Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method

Okur, Asim,Miller, Benjamin T.,Joo, Keehyoung,Lee, Jooyoung,Brooks, Bernard R. American Chemical Society 2013 Journal of chemical theory and computation Vol.9 No.2

<P>Temperature replica exchange molecular dynamics (T-REM) has been successfully used to improve the conformational search for model peptides and small proteins. However, for larger and more complicated systems, the use of T-REM is computationally intensive since the complexity of the free energy landscape and number of required replicas increase with system size. Achieving convergence of systems with slow transition kinetics is often difficult. Several methods have been proposed to overcome the size and convergence speed issues of standard T-REM. One of these is the Reservoir Replica Exchange Method (R-REM), in which the conformational search and temperature equilibration are separated by exchanging with a pre-existing reservoir of structures. This approach allows the integration of computationally efficient search algorithms with replica exchange. The Conformational Space Annealing (CSA) method has been shown to be able to determine the global energy minimum of proteins efficiently and has been used in structure prediction successfully. CSA uses a genetic algorithm to generate a diverse set of conformations to determine the minimum energy structure. We combine these methods by using conformations generated by the CSA method to build a reservoir. R-REM is then used to seed the top replica with the structures from the reservoir; fast convergence at every temperature is observed. The efficiency of this method is then demonstrated with model peptides and small proteins, and significant improvement of efficiency is observed while maintaining the overall shape of the free energy landscape.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2013/jctcce.2013.9.issue-2/ct300996m/production/images/medium/ct-2012-00996m_0011.gif'></P>

Lack of Impact of Age on Acute Side Effects and Tolerance of Curative Radiation Therapy

Yucel, Birsen,Okur, Yillar,Akkas, Ebru Atasever,Eren, Mehmet Fuat Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.2

Aim: The aim of this study was to determine the impact of age on the occurrence, severity, and timing of acute side effects related to radiotherapy. Materials and Methods: We analysed the data of 423 patients. Results: Of the patients, 295 (70%) were under the age of 65 (group 1) and 128 (30%) were over the age of 65 (group 2). The frequencies of radiotherapy-induced side effects were 89% in group 1 and 87% in group 2 (p=0.286). The mean times to occurrence were $2.5{\pm}0.1$ weeks in group 1 and $2.2{\pm}0.1$ weeks in group 2 (p=0.013). Treatment was ended in 2% of patients in group 1 and 6% of those in group 2 (p=0.062). Treatment interruption was identified in 18% of patients in group 1 and 23% in group 2 (p=0.142). Changes in performance status were greater in older patients (p=0.013). There were no significant differences according to the frequency or severity of side effects, except skin and genitourinary complications, between the groups. Conclusions: Early normal tissue reactions were not higher in older versus younger patients, though there was a tendency towards an earlier appearance.

Evaluation of prolonged pain in preterm infants with pneumothorax using heart rate variability analysis and EDIN (Échelle Douleur Inconfort Nouveau-Né, neonatal pain and discomfort scale) scores

Buyuktiryaki, Mehmet,Uras, Nurdan,Okur, Nilufer,Oncel, Mehmet Yekta,Simsek, Gulsum Kadioglu,Isik, Sehribanu Ozluer,Oguz, Serife Suna The Korean Pediatric Society 2018 Clinical and Experimental Pediatrics (CEP) Vol.61 No.10

Purpose: The EDIN scale (${\acute{E}}chelle$ Douleur Inconfort Nouveau-$N{\acute{e}}$, neonatal pain and discomfort scale) and heart rate variability has been used for the evaluation of prolonged pain. The aim of our study was to assess the value of the newborn infant parasympathetic evaluation (NIPE) index and EDIN scale for the evaluation of prolonged pain in preterm infants with chest tube placement due to pneumothorax. Methods: This prospective observational study assessed prolonged pain in preterm infants with a gestational age between 33 and 35 weeks undergoing installation of chest tubes. Prolonged pain was assessed using the EDIN scale and NIPE index. Results: There was a significant correlation between the EDIN scale and NIPE index (r=-0.590, P=0.003). Prolonged pain is significantly more severe in the first 6 hours following chest tube installation (NIPE index: 60 [50-86] vs. 68 [45-89], P<0.002; EDIN score: 8 [7-11] vs. 6 [4-8], P<0.001). Conclusion: Prolonged pain can be accurately assessed with the EDIN scale and NIPE index. However, evaluation with the EDIN scale is time-consuming. The NIPE index can provide instantaneous assessment of prolonged and continuous pain.

Transumbilical scarless surgery with thoracic trocar

Ibrahim Uygun,Mehmet Hanifi Okur,Bahattin Aydogdu,Mehmet Serif Arslan,Hasan Cimen,,Selcuk Otcu 대한외과학회 2013 Annals of Surgical Treatment and Research(ASRT) Vol.84 No.6

Purpose: Single-site laparoscopic surgery has become increasingly common. We herein report an easy and low-cost thoracic trocar technique (TTT) for these types of procedures and recommend the simpler name “transumbilical scarless surgery” (TUSS) to minimize confusion in nomenclature. Methods: We retrospectively reviewed patients who underwent TUSS by TTT using a thoracic trocar and surgical glove in our hospital between November 2011 and November 2012. Operating time, postoperative stay, and complications were detailed. Results: A total of 101 TUSS by TTT were successfully performed, comprising appendectomy (n = 63), ovarian cyst excision (n = 7), splenectomy (n = 5), nephroureterectomy (n = 5), orchidopexy (n = 4), pyeloplasty (n = 3), nephrolithotomy (n = 2), orchiectomy (n = 2), varicocelectomy (n = 2), lymphangioma excision (n = 2), ureterectomy (n = 1), Morgagni diaphragmatic hernia repair (n = 1), ovarian detorsion (n = 1), antegrade continence enema (n = 1), intestinal resection anastomosis (n = 1), and intestinal duplication excision (n = 1). Kirschner wires were used for some organ traction. Nine patients required an additional port, but no major complications occurred. The postoperative stay (mean ± standard deviation) was 3.2 ± 1.4 days, and operating time was 58.9 ± 38.3 minutes. Conclusion: We recommend the simpler name of TUSS to minimize confusion in nomenclature for all transumbilical single-incision laparoendoscopic surgeries. TTT is an easy and low-cost TUSS technique.

Vibrations of a Box-Sectional Cantilever Timoshenko Beam with Multiple Cracks

Ahmet Can Altunışık,Fatih Yesevi Okur,Volkan Kahya 한국강구조학회 2019 International Journal of Steel Structures Vol.19 No.2

This paper considers a Timoshenko cantilever beam with box cross-section including multiple cracks. Under six damage scenarios, the problem is solved analytically by the transfer matrix method, and numerically by the fi nite element method. Results are validated by the experimental measurements with the aid of ambient vibration tests, that use Enhanced Frequency Domain Decomposition and Stochastic Subspace Identifi cation methods. Measured and calculated natural frequencies and mode shapes for undamaged and damaged beams are compared with each other. Modal assurance criterion and coordinated modal assurance criterion values are obtained from two set of measurements to establish the correlation between the measured and calculated mode shapes for the damage location identifi cation.

Evaluation of prolonged pain in preterm infants with pneumothorax using heart rate variability analysis and EDIN (Échelle Douleur Inconfort Nouveau-Né, neonatal pain and discomfort scale) scores

Mehmet Buyuktiryaki,Nurdan Uras,Nilufer Okur,Mehmet Yekta Oncel,Gulsum Kadioglu Simsek,Sehribanu Ozluer Isik,Serife Suna Oguz 대한소아청소년과학회 2018 Clinical and Experimental Pediatrics (CEP) Vol.61 No.10

Purpose: The EDIN scale (Échelle Douleur Inconfort Nouveau-Né, neonatal pain and discomfort scale) and heart rate variability has been used for the evaluation of prolonged pain. The aim of our study was to assess the value of the newborn infant parasympathetic evaluation (NIPE) index and EDIN scale for the evaluation of prolonged pain in preterm infants with chest tube placement due to pneumothorax. Methods: This prospective observational study assessed prolonged pain in preterm infants with a gestational age between 33 and 35 weeks undergoing installation of chest tubes. Prolonged pain was assessed using the EDIN scale and NIPE index. Results: There was a significant correlation between the EDIN scale and NIPE index (r=-0.590, P= 0.003). Prolonged pain is significantly more severe in the first 6 hours following chest tube installation (NIPE index: 60 [50–86] vs. 68 [45–89], P<0.002; EDIN score: 8 [7–11] vs. 6 [4–8], P<0.001). Conclusion: Prolonged pain can be accurately assessed with the EDIN scale and NIPE index. However, evaluation with the EDIN scale is time-consuming. The NIPE index can provide instantaneous assessment of prolonged and continuous pain.

Optimal sensor placements for system identification of concrete arch dams

Altunisik, Ahmet Can,Sevim, Baris,Sunca, Fezayil,Okur, Fatih Yesevi Techno-Press 2021 Advances in concrete construction Vol.11 No.5

This paper investigates the optimal sensor placements and capabilities of this procedure for dynamic characteristics identification of arch dams. For this purpose, a prototype arch dam is constructed in laboratory conditions. Berke arch dam located on the Ceyhan River in city of Osmaniye is one of the highest arch dam constructed in Turkey is selected for field verification. The ambient vibration tests are conducted using initial candidate sensor locations at the beginning of the study. Enhanced Frequency Domain Decomposition and Stochastic Subspace Identification methods are used to extract experimental dynamic characteristics. Then, measurements are repeated according to optimal sensor locations of the dams. These locations are specified using the Effective Independence Method. To determine the optimal sensor locations, the target mode shape matrices which are obtained from ambient vibration tests of the selected dam with a large number of accelerometers are used. The dynamic characteristics obtained from each ambient vibrations tests are compared with each other. It is concluded that the dynamic characteristics obtained from initial measurements and those obtained from a limited number of sensors are compatible with each other. This situation indicates that optimal sensor placements determined by the Effective Independence Method are useful for dynamic characteristics identification of arch dams.

Pigeon Inspired Optimization of Bayesian Network Structure Learning and a Comparative Evaluation

Shahab Wahhab Kareem,Mehmet Cudi Okur 서울대학교 인지과학연구소 2019 Journal of Cognitive Science Vol.20 No.4

Bayesian networks are useful analytical models for designing the structure of knowledge in machine learning. Probabilistic dependency relationships among the variables can be represented by Bayesian networks. One strategy of a structure learning Bayesian Networks is the score and search technique. In this paper, we present a new method for structure learning of the Bayesian network which is based on Pigeon Inspired Optimization (PIO) Algorithm. The proposed algorithm is a simple one with fast convergence rate. In nature, the navigational ability of pigeons is unbelievable and highly impressive. In accordance with the PIO search algorithm, a set of directed acyclic graphs is defined. Every graph owns a score which shows its fitness. The algorithm is iterated until it gets the best solution or a satisfactory network structure using map and compass, and landmark operator. In this work, the proposed method compared with Simulated Annealing, Bee optimization and Simulated Annealing as a hybrid algorithm, Bee optimization and Greedy search as a hybrid algorithm, and Greedy Search using BDeu score function. We also investigated the confusion matrix performances of the methods. The paper presents the results of extensive evaluations of these algorithms based on common benchmark data sets. The results indicate that the proposed algorithm has better performance than the other algorithms and produces higher scores and accuracy values.

Series D : Are the Primary School Teachers of the Future Ready to Solve the Word Problems without Algebra?

( Enver Tatar ),( Tevfik Isleyen ),( Muzaffer Okur ) 한국수학교육학회 2005 수학교육연구 Vol.9 No.4

Factors Associated with Mammographic Density in Postmenopausal Women

( Emel Kiyak Caglayan ),( Kasim Caglayan ),( Ismet Alkis ),( Ergin Arslan ),( Aylin Okur ),( Oktay Banli ),( Yaprak Engin-ustun ) 대한폐경학회 2015 대한폐경학회지 Vol.21 No.2

Objectives: Breast density increases the risk of breast cancer, but also in the interpretation of mammography is also important. This study examine the risk factors affecting breast density in postmenopausal women. Methods: Between January 2013 and January 2014, 215 patients admitted to The Clinics of Gynecology and Obstetrics with complaints of menopause were taken. According to the results of mammography, Group I (non-dense, n = 175) and Group II (dense, n = 40) were created. The informations of the caseswere analyzed retrospectively. Results: In Group I, body mass index (BMI), number of pregnancies, parity were significantly higher than group II (P < 0.05). In group II, the withdrawal period of menstruation and progesterone levels were significantly higher (P < 0.05). In logistic regression analysis, BMI for dense breasts and number of pregnancies were found to be an independent risk factor (P < 0.05). Conclusion: Increased BMI, pregnancy and parity, result of reduction in density , but longer duration of menopause and increased progesterone cause an increase in density. BMI and the number of pregnancy was found to be independent risk factors for reducing breast density. (J Menopausal Med 2015;21:82-88)