Search results for: Serdal Kirmizialtin

Authors: Amani Tahat, Serdal Kirmizialtin

Abstract:

Trajectory fragment methods such as Markov State Models (MSM), Milestoning (MS) and Transition Path sampling are the prime choice of extending the timescale of all atom Molecular Dynamics simulations. In these approaches, a set of structures that covers the accessible phase space has to be chosen a priori using cluster analysis. Structural clustering serves to partition the conformational state into natural subgroups based on their similarity, an essential statistical methodology that is used for analyzing numerous sets of empirical data produced by Molecular Dynamics (MD) simulations. Local transition kernel among these clusters later used to connect the metastable states using a Markovian kinetic model in MSM and a non-Markovian model in MS. The choice of clustering approach in constructing such kernel is crucial since the high dimensionality of the biomolecular structures might easily confuse the identification of clusters when using the traditional hierarchical clustering methodology. Of particular interest, in the case of MS where the milestones are very close to each other, accurate determination of the milestone identity of the trajectory becomes a challenging issue. Throughout this work we present two cluster analysis methods applied to the cis–trans isomerism of dinucleotide AA. The choice of nucleic acids to commonly used proteins to study the cluster analysis is two fold: i) the energy landscape is rugged; hence transitions are more complex, enabling a more realistic model to study conformational transitions, ii) Nucleic acids conformational space is high dimensional. A diverse set of internal coordinates is necessary to describe the metastable states in nucleic acids, posing a challenge in studying the conformational transitions. Herein, we need improved clustering methods that accurately identify the AA structure in its metastable states in a robust way for a wide range of confused data conditions. The single linkage approach of the hierarchical clustering available in GROMACS MD-package is the first clustering methodology applied to our data. Self Organizing Map (SOM) neural network, that also known as a Kohonen network, is the second data clustering methodology. The performance comparison of the neural network as well as hierarchical clustering method is studied by means of computing the mean first passage times for the cis-trans conformational rates. Our hope is that this study provides insight into the complexities and need in determining the appropriate clustering algorithm for kinetic analysis. Our results can improve the effectiveness of decisions based on clustering confused empirical data in studying conformational transitions in biomolecules.

Keywords: milestoning, self organizing map, single linkage, structure clustering

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Authors: Halit Turan, Mehmet Ozturk, Serdal Akyuz

Abstract:

General Framework Agreement for Peace (Dayton Peace Agreement) in Bosnia and Herzegovina (GFAP), is one of the most challenging issues in the contemporary peace studies scholarship. It is clear that this agreement has created an exceptional state structure which Bosnia and Herzegovina has still executed for 20 years. The agreement, signed reluctantly by warring sides to end war, has carried out reaching the present day. Demonstrations held by unemployed people in the early of 2014 can be seen as a symptom of discontent about low economic wealth level which is a clear consequence of agreement. This paper lays out the influences of problems stemmed from the agreement to the future of country especially in terms of economic issues.

Keywords: Bosnia and Herzegovina, dayton peace agreement, economic problems, social discontent

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Authors: Serdal AKYUZ

Abstract:

The smart power is the use of soft and hard power together in consideration of existing circumstances. Soft power can be defined as the capability of changing perception of any target mass by employing policies based on legality. The hard power, generally, uses military and economic instruments which are the concrete indicator of general power comprehension. More than providing a balance between soft and hard power, smart power creates a proactive combination by assessing existing resources. Military targeting process (MTP), as stated in smart power methodology, benefits from a wide scope of lethal and non-lethal weapons to reach intended end state. The Smart powers components can be used in military targeting process similar to using of lethal or non-lethal weapons. This paper investigates the current use of Smart power concept, MTP and presents a new approach to MTP from smart power concept point of view.

Keywords: future security environment, hard power, military targeting process, soft power, smart power

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Authors: Serdal Akyüz, Halit Turan, Mehmet Öztürk

Abstract:

The future security environment will have new battlefield and enemies. The boundaries of battlefield and the identity of enemies cannot be noticed easily. The politicians may not want to lose their soldiers in very risky operations. This approach will pave the way for smart machines like war robots and new drones. These machines will have the decision-making ability and act simultaneously. This ability can change the military targeting process. Military targeting process (MTP) benefits from a wide scope of lethal and non-lethal weapons to reach an intended end-state. This process is now managed by people but in the future smart machines can do it by themselves. At first sight, this development seems useful for humanity owing to decrease the casualties in war. Using robots -which can decide, detect, deliver and asses without human support- for homeland security and against terrorist has very crucial risks and threats. Besides, it can decrease the havoc but also increase the collateral damages. This paper examines the current use of smart war machines, military targeting process and presents a new approach to MTP from lethal autonomy concept's point of view.

Keywords: the autonomous weapon systems, the lethal autonomy, military targeting process (MTP)

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Authors: Mehmet Ozturk, Serdal Akyuz, Halit Turan

Abstract:

By the evolving technology, the nature of the war has been changed since the beginning of the history. In the first generation war, the bayonet came to the fore in battlefields; successively; in the second-generation firepower; in the third generation maneuver. Today, in the fourth-generation, fighters, sides, and even fighters’ borders are unclear; consequently, lines of the battles have lost their significance. Furthermore, the actors in the battles can be state or non-state, military, paramilitary or civilian. In order to change the balance according to their interests, parties have utilized the urban areas as warfare. The main reason for using urban areas as a battlefield is the imbalance between parties. To balance the power strength, exploiting technological developments has utmost importance. There are many newly developed technologies for urban warfare such as change in the size of the unmanned aerial vehicle, increased usage of unmanned ground vehicles (especially in supply and evacuation purposes), systems showing the behind of the wall, simulations used for educational purposes. This study will focus on the technological equipment being used for urban warfare.

Keywords: urban warfare, unmanned ground vehicles, technological developments, nature of the war

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Authors: Serdal Pamuk, Irem Cay

Abstract:

Our model is based on the theory of reinforced random walks coupled with Michealis-Menten mechanisms which view endothelial cell receptors as the catalysts for transforming both tumor and macrophage derived tumor angiogenesis factor (TAF) into proteolytic enzyme which in turn degrade the basal lamina. The model consists of two main parts. First part has seven differential equations (DE’s) in one space dimension over the capillary, whereas the second part has the same number of DE’s in two space dimensions in the extra cellular matrix (ECM). We connect these two parts via some boundary conditions to move the cells into the ECM in order to initiate capillary formation. But, when does this movement begin? To address this question we estimate the thresholds that activate the transport equations in the capillary. We do this by using steady-state analysis of TAF equation under some assumptions. Once these equations are activated endothelial, pericyte and macrophage cells begin to move into the ECM for the initiation of angiogenesis. We do believe that our results play an important role for the mechanisms of cell migration which are crucial for tumor angiogenesis. Furthermore, we estimate the long time tendency of these three cells, and find that they tend to the transition probability functions as time evolves. We provide our numerical solutions which are in good agreement with our theoretical results.

Keywords: angiogenesis, capillary formation, mathematical analysis, steady-state, transition probability function

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Authors: Bahadir Batar, Elif Serdal, Berna Erdal, Hasan Ogul

Abstract:

Micro-ribonucleic acids (miRNAs) are small short non-coding ribonucleic acid molecules about 22 nucleotides long. miRNAs play a key role in response to chemotherapeutic agents. WW domain-containing oxidoreductase (WWOX) gene encodes a tumor suppressor protein. Loss or reduction of Wwox protein is observed in many breast cancer cases. WWOX protein deficiency is increased in triple-negative breast cancer (TNBC). TNBC is a heterogeneous, highly aggressive, and difficult to treat tumor type. WWOX loss contributes to resistance to cisplatin therapy in patients with TNBC. Here, the aim of the study was to investigate the potential role of miRNAs in cisplatin therapy resistance of WWOX-deficient TNBC cells. This was a cell culture study. miRNA expression profiling was analyzed by LightCycler 480 system. miRNA Set Enrichment Analysis tool was used to integrate experimental data with literature-based biological knowledge to infer a new hypothesis. Increased miR-182 and decreased miR-214 were significantly correlated with cisplatin resistance in WWOX-deficient TNBC cells. miR-182 and miR-214 may involve in cisplatin resistance of WWOX-deficient TNBC cells by deregulating the DNA repair, apoptosis, or protein kinase B signaling pathways. These data highlight the mechanism by which WWOX regulates cisplatin resistance of TNBC and the potential use of WWOX as a predictor biomarker for cisplatin resistance.

Keywords: cisplatin, microRNA, triple-negative breast cancer, WWOX

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Authors: Serdal Sabanci, Mutlu Çevik, Derya Tezcan, Cansu Çelebi, Filiz Içier

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Ultrasound is defined as sound waves having frequencies higher than 20 kHz, which is greater than the limits of the human hearing range. In recent years, ultrasonic treatment is an emerging technology being used increasingly in the food industry. It is applied as an alternative technique for different purposes such as microbial and enzyme inactivation, extraction, drying, filtration, crystallization, degas, cutting etc. Red beetroot (Beta vulgaris L.) is a root vegetable which is rich in mineral components, folic acid, dietary fiber, anthocyanin pigments. In this study, the application of low frequency high intensity ultrasound to the red beetroot slices and red beetroot juice for different treatment times (0, 5, 10, 15, 20 min) was investigated. Ultrasonicated red beetroot slices were also squeezed immediately. Changes on colour, betanin, pH and titratable acidity properties of red beetroot juices (the ultrasonicated juice (UJ) and the juice from ultrasonicated slices (JUS)) were determined. Although there was no significant difference statistically in the changes of color value of JUS samples due to ultrasound application (p>0.05), the color properties of UJ samples ultrasonicated for low durations were statistically different from raw material (p<0.05). The difference between color values of UJ and raw material disappeared (p>0.05) as the ultrasonication duration increased. The application of ultrasound to red beet root slices adversely affected and decreased the betanin content of JUS samples. On the other hand, the betanin content of UJ samples increased as the ultrasonication duration increased. Ultrasound treatment did not affect pH and titratable acidity of red beetroot juices statistically (p>0.05). The results suggest that ultrasound technology is the simple and economical technique which may successfully be employed for the processing of red beetroot juice with improved color and betanin quality. However, further investigation is still needed to confirm this.

Keywords: red beetroot, ultrasound, color, betanin

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