actin expressions were followed by immunostaining revealing a 9- and 10-fold increase during long-term culture. Overall, a single-step and non-toxic protocol was developed for extraction and gelation of PSH. Obtained results unveiled that PSH scaffold provided a favorable 3D microenvironment for cells, holding promise for further tissue engineering applications. © 2024 Elsevier B.V.
Assessment of Undergraduate Health Students' Perception and Satisfaction on Training and Participation in Community Health Outreach
(Springer, 2023) Adegbore, Abidemi Kafayat; Adedokun, Amudatu Ambali; Adegoke, Juliet Ifeoluwa; Lawal, Maruf Ayobami; Oke, Muse
AimThe need to improve training of health professionals has increased in recent years due to increasing frequencies of public health events. Consequently, a descriptive cross-sectional survey was carried out to determine the level of satisfaction and knowledge acquired by undergraduate students in the health sciences during a community health outreach program.Subject and methodsStudents were invited to complete an online-administered questionnaire (consisting of both open- and closed-ended questions) to assess their perceptions and experiences on the community health outreach program. Additionally, the survey was carried out to assess the quality of training provided and obtain suggestions for further improvements. Responses were collected and analysed using Microsoft Excel.ResultsMost respondents (>83%) reported satisfaction with the community diagnosis and community intervention briefing and training sessions. All respondents reported familiarity with standard community health outreach instruments and were capable of identifying environmental health risk factors that may contribute to the spread of communicable diseases. Interestingly, respondents reported greater appreciation of health challenges faced by rural communities. However, respondents expressed dissatisfaction with the duration of the outreach program (24%) and funding (15%).ConclusionAlthough respondents reported overall satisfaction with the organization and execution of the health outreach program, certain aspects of the program were deemed unsatisfactory. Despite the shortcomings, we believe that our student-centred learning strategy is readily adaptable for training future healthcare professionals and improving health literacy of rural communities, particularly in sub-Saharan Africa.
Citation - WoS: 3
Citation - Scopus: 3
Automated Labeling of Cancer Textures in Larynx Histopathology Slides Using Quasi-Supervised Learning
(Science Printers and Publishers Inc., 2014) Önder, Devrim; Sarıoğlu, Sülen; Karaçalı, Bilge
OBJECTIVE: To evaluate the performance of a quasisupervised statistical learning algorithm, operating on datasets having normal and neoplastic tissues, to identify larynx squamous cell carcinomas. Furthermore, cancer texture separability measures against normal tissues are to be developed and compared either for colorectal or larynx tissues. STUDY DESIGN: Light microscopic digital images from histopathological sections were obtained from laryngectomy materials including squamous cell carcinoma and nonneoplastic regions. The texture features were calculated by using co-occurrence matrices and local histograms. The texture features were input to the quasisupervised learning algorithm. RESULTS: Larynx regions containing squamous cell carcinomas were accurately identified, having false and true positive rates up to 21% and 87%, respectively. CONCLUSION: Larynx squamous cell carcinoma versus normal tissue texture separability measures were higher than colorectal adenocarcinoma versus normal textures for the colorectal database. Furthermore, the resultant labeling performances for all larynx datasets are higher than or equal to that of colorectal datasets. The results in larynx datasets, in comparison with the former colorectal study, suggested that quasi-supervised texture classification is to be a helpful method in histopathological image classification and analysis.
Citation - WoS: 40
Citation - Scopus: 45
Bioactive Diatomite and Poss Silica Cage Reinforced Chitosan/Na-carboxymethyl Cellulose Polyelectrolyte Scaffolds for Hard Tissue Regeneration
(Elsevier, 2019) Tamburacı, Sedef; Kimna, Ceren; Tıhmınlıoğlu, Funda
Recently, natural polymers are reinforced with silica particles for hard tissue engineering applications to induce bone regeneration. In this study, as two novel bioactive agents, effects of diatomite and polyhedral oligomeric silsesquioxanes (POSS) on chitosan (CS)/Na-carboxymethylcellulose (Na-CMC) polymer blend scaffolds are examined. In addition, the effect of silica reinforcements was compared with Si-substituted nano-hydroxyapatite (Si-Hap) particles. The morphology, physical and chemical structures of the scaffolds were characterized with SEM, liquid displacement, FT-IR, mechanical analysis, swelling and degradation studies. The particle size and the crystal structure of diatomite, POSS and Si-Hap particles were determined with DLS and XRD analyses. In vitro studies were performed to figure out the cytotoxicity, proliferation, ALP activity, osteocalcin production and biomineralization to demonstrate the promising use of natural silica particles in bone regeneration. Freeze-dried scaffolds showed 190-307 mu m pore size range and 61-70% porosity. Both inorganic reinforcements increased the mechanical strength, enhanced the water uptake capacity and fastened the degradation rate. The nanocomposite scaffolds did not show any cytotoxic effect and enhanced the surface mineralization in osteogenic medium. Thus, diatomite and POSS cage structures can be potential reinforcements for nanocomposite design in hard tissue engineering applications.
Citation - WoS: 9
Citation - Scopus: 10
Biofouling-Resistant Ultrafiltration Membranes Via Codeposition of Dopamine and Cetyltrimethylammonium Bromide With Retained Size Selectivity and Water Flux
(American Chemical Society, 2022-08-10) Cihanoğlu, Aydın; Schiffman, Jessica D.; Alsoy Altınkaya, Sacide
Biofouling is a serious problem in ultrafiltration (UF) membrane applications. Modifying the surface of membranes with low molecular weight, commercially available antibacterial chemistries is an excellent strategy to mitigate biofouling. Herein, we report a new strategy to impart antibacterial and anti-biofouling behavior without changing the support membrane’s size selectivity and pure water permeance (PWP). To this end, a strong antibacterial agent, cetyltrimethylammonium bromide (CTAB), was codeposited with dopamine onto commercial polyethersulfone (PES) UF membranes in the presence of nitrogen (N2) gas backflow. The PWP and pore size of the support membrane did not change with codeposition, confirming the benefit of N2 backflow in mitigating the solution intrusion phenomenon. X-ray photoelectron spectroscopy (XPS), surface ζ potentials, and contact angle measurements confirmed the successful codeposition of polydopamine (PDA) and CTAB onto the membrane. Among three different CTAB concentrations systematically investigated, the membrane functionalized with CTAB at the critical micelle concentration (CMC) provided the best anti-biofouling activity against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and retained its surface ζ potential after being stored in 1 M NaCl (pH = 6.8) for 3 months. Our results demonstrate the potential of using a facile, one-step approach to modify commercial UF membranes without compromising their pore size or flux, while simultaneously endowing antibacterial activity.
Citation - WoS: 5
Citation - Scopus: 5
Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models
(Academic Press Inc., 2024) Güler,G.; Acikgoz,E.; Mukhtarova,G.; Oktem,G.
Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc.
Citation - WoS: 14
Citation - Scopus: 18
Comparison of Antimicrobial Activity of Allium Sativum Cloves From China and Taskopru, Turkey
(Hindawi Publishing Corporation, 2018) Yetgin, Ali; Canlı, Kerem; Altuner, Ergin Murat
In this study, antimicrobial activities of two different samples of Allium sativum L. from Turkey (TR) (Taskopru, Kastamonu, Turkey) and China (CN) were determined. A broad spectrum of Gram-negative and Gram-positive bacteria (17 bacteria) including species of Bacillus, Enterobacter, Enterococcus, Escherichia, Klebsiella, Listeria, Pseudomonas, Salmonella, and Staphylococcus were used for testing antibacterial activity. In addition, antifungal activity against Candida albicans was also investigated. Antimicrobial activity was tested by using 3 different processes (chopping, freezing, and slicing by the disk diffusion method). The results showed that TR garlic presented more antimicrobial activity than CN garlic. Mechanism of activity of CN garlic could be proposed to be different from that of TR garlic.
Citation - WoS: 13
Citation - Scopus: 18
Database Covering the Prayer Movements Which Were Not Available Previously
(Nature Publishing Group, 2023-05-12) Mihçin, Şenay; Şahin, Ahmet Mert; Yılmaz, Mehmet; Alpkaya, Alican Tuncay; Tuna, Merve; Akdeniz, Sevinç; Can, Nuray Korkmaz; Tosun, Aliye; Şahin, Serap
Lower body implants are designed according to the boundary conditions of gait data and tested against. However, due to diversity in cultural backgrounds, religious rituals might cause different ranges of motion and different loading patterns. Especially in the Eastern part of the world, diverse Activities of Daily Living (ADL) consist of salat, yoga rituals, and different style sitting postures. A database covering these diverse activities of the Eastern world is non-existent. This study focuses on data collection protocol and the creation of an online database of previously excluded ADL activities, targeting 200 healthy subjects via Qualisys and IMU motion capture systems, and force plates, from West and Middle East Asian populations with a special focus on the lower body joints. The current version of the database covers 50 volunteers for 13 different activities. The tasks are defined and listed in a table to create a database to search based on age, gender, BMI, type of activity, and motion capture system. The collected data is to be used for designing implants to allow these sorts of activities to be performed.
Citation - WoS: 48
Citation - Scopus: 51
Development of Si Doped Nano Hydroxyapatite Reinforced Bilayer Chitosan Nanocomposite Barrier Membranes for Guided Bone Regeneration
(Elsevier, 2021) Tamburacı, Sedef; Tıhmınlıoğlu, Funda
Guided Bone Regeneration (GBR) is a widely used process for the treatment of periodontal defects to prevent the formation of surrounding soft tissue at the periodontal defect and to provide hard tissue regeneration. Recently GBR designs have focused on the development of resorbable natural polymer-based barrier membranes due to their biodegradability and excellent biocompatibility. The aim of this study is to fabricate a novel bilayer nanocomposite membrane with microporous sublayer composed of chitosan and Si doped nanohydroxyapatite particles (Si-nHap) and chitosan/PEO nanofiber upper layer. Bilayer membrane was designed to prevent epithelial and fibroblastic cell migration and growth impeding bone formation with its upper layer and to support osteogenic cell bioactivity at the defect site with its sublayer. Microporous and nanofiber layers were fabricated by using freeze-drying and electrospinning techniques respectively. The effect of Si-nHap content on the morphological, mechanical and physical properties of the composites were investigated using SEM, AFM, micro-Ct, compression test, water uptake capacity and enzymatic degradation study. Antimicrobial properties of nanocomposite membranes were investigated with tube dilution and disk diffusion methods. In vitro cytotoxicity of bilayer membranes was evaluated. Saos-2 and NIH/3T3 proliferation studies were carried out on each layer. In vitro bioactivity of Saos-2 and NIH/3T3 cells were evaluated with ALP activity and hydroxyproline content respectively. Results showed that Si-nHap incorporation enhanced the mechanical and physical properties as well as controlling biodegradability of the polymer matrix. Besides, Si-nHap loading induced the bioactivity of Saos-2 cells by enhancing cell attachment, spreading and biomineralization on the material surface. Thus, results supported that designed bilayer nanocomposite membranes can be used as a potential biomaterial for guided bone regeneration in periodontal applications.
Citation - WoS: 61
Citation - Scopus: 71
Diatomite Reinforced Chitosan Composite Membrane as Potential Scaffold for Guided Bone Regeneration
(Elsevier Ltd., 2017-11) Tamburacı, Sedef; Tıhmınlıoğlu, Funda
In this study, natural silica source, diatomite, incorporated novel chitosan based composite membranes were fabricated and characterized for bone tissue engineering applications as possible bone regeneration membrane. The effect of diatomite loading on the mechanical, morphological, chemical, thermal and surface properties, wettability and in vitro cytotoxicity and cell proliferation on of composite membranes were investigated and observed by tensile test, atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), protein adsorption assay, air/water contact angle analysis and WST-1 respectively. Swelling studies were also performed by water absorption capacity determination. Results showed that incorporation of diatomite to the chitosan matrix increased the surface roughness, swelling capacity and tensile modulus of membranes. An increase of about 52% in Young's modulus was achieved for 10 wt% diatomite composite membranes compared with chitosan membranes. High cell viability results were obtained with indirect extraction method. Besides, in vitro cell proliferation and ALP activity results showed that diatom incorporation significantly increased the ALP activity of Saos-2 cells cultured on chitosan membranes. The novel composite membranes prepared in the present study with tunable properties can be considered as a potential candidate as a scaffold in view of its enhanced physical & chemical properties as well as biological activities for bone tissue engineering applications.
Citation - WoS: 11
Citation - Scopus: 11
Effect of Alkali Metal Hydroxides on the Morphological Development and Optical Properties of Ceria Nanocubes Under Hydrothermal Conditions
(American Scientific Publishers, 2011-04-01) Kepenekçi, Özlem; Eanes, Mehtap; Demir, Mustafa Mustafa
Nanocrystalline cerium(IV) oxide (CeO2, ceriaceria) particles were produced via the hydrothermal treatment of cerium nitrate hexahydrate with various alkali metal hydroxides (MOH: M = Li, Na, K). Experimental conditions such as [MOH], reaction temperature, and reaction time were studied. Particle morphology as well as size of crystallites was precisely controlled by choice of experimental conditions. While rod-shaped particles were obtained at 120 C, well-defined nanocubes were formed at higher temperatures regardless of the choice of MOH. Examination of particle growth kinetics, in the final stages of crystallization, showed that particle growth rate is controlled by two different mechanisms. Grain boundary diffusion controls the particle growth in the presence of NaOH with an activation energy of 113.8 kj/mol and surface diffusion for LiOH ad KOH with the activation energy of 43.0–150.9 kj/mol, respectively. In addition, the particles exhibit strong violet and blue emissions at 400 nm and 370 nm. The former emission originates from excitation of a wide band gap of CeO2. The latter one is attributed to the trivalency of the cerium ion and appears to be sensitive to all the experimental conditions studied. Both extending reaction time and increasing temperature reduce the intensity of the 370 nm emission and increase the intensity of the 400 nm emission.
Citation - WoS: 24
Effect of pH and Hydration on the Normal and Lateral Interaction Forces Between Alumina Surfaces
(2006) Polat, Mehmet; Sato, Kimiyasu; Nagaoka, Takaaki; Watari, Koji
Normal and lateral interaction forces between alumina surfaces were measured using Atomic Force Microscopy-Colloid Probe Method at different pH. The normal force curves exhibit a well-defined repulsive barrier and an attractive minimum at acidic pH and the DLVO theory shows excellent agreement with the data. The normal forces are always repulsive at basic pH and the theory fails to represent the measurements. Lateral forces are almost an order of magnitude smaller in the basic solutions. These differences, which have important implications in the study of stability and rheology, are attributed to the hydration of the alumina surface at basic pH. © 2013 Elsevier B.V., All rights reserved.
Citation - WoS: 12
Effects of Fat Reduction on the Stability, Microstructure, Rheological and Color Characteristics of White-Brined Cheese Emulsion With Different Emulsifying Salt Amounts
(Korean Society for Food Science of Animal Resources, 2018) Urgu, Müge; Ünlütürk, Sevcan; Koca, Nurcan
Cheese emulsion is an intermediate product for the production of cheese powder and needs to be stable, homogeneous and pumpable characteristics to convey to the spray drier. This study was conducted to evaluate the effects of fat reduction and emulsifying salt (ES) amount in cheese emulsion systems on the physicochemical characteristics. Reduced-fat (RF) and full-fat (FF) white-brined cheese emulsions were produced with different dry matters (DM; 15%-25% excluding ES) and ES concentrations (0%-3% based on cheese weight). Stable cheese emulsion was obtained at lower DM in RF cheese emulsion than that of FF cheese emulsion. Reduction in the amount of ES resulted in instability of both emulsions. Apparent viscosity with pseudoplastic flow behavior significantly increased with the decrease of fat content in stable cheese emulsions. Microstructure of emulsions appeared to be related to the fat content, stability and degree of emulsification. Reduction of fat content caused to get less lightness and more greenness in color, whereas yellowness was significantly decreased by increase in the amount of ES. In conclusion, fat reduction resulted in higher viscosities of cheese emulsion due to inducing the increment of protein, and the addition amount of ES considered as very important factor to produce stable cheese emulsion without protein precipitation or cream separation. Therefore, for preparation of RF cheese emulsion using a variety of white-brined cheese, lower amounts of DM would be suggested in this study to obtain homogenous droplets in the atomizing process of spray drying.
Citation - WoS: 5
Citation - Scopus: 9
Efficient Privacy-Preserving Whole-Genome Variant Queries
(Oxford University Press, 2022-04) Akgün, Mete; Pfeifer, Nico; Kohlbacher, Oliver
Motivation: Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data. Results: We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.
Citation - WoS: 60
Citation - Scopus: 64
Electrospun Gelma Fibers and P(hema) Matrix Composite for Corneal Tissue Engineering
(Elsevier Ltd., 2021) Arıca, Tuğçe A.; Güzelgülgen, Meltem; Yıldız, Ahu Arslan; Demir, Mustafa Muammer
The development of biocompatible and transparent three-dimensional materials is desirable for corneal tissue engineering. Inspired from the cornea structure, gelatin methacryloyl-poly(2-hydroxymethyl methacrylate) (GelMA-p(HEMA)) composite hydrogel was fabricated. GelMA fibers were produced via electrospinning and covered with a thin layer of p(HEMA) in the presence of N,N?-methylenebisacrylamide (MBA) as cross-linker by drop-casting. The structure of resulting GelMA-p(HEMA) composite was characterized by spectrophotometry, microscopy, and swelling studies. Biocompatibility and biological properties of the both p(HEMA) and GelMA-p(HEMA) composite have been investigated by 3D cell culture, red blood cell hemolysis, and protein adsorption studies (i.e., human serum albumin, human immunoglobulin and egg white lysozyme). The optical transmittance of the GelMA-p(HEMA) composite was found to be approximately 70% at 550 nm. The GelMA-p(HEMA) composite was biocompatible with tear fluid proteins and convenient for cell adhesion and growth. Thus, as prepared hydrogel composite may find extensive applications in future for the development of corneal tissue engineering as well as preparation of stroma of the corneal material. © 2020 Elsevier B.V.
Citation - WoS: 7
Citation - Scopus: 6
Engineered Silica Nanoparticles Are Biologically Safe Vehicles To Deliver Drugs or Genes To Liver Cells
(Elsevier Ltd., 2021) Tüncel, Özge; Kahraman, Erkan; Bağcı, Gülsün; Atabey, Neşe; Özçelik, Serdar
Engineered silica nanoparticles (SiNP) are emerging materials for medical applications. Evaluating biological responses of specific cells treated with engineered silica nanoparticles is however essential. We synthesized and characterized the physicochemical properties of silica nanoparticles with two different sizes of 10 and 100 nm (10SiNP and 100SiNP) dispersed in cell culture medium. HuH-7, an epithelial-like human hepatoblastoma cell line and SK-HEP-1, a liver sinusoidal endothelial cell line (LSEC) are employed to evaluate their biological responses for the SiNP treatment. Primary human lymphocytes are used to assess genotoxicity recommended by OECD guidelines while erythrocytes are used to assess hemolytic activity. The engineered silica nanoparticles are not able to produce radical species, to alter the mitochondrial membrane potential, and induce any adverse effects on cell proliferation. The colony formation ability of HuH-7 hepatoblastoma cells was not affected following the SiNP treatment. Furthermore, SiNPs do not induce hemolysis of red blood cells and are not genotoxic. These findings suggest that SiNPs regardless of the size, amount, and incubation time are biologically safe vehicles to deliver drugs or genes to the liver. © 2020 Elsevier B.V.
Estimation of Heat Production Rate Using Thermal Data During Exercise in Indoor Environments: a Study of Heat Storage Rate in Male Athletes
(Springer, 2024) Balcı, Görkem Aybars; Avcı, Ali Berkay; Çolakoğlu, Muzaffer; Başaran, Tahsin
The increasing preference for indoor exercise spaces highlights the relationship between indoor thermal environments and physiological responses, particularly concerning thermal comfort during physical activity. Determining the metabolic heat production rate during exercise is essential for optimizing the thermal comfort, well-being, and performance of individuals engaged in physical activities. This value can be determined during the activity using several methods, including direct calorimetry measurement, indirect calorimetry that uses analysis of respiratory gases, or approximations using collected data such as speed, body mass, and heart rate. The study aimed to calculate the metabolic heat production rate by infrared thermal evaluation (ITE) based on the body's thermal balance approach and compare it with the values determined by indirect calorimetry (IC). Fourteen participants volunteered for the study, using a cycling ergometer in a controlled climatic chamber. After the familiarization sessions, maximal O2 intake levels (VO2max) were determined through maximal graded exercise tests. Subsequently, constant work rate exercise tests were performed at 60% of VO2max for 20 min. The metabolic heat production rates were calculated by IC and ITE for each athlete individually. Respiratory gases were used to determine IC, while body skin and core temperatures, along with physical environmental data, were applied to calculate ITE using the human body thermal balance approximation of ASHRAE. According to the results, heat storage rates were misleading among the body's heat transfer modes, particularly during the first 8 min of the exercise. ITE showed a moderate level of correlation with IC (r: 0.03-0.86) with a higher level of dispersion relative to the mean (CV%: 12-84%). Therefore, a new equation (ITEnew) for the heat storage rates was proposed using the experimental data from this study. The results showed that ITEnew provided more precise estimations for the entire exercise period (p > 0.05). Correlations between ITEnew and IC values were consistently strong throughout the exercise period (r: 0.62-0.85). It can be suggested that ITEnew values can predict IC during the constant work rate steady-state exercise.
Citation - WoS: 5
Citation - Scopus: 5
Excessive Replacement Changes Drive Evolution of Global Sheep Prion Protein (prnp) Sequences
(Springer, 2022-05) Sezgin, Efe; Teferedegn, Eden Yitna; Ün, Cemal; Yaman, Yalçın
Sheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.
Citation - Scopus: 19
Feature Selection Has a Large Impact on One-Class Classification Accuracy for Micrornas in Plants
(Hindawi Publishing Corporation, 2016) Yousef, Malik; Demirci, Müşerref Duygu Saçar; Khalifa, Waleed; Allmer, Jens
MicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently computational miRNA detection is mainly performed using machine learning and in particular two-class classification. For machine learning, the miRNAs need to be parametrized and more than 700 features have been described. Positive training examples for machine learning are readily available, but negative data is hard to come by. Therefore, it seems prerogative to use one-class classification instead of two-class classification. Previously, we were able to almost reach two-class classification accuracy using one-class classifiers. In this work, we employ feature selection procedures in conjunction with one-class classification and show that there is up to 36% difference in accuracy among these feature selection methods. The best feature set allowed the training of a one-class classifier which achieved an average accuracy of 95.6% thereby outperforming previous two-class-based plant miRNA detection approaches by about 0.5%. We believe that this can be improved upon in the future by rigorous filtering of the positive training examples and by improving current feature clustering algorithms to better target pre-miRNA feature selection.

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