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https://hdl.handle.net/20.500.12939/79

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Foam-based antibacterial hydrogel composed of carboxymethyl cellulose/polyvinyl alcohol/cerium oxide nanoparticles for potential wound dressing
(2024) Orhan, Burcu; Karadeniz, Duygu; Kalaycıoğlu, Zeynep; Kaygusuz, Hakan; Torlak, Emrah; Erim, F. Bedia
Foam-based wound dressing materials produced by dispersing gas phases in a polymeric material are soft, adapt to the body shape, and allow the absorption of wound exudate due to their porous structure. Most of these formulations are based on synthetic substances such as polyurethane. However, biopolymers have entered the field as a new player thanks to their biocompatible and sustainable nature. Incorporating biopolymers in formulations is gaining interest in scientific literature, and we extend this approach by adding antibacterial cerium oxide nanoparticles to biopolymer formulation. We introduce a novel biopolymer composite of carboxymethyl cellulose (CMC), polyvinyl alcohol (PVA), and cerium oxide nanoparticles (CeO2 NPs), namely PVA-CMC@CeO2. This mixture was first foamed and then cross-linked with sodium tetraborate solution, followed by a freeze-thaw process. After the novel material's spectroscopic, structural, and morphological characterization, we investigated its swelling, drug-delivery, antibacterial, and biodegradability properties PVA-CMC@CeO2 dressing effectively inhibits Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) growth and delivers the antibiotic drug silver sulfadiazine for up to 6 h. The antibacterial properties, good swelling, and drug release profile of the blend material show promising potential in wound care applications.
Tunable fano resonance in mid-infrared region based on asymmetric graphene nanoribbon arrays
(2024)
An asymmetric graphene nanoribbon structure is presented to reach plasmonic Fano resonance in mid-infrared region when illuminated by a TM polarized light. Each mode of the Fano resonance is connected to the resonance mode occurred around each of nanoribbons with different width in the structure. Numerical studies show that the position and amplitude of the double resonances can be actively adapted via geometrical modification of the graphene structure or altering the doping level. Moreover, simulation results show highly remarkable enhancement in normalized electric field intensity for the asymmetric graphene structure compared to its symmetric counterparts. This feature is advantageous for construction of high sensitivity instruments such as sensors or filters.
Formulas and relations for bernoulli-type numbers and polynomials derıve from bessel function
(Korean Mathematical Society, 2023) Şimşek, Selin Selen Özbek; Şimşek, Yılmaz
The main purpose of this paper is to give some new identities and properties related to Bernoulli type numbers and polynomials associated with the Bessel function of the first kind. We give symmetric properties of the Bernoulli type numbers and polynomials. Moreover, using generating functions and the Faà di Bruno’s formula, we derive some new formulas and relations related to not only these polynomials, but also the Bernoulli numbers and polynomials and the Euler numbers and polynomials.
Reversible codes and applications to DNA codes over (F42t[u]/(u2 - 1)
(American Institute of Mathematical Sciences, 2023) Alsuraiheed, Turki; Öztaş, Elif Segah; Ali, Shakir; Yılgör, Merve Bulut
Let n ≥ 1 be a fixed integer. Within this study, we present a novel approach for discovering reversible codes over rings, leveraging the concept of r-glifted polynomials. This technique allows us to achieve optimal reversible codes. As we extend our methodology to the domain of DNA codes, we establish a correspondence between 4t-bases of DNA and elements within the ring (formula presented). By employing a variant of r-glifted polynomials, we successfully address the challenges of reversibility and complementarity in DNA codes over this specific ring. Moreover, we are able to generate reversible and reversible-complement DNA codes that transcend the limitations of being linear cyclic codes generated by a factor of xn − 1.
COVID-19 modeling based on real geographic and population data
(Turkiye Klinikleri, 2023) Baysazan, Emir; Berker, A. Nihat; Mandal, Hasan; Kaygusuz, Hakan
Background/aim: Intercity travel is one of the most important parameters for combating a pandemic. The ongoing COVID-19 pandemic has resulted in different computational studies involving intercity connections. In this study, the effects of intercity connections during an epidemic such as COVID-19 are evaluated using a new network model. Materials and methods: This model considers the actual geographic neighborhood and population density data. This new model is applied to actual Turkish data by means of provincial connections and populations. A Monte Carlo algorithm with a hybrid lattice model is applied to a lattice with 8802 data points. Results: Around Monte Carlo step 70, the number of active cases in Türkiye reaches up to 8.0% of the total population, which is followed by a second wave at around Monte Carlo step 100. The number of active cases vanishes around Monte Carlo step 160. Starting with İstanbul, the epidemic quickly expands between steps 60 and 100. Simulation results fit the actual mortality data in Türkiye. Conclusion: This model is quantitatively very efficient in modeling real-world COVID-19 epidemic data based on populations and geographical intercity connections, by means of estimating the number of deaths, disease spread, and epidemic termination.
Encryption and decryption of the data by using the terms of the Lucas Series
(2021) Duman, Mehmet; Güney Duman, Merve
The sequence, whose initial condition is 2 and 1, obtained by summing the two terms preceding it, is called the Lucas sequence. The terms of this series continue as 2, 1, 3, 4, 7, 11, 18, 29, ... respectively. The features of the Lucas sequence have been studied in many projects in the literature and many studies have been done on Lucas series in applied sciences. Cryptology is the science that deals with encrypting data, transferring it securely from one point to another, and converting the encrypted data to the previous one. It includes cryptography and cryptoanalysis. Different encryption-decryption methods have been developed to ensure the security of the data from the past to the present. Some of these are Caesar, Affine, Vigenere and RSA. There are two types of encryption systems in cryptology. The first one is symmetric (secret key) encryption and the another one is asymmetric (public key) encryption. In this study; using the features of the Lucas sequence, studies on cryptology, which deals with the correct encryption, transfer and decryption of data, have been carried out and an example of cryptology algorithm has been given. With Lucas cipher, the letters in the alphabet and the space character are each mapped to the terms of the Lucas sequence. Later, starting from the first term of the Lucas sequence, the encryption was strengthened by adding Lucas terms. As a result, the text to be encrypted has been turned into a symbolic representation of the numbers. Then, the necessary information for deciphering the text which is encrypted with numbers is given.
Sustainable alginate-carboxymethyl cellulose superabsorbents prepared by a novel quasi-cryogelation method
(Springer, 2022) Orhan, Burcu; Kaygusuz, Hakan; Erim, F. Bedia
The research in biopolymer-based superabsorbents is gaining importance in the green chemistry feld thanks to their environmentally friendly properties. In this study, a biopolymer-based superabsorbent made of calcium ion crosslinked alginate/ carboxymethyl cellulose composite was prepared by a new quasi-cryogelation process, where the complete ionic gelation takes place before the freezing step, in contrast to the conventional cryogelation technique in which gelation occurs under semi-frozen conditions. Thanks to the facile quasi-cryogelation method, the morphology of the gels changed and a signifcant increase in water absorption properties has been achieved. The swelling properties of the material were investigated in distilled water and diferent physiological fuids. Results show that the proposed material shows good water absorption property where a water absorption of 2343% was reached and even after fve cycles this value was 1200%. As a result, this study reports a biopolymer-based sustainable superabsorbent which is appropriate for various applications such as the removal of pollutants from water or diaper production.
Role of Gauss-Bonnet corrections in a DGP brane gravitational collapse
(2022) Tavakoli, Yaser; Ardabili, Ahad K.; Bouhmadi-Lopez, Mariam; Moniz, Paulo Vargas
An Oppenheimer-Snyder (OS)-type collapse is considered for a Dvali-Gabadadze-Porrati (DGP) brane, whereas a Gauss-Bonnet (GB) term is provided for the bulk. We study the combined effect of the DGP induced gravity plus the GB curvature, regarding any modification of the general relativistic OS dynamics. Our paper has a twofold objective. On the one hand, we investigate the nature of singularities that may arise at the collapse end state. It is shown that all dynamical scenarios for the contracting brane would end in one of the following cases, depending on conditions imposed: either a central shell-focusing singularity or what we designate as a ???sudden collapse singularity.??? On the other hand, we also study the deviations of the exterior spacetime from the standard Schwarzschild geometry, which emerges in our modified OS scenario. Our purpose is to investigate whether a black hole always forms regarding this brane world model. We find situations where a naked singularity emerges instead.
Effective photocatalytic degradation of malachite green dye by Fe(III)-Cross-linked alginate-carboxymethyl cellulose composites
(2022) Karadeniz, Duygu; Kahya, Nilay; Erim, F. Bedia
Fe(III) ion cross-linked alginate-carboxymethyl cellulose composite beads (Fe@(Alg-CMC)) were prepared and used as a novel photocatalyst for the degradation of malachite green (MG) dye. Fe (III) ions bound to the carboxyl groups of the biopolymer composite provided reactive radicals under UV light, and degradation of the dye in an aqueous solution occurred at a high percentage and in a short time. Unlike Fenton’s reaction, effective degra- dation of the dye was carried out without adding H2O2 to the medium. Optimum conditions of dye degradation were investigated. Under UV-A light, 98.8%±0.7% dye degradation was achieved at pH 4 of 10 ppm MG solution with 0.1 g of Fe@(Alg-CMC) beads in 30 min. Experimental results fitted Langmuir-Hinshelwood kinetic modeling, which explains the kinetics of the heterogeneous catalytic processes. A rate constant (k) of 0.115 ± 0.001 min
Angiotensin (1-7) peptide replacement therapy with plasma transfusion in COVID-19
(Transfusion and Apheresis Science, 2022) Önal, Hasan; Üçüncü Ergun, Nurcan; Arslan, Bengü; Topuz, Şeyma; Yılmaz Semerci, Seda; Topuzoğulları, Murat; Kalkan, Ali; Aydın Yoldemir, Şengül; Suner, Nurettin; Kocataş, Ali
Aim: To determine whether convalescent angiotensin (1−7) peptide replacement therapy with plasma (peptide plasma) transfusion can be beneficial in the treatment of critically ill patients with severe coronavirus 2 (SARS-CoV-2) infection. Study design: Case series of 9 critically ill patients with laboratory-confirmed COVID-19 who met the following criteria: severe pneumonia with rapid progression and continuously high viral load despite antiviral treatment. Peptide plasma: Plasma with angiotensin (1−7) content 8–10 times higher than healthy plasma donors was obtained from suitable donors. Peptide plasma transfusion was applied to 9 patients whose clinical status and/or laboratory profile deteriorated and who needed intensive care for 2 days. Results: In our COVID-19 cases, favipiravir, low molecular weight heparin treatment, which is included in the treatment protocol of the ministry of health, was started. Nine patients with oxygen saturation of 93% and below despite nasal oxygen support, whose clinical and/or laboratory deteriorated, were identified. The youngest of the cases was 36 years old, and the oldest patient was 85 years old. 6 of the 9 cases had male gender. 3 cases had been smoking for more than 10 years. 4 cases had at least one chronic disease. In all of our cases, SARS CoV2 lung involvement was bilateral and peptide plasma therapy was administered in cases when oxygen saturation was 93% and below despite nasal oxygen support of 5 liters/minute and above, and intensive care was required. Although it was not reflected in the laboratory parameters in the early period, 8 patients whose saturations improved with treatment were discharged without the need for intensive care. However, a similar response was not obtained in one case. Oxygen requirement increased gradually and, he died in intensive care process. An increase of the platelet count was observed in all cases following the peptide plasma treatment. Conclusion: In this preliminary case series of 9 critically ill patients with COVID-19, administration of plasma containing angiotensin (1−7) was followed by improvement in their clinical status. The limited sample size and study design preclude a definitive statement about the potential effectiveness of this treatment, and these observations require evaluation in clinical trials.
Heterologous expression, biochemical characterisation and computational analysis of Bacteroides fragilis enolase
(2022) Uğureli, Erennur; Koçer, Sinem; Sarıyer, Emrah; Mutlu, Ozal; İnci, Tuğba Gül; Turgut Balık, Dilek
Bacteriodes fragilis is an anaerobic bacterium found in the human intestinal flora. In this study, BfEno was targeted with a structure-based drug design approach because inhibition of this enzyme may prevent both the aerobic and anaerobic pathways due to its role in the glycolytic pathway. First, the gene encoding BfEno was cloned, expressed and the protein produced over 95% purity. The Km and Vmax values of BfEno were determined as 314.9 µM and 256.2 µmol/min.mg, respectively. Drug-like chemicals were retrieved from the ZINC database for high-throughput virtual screening analyses. As a result of screening study, the ZINC91441604 has been proposed to bind to the active site of the enzyme and remain stable. The same compound exhibited weak binding to the human enolases than the bacterial enolase. Hence, ZINC91441604 may be proposed as a novel candidate for further in vitro and in vivo drug analysis towards the treatment of B. fragilis infections.
Detection and classification of skin lesion based neural networks
(IEEE, 2021) Abdullah, Hadeel N.; Abdullah, Aseel N.; Halef, Nejat H.; Abduljaleel, Hala K.
Skin cancers emerge from the skin due to the growth of untypical cells that dispersal to other parts of the body. Through early detection, very high success rates can be achieved in treating most cases of skin cancer, including the most aggressive and deadly forms and types. The objective of this work is brief as follows: First, to collect a real database from Al-Kindi Hospital and Baghdad Medical City. Next, choose smart classification methods for the early detection of skin lesions. Second, propose a new technique for reducing database noise obtained based on convolutional neural networks (CNN). Third, a new algorithm has been proposed for dividing a cutaneous lesion into cutaneous images based on the straight active-contour and morphological processes.
Retinal fundus images of optical disk detection
(IEEE, 2021) Elwiya, Lina; Mohammed, Alaa Hamid; Jasim, Zinah Khalid Jasim
Optical circle identification (OD) is a significant advance in the programmed division and investigation of pictures of the retina. In this article, another approach is proposed for recognizing RE cutoff points from shading retinal fundus pictures. Morphological factors and differentiation improvement methods are utilized related to a Gaussian contrast (DOG) channel to acquire an OD limit. Our proposed calculation makes a high progress rate with comparative computational time. The exhibition of our proposed strategy was assessed on 1660 pictures addressing six freely accessible informational collections; STARE, DRIVE, ARIA, DIARETDB1, DIARETDB0, and MESSIDOR informational indexes. The trial results show that the pictures from the DRIVE, ARIA, DIARETDB1 and DIARETDB0 datasets have a 100% achievement rate, which is superior to the precision of the most recent age techniques, which is under 99% for the ARIA, DIARETDB1 and DIARETDB0 informational indexes. While coming to 98.8% and 99.83% for the STARE and MESSIDOR datasets individually, the calculation runs with a normal computational season of 1.2 seconds.
Efficient energy and QoS based routing algorithm for wireless body area network
(IEEE, 2021) Ojelade, Afolabi K.; Ibrahim, Abdullahi Abdu; Ata, Oğuz
—In this study, a Novel architecture comprising a sink node is designed to minimize power consumption as well as improve quality of service (QoS) of wireless body area network (WBAN). Furthermore, in the quest to enhance the network lifetime and QoS, we utilized MAC protocol to classify the physiological attributes into normal and critical data. A routing protocol known as Efficient Energy and QoS (EEQ) algorithm is implemented to transmit the normal data through the shortest and appropriate route. According to the EEQ algorithm, the weight value is considered based on parameters such as network lifetime, link stability and throughput. The data is conveyed through the path having the highest weight value. However, the data is encrypted using RSA algorithm. In order to compare EEQ with other existing protocols, a number of simulations is executed on OMNet++ software to show that the proposed work outperforms other related research works.
Electronic health records system using blockchain technology
(Special Issue on Current Trends in Management and Information Technology, 2021) Hasan, Q. H.; Yassin, Ali A.; Ata, Oğuz
Blockchain technology is one of the most important and disruptive technologies in the world. Nowadays the healthcare center needs to share patient databases over all departments of the healthcare centers. Although, electronic healthcare records overcome several problems compared with manual records, but still suffer from many issues such as security, the privacy of patient data overall as we should transfer over a database from a central database to a decentralized database. In this paper, we proposed a good security system to manage the data of patients based on blockchain technology and a decentralized database. Depending on decentralized database and blockchain. Our proposed system provides the secure exchange of patient data, reliability, and high efficiency in sharing data during transaction data network equivalence checking to perform this validation of patient information in the blockchain and healthcare centers.
CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics
(TÜBİTAK, 2021) Doğan, Ayça; Gurbaov, Rafig; Severcan, Mete; Severcan, Feride
From the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes in some functional groups belonging to lipids, proteins and nucleic acids. In addition, the non-vaccinated and vaccinated groups were successfully separated from each other by principal component analysis (PCA) and linear discriminant analysis (LDA). This proof-of-concept study will encourage future studies on CoronaVac as well as other vaccines and will lead to make a comparison between different vaccines to establish a better understanding of the vaccination outcomes on serum biomolecules.
Development of high accuracy classifier for the speaker recognition system
(Hindawi, 2021) Al-Hassani, Raghad Tariq; Atilla, Doğu Çağdaş; Aydın, Çağatay
Speech signal is enriched with plenty of features used for biometrical recognition and other applications like gender and emotional recognition. Channel conditions manifested by background noise and reverberation are the main challenges causing feature shifts in the test and training data. In this paper, a hybrid speaker identification model for consistent speech features and high recognition accuracy is made. Features using Mel frequency spectrum coefficients (MFCC) have been improved by incorporating a pitch frequency coefficient from speech time domain analysis. In order to enhance noise immunity, we proposed a single hidden layer feed-forward neural network (FFNN) tuned by an optimized particle swarm optimization (OPSO) algorithm. The proposed model is tested using 10-fold cross-validation over different levels of Adaptive White Gaussian Noise (AWGN) (0-50 dB). A recognition accuracy of 97.83% was obtained from the proposed model in clean voice environments. However, a noisy channel is realized with lesser impact on the proposed model as compared with other baseline classifiers such as plain-FFNN, random forest (RF), -nearest neighbour (KNN), and support vector machine (SVM).
Genomic chronicle of SARS-CoV-2: A mutational analysis with over 1 million genome sequences
(TÜBİTAK, 2021) Uğurel, Osman Mutluhan; Ata, Oğuz; Turgut Balık, Dilek
Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.
Bronchopulmonary dysplasia and wnt pathway-associated single nucleotide polymorphisms
(Springer Nature, 2021) Akat, Ayberk; Semerci, Yılmaz; Uğurel, Osman Mutluhan; Erdemir, Ayşegül; Danhaive, Olivier; Çetinkaya, Merih; Turgut-Balık, Dilek
Aim: Genetic variants contribute to the pathogenesis of bronchopulmonary dysplasia (BPD). The aim of this study is to evaluate the association of 45 SNPs with BPD susceptibility in a Turkish premature infant cohort. Methods: Infants with gestational age <32 weeks were included. Patients were divided into BPD or no-BPD groups according to oxygen need at 28 days of life, and stratified according to the severity of BPD. We genotyped 45 SNPs, previously identified as BPD risk factors, in 192 infants. Results: A total of eight SNPs were associated with BPD risk at allele level, two of which (rs4883955 on KLF12 and rs9953270 on CHST9) were also associated at the genotype level. Functional relationship maps suggested an interaction between five of these genes, converging on WNT5A, a member of the WNT pathway known to be implicated in BPD pathogenesis. Dysfunctional CHST9 and KLF12 variants may contribute to BPD pathogenesis through an interaction with WNT5A. Conclusions: We suggest investigating the role of SNPs on different genes which are in relation with the Wnt pathway in BPD pathogenesis. We identified eight SNPs as risk factors for BPD in this study. In-silico functional maps show an interaction of the genes harboring these SNPs with the WNT pathway, supporting its role in BPD pathogenesis. Trial registration: NCT03467828. Impact: It is known that genetic factors may contribute to the development of BPD in preterm infants. Further studies are required to identify specific genes that play a role in the BPD pathway to evaluate them as a target for therapeutic interventions. Our study shows an association of BPD predisposition with certain polymorphisms on MBL2, NFKBIA, CEP170, MAGI2, and VEGFA genes at allele level and polymorphisms on CHST9 and KLF12 genes at both allele and genotype level. In-silico functional mapping shows a functional relationship of these five genes with WNT5A, suggesting that Wnt pathway disruption may play a role in BPD pathogenesis.
5 ghz wi-fi effects on escherıchıa colı, caenorhabdıtıs elegans and human neuroblastoma cells
(Mugla Journal of Science and Technology, 2021) Dinç, Bircan
The use of 5 GHz Wi-Fi has spread and potential effects on microorganisms and human health are still under investigation. To investigate the possible effects for that, experiments were performed using three different microorganisms, Escherichia coli, SH-SY5Y human neuroblastoma cells and Caernohabditis elegans. The maximum allowed temperature for the Wi-Fi Access Point (AP) was considered in the measurement setup in order not to harm the internal circuitry of the router which can result impact the performance of the router. Suspension turbidity, optical density measurements and simultaneous counting of E. coli were performed. It was observed that 5 GHz Wi-Fi exposure slow down the E. coli growth rate at the same temperature conditions with sham exposed groups especially after the first 6 h. 5 GHz Wi-Fi induced decrease in cell viability remarkably for the cells seeded at densities 20,40, 100 (×103) and viability values were varied between 20 and 30%. C. elegans which is a nematode, plays key role in nutrient cycling and soil fertilization was affected by the radiation and egg-laying rates changed by 27.49%.

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