Scopus İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395

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3-State Protein Secondary Structure Prediction based on SCOPe Classes
(INST TECNOLOGIA PARANARUA PROF ALGACYR MUNHOZ MADER 3775-CIC, 81350-010 CURITIBA-PARANA, BRAZIL, 2021) Atasever, Sema; Azgınoglu, Nuh; Erbay, Hasan; Aydın, Zafer; 0000-0002-2295-7917; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Atasever, Sema
Abstract Improving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q3 accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSIPRED on the SCOPe test datasets and found that our method outperformed PSIPRED.
4D-QSAR investigation and pharmacophore identification of pyrrolo[2,1-c][1,4]benzodiazepines using electron conformational–genetic algorithm method
(Taylor and Francis Ltd., 2016) Özalp, A.; Yavuz, S.Ç.; Sabancı, N.; Çapur, F.; Kökbudak, Z.; Sarıpınar, E.; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Çopur, Fatih
In this paper, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational–genetic algorithm (EC–GA) method as 4D-QSAR analysis. Using the data obtained from quantum chemical calculations at PM3/HF level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as the template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal the electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, the nonlinear least square regression method and genetic algorithm were performed. For four types of activity including the GI50, TGI, LC50 and IC50 of the pyrrolo[2,1-c][1,4] benzodiazepine series, the r2 train, r2 test and q2 values were 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, 0.600; and 0.776, 0.722, 0.687, respectively.
Adaptive Fault Detection Scheme Using an Optimized Self-healing Ensemble Machine Learning Algorithm
(CHINA ELECTRIC POWER RESEARCH INST, 2022) Yavuz, Levent; Soran, Ahmet; Onen, Ahmet; Li, Xiangjun; Muyeen, S. M.; 0000-0003-1398-9447; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Yavuz, Levent; Soran, Ahmet
This paper proposes a new cost-efficient, adaptive, and self-healing algorithm in real time that detects faults in a short period with high accuracy, even in the situations when it is difficult to detect. Rather than using traditional machine learning (ML) algorithms or hybrid signal processing techniques, a new framework based on an optimization enabled weighted ensemble method is developed that combines essential ML algorithms. In the proposed method, the system will select and compound appropriate ML algorithms based on Particle Swarm Optimization (PSO) weights. For this purpose, power system failures are simulated by using the PSCAD-Python co-simulation. One of the salient features of this study is that the proposed solution works on real-time raw data without using any pre-computational techniques or pre-stored information. Therefore, the proposed technique will be able to work on different systems, topologies, or data collections. The proposed fault detection technique is validated by using PSCAD-Python co-simulation on a modified and standard IEEE-14 and standard IEEE-39 bus considering network faults which are difficult to detect.
Addressing the Modern Regimes of Urban Spectacle: Revisiting the Ottoman General Exhibition of 1863 in Istanbul
(SAGE Publications Inc., 2022) Tozoglu, Ahmet Erdem; 0000-0002-8434-7882; AGÜ, Mimarlık Fakültesi, Mimarlık Bölümü; Tozoglu, Ahmet Erdem
One of the most spectacular events of the Ottoman experience of modernity was the inauguration of the Ottoman General Exposition in Istanbul in 1863. The ancient Hippodrome, which is one of the most prominent venues of the city and the setting of memorable celebrations and festivals for centuries, hosted the event and provided the visitors with the opportunity to become part of the modern regimes of gaze and spectacle. This article posits three observer roles to reveal the multilayered structure of urban spectacle in mid-century Istanbul, namely the sultanic gaze, spectacle of the ordinary citizens, and the mediated experience of the foreigner. To understand the particularities of each position, I utilize several visual and textual documents about the exhibition event. Though just a single case in Ottoman urban history, the exposition enables us to understand how the new manner of modern urban spectacle emerged during a spectacular public event in Istanbul.
Adjustment speed of debt maturity: Evidence from financial crises in East Asia
(Bank Indonesia Institute, 2021) Hasan Tekin; Ali Yavuz Polat; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Polat, Ali Yavuz
We investigate the change in adjustment speed of debt maturity for East Asian firms between 1990 and 2017 by including two exogenous shocks: the Asian Financial Crisis 1997-1998 (AFC) and the Global Financial Crisis 2007-2009 (GFC). We employ the least square dummy variable correction and find that East Asian firms have a slower adjustment of long-term debt over time. Besides, the decrease in adjustment speed of long-term debt after the GFC is more compared to the decrease after the AFC. Further analysis shows the optimal debt maturity differs across countries and industries. Another important implication of our results is that firms in high governance countries are more likely to close the gap between the actual and target debt maturity in time. Overall, debt holders and investors should consider financial uncertainties. © 2021 Ege Universitesi. All rights reserved.
Admissible invariants of genus 3 curves
(Springer New York LLC, 2015) Cinkir, Zubeyir; AGÜ, Mühendislik Fakültesi, Endüstri Mühendisliği Bölümü; Çinkir, Zübeyir
Several invariants of polarized metrized graphs and their applications in Arithmetic Geometry are studied recently. In this paper, we explicitly calculated these admissible invariants for all curves of genus 3. We find the sharp lower bound for the invariants φ, λ and ε for all polarized metrized graphs of genus 3. This improves the lower bound given for Effective Bogomolov Conjecture for such curves.
The Age Structure, Stringency Policy, Income, and Spread of Coronavirus Disease 2019: Evidence From 209 Countries
(FRONTIERS MEDIA SAAVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE CH-1015, SWITZERLAND, 2021) Bilgili, Faik; Dundar, Munis; Kuskaya, Sevda; Lorente, Daniel Balsalobre; Unlu, Fatma; Gencoglu, Pelin; Mugaloglu, Erhan; 0000-0001-5362-6259; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Mugaloglu, Erhan
This article aims at answering the following questions: (1) What is the influence of age structure on the spread of coronavirus disease 2019 (COVID-19)? (2) What can be the impact of stringency policy (policy responses to the coronavirus pandemic) on the spread of COVID-19? (3) What might be the quantitative effect of development levelincome and number of hospital beds on the number of deaths due to the COVID-19 epidemic? By employing the methodologies of generalized linear model, generalized moments method, and quantile regression models, this article reveals that the shares of median age, age 65, and age 70 and older population have significant positive impacts on the spread of COVID-19 and that the share of age 70 and older people in the population has a relatively greater influence on the spread of the pandemic. The second output of this research is the significant impact of stringency policy on diminishing COVID-19 total cases. The third finding of this paper reveals that the number of hospital beds appears to be vital in reducing the total number of COVID-19 deaths, while GDP per capita does not affect much the level of deaths of the COVID-19 pandemic. Finally, this article suggests some governmental health policies to control and decrease the spread of COVID-19.
Aguhyper: a hyperledger-based electronic health record management framework
(PEERJ INC, 2024) Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu; 0000-0003-4983-2417; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off-chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper’s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identified in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper’s implementation configurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes significantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the field.
Airbnb and COVID-19: SPACE-TIME vulnerability effects in six world-cities
(Elsevier, 2022) Kourtit, Karima; Nijkamp, Peter; Östh, John; Türk, Umut; 0000-0002-8440-7048; 0000-0002-4068-8132; 0000-0002-7171-994X; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü
This study examines the COVID-19 vulnerability and subsequent market dynamics in the volatile hospitality market worldwide, by focusing in particular on individual Airbnb bookings-data for six world-cities in various continents over the period January 2020–August 2021. This research was done by: (i) looking into factual survival rates of Airbnb accommodations in the period concerned; (ii) examining place-based impacts of intracity location on the economic performance of Airbnb facilities; (iii) estimating the price responses to the pandemic by means of a hedonic price model. In our statistical analyses based on large volumes of time- and space-varying data, multilevel logistic regression models are used to trace ‘corona survivability footprints’ and to estimate a hedonic price-elasticity-of-demand model. The results reveal hardships for the Airbnb market as a whole as well as a high volatility in prices in most cities. Our study highlights the vulnerability and ‘corona echoeffects’ on Airbnb markets for specific accommodation segments in several large cities in the world. It adds to the tourism literature by testing the geographic distributional impacts of the corona pandemic on customers’ choices regarding type and intra-urban location of Airbnb accommodations.
All-polymer ultrasonic transducer design for an intravascular ultrasonography application
(TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, ATATURK BULVARI NO 221, KAVAKLIDERE, ANKARA, 00000, TURKEY, 2019) Hah, Dooyoung; AGÜ, Mühendislik Fakültesi, Elektrik & Elektronik Mühendisliği Bölümü; Hah, Dooyoung
Intravascular ultrasonography (IVUS), a medical imaging modality, is used to obtain cross-sectional views of blood vessels from inside. In IVUS, transducers are brought to the proximity of the imaging targets so that high-resolution images can be obtained at high frequency without much concern of signal attenuation. To eliminate mechanical rotation rendered in conventional IVUS, it is proposed to manufacture a transducer array on a flexible substrate and wrap it around a cylindrical frame. The transducer of consideration is a capacitive micromachined ultrasonic transducer (CMUT). The whole device needs to be made out of polymers to be able to endure a high degree of bending (radius: 1 mm) Bending of the devices leads to considerable changes in the device characteristics, including resonant frequency and pull-in voltage due to geometrical dimension changes and stress induced. The main purpose of this work is to understand the effect of bending on the device characteristics by means of finite element analysis. Another objective of the work is to understand the relationships between such an effect and the device geometries. It is learned that the bending-induced stress depends strongly on anchor width, membrane thickness, and substrate thickness. It is also learned that resonant frequency and pull-in voltage become lower in most cases because of using a flexible substrate in comparison to those of the device on a rigid substrate. Bending-induced stress increases the spring constant and hence increases resonant frequency and pull-in voltage, although this effect is relatively weaker. For most of the device geometries, pull-in voltage is too high for the polymer material to endure. This is the main drawback of the all-polymer CMUT. In order to meet the design goal of 20 MHz resonant frequency, the membrane radius has to be smaller than 7.7 mu m for a thickness of 3 mu m.
All-Surface Induction Heating With High Efficiency and Space Invariance Enabled by Arraying Squircle Coils in Square Lattice
(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA, 2018) Kilic, Veli Tayfun; Unal, Emre; Yilmaz, Namik; Demir, Hilmi Volkan; AGÜ, Mühendislik Fakültesi, Elektrik & Elektronik Mühendisliği Bölümü;
This paper reports an all-surface induction heating system that enables efficient heating at a constant speed all over the surface independent of the specific location on the surface. In the proposed induction system, squircle coils are placed tangentially in a two-dimensional square lattice as opposed to commonly used hexagonal packing. As a proof-of-concept demonstration, a simple model setup was constructed using a 3 x 3 coil array along with a steel plate to be inductively heated. To model surface heating, a set of six locations for the plate was designated considering symmetry points. For all of these cases, power dissipated by the system and the plate's transient heating were recorded. Independent from the specific plate position, almost equal heating speeds were measured for the similar levels of dissipated energies in the system. Using full three-dimensional electromagnetic solutions, the experimental results were also verified. The findings indicate that the proposed system is proved to enable energy efficient space-invariant heating in all-surface induction hobs.
Alzheimer Disease Associated Loci: APOE Single Nucleotide Polymorphisms in Marmara Region
(MDPI, 2024) Ismail, Aya Badeea; Dundar, Mehmet Sait; Erguzeloglu, Cemre Ornek; Ergoren, Mahmut Cerkez; Alemdar, Adem; Ozemri Sag, Sebnem; Temel, Sehime Gulsun; 0000-0002-0336-4825; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Dundar, Mehmet Sait
Alzheimer’s disease (AD) is a major global health challenge, especially among individuals aged 65 or older. According to population health studies, Turkey has the highest AD prevalence in the Middle East and Europe. To accurately determine the frequencies of common and rare APOE single nucleotide polymorphisms (SNPs) in the Turkish population residing in the Marmara Region, we conducted a retrospective study analyzing APOE variants in 588 individuals referred to the Bursa Uludag University Genetic Diseases Evaluation Center. Molecular genotyping, clinical exome sequencing, bioinformatics analysis, and statistical evaluation were employed to identify APOE polymorphisms and assess their distribution. The study revealed the frequencies of APOE alleles as follows: ε4 at 9.94%, ε2 at 9.18%, and ε3 at 80.68%. The gender-based analysis in our study uncovered a tendency for females to exhibit a higher prevalence of mutant genotypes across various SNPs. The most prevalent haplotype observed was ε3/ε3, while rare APOE SNPs were also identified. These findings align with global observations, underscoring the significance of genetic diversity and gender-specific characteristics in comprehending health disparities and formulating preventive strategies.
AMP-GSM: Prediction of Antimicrobial Peptides via a Grouping–Scoring–Modeling Approach
(MDPI, 2023) Soylemez, Ummu Gulsum; Yousef, Malik; Bakir-Gungor, Burcu; 0000-0002-6602-772X; 0000-0002-2272-6270; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Soylemez, Ummu Gulsum; Bakir-Gungor, Burcu
Due to the increasing resistance of bacteria to antibiotics, scientists began seeking new solutions against this problem. One of the most promising solutions in this field are antimicrobial peptides (AMP). To identify antimicrobial peptides, and to aid the design and production of novel antimicrobial peptides, there is a growing interest in the development of computational prediction approaches, in parallel with the studies performing wet-lab experiments. The computational approaches aim to understand what controls antimicrobial activity from the perspective of machine learning, and to uncover the biological properties that define antimicrobial activity. Throughout this study, we aim to develop a novel prediction approach that can identify peptides with high antimicrobial activity against selected target bacteria. Along this line, we propose a novel method called AMP-GSM (antimicrobial peptide-grouping-scoring-modeling). AMP-GSM includes three main components: grouping, scoring, and modeling. The grouping component creates sub-datasets via placing the physicochemical, linguistic, sequence, and structure-based features into different groups. The scoring component gives a score for each group according to their ability to distinguish whether it is an antimicrobial peptide or not. As the final part of our method, the model built using the top-ranked groups is evaluated (modeling component). The method was tested for three AMP prediction datasets, and the prediction performance of AMP-GSM was comparatively evaluated with several feature selection methods and several classifiers. When we used 10 features (which are members of the physicochemical group), we obtained the highest area under curve (AUC) value for both the Gram-negative (99%) and Gram-positive (98%) datasets. AMP-GSM investigates the most significant feature groups that improve AMP prediction. A number of physico-chemical features from the AMP-GSM's final selection demonstrate how important these variables are in terms of defining peptide characteristics and how they should be taken into account when creating models to predict peptide activity.
Analysis of CO 2 emissions and energy consumption by sources in MENA countries: evidence from quantile regressions
(Springer Nature 2021, 2021) Majed Alharthi; Eyup Dogan; Dilvin Taskin; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü; Dogan, Eyup
The development of economies and energy usage can significantly impact the carbon dioxide (CO2) emissions in the Middle East and North Africa (MENA) countries. Therefore, this study aims to analyze the factors that determine CO2 emissions in MENA under the environmental Kuznets curve (EKC) framework by applying novel quantile techniques on data for CO2 emissions, real income, renewable and non-renewable energy consumption, and urbanization over the period from 1990 to 2015. The results from the estimations suggest that renewable energy consumption significantly reduces the level of emissions; furthermore, its impact increases with higher quantiles. In addition, non-renewable energy consumption increases CO2 emissions, while its magnitude decreases with higher quantiles. The empirical results also confirm the validity of EKC hypothesis for the panel of MENA economies. Policymakers in the region should implement policies and regulations to promote the adoption and use of renewable energy to mitigate carbon emissions.
Analysis of coronary angiography related psychophysiological responses
(BMC, CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2011) Okkesim, Sukru; Kara, Sadik; Kaya, Mehmet G.; Asyali, Musa H.; AGÜ, Mimarlık Fakültesi, Mimarlık Bölümü;
Background: Coronary angiography is an important tool in diagnosis of cardiovascular diseases. However, it is the administration is relatively stressful and emotionally traumatic for the subjects. The aim of this study is to evaluate psychophysiological responses induced by the coronary angiography instead of subjective methods such as a questionnaire. We have also evaluated the influence of the tranquilizer on the psychophysiological responses. Methods: Electrocardiography (ECG), Blood Volume Pulse (BVP), and Galvanic Skin Response (GSR) of 34 patients who underwent coronary angiography operation were recorded. Recordings were done at three phases: "1 hour before," "during," and "1 hour after" the coronary angiography test. Total of 5 features obtained from the physiological signals were compared across these three phases. Sixteen of the patients were administered 5 mg of a tranquilizer (Diazepam) before the operation and remaining 18 were not. Results: Our results indicate that there is a strong correlation between features (LF/HF, Bk, DN1/DN2, skin conductance level and seg_mean) in terms of reflecting psychophysiological responses. However only DN1/DN2 feature has statistically significant differences between angiography phases (for diazepam: p = 0.0201, for non_diazepam p = 0.0224). We also note that there are statistically significant differences between the diazepam and non-diazepam groups for seg_mean features in "before", "during" and "after" phases (p = 0.0156, 0.0282, and 0.0443, respectively). Conclusions: The most intense sympathetic activity is observed in the "during" angiography phase for both of the groups. The obtained features can be used in some clinical studies where generation of the customized/individual diagnoses styles and quantitative evaluation of psychophysiological responses is necessary.
Analysis of mosaic mortars from the Roman, Byzantine and Early Islamic periods sourced from Gerasa’s Northwest Quarter
(SPRINGER OPEN, 2024) Ball, Richard J.; Ansell, Martin P.; Su-Cadirci, Tuğçe Büşra; Baki, Vahiddin Alperen; Fletcher, Philip J.; Lichtenberger, Achim; Raja, Rubina; Wootton, Will; 0000-0001-6617-0924; AGÜ, Mimarlık Fakültesi, Mimarlık Bölümü; Su-Cadirci, Tuğçe Büşra
This study analyses and compares around 650 years of mosaic mortar production spanning the Roman, late Roman and Umayyad periods, at Gerasa/Jerash in Jordan, offering a better understanding of composition, structural features, and manufacturing processes. It assesses the value of optical and electron microscopy examination of morphological and textural features, pore structure using MIP, and composition studies using EDX, XRD, FTIR, TGA, and Raman spectroscopy. The study indicated high density lime adhesive was used compared to other mortars. Wood was used as a fuel when producing the lime and natural fibres were incorporated when manufacturing mortars. Aggregates were primarily calcitic with a small proportion of silica-based aggregates. Key outcomes of the study conclude that early Roman mortars were of highest quality, which was demonstrated through the careful selection of materials including different stone for lime and tesserae, and differences between layers. Late Roman mortars used the same slaked lime plus fibres and charcoal. Mortars dating from the Umayyad period also had the same higher lime content than late Roman, but higher porosity with fibres and charcoal. In general, the mortars showed slight differences in content and aggregate; different stone for lime and tesserae. The research attests to underlying traditions as well as changes in mortar mixes and methods according to context and time. The resulting data is contextualized within local and regional approaches.
Analysis of optical gyroscopes with vertically stacked ring resonators
(TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEYATATURK BULVARI NO 221, KAVAKLIDERE, ANKARA 00000, TURKEY, 2021) Hah, Dooyoung; 0000-0002-1290-0597; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Hah, Dooyoung
Without any moving part, optical gyroscopes exhibit superior reliability and accuracy in comparison to mechanical sensors. Microring-resonator-based optical gyroscopes emerged as alternatives for bulky conventional Sagnac interferometer sensors, especially attractive for applications with limited footprints. Previously, it has been reported that planar incorporation of multiple resonators does not bring about improvement in sensitivity for a given area because the increase in Sagnac phase accumulation does not outrun the increase of area. Therefore, it was naturally suggested to consider vertical stacking of ring resonators because then, the resonators can share the same footprint. In this work, sensitivity performances of such configurations with vertically stacked microring resonators are analyzed and compared to that of a basic (single-resonator) configuration. Through comprehensive study, it is learned that the sensitivity performance of the devices with vertically-stacked resonators (either with a single bus waveguide or with two bus waveguides) does not exceed that of the basic sensor device (single resonator with one bus waveguide), i.e. the basic structure is yet to be remained as the most efficient configuration.
Analysis of the in vitro nanoparticle-cell interactions via a smoothing-splines mixed-effects model
(TAYLOR & FRANCIS LTD, 2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND, 2016) Dogruoz, Elifnur; Dayanik, Savas; Budak, Gurer; Sabuncuoglu, Ihsan; AGÜ, Mühendislik Fakültesi, Endüstri Mühendisliği Bölümü;
A mixed-effects statistical model has been developed to understand the nanoparticle (NP)-cell interactions and predict the rate of cellular uptake of NPs. NP-cell interactions are crucial for targeted drug delivery systems, cell-level diagnosis, and cancer treatment. The cellular uptake of NPs depends on the size, charge, chemical structure, and concentration of NPs, and the incubation time. The vast number of combinations of these variable values disallows a comprehensive experimental study of NP-cell interactions. A mathematical model can, however, generalize the findings from a limited number of carefully designed experiments and can be used for the simulation of NP uptake rates, to design, plan, and compare alternative treatment options. We propose a mathematical model based on the data obtained from in vitro interactions of NP-healthy cells, through experiments conducted at the Nanomedicine and Advanced Technologies Research Center in Turkey. The proposed model predicts the cellular uptake rate of silica, polymethyl methacrylate, and polylactic acid NPs, given the incubation time, size, charge and concentration of NPs. This study implements the mixed-model methodology in the field of nanomedicine for the first time, and is the first mathematical model that predicts the rate of cellular uptake of NPs based on sound statistical principles. Our model provides a cost-effective tool for researchers developing targeted drug delivery systems.
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; AGÜ, Mühendislik Fakültesi, Mühendislik Bilimleri Bölümü; 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.
Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
(Frontiers Media S.A., 2023) Gumustop, Ismail; Ortakci, Fatih; 0000-0003-1319-0854; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü; Gumustop, Ismail; Ortakci, Fatih
Leuconostoc pseudomesenteroides is a lactic acid bacteria species widely exist in fermented dairy foods, cane juice, sourdough, kimchi, apple dumpster, caecum, and human adenoid. In the dairy industry, Ln. pseudomesenteroides strains are usually found in mesophilic starter cultures with lactococci. This species plays a crucial role in the production of aroma compounds such as acetoin, acetaldehyde, and diacetyl, thus beneficially affecting dairy technology. We performed genomic characterization of 38 Ln. pseudomesenteroides from diverse ecological niches to evaluate this species’ genetic diversity and biotechnological potential. A mere ~12% of genes conserved across 38 Ln. pseudomesenteroides genomes indicate that accessory genes are the driving force for genotypic distinction in this species. Seven main clades were formed with variable content surrounding mobile genetic elements, namely plasmids, transposable elements, IS elements, prophages, and CRISPR-Cas. All but three genomes carried CRISPR-Cas system. Furthermore, a type IIA CRISPR-Cas system was found in 80% of the CRISPR-Cas positive strains. AMBR10, CBA3630, and MGBC116435 were predicted to encode bacteriocins. Genes responsible for citrate metabolism were found in all but five strains belonging to cane juice, sourdough, and unknown origin. On the contrary, arabinose metabolism genes were only available in nine strains isolated from plant-related systems. We found that Ln. pseudomesenteroides genomes show evolutionary adaptation to their ecological environment due to niche-specific carbon metabolism and forming closely related phylogenetic clades based on their isolation source. This species was found to be a reservoir of type IIA CRISPR-Cas system. The outcomes of this study provide a framework for uncovering the biotechnological potential of Ln. pseudomesenteroides and its future development as starter or adjunct culture for dairy industry.

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