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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.
An accurate investigation of the mechanical response and damage model of aluminum 7068
(Abdullah Gül Üniversitesi, 2018) Karaveli, Kadir Kaan; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Karaveli, Kadir Kaan
The promising combination of high strength, high toughness, low density and corrosion resistivity have made aluminium (Al) alloys the material of choice in various applications, from buildings to aerospace, for decades. Especially, Al 7068 alloy is one of the recently developed materials used mostly in defence and automobile industries due to their exceptional mechanical properties. In this master thesis, the mechanical response and Johnson-Cook damage model of Al 7068-T651 alloy was investigated. Specifically, different Johnson-Cook damage parameters were determined for different application areas considering the maximum, minimum and average results. These damage parameters can be used for accurate Finite Element Analysis simulations. To determine these damage parameters tensile tests were conducted on notched and smooth specimen son both rolling direction and perpendicular to the rolling direction. The notch radius were selected as smooth, 0.4 mm, 0.8 mm and 2 mm to provide different stress triaxiality values and observe the mechanical response at these triaxiality values. Tensile tests were repeated seven times to obtain the accurate results. The final cross-sectional areas of fractured specimens were calculated through optical microscopy. The effects of stress triaxiality factor and rolling direction on the mechanical properties of Al 7068-T651 alloy were successfully investigated. All damage parameters were calculated via LevenbergMarquardt optimization method. Overall, three different Johnson-Cook damage parameters based on minimum, average and maximum equivalent strain values were calculated. These Johnson-Cook ii damage parameters can be utilized for the accurate damage simulations of different applications in Finite Element Analysis, which is a computational technique and is used to obtain approximate solution of several engineering problems
Accurate Prediction of Residual Stresses in Machining of Inconel 718 Alloy through Crystal Plasticity Modelling
(Afyon Kocatepe Üniversitesi, 2023) Kesriklioglu, Sinan; Kapci, Mehmet Fazil; Büyükçapar,Rıdvan; Çetin , Barış; Yılmaz, Okan Deniz; Bal, Burak; 0000-0002-2914-808X; 0000-0003-3297-5307; 0000-0002-2550-7911; 0000-0002-7389-9155; AGÜ, Mühendislik Fakültesi, Makine Mühendisliği Bölümü; Kesriklioglu, Sinan; Kapci, Mehmet Fazil; Büyükçapar, Rıdvan; Bal, Burak
Determination and assessment of residual stresses are crucial to prevent the failure of the components used in defense, aerospace and automotive industries. The objective of this study is to present a material method to accurately predict the residual stresses induced during machining of Inconel 718. Orthogonal cutting tests were performed at various cutting speeds and feeds, and the residual stresses after machining of Inconel 718 were characterized by X-ray diffraction. A viscoplastic self-consistent crystal plasticity model was developed to import the microstructural inputs of this superalloy into a commercially available finite element software (Deform 2D). In addition, same simulations were carried out with classical Johnson - Cook material model. The simulation and experimental results showed that the crystal plasticity based multi-scale and multi-axial material model significantly improved the prediction accuracy of machining induced residual stresses of Inconel 718 when compared to the existing model, and it can be used to minimize the surface defects and cost of production trials in machining of difficult-to-cut materials.
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.
Advantage of co-culture strategy for targeted cancer treatment and in vitro studies
(ELSEVIERRADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS, 2021) Bayram, Nurun Nisa; Isoglu, Sevil Dincer; Baran, Yael; Ulu, Gizem Tugce; AGÜ, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü; Bayram, Nurun Nisa; Isoglu, Sevil Dincer
Advantage of co-culture strategy for targeted cancer treatment and in vitro studies
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.
Agency Theory: A Review in Finance
(TÜBİTAK ULAKBİM Ulusal Akademik Ağ ve Bilgi Merkezi Cahit Arf Bilgi Merkezi, 2020) Ali Yavuz POLAT; Hasan TEKİN; AGÜ, Yönetim Bilimleri Fakültesi, Ekonomi Bölümü
The problems of agency and risk sharing arise due to the separation of ownership and control of a large firm, when conflicts of interest exist between principals (owners) and agents (managers). The main source of these problems is asymmetric information, which implies an agency cost for the principal. Agency theory, which is still one of the fundamental theories in corporate finance, focuses on minimizing costs in agency relations. This study critically evaluates the principal-agent relations, focusing on the interaction between the shareholder-manager and bondholder-shareholder in corporate finance.
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.
AKP’NİN SURİYELİ GÖÇMEN SÖYLEMİNİ TÜRKİYE’NİN JEOPOLİTİK SENARYOSUYLA BİRLİKTE OKUMAK
(TÜBİTAK ULAKBİM Ulusal Akademik Ağ ve Bilgi Merkezi Cahit Arf Bilgi Merkezi, 2020) Özgür BALKILIÇ; Fatma Armağan TEKE LLOYD; AGÜ, İnsan ve Toplum Bilimleri Fakültesi, Psikoloji Bölümü
AKP Suriyeli mülteci krizi ile baş etmek için uzun bir süre boyunca açık kapı politikası uygulamasına karşın, 2011-2018 yılları arasında konu üzerine geliştirdiği söylemsel pratiği kafa karıştırıcıydı. Zira, bu söylemsel pratik uluslararası göçkuramları ve pratikleri örüntüsünü tam olarak takip etmiyordu. Aslında AKP için göçmen krizi,Batı’nın ahlaki ve lider lik sorunlarının geniş yansımasının bir ürünüydü. Suriye göçmen krizini uluslararası sistemin bir çöküşünün sonucu olarak okuyan Türkiye’nin dışpolitika pratiklerini temellendirdiği ve meşrulaştırdığıjeopolitik senaryosu AKP’nin görünürde kafa karıştırıcı söylemini kavramamız için bize analitik bir çerçeve sunabilir. Bu makale söz konusu söylemde iki temaya odaklanmaktadır. Birincisi, AKP Suriyeli göçmenleri tanımlarken resmi düzenlemelerde belirtilen herhangi bir statüden ziyade dini temelli bir “misafir” kavramına başvurmaktadır. İkincisi, AKP Suriyeli mülteci krizini, içerisinde Türkiye’ye bir liderlik rolü payesi biçecek şekilde, uluslararasısistemin daha geniş siyasi ve ahlaki bir krizinin bir sonucu olarak ele almaktadır.
Akut Böbrek Hasarında Nötrofil Jelatinaz İlişkili Lipokalin ile Mortalite İlişkisi
(GALENOS YAYINCILIK, ERKAN MOR, MOLLA GURANI CAD 21-1, FINDIKZADE, ISTANBUL 34093, TURKEY, 2018) Aksebzeci, Bekir Hakan; Kayaaltı, Seda; Kayaaltı, Ömer; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Biyomühendislik Bölümü;
Objective: Almost half of intensive care patients are affected by acute kidney injury (AKI). The purpose of this study is to determine parameters that can be used for predicting of early (within 28 days) and late (within 90 days) mortality in patients who are followed-up with AKI in intensive care units. Materials and Methods: In this study, a dataset that contains 50 patients with AKI in intensive care units was used. This dataset contains blood urea nitrogen, creatinine, plasma and urinary neutrophil gelatinase-associated hpocalin (NGAL), lactate dehydrogenase, alkaline phosphatase and gammaglutamyl transpeptidase values of patients who were admitted to intensive care for various reasons and who developed AKI on the days 1, 3 and 7. In addition to these values, laboratory results such as serum electrolytes on day 1, blood gas; vital signs such as mean arterial pressure, central venous pressure; and demographic data were also recorded. Data mining techniques were applied to determine correlation between all of these data and mortality. Results: The threshold level of urinary NGAL on day 7 was determined to be 69 ng/mL, and strong correlation was found between this threshold level and early mortality. Similarly, the threshold level of plasma NGAL on day 7 was determined to be 150 ng/mL, and this was highly correlated with early mortality. Besides, strong correlation was also found between the difference in the urinary NGAL levels on day 1 and 7, and early mortality. Conclusion: In this study, plasma and urinary NGAL levels were found to be closely related to early mortality in patients who were followed-up with AKI in intensive care units. On the other hand, any parameter associated with late mortality was not found.
Akut Myeloid Lösemi Tedavisi için Hedgehog Ve Otofaji Yolaklarının Düzenlenmesi
(TUBİTAK, 2019) EL KHATIB, Mona; AGÜ, Yaşam ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümü; EL KHATIB, Mona
Akut myeloid lösemi (AML) çeşitli moleküler aberasyonlar ve sinyal yolaklarındaki bozuklukları içeren klonal hastalıklar ile karakterize edilen bir grup heterojen malignanttır. Hedgehog (HH) sinyal yolağı birçok kanserde deregüle edilen evrimsel olarak korunan bir sinyal yolağıdır. HH sinyal yolağı lizozomal degradasyon prosesi otofajinin temel regülatörü olan PI3K/AKT/mTOR aksesini de içeren diğer sinyal yolakları ile karşılıklı iletişim halindedir. Bu sinyal yolakları AML’de deregüle edilmiştir. Birçok çalışmada otofajinin AML için bir kaçış mekanizması olabileceği ortaya konulmuştur. Bizim çalışmamızda, HH ve otofaji yolaklarının farklı AML türleri üzerine etkileri incelenmiştir. Çalışmamızda KML hücresi olan K562 ve CMK, MV4-11, MOLM-13 ve NB4 AML hücreleri GLI1 inhibitörü GANT61 ve farklı otofaji modülatörleri ile muamele edilmiştir.MTT sonuçları NB4, MOLM-13 ve MV4-11hücre proliferasyonun GLI inhibisyonu sonrasında düştüğünü ancak CMK’nin diğer AML hücre hatlarına kıyasla GLI inhibisyonuna daha az sensitif olduğunu ortaya koymuştur. Daha sonra, otofaji modülasyonunun farklı AML hücre hatlarının proliferasyonu üzerine etkileri incelenmiştir. Otofajinin gerek otofagozom-lizozom füzyonu aşamasında gerekse otofagolizozomal degradasyon aşamasında inhibisyonunun ilaç konsantrasyonu ve muamele süresine bağlı olarak AML sağkalımını azalttığı gözlemlenmiştir. Otofaji modülatörleri ve GANT61’in kombinasyonunun MOLM-13 hücre hattı üzerinde sinerjistik bir etkisinin olduğu fakat CMK hücre hattı üzerinde sinerjistik etkisinin olmadığı gözlemlenmiştir. GANT61 muamelesinin AML hücre hatlarında otofajiyi artırdığı LC3II ekspresyonu ile western blot yöntemi ile ortaya konulmuştur. Buna ek olarak, kombinasyonun MOLM-13 hücresinde LC3II’yi artırdığı gözlenirken, bu oran CMK hücre hattında daha düşüktür. AKT proteinin ekspresyonu ilaca ve hücre hattına gore farklılık göstermektedir. Sonuç olarak, HH ve otofaji sinyal yolaklarının hedeflenmesi MOLM-13 hücre hattı için umut vaatedici bir terapi iken, CMK hücre hattında benzer sonuçlara ulaşılamamıştır.
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.

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