Araştırma Çıktıları / Research Outputs
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Article Citation Count: 016S Bacterial Metagenomic Analysis of Herby Cheese (Otlu Peynir) Microbiota(Istanbul Univ-cerrahpasa, 2021) Sudağıdan, Mert; Yurt, Mediha Nur Zafer; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Ömeroğlu, Esra Ersoy; Uçak, Samet; Aydın, AliCheese microbiota may contain various bacterial species due to the use of different types of milk, rennet, and herbs. In this study, the distribution of the dominant bacteria present in the microbiota of herby cheese samples (n = 13) were examined by the next generation sequencing (NGS) technique. DNA was extracted both directly from cheese samples and after pre-enrichment. The metagenomic analysis of the NGS results revealed that Firmicutes were dominant both in DNA directly extracted from herby cheese (KOP), and pre-enriched samples (OP), at the phylum level. At the genus level, Lactobacillus, Lactococcus, and Streptococcus were dominant in the KOP samples, whereas in the OP samples, Enterococcus, Streptococcus, and Bacillus were determined as the dominant bacterial genera. Although Lactococcus raffinolactis and Streptococcus salivarius were dominant in the KOP samples, Enterococcus faecalis and S. salivarius were dominant in the OP samples. The Shannon species diversity index and principal coordinates analysis (PCoA) were used to determine the distribution in KOP and OP samples at the genus level. The PCoA of KOP-10, KOP-11, KOP-2, and KOP-7, KOP-3, and KOP-6 samples showed the wide distribution, whereas KOP-5, KOP-8, KOP-9, and KOP-14 herby cheese samples were closely related. The OP samples, especially OP-7 and OP-14, showed wide distribution in comparison to other OP samples. Finally, the dominant bacterial communities were identified by DNAbased metagenomic analysis, and this is the first report to elucidate the microbiota of herby cheese produced in Turkey using the NGS technique.Article Citation Count: 8Absorption and optical conduction in InSe/ZnSe/InSe thin film transistors(World Scientific Publ Co Pte Ltd, 2016) Qasrawı, Atef Fayez Hasan; Qasrawi, A. F.; Department of Electrical & Electronics EngineeringIn this work, (n)InSe/(p)ZnSe and (n)InSe/(p)ZnSe/(n)InSe heterojunction thin film transistor (TFT) devices are produced by the thermal evaporation technique. They are characterized by means of X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersion X-ray spectroscopy and optical spectroscopy techniques. While the InSe films are found to be amorphous, the ZnSe and InSe/ZnSe films exhibited polycrystalline nature of crystallization. The optical analysis has shown that these devices exhibit a conduction band offsets of 0.47 and valence band offsets of 0.67 and 0.74 eV, respectively. In addition, while the dielectric spectra of the InSe and ZnSe displayed resonance peaks at 416 and 528 THz, the dielectric spectra of InSe/ZnSe and InSe/ZnSe/InSe layers indicated two additional peaks at 305 and 350 THz, respectively. On the other hand, the optical conductivity analysis and modeling in the light of free carrier absorption theory reflected low values of drift mobilities associated with incident alternating electric fields at terahertz frequencies. The drift mobility of the charge carrier particles at femtoseconds scattering times increased as a result of the ZnSe sandwiching between two InSe layers. The valence band offsets, the dielectric resonance at 305 and 350 THz and the optical conductivity values nominate TFT devices for use in optoelectronics.Article Citation Count: 0An adaptive element division algorithm for accurate evaluation of singular and near singular integrals in 3D(Tubitak Scientific & Technological Research Council Turkey, 2021) Yazıcı, Ali; Baranoglu, Besim; Baranoğlu, Besim; Software Engineering; Manufacturing EngineeringAn adaptive algorithm for evaluation of singular and near singular integrals in 3D is presented. The algorithm is based on successive adaptive/selective subdivisions of the element until a prescribed error criteria is met. For evaluating the integrals in each subdivision, Gauss quadrature is applied. The method is computationally simple, memory efficient and can be applied for both triangular and quadrilateral elements, including the elements with nonplanar and/or curved surfaces. To assess the method, several examples are discussed. It has shown that the algorithm performs well for singular and near-singular integral examples presented in the paper and evaluates the integrals with very high accuracy.Article Citation Count: 0An adaptive element division algorithm for accurate evaluation of singular and near singular integrals in 3D(Turkiye Klinikleri, 2021) Yazıcı, Ali; Baranoğlu,B.; Baranoğlu, Besim; Software Engineering; Manufacturing EngineeringAn adaptive algorithm for evaluation of singular and near singular integrals in 3D is presented. The algorithm is based on successive adaptive/selective subdivisions of the element until a prescribed error criteria is met. For evaluating the integrals in each subdivision, Gauss quadrature is applied. The method is computationally simple, memory efficient and can be applied for both triangular and quadrilateral elements, including the elements with nonplanar and/or curved surfaces. To assess the method, several examples are discussed. It has shown that the algorithm performs well for singular and near-singular integral examples presented in the paper and evaluates the integrals with very high accuracy. © TÜBİTAKArticle Citation Count: 1Adaptive Stimulus Design for Dynamic Recurrent Neural Network Models(Frontiers Media Sa, 2019) Doruk, Reşat Özgür; Zhang, Kechen; Electrical-Electronics EngineeringWe present an adaptive stimulus design method for efficiently estimating the parameters of a dynamic recurrent network model with interacting excitatory and inhibitory neuronal populations. Although stimuli that are optimized for model parameter estimation should, in theory, have advantages over nonadaptive random stimuli, in practice it remains unclear in what way and to what extent an optimal design of time-varying stimuli may actually improve parameter estimation for this common type of recurrent network models. Here we specified the time course of each stimulus by a Fourier series whose amplitudes and phases were determined by maximizing a utility function based on the Fisher information matrix. To facilitate the optimization process, we have derived differential equations that govern the time evolution of the gradients of the utility function with respect to the stimulus parameters. The network parameters were estimated by maximum likelihood from the spike train data generated by an inhomogeneous Poisson process from the continuous network state. The adaptive design process was repeated in a closed loop, alternating between optimal stimulus design and parameter estimation from the updated stimulus-response data. Our results confirmed that, compared with random stimuli, optimally designed stimuli elicited responses with significantly better likelihood values for parameter estimation. Furthermore, all individual parameters, including the time constants and the connection weights, were recovered more accurately by the optimal design method. We also examined how the errors of different parameter estimates were correlated, and proposed heuristic formulas to account for the correlation patterns by an approximate parameter-confounding theory. Our results suggest that although adaptive optimal stimulus design incurs considerable computational cost even for the simplest excitatory-inhibitory recurrent network model, it may potentially help save time in experiments by reducing the number of stimuli needed for network parameter estimation.Article Citation Count: 21Adopting of Agile methods in Software Development Organizations: Systematic Mapping(Assoc information Communication Technology Education & Science, 2017) Mıshra, Alok; Mishra, Alok; Software EngineeringAdoption of agile methods in the software development organization is considered as a powerful solution to deal with the quickly changing and regularly developing business environment and fully-educated customers with constantly rising expectation, such as shorter time periods and an extraordinary level of response and service. This study investigates the adoption of agile approaches in software development organizations by using systematic mapping. Six research questions are identified, and to answer these questions a number of research papers have been reviewed in electronic databases. Finally, 25 research papers are examined and answers to all research questions are provided.Article Citation Count: 25Amine-functionalized graphene nanosheet-supported PdAuNi alloy nanoparticles: efficient nanocatalyst for formic acid dehydrogenation(Royal Soc Chemistry, 2018) Kaya, Murat; Yurderi, Mehmet; Kaya, Murat; Aydemir, Murat; Baysal, Akin; Durap, Feyyaz; Zahmakiran, Mehmet; Chemical EngineeringFormic acid (HCOOH), a major by-product of biomass processing with high energy density, stability and non-toxicity, has a great potential as a safe and a convenient liquid hydrogen (H-2) storage material for combustion engines and fuel cell applications. However, high-purity hydrogen release from the catalytic decomposition of aqueous formic acid solution at desirable rates under mild conditions stands as a major challenge that needs to be solved for the practical use of formic acid in on-demand hydrogen generation systems. Described herein is a new nanocatalyst system comprised of 3-aminopropyltriethoxysilane-functionalized graphene nanosheet-supported PdAuNi alloy nanoparticles (PdAuNi/f-GNS), which can reproducibly be prepared by following double solvent method combined with liquid-phase chemical reduction, all at room temperature. PdAuNi/f-GNS selectively catalyzes the decomposition of aqueous formic acid through the dehydrogenation pathway (similar to 100% H-2 selectivity), in the absence of any promoting additives (alkali formates, Bronsted bases, Lewis bases, etc.). PdAuNi/f-GNS nanocatalyst provides CO-free H-2 generation with a turnover frequency of 1090 mol H-2 mol metal(-1) h(-1) in the additive-free dehydrogenation of formic acid at almost complete conversion (>= 92%) even at room temperature. The catalytic activity provided by PdAuNi/f-GNS nanocatalyst is higher than those obtained with the heterogeneous catalysts reported to date for the additive-free dehydrogenation of formic acid. Moreover, PdAuNi/f-GNS nanoparticles show high durability against sintering, clumping and leaching throughout the catalytic runs, so that the PdAuNi/f-GNS nanocatalyst retains almost its inherent catalytic activity and selectivity at the end of the 10th recycle.Article Citation Count: 25Amine-functionalized graphene nanosheet-supported PdAuNi alloy nanoparticles: efficient nanocatalyst for formic acid dehydrogenation(Royal Society of Chemistry, 2018) Kaya, Murat; Yurderi,M.; Kaya,M.; Aydemir,M.; Baysal,A.; Durap,F.; Zahmakiran,M.; Chemical EngineeringFormic acid (HCOOH), a major by-product of biomass processing with high energy density, stability and non-toxicity, has a great potential as a safe and a convenient liquid hydrogen (H2) storage material for combustion engines and fuel cell applications. However, high-purity hydrogen release from the catalytic decomposition of aqueous formic acid solution at desirable rates under mild conditions stands as a major challenge that needs to be solved for the practical use of formic acid in on-demand hydrogen generation systems. Described herein is a new nanocatalyst system comprised of 3-aminopropyltriethoxysilane-functionalized graphene nanosheet-supported PdAuNi alloy nanoparticles (PdAuNi/f-GNS), which can reproducibly be prepared by following double solvent method combined with liquid-phase chemical reduction, all at room temperature. PdAuNi/f-GNS selectively catalyzes the decomposition of aqueous formic acid through the dehydrogenation pathway (∼100% H2 selectivity), in the absence of any promoting additives (alkali formates, Brønsted bases, Lewis bases, etc.). PdAuNi/f-GNS nanocatalyst provides CO-free H2 generation with a turnover frequency of 1090 mol H2 mol metal−1 h−1 in the additive-free dehydrogenation of formic acid at almost complete conversion (≥92%) even at room temperature. The catalytic activity provided by PdAuNi/f-GNS nanocatalyst is higher than those obtained with the heterogeneous catalysts reported to date for the additive-free dehydrogenation of formic acid. Moreover, PdAuNi/f-GNS nanoparticles show high durability against sintering, clumping and leaching throughout the catalytic runs, so that the PdAuNi/f-GNS nanocatalyst retains almost its inherent catalytic activity and selectivity at the end of the 10th recycle. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.Article Citation Count: 1Analyzing two decades of intimate partner femicide-suicides in T?rkiye*(Elsevier Sci Ltd, 2023) Cavlak, Mehmet; Odabasi, Aysun Balseven; Mutlu, Niluefer Dilara Ar; Erbaydar, Nueket PaksoyIntimate partner femicide-suicide (IPF-S) is an understudied subgroup of homicide-suicide deaths. Limited research has been conducted on IPF-Ss in the Eastern Mediterranean region. This study thus aimed to evaluate the characteristics of IPF-Ss that occurred in Turkiye between 2000 and 2019. IPF-Ss (n = 226) were extracted from electronic news stories. Data on victims, perpetrators, their relationships, and incidents of murder and suicide were collected. Descriptive statistics were calculated, and logistic regression analysis, mortality rates, and proportion of IPF-S in femicide calculations were conducted, showing that 13.3% of the femicides (n = 1699) were IPF-Ss. The IPF-Ss increased in 5-year intervals and were the highest during the 2015-2019 period (62.5%). Victims were married in 48.2% of the cases and 56% were aged <35 years, while 51.3% of the perpetrators were married and 52.6% were aged >40 years. In 42.0% of the cases, the perpetrator lived with the victim. Most (79.2%) of the cases took place in urban settlements, and the perpetrators used firearms in 84.1% of femicide cases. Firearm use was the most common method in cases where IPF-S was planned (OR = 2.98), when the IPF-S method was the same (OR = 29.6), and when the perpetrator committed suicide (OR = 7.82). In addition, it was found that firearm ownership is an important risk factor for IPF-S in Turkiye. Therefore, we recommend legislation to restrict firearms, as well as new measures to prevent illegal access to weapons.Article Citation Count: 0ANN-assisted forecasting of adsorption efficiency to remove heavy metals(Tubitak Scientific & Technological Research Council Turkey, 2019) Balku, Şaziye; Balku, Şaziye; Özalp Yaman, Şeniz; Energy Systems Engineering; Chemical EngineeringIn wastewater treatment, scientific and practical models utilizing numerical computational techniques suchas artificial neural networks (ANNs) can significantly help to improve the process as a whole through adsorption systems.In the modeling of the adsorption efficiency for heavy metals from wastewater, some kinetic models have been used such as pseudo first-order and second-order. The present work develops an ANN model to forecast the adsorption efficiency of heavy metals such as zinc, nickel, and copper by extracting experimental data from three case studies. To do this, we apply trial-and-error to find the most ideal ANN settings, the efficiency of which is determined by mean square error (MSE) and coefficient of determination (R2). According to the results, the model can forecast adsorption efficiency percent (AE%) with a tangent sigmoid transfer function (tansig) in the hidden layer with 10 neurons and a linear transferfunction (purelin) in the output layer. Furthermore, the Levenberg–Marquardt algorithm is seen to be most ideal for training the algorithm for the case studies, with the lowest MSE and high R2 . In addition, the experimental results and the results predicted by the model with the ANN were found to be highly compatible with each other.Article Citation Count: 16Applicability of Weyuker's Properties on OO Metrics: Some Misunderstandings(Comsis Consortium, 2008) Akman, Kamil İbrahim; Akman, Ibrahim; Mısra, Sanjay; Computer EngineeringWeyuker's properties have been suggested as a guiding tool in identification of a good and comprehensive complexity measure by several researchers. Weyuker proposed nine properties to evaluate complexity measure for traditional programming. However, they are extensively used for evaluating object-oriented (OO) metrics, although the object-oriented features are entirely different in nature. In this paper, two recently reported OO metrics were evaluated and, based on it; the usefulness and relevance of these properties for evaluation purpose for object-oriented systems is discussed.Article Citation Count: 2Application of Agent Methodology in Healthcare Information Systems(Assoc information Communication Technology Education & Science, 2017) Mıshra, Alok; Mishra, Alok; Software EngineeringThis paper presents a case study to describe the features and the phases of the two agent methodologies. The Gaia methodology for agent oriented analysis and design, Tropos is a detailed agent oriented software engineering methodology to explore each methodology's ability to present solutions for small problems. Also we provide an attempt to discover whether the methodology is in fact understandable and usable. In addition we were collecting and taking notes of the advantages and weaknesses of these methodologies during the study analysis for each methodology and the relationships among their models. The Guardian Angle: Patient-Centered Health Information System (GA: PCHIS) is the personal system to help track, manage, and interpret the subject's health history, and give advice to both patient and provider is used as the case study throughout the paper.Article Citation Count: 1An application of spectral theory of the Laplace operator(Taylor & Francis Ltd, 2013) Hüseyin, Hüseyin Şirin; MathematicsWe describe the structure of arbitrary rapidly decreasing functions of the Laplace operator. Combining this with the spectral data of the periodic Laplace operator we develop a generalization of the classical Poisson summation formula.Article Citation Count: 7Applying Emmert's Law to the Poggendorff illusion(Frontiers Research Foundation, 2015) Talaslı, Umur; Inan, Asli Bahar; İnan, Aslı Bahar; Department of PsychologyThe Poggendorff illusion was approached with a novel perspective, that of applying Emmert's Law to the situation. The extensities between the verticals and the transversals happen to be absolutely equal in retinal image size, whereas the registered distance for the verticals must be smaller than that of the transversals due to the fact that the former is assumed to occlude the latter. This combination of facts calls for the operation of Emmert's Law, which results in the shrinkage of the occluding space between the verticals. Since the retinal image shows the transversals to be in contact with the verticals, the shrinkage must drag the transversals inwards in the cortical representation in order to eliminate the gaps. Such dragging of the transversals produces the illusory misalignment, which is a dictation of geometry. Some of the consequences of this new explanation were tested in four different experiments. In Experiment 1, a new illusion, the tilting of an occluded continuation of an oblique line, was predicted and achieved. In Experiments 2 and 3, perceived nearness of the occluding entity was manipulated via texture density variations and the predicted misalignment variations were confirmed by using a between-subjects and within-subjects designs, respectively. In Experiment 4, tilting of the occluded segment of the transversal was found to vary in the predicted direction as a result of being accompanied by the same texture cues used in Experiments 2 and 3.Article Citation Count: 0An approach for performance prediction of saturated brushed permanent magnet\rdirect current (DC) motor from physical dimensions(Tubitak Scientific & Technological Research Council Turkey, 2022) Ertan, Hulusi Bülent; Asl, Rasul Tarvirdilu; Zeinali, Reza; Ertan, Hulusi Bulent; Electrical-Electronics EngineeringAn analytical approach for performance prediction of saturated brushed permanent magnet direct current\r(DC) motors is proposed in this paper. In case of a heavy saturation in the stator back core of electrical machines, some\rflux completes its path through the surrounding air, and the conventional equivalent circuit cannot be used anymore.\rThis issue has not been addressed in the literature. The importance of considering the effect of the flux penetrating\rthe surrounding air is shown in this paper using finite element simulations and experimental results, and an analytical\rapproach is proposed to consider this effect on magnet operating point determination and performance prediction of\rsaturated brushed permanent magnet DC motors. An analytical method is also presented to determine the boundary\rradius of the surrounding air for obtaining accurate results in finite element (FE) solutions and analytical calculations.\rAn analytical approach based on Carter’s coefficient is also proposed to calculate the effective length of the magnet when\rthe length of the magnet and rotor length are not the same. The accuracy of the proposed analytical model is illustrated\rusing finite element simulations and experimental results. With this accuracy, this analytical model is very suitable to\rbe used for reliable and quick mathematical design optimization.Article Citation Count: 17The approximation by q-Bernstein polynomials in the case q ↓ 1(Springer Basel Ag, 2006) Ostrovska, Sofiya; MathematicsLet B-n (f, q; x), n = 1, 2, ... , 0 < q < infinity, be the q-Bernstein polynomials of a function f, B-n (f, 1; x) being the classical Bernstein polynomials. It is proved that, in general, {B-n (f, q(n); x)} with q(n) down arrow 1 is not an approximating sequence for f is an element of C[0, 1], in contrast to the standard case q(n) up arrow 1. At the same time, there exists a sequence 0 < delta(n) down arrow 0 such that the condition 1 <= q(n) <= delta(n) implies the approximation of f by {B-n(f, qn; x)} for all f is an element of C[0, 1].Article Citation Count: 3The approximation of all continuous functions on [0,1] by q-Bernstein polynomials in the case q → 1+(Springer Basel Ag, 2008) Ostrovska, Sofiya; MathematicsSince for q > 1, the q-Bernstein polynomials B-n,B-q(f;.) are not positive linear operators on C[0, 1], their convergence properties are not similar to those in the case 0 < q = 1. It has been known that, in general, B-n,B-qn(f;.) does not approximate f is an element of C[0, 1] if q(n) -> 1(+), n ->infinity, unlike in the case q(n) -> 1(-). In this paper, it is shown that if 0 <= q(n) - 1 = o(n(-1)3(-n)), n -> infinity, then for any f is an element of C[0, 1], we have: B-n,B-qn(f; x) -> f(x) as n -> infinity, uniformly on [ 0,1].Article Citation Count: 2Assessment of pulmonary arterial hemodynamic and vascular changes by pulmonary pulse transit time in patients with human immunodeficiency virus infection(Wolters Kluwer Medknow Publications, 2021) Erdol, Mehmet Akif; Acar, Burak; Ertem, Ahmet Goktug; Karanfil, Mustafa; Yayla, Cagri; Demirtas, Koray; Akcay, Adnan BurakIntroduction: Pulmonary arterial hypertension and human immunodeficiency virus (HIV) infection is a well-known association. Pulmonary pulse transit time (pPTT) is a recent echocardiographic marker that might be used for evaluation of pulmonary arterial stiffness (PAS) in patients with HIV infection. We aimed to investigate whether pPTT elevated in patients with HIV infection compared to healthy controls and its association with echocardiographic indices of right ventricular functions. Materials and Methods: Fifty HIV (+) patients from infectious disease outpatient clinics and fifty age- and sex-matched HIV (-) healthy volunteers were enrolled in this study. pPTT was measured from pulmonary vein flow velocity as the time interval between the R-wave in the electrocardiography and corresponding peak late systolic was then calculated as the mean from two separate pw-Doppler measurements. Results: pPTT, tricuspid annular peak systolic excursion (TAPSE) and right ventricle fractional area change (FAC) were significantly lower in patients with HIV than control patients (177.1 +/- 34.9 vs. 215.7 +/- 35.7 msn, P < 0.001; 2.33 +/- 0.28 vs. 2.19 +/- 0.22, P = 0.039; 45 [4.25] vs. 41.1 [4.0], P = 0.032, respectively). pPTT was positively correlated with FAC, TAPSE and cluster of differentiation 4 count (r = 0.210; P = 0.036, r = 0.256; P = 0.041, r = 0.304; P = 0.044, respectively). Conclusion: Our study showed that pPTT, TAPSE, and right ventricle FAC levels were lower in patients with HIV infection. pPTT is an important predictor in patients with HIV expected to develop pulmonary vascular pathology.Article Citation Count: 15Assessment of Shock Models for a Particular Class of Intershock Time Distributions(Springer, 2022) Kus, Coskun; Eryılmaz, Serkan; Tuncel, Altan; Eryilmaz, Serkan; Industrial EngineeringIn this paper, delta and extreme shock models and a mixed shock model which combines delta-shock and extreme shock models are studied. In particular, the interarrival times between successive shocks are assumed to belong to a class of matrix-exponential distributions which is larger than the class of phase-type distributions. The Laplace -Stieltjes transforms of the systems' lifetimes are obtained in a matrix form. Survival functions of the systems are approximated based on the Laplace-Stieltjes transforms. The results are applied for the reliability evaluation of a certain repairable system consisting of two components.Article Citation Count: 11Atomistic Engineering of Chemiluminogens: Synthesis, Properties and Polymerization of 2,3-Dihydro-Pyrrolo[3,4-d]Pyridazine-1,4-Dione Scaffolds(Springer/plenum Publishers, 2017) Tirkeş, Seha; Cihaner, Atilla; Tirkes, Seha; Cihaner, Atilla; Algi, Fatih; Chemical EngineeringTwo chemiluminescent compounds containing 2,5-di(thien-2-yl)pyrrole and pyridazine units, namely 5,7-di(thiophen-2-yl)-2,3-dihydro-1H-pyrrolo[3,4-d]pyridazine-1,4(6H)-dione (5) and 6-phenyl-5,7-di(thiophen-2-yl)-2,3-dihydro-1H-pyrrolo[3,4-d]pyridazine-1,4(6H)-dione (6), were successfully synthesized and electrochemically polymerized. The compounds have chemiluminescent properties and glow in the presence of hydrogen peroxide in basic medium. The intensity of the glow can be increased dramatically by using Fe3+ ions, hemin (1.0 ppm) or blood samples (1.0 ppm) as catalyst. The compounds 5 and 6 have one well-defined irreversible oxidation peak at 1.08 V and 1.33 V vs Ag/AgCl, respectively. Electrochemical polymerization of both 5 and 6 were carried out successfully by repeating potential scanning in the presence of BF3. Et2O in an electrolyte solution of 0.1 M LiClO4 dissolved in acetonitrile. The electronic band gaps (E-g) of the polymers P5 and P6 were found to be 2.02 eV and 2.16 eV, respectively. On the other hand, the corresponding polymers are electroactive and exhibited electrochromic features.