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1. Golden Sine Algorithm: A Novel Math-Inspired Algorithm

Author

TANYILDIZI, E. and DEMIR, G.

Subjects
artificial intelligence, computational intelligence, evolutionary computation, heuristic algorithms, optimization, Electrical engineering. Electronics. Nuclear engineering, TK1-9971, Computer engineering. Computer hardware, TK7885-7895
Abstract

In this study, Golden Sine Algorithm (Gold-SA) is presented as a new metaheuristic method for solving optimization problems. Gold-SA has been developed as a new search algorithm based on population. This math-based algorithm is inspired by sine that is a trigonometric function. In the algorithm, random individuals are created as many as the number of search agents with uniform distribution for each dimension. The Gold-SA operator searches to achieve a better solution in each iteration by trying to bring the current situation closer to the target value. The solution space is narrowed by the golden section so that the areas that are supposed to give only good results are scanned instead of the whole solution space scan. In the tests performed, it is seen that Gold-SA has better results than other population based methods. In addition, Gold-SA has fewer algorithm-dependent parameters and operators than other metaheuristic methods, increasing the importance of this method by providing faster convergence of this new method.

Published
2017
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3. Weekly cumulated throughfall and rain data, April-August 2019, Hainich, Germany, project AquaDiva [Data set]

Author

Demir, G., Hildebrandt, Anke, Filipzik, J., Demir, G., Hildebrandt, Anke, and Filipzik, J.

Abstract

Root water uptake depends on soil moisture which is primarily fed by throughfall in forests. Several biotic and abiotic elements shape the spatial distribution of throughfall. It is well documented that throughfall patterns result in reoccurring higher and lower water inputs at certain locations. However, how the spatial distribution of throughfall affects root water uptake patterns remains unresolved. Therefore, we investigate root water uptake patterns by considering spatial patterns of throughfall and soil water in addition to soil and neighboring tree characteristics. In a beech-dominated mixed deciduous forest in a temperate climate, we conducted intensive throughfall sampling at locations paired with soil moisture sensors during the 2019 growing season. We employed a linear mixed-effects model to understand controlling factors in root water uptake patterns. Our results show that soil water patterns and interactions among neighboring trees are the most significant factors regulating root water uptake patterns. Temporally stable throughfall patterns did not influence root water uptake patterns. Similarly, soil properties were unimportant for spatial patterns of root water uptake. We found that wetter locations (rarely associated with throughfall hotspots) promoted greater root water uptake. Root water uptake in monitored soil layers also increased with neighborhood species richness. Ultimately our findings suggest that complementarity mechanisms within the forest stand, in addition to soil water variability and availability, govern root water uptake patterns.

Published
2024

4. High-resolution throughfall measurement design since 2019, Hainich, Germany, project AquaDiva [Data set]

Author

Demir, G., Metzger, J.C., Hildebrandt, Anke, Demir, G., Metzger, J.C., and Hildebrandt, Anke

Abstract

Root water uptake depends on soil moisture which is primarily fed by throughfall in forests. Several biotic and abiotic elements shape the spatial distribution of throughfall. It is well documented that throughfall patterns result in reoccurring higher and lower water inputs at certain locations. However, how the spatial distribution of throughfall affects root water uptake patterns remains unresolved. Therefore, we investigate root water uptake patterns by considering spatial patterns of throughfall and soil water in addition to soil and neighboring tree characteristics. In a beech-dominated mixed deciduous forest in a temperate climate, we conducted intensive throughfall sampling at locations paired with soil moisture sensors during the 2019 growing season. We employed a linear mixed-effects model to understand controlling factors in root water uptake patterns. Our results show that soil water patterns and interactions among neighboring trees are the most significant factors regulating root water uptake patterns. Temporally stable throughfall patterns did not influence root water uptake patterns. Similarly, soil properties were unimportant for spatial patterns of root water uptake. We found that wetter locations (rarely associated with throughfall hotspots) promoted greater root water uptake. Root water uptake in monitored soil layers also increased with neighborhood species richness. Ultimately our findings suggest that complementarity mechanisms within the forest stand, in addition to soil water variability and availability, govern root water uptake patterns.

Published
2024

5. Root water uptake patterns are controlled by tree species interactions and soil water variability

Author

Demir, G., Guswa, A.J., Filipzik, J., Metzger, J.C., Römermann, C., Hildebrandt, Anke, Demir, G., Guswa, A.J., Filipzik, J., Metzger, J.C., Römermann, C., and Hildebrandt, Anke

Abstract

Root water uptake depends on soil moisture which is primarily fed by throughfall in forests. Several biotic and abiotic elements shape the spatial distribution of throughfall. It is well documented that throughfall patterns result in reoccurring higher and lower water inputs at certain locations. However, how the spatial distribution of throughfall affects root water uptake patterns remains unresolved. Therefore, we investigate root water uptake patterns by considering spatial patterns of throughfall and soil water in addition to soil and neighboring tree characteristics. In a beech-dominated mixed deciduous forest in a temperate climate, we conducted intensive throughfall sampling at locations paired with soil moisture sensors during the 2019 growing season. We employed a linear mixed-effects model to understand controlling factors in root water uptake patterns. Our results show that soil water patterns and interactions among neighboring trees are the most significant factors regulating root water uptake patterns. Temporally stable throughfall patterns did not influence root water uptake patterns. Similarly, soil properties were unimportant for spatial patterns of root water uptake. We found that wetter locations (rarely associated with throughfall hotspots) promoted greater root water uptake. Root water uptake in monitored soil layers also increased with neighborhood species richness. Ultimately our findings suggest that complementarity mechanisms within the forest stand, in addition to soil water variability and availability, govern root water uptake patterns.

Published
2024

6. High-resolution soil water content, March-August 2019, Hainich, Germany, project AquaDiva [Data set]

Author

Demir, G., Hildebrandt, Anke, Filipzik, J., Demir, G., Hildebrandt, Anke, and Filipzik, J.

Abstract

Root water uptake depends on soil moisture which is primarily fed by throughfall in forests. Several biotic and abiotic elements shape the spatial distribution of throughfall. It is well documented that throughfall patterns result in reoccurring higher and lower water inputs at certain locations. However, how the spatial distribution of throughfall affects root water uptake patterns remains unresolved. Therefore, we investigate root water uptake patterns by considering spatial patterns of throughfall and soil water in addition to soil and neighboring tree characteristics. In a beech-dominated mixed deciduous forest in a temperate climate, we conducted intensive throughfall sampling at locations paired with soil moisture sensors during the 2019 growing season. We employed a linear mixed-effects model to understand controlling factors in root water uptake patterns. Our results show that soil water patterns and interactions among neighboring trees are the most significant factors regulating root water uptake patterns. Temporally stable throughfall patterns did not influence root water uptake patterns. Similarly, soil properties were unimportant for spatial patterns of root water uptake. We found that wetter locations (rarely associated with throughfall hotspots) promoted greater root water uptake. Root water uptake in monitored soil layers also increased with neighborhood species richness. Ultimately our findings suggest that complementarity mechanisms within the forest stand, in addition to soil water variability and availability, govern root water uptake patterns.

Published
2024

7. Root water uptake, May-July 2019, Hainich, Germany, project AquaDiva [Data set]

Author

Demir, G., Hildebrandt, Anke, Demir, G., and Hildebrandt, Anke

Abstract

Root water uptake depends on soil moisture which is primarily fed by throughfall in forests. Several biotic and abiotic elements shape the spatial distribution of throughfall. It is well documented that throughfall patterns result in reoccurring higher and lower water inputs at certain locations. However, how the spatial distribution of throughfall affects root water uptake patterns remains unresolved. Therefore, we investigate root water uptake patterns by considering spatial patterns of throughfall and soil water in addition to soil and neighboring tree characteristics. In a beech-dominated mixed deciduous forest in a temperate climate, we conducted intensive throughfall sampling at locations paired with soil moisture sensors during the 2019 growing season. We employed a linear mixed-effects model to understand controlling factors in root water uptake patterns. Our results show that soil water patterns and interactions among neighboring trees are the most significant factors regulating root water uptake patterns. Temporally stable throughfall patterns did not influence root water uptake patterns. Similarly, soil properties were unimportant for spatial patterns of root water uptake. We found that wetter locations (rarely associated with throughfall hotspots) promoted greater root water uptake. Root water uptake in monitored soil layers also increased with neighborhood species richness. Ultimately our findings suggest that complementarity mechanisms within the forest stand, in addition to soil water variability and availability, govern root water uptake patterns.

Published
2024

8. Design of the ONERA M6 wing by shape optimization under uncertainty

Author

Görgülüarslan, R.M., Demir, G., Aradağ, S., Görgülüarslan, R.M., Demir, G., and Aradağ, S.

Abstract

Aerodynamic shape optimization processes are often used for complex problems that meet single or multi-objective design requirements. The robust aerodynamic shape optimization techniques with a high number of design variables that consider uncertainties have a huge computational burden compared to the traditional aerodynamic shape optimization techniques without considering uncertainties. To overcome this issue, in this study, the proper orthogonal decomposition is integrated with the inductive design exploration method to use for the robust shape optimization of the ONERA M6 wing. The proper orthogonal decomposition method is utilized for reducing the number of design variables of the wing geometry. The cost due to the computational fluid dynamics analysis is mitigated by incorporating the proper orthogonal decomposition with a surrogate modeling technique called the radial basis function. The robust optimization is conducted by the proposed approach based on the inductive design exploration method by accounting for uncertainties of the Mach number in the transonic flow regime. The agreement between the performance predictions of the robust designs and the computational fluid dynamics analysis results showed the effectiveness of the proposed approach. © 2024 Gazi Universitesi Muhendislik-Mimarlik. All rights reserved.

Published
2024

9. High-resolution throughfall measurement design, Hainich, Germany, project AquaDiva [Data set]

Author

Metzger, J.C., Hildebrandt, Anke, Demir, G., Filipzik, J., Metzger, J.C., Hildebrandt, Anke, Demir, G., and Filipzik, J.

Abstract

Throughfall heterogeneity induced by the redistribution of precipitation in vegetation canopies has repeatedly been hypothesized to affect the variation in the soil water content and runoff behavior, especially in forests. However, observational studies relating the spatial variation in the soil water content directly to net precipitation are rare, and few confirm modeling hypotheses. Here, we investigate whether throughfall patterns affect the spatial heterogeneity in the soil water response in the main rooting zone. We assessed rainfall, throughfall and soil water content (at two depths, 7.5 and 27.5 cm) on a 1 ha temperate mixed-beech forest plot in Germany during the 2015 and 2016 growing seasons using independent, high-resolution, stratified, random designs. Because the throughfall and soil water content cannot be measured at the same location, we used kriging to derive the throughfall values at the locations where the soil water content was measured. We first explored the spatial variation and temporal stability of throughfall and soil water patterns and subsequently evaluated the effects of input (throughfall), soil properties (field capacity and macroporosity), and vegetation parameters (canopy cover and distance to the next tree) on the soil water content and dynamics.   Throughfall spatial patterns were related to canopy density. Although spatial autocorrelation decreased with increasing event sizes, temporally stable throughfall patterns emerged, leading to reoccurring higher- and lower-input locations across precipitation events. Linear mixed-effects model analysis showed that soil water content patterns were poorly related to spatial patterns of throughfall and that they were more influenced by unidentified, but time constant, factors.   Instead of the soil water content itself, the patterns of its increase after rainfall corresponded more closely to throughfall patterns: more water was stored in the soil in areas where throughfall was

Published
2023

10. Throughfall spatial patterns translate into spatial patterns of soil moisture dynamics – empirical evidence

Author

Fischer-Bedtke, C., Metzger, J.C., Demir, G., Wutzler, T., Hildebrandt, Anke, Fischer-Bedtke, C., Metzger, J.C., Demir, G., Wutzler, T., and Hildebrandt, Anke

Abstract

Throughfall heterogeneity induced by the redistribution of precipitation in vegetation canopies has repeatedly been hypothesized to affect the variation in the soil water content and runoff behavior, especially in forests. However, observational studies relating the spatial variation in the soil water content directly to net precipitation are rare, and few confirm modeling hypotheses. Here, we investigate whether throughfall patterns affect the spatial heterogeneity in the soil water response in the main rooting zone. We assessed rainfall, throughfall and soil water content (at two depths, 7.5 and 27.5 cm) on a 1 ha temperate mixed-beech forest plot in Germany during the 2015 and 2016 growing seasons using independent, high-resolution, stratified, random designs. Because the throughfall and soil water content cannot be measured at the same location, we used kriging to derive the throughfall values at the locations where the soil water content was measured. We first explored the spatial variation and temporal stability of throughfall and soil water patterns and subsequently evaluated the effects of input (throughfall), soil properties (field capacity and macroporosity), and vegetation parameters (canopy cover and distance to the next tree) on the soil water content and dynamics. Throughfall spatial patterns were related to canopy density. Although spatial autocorrelation decreased with increasing event sizes, temporally stable throughfall patterns emerged, leading to reoccurring higher- and lower-input locations across precipitation events. Linear mixed-effects model analysis showed that soil water content patterns were poorly related to spatial patterns of throughfall and that they were more influenced by unidentified, but time constant, factors. Instead of the soil water content itself, the patterns of its increase after rainfall corresponded more closely to throughfall patterns: more water was stored in the soil in areas where throughfall was elevated. Furthermore

Published
2023

11. Talactoferrin alfa versus placebo in patients with refractory advanced non-small-cell lung cancer (FORTIS-M trial)

Author

Della-Fiorentina, S., Begbie, S., Jennens, R., Dass, J., Pittman, K., Ivanova, N., Koynova, T., Petrov, P., Tomova, A., Tzekova, V., Couture, F., Hirsh, V., Burkes, R., Sangha, R., Ambrus, M., Janaskova, T., Musil, J., Novotny, J., Zatloukal, P., Jakesova, J., Klenha, K., Roubec, J., Vanasek, J., Fayette, J., Barlesi, F., Bennouna-Louridi, J., Chouaid, C., Mazières, J., Vallerand, H., Robinet, G., Souquet, P.-J., Spaeth, D., Schott, R., Lena, H., Martinet, Y., El Kouri, C., Baize, N., Scherpereel, A., Molinier, O., Fuchs, F., Josten, K.M., Manegold, C., Marschner, N., Schneller, F., Overbeck, T., Thomas, M., von Pawel, J., Reck, M., Schuette, W., Hagen, V., Schneider, C.-P., Georgoulias, V., Varthalitis, I., Zarogoulidis, K., Syrigos, K., Papandreou, C., Bocskei, C., Csanky, E., Juhasz, E., Losonczy, G., Mark, Z., Molnar, I., Papai-Szekely, Z., Tehenes, S., Vinkler, I., Almel, S., Bakshi, A., Bondarde, S., Maru, A., Pathak, A., Pedapenki, R.M., Prasad, K., Prasad, S.V.S.S., Kilara, N., Gorijavolu, D., Deshmukh, C.D., John, S., Sharma, L.M., Amoroso, D., Bajetta, E., Bidoli, P., Bonetti, A., De Marinis, F., Maio, M., Passalacqua, R., Cascinu, S., Bearz, A., Bitina, M., Brize, A., Purkalne, G., Skrodele, M., Baba, A.A., Ratnavelu, K., Saw, M.H., Samson-Fernando, M.C., Ladrera, G.E., Jassem, J., Koralewski, P., Serwatowski, P., Krzakowski, M., Cebotaru, C., Filip, D., Ganea-Motan, D.E., Ianuli, C.H., Manolescu, I.G., Udrea, A., Burdaeva, O., Byakhov, M., Filippov, A., Lazarev, S., Mosin, I., Orlov, S., Udovitsa, D., Khorinko, A., Protsenko, S., Chang, A., Lim, H.L., Tan, Y.O., Tan, E.H., Bastus Piulats, R., Garcia-Foncillas, J., Valdivia, J., de Castro, J., Domine Gomez, M., Kim, S.W., Lee, J.-S., Kim, H.K., Lee, J.S., Shin, S.W., Kim, D.-W., Kim, Y.-C., Park, K.C., Chang, C.-S., Chang, G.-C., Goan, Y.-G., Su, W.-C., Tsai, C.-M., Kuo, H.-P., Benekli, M., Demir, G., Gokmen, E., Sevinc, A., Crawford, J., Giaccone, G., Haigentz, M., Owonikoko, T., Agarwal, M., Pandit, S., Araujo, R., Vrindavanam, N., Bonomi, P., Berg, A., Wade, J., Bloom, R., Amin, B., Camidge, R., Hill, D., Rarick, M., Flynn, P., Klein, L., Lo Russo, K., Neubauer, M., Richards, P., Ruxer, R., Savin, M., Weckstein, D., Rosenberg, R., Whittaker, T., Richards, D., Berry, W., Ottensmeier, C., Dangoor, A., Steele, N., Summers, Y., Rankin, E., Rowley, K., Giridharan, S., Kristeleit, H., Humber, C., Taylor, P., Ramalingam, S., Perez-Soler, R., Douillard, J.-Y., Thatcher, N., Wang, Y., Pultar, P., Zhu, J., and Malik, R.

Published
2013
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13. A Multi-Objective Robust Aircraft Wing Shape Optimization Approach

Author

Demir G., Aradag S., Görgülüarslan, Recep Muhammet, Demir G., Aradag S., and Görgülüarslan, Recep Muhammet

Abstract

AIAA Aviation and Aeronautics Forum and Exposition, AIAA AVIATION Forum 2021 -- 2 August 2021 through 6 August 2021 -- -- 273499, A robust aerodynamic shape optimization problem is one of the most challenging processes due to the high number of design parameters. The consideration of uncertainties causes a considerable computational burden. Therefore, the reduction of the number of required design variables has a significant impact on computational efficiency. In this study, Proper Orthogonal Decomposition (POD) method is utilized to extract the essential feature of the design variables for an aircraft wing geometry. The design exploration is conducted with the reduced-order parametric model constructed with POD rather than using the more complex or high-dimensional system. The Radial Basis Function (RBF) interpolation technique is implemented to estimate the unknown field available in the design space. Model-form uncertainties originating from the turbulence model required for the CFD analyses are determined using the eigenspace perturbation methodology. Robust solutions that satisfy the design requirements are obtained while taking uncertainties into account using Inductive Design Exploration Method (IDEM). The results of the case study show that geometric filtration using POD-RBF based IDEM computation approach is an alternative multi-objective robust optimization framework. © 2021, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

Published
2022

14. A Multi-Objective Robust Aircraft Wing Shape Optimization Approach

Author

Aradag S., Demir G., Görgülüarslan, Recep Muhammet, Aradag S., Demir G., and Görgülüarslan, Recep Muhammet

Abstract

AIAA Aviation and Aeronautics Forum and Exposition, AIAA AVIATION Forum 2021 -- 2 August 2021 through 6 August 2021 -- -- 273499, A robust aerodynamic shape optimization problem is one of the most challenging processes due to the high number of design parameters. The consideration of uncertainties causes a considerable computational burden. Therefore, the reduction of the number of required design variables has a significant impact on computational efficiency. In this study, Proper Orthogonal Decomposition (POD) method is utilized to extract the essential feature of the design variables for an aircraft wing geometry. The design exploration is conducted with the reduced-order parametric model constructed with POD rather than using the more complex or high-dimensional system. The Radial Basis Function (RBF) interpolation technique is implemented to estimate the unknown field available in the design space. Model-form uncertainties originating from the turbulence model required for the CFD analyses are determined using the eigenspace perturbation methodology. Robust solutions that satisfy the design requirements are obtained while taking uncertainties into account using Inductive Design Exploration Method (IDEM). The results of the case study show that geometric filtration using POD-RBF based IDEM computation approach is an alternative multi-objective robust optimization framework. © 2021, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

Published
2022

15. Spatial variation of grassland canopy affects soil wetting patterns and preferential flow

Author

Demir, G., Michalzik, B., Filipzik, J., Metzger, J.C., Hildebrandt, Anke, Demir, G., Michalzik, B., Filipzik, J., Metzger, J.C., and Hildebrandt, Anke

Abstract

Canopies shape net precipitation patterns, which are spatially heterogeneous and control soil moisture response to rainfall. The vast majority of studies on canopy water fluxes were conducted in forests. In contrast, grassland canopies are often assumed to be spatially homogeneous, therefore likely not inducing patches of heterogeneity at and below the soil surface. However, some studies on short-structured vegetation, such as grasslands, proposed the importance of canopy-induced heterogeneity for net precipitation. Still, systematic investigations on the effects on soil wetting patterns are missing. Therefore, in this study, we investigated soil moisture response to rainfall in a managed temperate grassland by exploring the individual impacts of spatially varying throughfall, vegetation height, and antecedent soil moisture status on the soil wetting patterns. We applied linear mixed effects models to disentangle the role of grassland canopy versus abiotic drivers. The spatial average soil water response showed diminishing water amounts stored in the upper parts of the soil as the growing season progressed and the soils dried, indicating bypass flow. Spatial variation of grass height was a significant driver of soil wetting patterns along with precipitation and antecedent soil moisture status. Soil wetting was suppressed in locations with tall canopies, although surprisingly, this was not directly related to throughfall patterns. Instead, our results suggest that seasonally drier conditions and the spatial difference in grass development amplify fast flow processes. Ultimately, our results confirm that spatial variation of the canopy affects soil moisture wetting patterns not only in forests but indicate a strong influence of preferential flow on soil water patterns in managed grassland as well.

Published
2022

17. Continuous glucose monitoring in children with glycogen storage disease type I

Author

Kasapkara, C.S., Demir, G. Cinasal, Hasanoglu, A., and Tumer, L.

Subjects
Medical research, Medicine, Experimental, Blood sugar -- Physiological aspects -- Health aspects, Glucose metabolism -- Research, Patient monitoring -- Methods, Food/cooking/nutrition, Health
Abstract

BACKGROUND/OBJECTIVES: Glycogen storage disease type I (GSD I) is an autosomal recessive metabolic disorder caused by defects in the glucose-6-phosphatase complex. Deficient activity in the glucose-6-phosphatase-α catalytic unit characterizes GSD Ia and defects in the glucose-6-phosphate transporter protein characterize GSD Ib. Type Ia involves the liver, kidney and intestine (and Ib also leukocytes), and the clinical manifestations are hepatomegaly, failure to thrive, severe fasting hypoglycemia within 3-4 h after a meal, hyperlactatemia, hyperuricemia and hyperlipidemia. The aim of the present study was to examine the safety and efficacy of a continuous subcutaneous glucose monitoring system to determine the magnitude and significance of hypoglycemia in GSD I and to evaluate the efficacy of the revised dietary treatment. SUBJECTS/METHODS: Sixteen children with GSD I were studied over a 72-h period. Continuous glucose monitoring (CGM) was repeated in all patients 3-6 months after the first monitoring to examine the effects of revised dietary instructions on glycemic control. RESULTS: All the patients completed the study without any major adverse events. Significant periods of asymptomatic hypoglycemia (below 4mmol/l, 70mg/dl) were noted. There was a close correlation between CGM sensor and capillary blood glucose values measured by a glucometer. CGM indicated a considerable reduction in duration of hypoglycemia, liver size and improvements in secondary metabolic derangements such as hyperlacticacidemia and hyperlipidemia. CONCLUSIONS: CGM could be applied in the clinical setting to help the physician to identify hypoglycemic events, and repeated CGM may serve as a safe and useful tool for the assessment of the long-term management of patients with GSD I. European Journal of Clinical Nutrition (2014) 68, 101-105; doi: 10.1038/ejcn.2013.186; published online 23 October 2013 Keywords: glycogen storage disease I; continuous glucose monitoring; metabolic parameters, INTRODUCTION Glycogen storage disease type I (GSD I), characterized by impaired production of glucose from glycogenolysis and gluconeogenesis, results from defects in the glucose 6-phosphate enzyme system. Glucose-6-phosphatase is affected [...]

Published
2014
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18. Changes in Anterior Chamber Angle and Pupillary Diameter after Implantation of a New Posterior Chamber Phakic Intraocular Lens

Author

Demir G, Akbaş Yb, Sucu Me, and Agca A

Subjects
medicine.medical_specialty, Materials science, genetic structures, Ophthalmology, medicine, Anterior chamber angle, Posterior chamber phakic intraocular lens
Abstract

Purpose: To evaluate the effect of the Eyecryl posterior chamber phakic intraocular lens (pIOL) on iridocorneal angle (ICA) parameters, anterior chamber depth (ACD), and pupillary size.Methods: The medical files of myopic patients who had implantation of the Eyecryl posterior chamber pIOL were reviewed retrospectively. Trabecular-iris space area at 500 and 750μm (TISA500, TISA750), angle opening distances at 500 and 750μm (AOD500, AOD750), anterior chamber depth (ACD), iridocorneal angle (ICA), and pupil diameter under different illumination conditions were analyzed preoperatively, and at 1 and 3 months postoperatively.Results: Ninety-three eyes of 48 patients were included in the study. The mean age of patients was 31.63 ±4.95 years (range, 21-54). The mean ICA decreased from 49.97° ± 6.33 before surgery to 30.75° ± 5.86 and 30.79° ± 5.74 at 1 and 3 months after surgery, respectively. The mean ACD was reduced from 3.23 ± 0.22 mm before surgery to 2.55 ± 0.34 mm and 2.46 ± 0.28 mm at 1 and 3 months after surgery, respectively. TISA500, TISA750, AOD500, and AOD750 were also reduced significantly after surgery. The mean pupil size under photopic, mesopic and scotopic illuminations decreased insignificantly by 1 month and continued to decrease significantly by 3 months after surgery.Conclusion: The implantation of the Eyecryl posterior chamber pIOL in myopic patients caused significant changes in anterior chamber parameters including ICA, ACD, TISA 500, TISA 750, AOD 500, AOD 750, and the pupil diameter under different illumination conditions.

Published
2021
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19. Computational fluid dynamics modelling of store separation for transonic generic store

Author

Demir G., Alemdaroğlu N., Demir G., and Alemdaroğlu N.

Abstract

In this study, two different well-known wind tunnel techniques; “Captive Trajectory Method “and “Grid Surveying Method “are simulated using Computational Fluid Dynamics (CFD) method. Time dependent behavior of a generic store during the release process from a delta wing under high transonic flow regime is determined. First of all, in captive trajectory simulation, simultaneous trajectory and attitude computations are accomplished by utilizing a reliable commercial flow solver called ANSYS Fluent. Secondly, aerodynamic grid database generation required for grid surveying approach is performed and the trajectory of the store is determined by using a standalone store separation module built in MATLAB Simulink. The numerical outputs are compared with available wind tunnel results conducted in Arnold Engineering Development Center. © 2018, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

Published
2021

20. Computational fluid dynamics modelling of store separation for transonic generic store

Author

Alemdaroğlu N., Demir G., Alemdaroğlu N., and Demir G.

Abstract

In this study, two different well-known wind tunnel techniques; “Captive Trajectory Method “and “Grid Surveying Method “are simulated using Computational Fluid Dynamics (CFD) method. Time dependent behavior of a generic store during the release process from a delta wing under high transonic flow regime is determined. First of all, in captive trajectory simulation, simultaneous trajectory and attitude computations are accomplished by utilizing a reliable commercial flow solver called ANSYS Fluent. Secondly, aerodynamic grid database generation required for grid surveying approach is performed and the trajectory of the store is determined by using a standalone store separation module built in MATLAB Simulink. The numerical outputs are compared with available wind tunnel results conducted in Arnold Engineering Development Center. © 2018, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

Published
2021

24. Comparison of Subthalamic Nucleus vs. Globus Pallidus Intern Deep Brain

Author

Celiker, O, Demir, G, Kocaoglu, M, Altug, F, and Acar, F

Subjects
endocrine system, surgical procedures, operative, nervous system, Advanced Parkinson's disease, Subthalamic nucleus, Globus pallidus, interna, Deep brain stimulation, therapeutics, nervous system diseases
Abstract

AIM: To compare the effects of subthalamic nucleus (STN) and globus pallidus interna (GPi) deep brain stimulation (DBS) on the motor outcome, gait and balance function, fall risk (FR), and non-motor symptoms in patients with advanced Parkinson's disease (PD).

Published
2019

26. Siponimod versus placebo in secondary progressive multiple sclerosis (EXPAND): a double-blind, randomised, phase 3 study

Author

Kappos, L., Bar-Or, A., Cree, B. A. C., Fox, R. J., Giovannoni, G., Gold, R., Vermersch, P., Arnold, D. L., Arnould, S., Scherz, T., Wolf, C., Wallstrom, E., Dahlke, F., Achiron, A., Achtnichts, L., Agan, K., Akman-Demir, G., Allen, A. B., Antel, J. P., Antiguedad, A. R., Apperson, M., Applebee, A. M., Ayuso, G. I., Baba, M., Bajenaru, O., Balasa, R., Balci, B. P., Barnett, M., Bass, A., Becker, V. U., Bejinariu, M., Bergh, F. T., Bergmann, A., Bernitsas, E., Berthele, A., Bhan, V., Bischof, F., Bjork, R. J., Blevins, G., Boehringer, M., Boerner, T., Bonek, R., Bowen, J. D., Bowling, A., Boyko, A. N., Boz, C., Bracknies, V., Braune, S., Brescia Morra, V., Brochet, B., Brola, W., Brownstone, P. K., Brozman, M., Brunet, D., Buraga, I., Burnett, M., Buttmann, M., Butzkueven, H., Cahill, J., Calkwood, J. C., Camu, W., Cascione, M., Castelnovo, G., Centonze, D., Cerqueira, J., Chan, A., Cimprichova, A., Cohan, S., Comi, G., Conway, J., Cooper, J. A., Corboy, J., Correale, J., Costell, B., Cottrell, D. A., Coyle, P. K., Craner, M., Cui, L., Cunha, L., Czlonkowska, A., da Silva, A. M., de Sa, J., de Seze, J., Debouverie, M., Debruyne, J., Decoo, D., Defer, G., Derfuss, T., Deri, N. H., Dihenia, B., Dioszeghy, P., Donath, V., Dubois, B., Duddy, M., Duquette, P., Edan, G., Efendi, H., Elias, S., Emrich, P. J., Estruch, B. C., Evdoshenko, E. P., Faiss, J., Fedyanin, A. S., Feneberg, W., Fermont, J., Fernandez, O. F., Ferrer, F. C., Fink, K., Ford, H., Ford, C., Francia, A., Freedman, M., Frishberg, B., Galgani, S., Garmany, G. P., Gehring, K., Gitt, J., Gobbi, C., Goldstick, L. P., Gonzalez, R. A., Grandmaison, F., Grigoriadis, N., Grigorova, O., Grimaldi, L. M. E., Gross, J., Gross-Paju, K., Gudesblatt, M., Guillaume, D., Haas, J., Hancinova, V., Hancu, A., Hardiman, O., Harmjanz, A., Heidenreich, F. R., Hengstman, G. J. D., Herbert, J., Herring, M., Hodgkinson, S., Hoffmann, O. M., Hofmann, W. E., Honeycutt, W. D., Hua, L. H., Huang, D., Huang, Y., Hupperts, R., Imre, P., Jacobs, A. K., Jakab, G., Jasinska, E., Kaida, K., Kalnina, J., Kaprelyan, A., Karelis, G., Karussis, D., Katz, A., Khabirov, F. A., Khatri, B., Kimura, T., Kister, I., Kizlaitiene, R., Klimova, E., Koehler, J., Komatineni, A., Kornhuber, A., Kovacs, K., Koves, A., Kozubski, W., Krastev, G., Krupp, L. B., Kurca, E., Lassek, C., Laureys, G., Lee, L., Lensch, E., Leutmezer, F., Li, H., Linker, R. A., Linnebank, M., Liskova, P., Llanera, C., Lu, J., Lutterotti, A., Lycke, J., Macdonell, R., Maciejowski, M., Maeurer, M., Magzhanov, R. V., Maida, E. -M., Malciene, L., Mao-Draayer, Y., Marfia, G. A., Markowitz, C., Mastorodimos, V., Matyas, K., Meca-Lallana, J., Merino, J. A. G., Mihetiu, I. G., Milanov, I., Miller, A. E., Millers, A., Mirabella, M., Mizuno, M., Montalban, X., Montoya, L., Mori, M., Mueller, S., Nakahara, J., Nakatsuji, Y., Newsome, S., Nicholas, R., Nielsen, A. S., Nikfekr, E., Nocentini, U., Nohara, C., Nomura, K., Odinak, M. M., Olsson, T., van Oosten, B. W., Oreja-Guevara, C., Oschmann, P., Overell, J., Pachner, A., Panczel, G., Pandolfo, M., Papeix, C., Patrucco, L., Pelletier, J., Piedrabuena, R., Pless, M., Polzer, U., Pozsegovits, K., Rastenyte, D., Rauer, S., Reifschneider, G., Rey, R., Rizvi, S. A., Robertson, D., Rodriguez, J. M., Rog, D., Roshanisefat, H., Rowe, V., Rozsa, C., Rubin, S., Rusek, S., Sacca, F., Saida, T., Salgado, A. V., Sanchez, V. E. F., Sanders, K., Satori, M., Sazonov, D. V., Scarpini, E. A., Schlegel, E., Schluep, M., Schmidt, S., Scholz, E., Schrijver, H. M., Schwab, M., Schwartz, R., Scott, J., Selmaj, K., Shafer, S., Sharrack, B., Shchukin, I. A., Shimizu, Y., Shotekov, P., Siever, A., Sigel, K. -O., Silliman, S., Simo, M., Simu, M., Sinay, V., Siquier, A. E., Siva, A., Skoda, O., Solomon, A., Stangel, M., Stefoski, D., Steingo, B., Stolyarov, I. D., Stourac, P., Strassburger-Krogias, K., Strauss, E., Stuve, O., Tarnev, I., Tavernarakis, A., Tello, C. R., Terzi, M., Ticha, V., Ticmeanu, M., Tiel-Wilck, K., Toomsoo, T., Tubridy, N., Tullman, M. J., Tumani, H., Turcani, P., Turner, B., Uccelli, A., Urtaza, F. J. O., Vachova, M., Valikovics, A., Walter, S., Van Wijmeersch, B., Vanopdenbosch, L., Weber, J. R., Weiss, S., Weissert, R., West, T., Wiendl, H., Wiertlewski, S., Wildemann, B., Willekens, B., Visser, L. H., Vorobeychik, G., Xu, X., Yamamura, T., Yang, Y. N., Yelamos, S. M., Yeung, M., Zacharias, A., Zelkowitz, M., Zettl, U., Zhang, M., Zhou, H., Zieman, U., Ziemssen, T., Bergmann A., Haas J., Mirabella M. (ORCID:0000-0002-7783-114X), Terzi M., Kappos, L., Bar-Or, A., Cree, B. A. C., Fox, R. J., Giovannoni, G., Gold, R., Vermersch, P., Arnold, D. L., Arnould, S., Scherz, T., Wolf, C., Wallstrom, E., Dahlke, F., Achiron, A., Achtnichts, L., Agan, K., Akman-Demir, G., Allen, A. B., Antel, J. P., Antiguedad, A. R., Apperson, M., Applebee, A. M., Ayuso, G. I., Baba, M., Bajenaru, O., Balasa, R., Balci, B. P., Barnett, M., Bass, A., Becker, V. U., Bejinariu, M., Bergh, F. T., Bergmann, A., Bernitsas, E., Berthele, A., Bhan, V., Bischof, F., Bjork, R. J., Blevins, G., Boehringer, M., Boerner, T., Bonek, R., Bowen, J. D., Bowling, A., Boyko, A. N., Boz, C., Bracknies, V., Braune, S., Brescia Morra, V., Brochet, B., Brola, W., Brownstone, P. K., Brozman, M., Brunet, D., Buraga, I., Burnett, M., Buttmann, M., Butzkueven, H., Cahill, J., Calkwood, J. C., Camu, W., Cascione, M., Castelnovo, G., Centonze, D., Cerqueira, J., Chan, A., Cimprichova, A., Cohan, S., Comi, G., Conway, J., Cooper, J. A., Corboy, J., Correale, J., Costell, B., Cottrell, D. A., Coyle, P. K., Craner, M., Cui, L., Cunha, L., Czlonkowska, A., da Silva, A. M., de Sa, J., de Seze, J., Debouverie, M., Debruyne, J., Decoo, D., Defer, G., Derfuss, T., Deri, N. H., Dihenia, B., Dioszeghy, P., Donath, V., Dubois, B., Duddy, M., Duquette, P., Edan, G., Efendi, H., Elias, S., Emrich, P. J., Estruch, B. C., Evdoshenko, E. P., Faiss, J., Fedyanin, A. S., Feneberg, W., Fermont, J., Fernandez, O. F., Ferrer, F. C., Fink, K., Ford, H., Ford, C., Francia, A., Freedman, M., Frishberg, B., Galgani, S., Garmany, G. P., Gehring, K., Gitt, J., Gobbi, C., Goldstick, L. P., Gonzalez, R. A., Grandmaison, F., Grigoriadis, N., Grigorova, O., Grimaldi, L. M. E., Gross, J., Gross-Paju, K., Gudesblatt, M., Guillaume, D., Haas, J., Hancinova, V., Hancu, A., Hardiman, O., Harmjanz, A., Heidenreich, F. R., Hengstman, G. J. D., Herbert, J., Herring, M., Hodgkinson, S., Hoffmann, O. M., Hofmann, W. E., Honeycutt, W. D., Hua, L. H., Huang, D., Huang, Y., Hupperts, R., Imre, P., Jacobs, A. K., Jakab, G., Jasinska, E., Kaida, K., Kalnina, J., Kaprelyan, A., Karelis, G., Karussis, D., Katz, A., Khabirov, F. A., Khatri, B., Kimura, T., Kister, I., Kizlaitiene, R., Klimova, E., Koehler, J., Komatineni, A., Kornhuber, A., Kovacs, K., Koves, A., Kozubski, W., Krastev, G., Krupp, L. B., Kurca, E., Lassek, C., Laureys, G., Lee, L., Lensch, E., Leutmezer, F., Li, H., Linker, R. A., Linnebank, M., Liskova, P., Llanera, C., Lu, J., Lutterotti, A., Lycke, J., Macdonell, R., Maciejowski, M., Maeurer, M., Magzhanov, R. V., Maida, E. -M., Malciene, L., Mao-Draayer, Y., Marfia, G. A., Markowitz, C., Mastorodimos, V., Matyas, K., Meca-Lallana, J., Merino, J. A. G., Mihetiu, I. G., Milanov, I., Miller, A. E., Millers, A., Mirabella, M., Mizuno, M., Montalban, X., Montoya, L., Mori, M., Mueller, S., Nakahara, J., Nakatsuji, Y., Newsome, S., Nicholas, R., Nielsen, A. S., Nikfekr, E., Nocentini, U., Nohara, C., Nomura, K., Odinak, M. M., Olsson, T., van Oosten, B. W., Oreja-Guevara, C., Oschmann, P., Overell, J., Pachner, A., Panczel, G., Pandolfo, M., Papeix, C., Patrucco, L., Pelletier, J., Piedrabuena, R., Pless, M., Polzer, U., Pozsegovits, K., Rastenyte, D., Rauer, S., Reifschneider, G., Rey, R., Rizvi, S. A., Robertson, D., Rodriguez, J. M., Rog, D., Roshanisefat, H., Rowe, V., Rozsa, C., Rubin, S., Rusek, S., Sacca, F., Saida, T., Salgado, A. V., Sanchez, V. E. F., Sanders, K., Satori, M., Sazonov, D. V., Scarpini, E. A., Schlegel, E., Schluep, M., Schmidt, S., Scholz, E., Schrijver, H. M., Schwab, M., Schwartz, R., Scott, J., Selmaj, K., Shafer, S., Sharrack, B., Shchukin, I. A., Shimizu, Y., Shotekov, P., Siever, A., Sigel, K. -O., Silliman, S., Simo, M., Simu, M., Sinay, V., Siquier, A. E., Siva, A., Skoda, O., Solomon, A., Stangel, M., Stefoski, D., Steingo, B., Stolyarov, I. D., Stourac, P., Strassburger-Krogias, K., Strauss, E., Stuve, O., Tarnev, I., Tavernarakis, A., Tello, C. R., Terzi, M., Ticha, V., Ticmeanu, M., Tiel-Wilck, K., Toomsoo, T., Tubridy, N., Tullman, M. J., Tumani, H., Turcani, P., Turner, B., Uccelli, A., Urtaza, F. J. O., Vachova, M., Valikovics, A., Walter, S., Van Wijmeersch, B., Vanopdenbosch, L., Weber, J. R., Weiss, S., Weissert, R., West, T., Wiendl, H., Wiertlewski, S., Wildemann, B., Willekens, B., Visser, L. H., Vorobeychik, G., Xu, X., Yamamura, T., Yang, Y. N., Yelamos, S. M., Yeung, M., Zacharias, A., Zelkowitz, M., Zettl, U., Zhang, M., Zhou, H., Zieman, U., Ziemssen, T., Bergmann A., Haas J., Mirabella M. (ORCID:0000-0002-7783-114X), and Terzi M.

Abstract

Background: No treatment has consistently shown efficacy in slowing disability progression in patients with secondary progressive multiple sclerosis (SPMS). We assessed the effect of siponimod, a selective sphingosine 1-phosphate (S1P) receptor1,5 modulator, on disability progression in patients with SPMS. Methods: This event-driven and exposure-driven, double-blind, phase 3 trial was done at 292 hospital clinics and specialised multiple sclerosis centres in 31 countries. Using interactive response technology to assign numbers linked to treatment arms, patients (age 18–60 years) with SPMS and an Expanded Disability Status Scale score of 3·0–6·5 were randomly assigned (2:1) to once daily oral siponimod 2 mg or placebo for up to 3 years or until the occurrence of a prespecified number of confirmed disability progression (CDP) events. The primary endpoint was time to 3-month CDP. Efficacy was assessed for the full analysis set (ie, all randomly assigned and treated patients); safety was assessed for the safety set. This trial is registered with ClinicalTrials.gov, number NCT01665144. Findings: 1651 patients were randomly assigned between Feb 5, 2013, and June 2, 2015 (1105 to the siponimod group, and 546 to the placebo group). One patient did not sign the consent form, and five patients did not receive study drug, all of whom were in the siponimod group. 1645 patients were included in the analyses (1099 in the siponimod group and 546 in the placebo). At baseline, the mean time since first multiple sclerosis symptoms was 16·8 years (SD 8·3), and the mean time since conversion to SPMS was 3·8 years (SD 3·5); 1055 (64%) patients had not relapsed in the previous 2 years, and 918 (56%) of 1651 needed walking assistance. 903 (82%) patients receiving siponimod and 424 (78%) patients receiving placebo completed the study. 288 (26%) of 1096 patients receiving siponimod and 173 (32%) of 545 patients receiving placebo had 3-month CDP (hazard ratio 0·79, 95% CI 0·65–0·95; relative

Published
2018

28. Conventional Morphology Versus PCR Sequencing, rep-PCR, and MALDI-TOF-MS for Identification of Clinical Aspergillus Isolates Collected Over a 2-Year Period in a University Hospital at Kayseri, Turkey

Author

Atalay, A., Koc, A.N., Suel, A., Sav, H., Demir, G., Elmali, F., Cakir, N., Seyedmousavi, S., and Medical Microbiology & Infectious Diseases

Subjects
lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4]
Abstract

Background: Aspergillus species cause a wide range of diseases in humans, including allergies, localized infections, or fatal disseminated diseases. Rapid detection and identification of Aspergillus spp. facilitate effective patient management. In the current study we compared conventional morphological methods with PCR sequencing, rep-PCR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the identification of Aspergillus strains. Materials and Methods: A total of 24 consecutive clinical isolates of Aspergillus were collected during 2012-2014. Conventional morphology and rep-PCR were performed in our Mycology Laboratory. The identification, evaluation, and reporting of strains using MALDI-TOFMS were performed by BioMerieux Diagnostic, Inc. in Istanbul. DNA sequence analysis of the clinical isolates was performed by the BMLabosis laboratory in Ankara. Results: Samples consisted of 18 (75%) lower respiratory tract specimens, 3 otomycosis (12.5%) ear tissues, 1 sample from keratitis, and 1 sample from a cutaneous wound. According to DNA sequence analysis, 12 (50%) specimens were identified as A. fumigatus, 8 (33.3%) as A. flavus, 3 (12.5%) as A. niger, and 1 (4.2%) as A. terreus. Statistically, there was good agreement between the conventional morphology and rep-PCR and MALDI-TOF methods; kappa values were K = 0.869, 0.871, and 0.916, respectively (P < 0.001). Conclusion: The good level of agreement between the methods included in the present study and sequence method could be due to the identification of Aspergillus strains that were commonly encountered. Therefore, it was concluded that studies conducted with a higher number of isolates, which include other Aspergillus strains, are required. J. Clin. Lab. Anal. 30:745-750, 2016. (C) 2016 Wiley Periodicals, Inc.

Published
2016

29. Bickerstaff's encephalitis and Miller Fisher syndrome associated with voltage-gated potassium channel and novel anti-neuronal antibodies

Author

Tüzün, E, Kürtüncü, M, Lang, B, Içöz, S, Akman-Demir, G, Eraksoy, M, and Vincent, A

Abstract

BACKGROUND: GQ1b antibody (GQ1b-Ab) is detected in approximately two-thirds of sera of patients with Bickerstaffs encephalitis (BE). Whilst some of the remaining patients have antibodies to other gangliosides, many patients with BE are reported to be seronegative. METHODS AND RESULTS: Voltage-gated potassium channel antibody (VGKC-Ab) at high titer was detected during the diagnostic work-up of one patient with BE. Sera of an additional patient with BE and nine patients with Miller Fisher syndrome (MF) (all GQ1b-Ab positive) were investigated for VGKC-Ab and other anti-neuronal antibodies by radioimmunoprecipitation using 125I-dendrotoxin-VGKC and immunohistochemistry, respectively. Two patients with MF exhibited moderate titer VGKC-Abs. Regardless of positivity for VGKC or GQ1b antibodies, serum IgG of all patients with BE and MF reacted with the molecular layer and Purkinje cells of the cerebellum in a distinctive pattern. CONCLUSION: Voltage-gated potassium channel antibodies might be involved in some cases of BE or MF. The common staining pattern despite different antibody results suggests that there might be other, as yet unidentified, antibodies associated with BE and MF.

Published
2016

30. DETECTION OF PHYSIOLOGICAL AND GENOTOXIC DAMAGES REFLECTING TOXICITY IN KALANCHOE CLONES

Author

Ibrahim Ilker Ozyigit, Yilmaz, S., Dogan, I., Sakcali, M. S., Tombuloglu, G., Goksel Demir, G., Doğan, İlhan, and Izmir Institute of Technology. Molecular Biology and Genetics

Subjects
RAPD-PCR, Photosynthetic pigments, genotoxicity, photosynthetic pigments, Genotoxicity, Heavy metal pollution, heavy metal pollution
Abstract

In order to make assessments in understanding of physiological and genotoxic effects of imposing cadmium (Cd) on photosynthetic pigment contents along with the changes occurring in genetic material of Kalanchoe plants were used in relation to various Cd-treatments. Young plantlets were originated from a single host plant as clones, and developed in vitro. Developed clones were grown in standard pots with daily watering of Hoagland solution (20 ml) containing different concentrations of cadmium chloride for two months. Cd concentrations of the collected samples were measured by employing ICP-OES and RAPD-PCR technique was applied for detecting the genotoxic effects of Cd. After two month of experimental period, the comparisons between unexposed and exposed Kalanchoe clone groups revealed reductions in photosynthetic pigment contents, especially at the highest level of Cd exposure and a genomic instability when application of Cd concentration increases. RAPD-PCR analyses demonstrated the distinguishable banding pattern in number and band intensities between Cd-treated and control groups. In addition, progressive Cd accumulations in leaves, stems and roots of plant samples were observed when the application of exposure level increased. Marmara University, Commission of Scientific Research ProjectMarmara University [FEN-C-YLP-040712-0283] This study was funded by Marmara University, Commission of Scientific Research Project under grant FEN-C-YLP-040712-0283.

Published
2016

31. Effects of amantadine on postural instability in Parkinson-s disease

Author

Topcular, B., Akman-Demir, G., Kaymaz, A., Altinkaya, A., Orken, D., Altindag, E., Tuncer, O. Gungor, Matur, ZELİHA, Altunrende, B., Yabalak, A., and MATUR, ZELİHA

Subjects
Topcular B., Altinkaya A., Kaymaz A., Yabalak A., Altunrende B., Matur Z., Tuncer O. G. , Altindag E., Orken D., Akman-Demir G., -Effects of amantadine on postural instability in Parkinson-s disease-, 19th International Congress of Parkinson-s Disease and Movement Disorders, California, Amerika Birleşik Devletleri, 14 - 18 Haziran 2015, cilt.30
Published
2015

32. registry study (A Turkish Oncology Group trial)

Author

Aykan, NF, Yalcin, S, Turhal, NS, Ozdogan, M, Demir, G, Ozkan, M, Yaren, A, Camci, C, Akbulut, H, Artac, M, Meydan, N, Uygun, K, Isikdogan, A, Unsal, D, Ozyilkan, O, Arican, A, Seyrek, E, Tekin, SB, Manavoglu, O, Ozet, A, Elkiran, T, and Disci, R

Subjects
Colorectal cancer, epidemiology, risk factors, Turkey
Abstract

Background/Aims: This study aimed to determine the epidemiological characteristics of colorectal cancer in Turkey. Materials and Methods: In this multicenter, prospective, and cross-sectional registry study, data for 968 patients with colorectal cancer from 21 centers in 7 geographic regions were analyzed. Results: Diagnosis was colon cancer in 662 (68.4%) and rectum cancer in 306 (31.6%) patients. In total, 60.9% of patients was male; mean age was 58.9 +/- 12.6 years. Among patients, 15.0% was drinking alcohol, 17.5% was smoking, 1.5% had familial history of polyposis, 15.0% had diabetes mellitus, 1.0% had inflammatory bowel disease. Fruit and vegetable consumption was low (= 3 times/week) in 47.4% of the patients. Median time-to diagnosis was 3.0 months and 4.0 months for patients with colon and rectum cancer, respectively. Mean body mass index was >25 in all group of patients. Distal rectum (61.3%) and sigmoid colon (36.8%) were the most common locations of cancer, for rectum and colon respectively. In total, 85.6% of patients were operated; 25.8% had emergency surgery. Low anterior resection rate was 64.2% in rectum cancer. In majority (89.8%) of the patients with rectum cancer who received preoperative treatment, conventional chemo-radiotherapy regimen was given. pTNM staging at diagnosis showed that stage III and IV patients were in majority (35.9% and 29.7%, respectively). Conclusion: Colon cancer is more frequent than rectum cancer in Turkey. Colorectal cancer patients are diagnosed at later stages. Most of the cases were operated. Interregional differences for risk factors are worthwhile for evaluation in future trials.

Published
2015

34. Effects of amantadine on postural instability in Parkinson-s disease

Author

Altinkaya, A., Akman-Demir, G., Yabalak, A., Topcular, B., Altindag, E., Gungor, O., Matur, ZELİHA, Altunrende, B., Kaymaz, A., and MATUR, ZELİHA

Subjects
Topcular B., Altinkaya A., Yabalak A., Kaymaz A., Altunrende B., Matur Z., Gungor O., Altindag E., Akman-Demir G., -Effects of amantadine on postural instability in Parkinson-s disease-, Joint Congress of European Neurology, İstanbul, Türkiye, 31 Mayıs - 03 Haziran 2014, cilt.21, ss.670, Topcular B., Altinkaya A., Yabalak A., Kaymaz A., Altunrende B., Matur Z., Gungor O., Altindag E., Demir G. A. , -Effects of amantadine on postural instability in Parkinson-s disease-, Joint Congress of European Neurology, İstanbul, Türkiye, 31 Mayıs - 03 Haziran 2014, cilt.261
Published
2014

35. (TOG)

Author

Tanriverdi, O, Kaytan-Saglam, E, Ulger, S, Bayoglu, IV, Turker, I, Ozturk-Topcu, T, Cokmert, S, Turhal, S, Oktay, E, Karabulut, B, Kilic, D, Kucukzeybek, Y, Oksuzoglu, B, Meydan, N, Kaya, V, Akman, T, Ibis, K, Saynak, M, Sen, CA, Uysal-Sonmez, O, Pilanci, KN, Demir, G, Saglam, S, Kocar, M, Menekse, S, Goksel, G, Yapar-Taskoylu, B, Yaren, A, Uyeturk, U, Avci, N, Denizli, B, and Ilis-Temiz, E

Subjects
Colorectal cancer, Brain metastasis, Prognosis
Abstract

Brain metastasis in colorectal cancer is highly rare. In the present study, we aimed to determine the frequency of brain metastasis in colorectal cancer patients and to establish prognostic characteristics of colorectal cancer patients with brain metastasis. In this cross-sectional study, the medical files of colorectal cancer patients with brain metastases who were definitely diagnosed by histopathologically were retrospectively reviewed. Brain metastasis was detected in 2.7 % (n = 133) of 4,864 colorectal cancer patients. The majority of cases were male (53 %), older than 65 years (59 %), with rectum cancer (56 %), a poorly differentiated tumor (70 %); had adenocarcinoma histology (97 %), and metachronous metastasis (86 %); received chemotherapy at least once for metastatic disease before brain metastasis developed (72 %), had progression with lung metastasis before (51 %), and 26 % (n = 31) of patients with extracranial disease at time the diagnosis of brain metastasis had both lung and bone metastases. The mean follow-up duration was 51 months (range 5-92), and the mean survival was 25.8 months (95 % CI 20.4-29.3). Overall survival rates were 81 % in the first year, 42.3 % in the third year, and 15.7 % in the fifth year. In multiple variable analysis, the most important independent risk factor for overall survival was determined as the presence of lung metastasis (HR 1.43, 95 % CI 1.27-4.14; P = 0.012). Brain metastasis develops late in the period of colorectal cancer and prognosis in these patients is poor. However, early screening of brain metastases in patients with lung metastasis may improve survival outcomes with new treatment modalities.

Published
2014

36. Taburan beberapa unsur dalam Veronica scutellata L. dari Bolu, Turki: Saling tindakan tanih-tumbuhan

Author

Ozyigit, I. I., Dogan, I., Demir, G., Eskin, B., Mustafa Keskin, Yalcin, I. E., TR100479, Doğan, İlhan, and Izmir Institute of Technology. Molecular Biology and Genetics

Subjects
Trace elements, Grassleaf speedwell, Autecology, Plant nutrition
Abstract

Veronica scutellata L. occurs in moist and wet habitats, such as ponds, marshes and other wetlands. This study was conducted on this species to examine its mineral element uptake status in terms of interactions between soil and plant. Experimental materials were taken from the Southern coast of Black Sea at coordinates 40°36'N and 31°16'E at an altitude of 1400 m above sea level from Bolu - Turkey; using standard methods and plant (root, stem and leaf parts) and soil mineral element measurements (Al, B, Ca, Cu, Fe, K, Mg, Mn, Na, Ni and Zn) were done. During the study, ICP-OES was employed for the measurement of mineral elements. It was observed that considerable amounts of B, Ca, K, Mg, Mn, Na and Zn are accumulated by the plant., Veronica scutellata L. wujud di habitat lembab dan basah seperti kolam, rawa dan tanah bencah lain. Kajian dijalankan ke atas spesies ini untuk meneliti status pengambilan unsur mineral daripada segi saling tindakan antara tanih dan tumbuhan. Bahan percubaan telah diambil dari Pantai Timur Laut Hitam pada koordinat 40º36’U dan 31º16’T pada altitud 1400 m atas paras laut dari Bolu, Turki dengan menggunakan kaedah piawai dan tumbuhan (bahagian akar, batang dan daun) dan pengukuran unsur mineral tanih (Al, B, Ca, Cu, Fe, K, Mg, Mn, Na, Ni dan Zn) telah dilakukan. Semasa kajian, ICP-OES telah digunakan bagi pengukuran unsur mineral. Telah diperhatikan bahawa sejumlah amaun B, Ca, K, Mg, Mn, Na dan Zn telah terkumpul oleh tumbuhan.

Published
2013

37. Mineral element uptake status of endemic Isoetes anatolica Prada & Rolleri populations from Bolu-Turkey

Author

Ozyigit, I. I., Dogan, I., Eskin, B., Keskin, M., Demir, G., IBRAHIM ERTUGRUL YALCIN, TR100479, Doğan, İlhan, and Izmir Institute of Technology. Molecular Biology and Genetics

Subjects
Environmental quality, Isoetes genus, Isoetes anatolica Prada & Rolleri, Abant Region, Mineral elements
Abstract

Isoetes genus is commonly known as the "quillworts" and considered to be "fern allies". There are about 200-250 species, with a cosmopolitan distribution but often scarce to rare. Isoetes genus members often grow in extremely sensitive aquatic environments such as temporary ponds, streams and lakes. They are therefore good indicators of environmental quality. Isoetes anatolica Prada & Rolleri is an endemic plant grows on calcareous sediment/soil on the edges of seasonal ponds located in a mountainous area near the southern coast of the Black Sea at 1400 m above sea level at Bolu, Turkey. In this study, mineral element uptake statuses of I. anatolica populations were studied on the background of plant-sediment/soil-water interactions. The study materials were collected from the place where this narrow endemic species only lives in the world (Abant Region, Bolu/Turkey) by using standard methods and plant and sediment/soil mineral element measurements (Al, B, Ca, Cu, Fe, K, Mg, Mn, Na, Ni and Zn) were done. ICP-OES was employed for the measurements during the study. Interrelations between mineral element contents in the sediment/soil, water and plant were discussed. The data revealed that I. anatolica is capable of accumulating considerable amounts of certain mineral elements (B, Ca, Mn and Na)., Marmara University, Commission of Scientific Research Project (FEN-D-040712-0291)

Published
2013

38. Mineral element distribution of cotton (Gossypium hirsutum L.) seedlings under different salinity levels

Author

Dogan, I., Ibrahim Ilker Ozyigit, Demir, G., TR100479, Doğan, İlhan, and Izmir Institute of Technology. Molecular Biology and Genetics

Subjects
Salinity, Salt stress, Cotton, Antioxidative enzymes, Gossypium hirsutum L
Abstract

Cotton (Gossypium hirsutum L.) is the world's leading natural fiber and second largest oilseed crop. In addition to textile manufacturing, cotton and cotton-by products are the sources of wealth of consumer based products, livestock feed, fertilizer, foodstuff and paper. High concentrations of NaCl in soils account for large decreases in the yield of a wide variety of crops all over the world. The present study was conducted to evaluate NaCl stress on mineral nutrient composition of cotton due to its economic importance. Cotton seeds were germinated in Magenta vessels containing Murshige and Skoog (MS) media for 15 days and then transferred in sterile jars containing MS exposed to different levels of NaCl (50, 100, 200 and 400 mM) treatments for 1 month. Uptake of some mineral nutrients (B, Ca, Fe, K, Mg, Mn, Na and Zn) by the plants was examined in roots and leaves by using an Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES). The data proved that plant growth and uptake and accumulation of microelements are altered extensively in cotton grown with NaCl. Excess NaCl reduces the uptake pattern of certain elements and increases that of others, the patterns depending on the element and the plant part being compared to the control., Marmara University, Commission of Scientific Research Project under grant FEN-A-030108-0016

Published
2012

39. Determination of heavy metal concentrations in tomato (lycopersicon esculentum miller) grown in different station types

Author

Osma, E., Ibrahim Ilker Ozyigit, Leblebici, Z., Demir, G., Serin, M., and Nevşehir Hacı Bektaş Veli Üniversitesi/fen-edebiyat fakültesi/moleküler biyoloji ve genetik bölümü/moleküler biyoloji ve genetik anabilim dalı

Subjects
Heavy metal, Fruit, İstanbul, Tomato
Abstract

In this study, washed and unwashed tomato fruits (Lycopersicon esculentum Miller) were collected from six different station types such as; brook coast, suburban area, industrial area, inner city, roadside and village (control) in Istanbul-Turkey, in 2009. Unwashed and washed fruit samples were used to analyze cadmium, chromium, copper, iron, nickel, lead and zinc concentrations by using inductively coupled plasma optical emission spectrometry. It was observed that washing procedure reduced concentrations of all heavy metals related to station types. In accordance with the results, the lowest and highest heavy metal accumulations measured in fruits were as follows; cadmium (0.17-0.40 µg/g dw), chrome (0.94-5.67 µg/g dw), copper (7.67-14.27 µg/g dw), iron (19.16-64.53 µg/g dw), nickel (1.02-11.64 µg/g dw), lead (4.31-5.51 µg/g dw) and zinc (1.36-3.07 µg/g dw). As a result, the relative abundance of heavy metals in tomato samples were observed as iron>copper>nickel>chrome>lead>zinc>cadmium. According to the results of this study, it can be said that tomato fruits reflect heavy metal amounts well in polluted areas such as urban, industrial and roadside when compared to unpolluted (control) areas with their washed and unwashed samples.

Published
2012

40. Steroid-responsive recurrent limbic encephalitis associated with small cell lung cancer and neuropil antibodies

Author

Tüzün, E, Yaka, E, Zuliani, L, Içöz, S, Baklan, B, Birişik, O, Kurd, P, Akman-Demir, G, Vincent, A, and Akdal, G

Abstract

Paraneoplastic limbic encephalitis (PLE) associated with small cell lung cancer (SCLC) often presents with antibodies to intracellular antigens and a poor outcome even after tumor resection and immunotherapy. We report a PLE patient presenting with generalized seizures, short-term memory impairment and medial temporal lobe hyperintensity in MRI. Initial screening revealed significantly elevated thyroid antibody levels suggesting Hashimoto's encephalopathy. Following methylprednisolone treatment, her seizures ceased, MRI findings disappeared and memory impairment showed a partial resolution in 5 months. Two months later, she developed further generalized seizures. Chest X-ray showed a mass lesion, which was demonstrated by needle biopsy to be a small cell lung carcinoma (SCLC). The panel of onconeural antibodies including cell-membrane antigens was negative. However, the patient's serum and cerebrospinal fluid IgG, obtained during both exacerbations, immunolabeled cytoplasm and dendrites of Purkinje cells, cerebellar and hippocampal molecular layers, basal ganglia, thalamus, and the surface of cultured hippocampal neurons, in a manner distinct from previously identified neuropil antibodies associated with SCLC. These neuropil antibodies appear to be associated with a favorable response to treatment. Further studies are required for determination of the target antigen.

Published
2011

41. In Vitro Testing for Genotoxicity of 4-CPA by Sister Chromatid Exchange in Human Lymphocyte Culture

Author

Baǧcı, Hüseyin, Baǧcı, Gülseren, Açıkbaş, İbrahim, and Demir, G.

Subjects
Plant cell culture, Cells, environmental exposure, tomato, Acetic acid, cytogenetics, Phenoxy herbicides, lymphocyte culture, 4-CPA, health hazard, Human lymphocytes, herbicide, phenoxyacetic acid derivative, Plant hormones, vegetable, human, Sister chromatid exchange, Cerrahi, 4 chlorophenoxyacetic acid, Toxicity, Concentration (process), Herbicides, human cell, questionnaire, genotoxicity, article, Hormones, Food products, Genes, food contamination, Phenoxyacetic acid, 4-CPA,Phenoxy herbicides,genotoxicity,sister chromatid exchange,tomato
Abstract

Certain phenoxyacetate derivatives used as plant growth regulators act as plant hormones. 2,4-D dichlorophenoxyacetic acid and 4-chlorophenoxyacetic acid are widely used in vegetable growing, especially tomatoes, in our region. These phenoxyacetic acid compounds are a potential hazard for the environment. There are conflicting results and inconsistent data about these herbicides in the literature. This is the first report of genotoxicity of 4-CPA evaluated by sister chromatid exchange in human lymphocyte culture. No significant change was found in sister chromatid exchange frequency at the tested 4-CPA concentration.

Published
2005

43. The Creative Village

Author

Demir, G. (author) and Demir, G. (author)

Abstract

Computational Architecture, Architecture, Architecture

Published
2012

44. Talactoferrin alfa versus placebo in patients with refractory advanced non-small-cell lung cancer (FORTIS-M trial)

Author

Ramalingam, S., primary, Crawford, J., additional, Chang, A., additional, Manegold, C., additional, Perez-Soler, R., additional, Douillard, J.-Y., additional, Thatcher, N., additional, Barlesi, F., additional, Owonikoko, T., additional, Wang, Y., additional, Pultar, P., additional, Zhu, J., additional, Malik, R., additional, Giaccone, G., additional, Della-Fiorentina, S., additional, Begbie, S., additional, Jennens, R., additional, Dass, J., additional, Pittman, K., additional, Ivanova, N., additional, Koynova, T., additional, Petrov, P., additional, Tomova, A., additional, Tzekova, V., additional, Couture, F., additional, Hirsh, V., additional, Burkes, R., additional, Sangha, R., additional, Ambrus, M., additional, Janaskova, T., additional, Musil, J., additional, Novotny, J., additional, Zatloukal, P., additional, Jakesova, J., additional, Klenha, K., additional, Roubec, J., additional, Vanasek, J., additional, Fayette, J., additional, Bennouna-Louridi, J., additional, Chouaid, C., additional, Mazières, J., additional, Vallerand, H., additional, Robinet, G., additional, Souquet, P.-J., additional, Spaeth, D., additional, Schott, R., additional, Lena, H., additional, Martinet, Y., additional, El Kouri, C., additional, Baize, N., additional, Scherpereel, A., additional, Molinier, O., additional, Fuchs, F., additional, Josten, K.M., additional, Marschner, N., additional, Schneller, F., additional, Overbeck, T., additional, Thomas, M., additional, von Pawel, J., additional, Reck, M., additional, Schuette, W., additional, Hagen, V., additional, Schneider, C.-P., additional, Georgoulias, V., additional, Varthalitis, I., additional, Zarogoulidis, K., additional, Syrigos, K., additional, Papandreou, C., additional, Bocskei, C., additional, Csanky, E., additional, Juhasz, E., additional, Losonczy, G., additional, Mark, Z., additional, Molnar, I., additional, Papai-Szekely, Z., additional, Tehenes, S., additional, Vinkler, I., additional, Almel, S., additional, Bakshi, A., additional, Bondarde, S., additional, Maru, A., additional, Pathak, A., additional, Pedapenki, R.M., additional, Prasad, K., additional, Prasad, S.V.S.S., additional, Kilara, N., additional, Gorijavolu, D., additional, Deshmukh, C.D., additional, John, S., additional, Sharma, L.M., additional, Amoroso, D., additional, Bajetta, E., additional, Bidoli, P., additional, Bonetti, A., additional, De Marinis, F., additional, Maio, M., additional, Passalacqua, R., additional, Cascinu, S., additional, Bearz, A., additional, Bitina, M., additional, Brize, A., additional, Purkalne, G., additional, Skrodele, M., additional, Baba, A.A., additional, Ratnavelu, K., additional, Saw, M.H., additional, Samson-Fernando, M.C., additional, Ladrera, G.E., additional, Jassem, J., additional, Koralewski, P., additional, Serwatowski, P., additional, Krzakowski, M., additional, Cebotaru, C., additional, Filip, D., additional, Ganea-Motan, D.E., additional, Ianuli, C.H., additional, Manolescu, I.G., additional, Udrea, A., additional, Burdaeva, O., additional, Byakhov, M., additional, Filippov, A., additional, Lazarev, S., additional, Mosin, I., additional, Orlov, S., additional, Udovitsa, D., additional, Khorinko, A., additional, Protsenko, S., additional, Lim, H.L., additional, Tan, Y.O., additional, Tan, E.H., additional, Bastus Piulats, R., additional, Garcia-Foncillas, J., additional, Valdivia, J., additional, de Castro, J., additional, Domine Gomez, M., additional, Kim, S.W., additional, Lee, J.-S., additional, Kim, H.K., additional, Lee, J.S., additional, Shin, S.W., additional, Kim, D.-W., additional, Kim, Y.-C., additional, Park, K.C., additional, Chang, C.-S., additional, Chang, G.-C., additional, Goan, Y.-G., additional, Su, W.-C., additional, Tsai, C.-M., additional, Kuo, H.-P., additional, Benekli, M., additional, Demir, G., additional, Gokmen, E., additional, Sevinc, A., additional, Haigentz, M., additional, Agarwal, M., additional, Pandit, S., additional, Araujo, R., additional, Vrindavanam, N., additional, Bonomi, P., additional, Berg, A., additional, Wade, J., additional, Bloom, R., additional, Amin, B., additional, Camidge, R., additional, Hill, D., additional, Rarick, M., additional, Flynn, P., additional, Klein, L., additional, Lo Russo, K., additional, Neubauer, M., additional, Richards, P., additional, Ruxer, R., additional, Savin, M., additional, Weckstein, D., additional, Rosenberg, R., additional, Whittaker, T., additional, Richards, D., additional, Berry, W., additional, Ottensmeier, C., additional, Dangoor, A., additional, Steele, N., additional, Summers, Y., additional, Rankin, E., additional, Rowley, K., additional, Giridharan, S., additional, Kristeleit, H., additional, Humber, C., additional, and Taylor, P., additional

Published
2013
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47. Autoantibodies to neuronal surface antigens in thyroid antibody-positive and -negative limbic encephalitis.

Author

Tuzun E, Erdag E, Durmus H, Brenner T, Turkoglu R, Kurtuncu M, Lang B, Akman-Demir G, Eraksoy M, Vincent A, Tüzün, Erdem, Erdağ, Ece, Durmus, Hacer, Brenner, Tanja, Türkoglu, Recai, Kürtüncü, Murat, Lang, Bethan, Akman-Demir, Gülşen, Eraksoy, Mefkure, and Vincent, Angela

Abstract

Background: Thyroid antibodies (Thy-Abs) are frequently detected in various autoimmune disorders in coexistence with other systemic autoantibodies. In association with an encephalopathy, they are often taken as evidence of Hashimoto's encephalitis (HE). However, the presence of Thy-Abs in a cohort of limbic encephalitis (LE) patients and their association with anti-neuronal autoimmunity has not been explored.Patients and Methods: We investigated thyroid and anti-neuronal antibodies in the sera of 24 LE patients without identified tumors by cell-based assay and radioimmunoassay and evaluated their clinical features.Results: There was a female predominance in Thy-Ab-positive LE patients. Five of the eight Thy-Ab-positive patients and six of the 16 Thy-Ab-negative patients had antibodies to voltage-gated potassium channel (VGKC), N-methyl-D-aspartate receptor (NMDAR) or undefined surface antigens on cultured hippocampal neurons. There were trends towards fewer VGKC antibodies (1/8 vs. 5/16, P = 0.159) and more NMDAR antibodies (2/8 vs. 1/16, P = 0.095) among the Thy-Ab-positive LE patients; antibodies to undefined surface antigens were only identified in Thy-Ab-positive patients (2/8 vs. 0/16, P = 0.018). There were no distinguishing clinical features between Thy-Ab-positive patients with and without neuronal antibodies. However, patients with anti-neuronal antibodies showed a better treatment response.Conclusion: Thy-Abs can be found in a high proportion of patients with non-paraneoplastic LE, often in association with antibodies to specific or as yet undefined neuronal surface antigens. These results suggest that acute idiopathic encephalitis patients with Thy-Abs should be closely monitored for ion-channel antibodies and it should not be assumed that they have HE. [ABSTRACT FROM AUTHOR]

Published
2011
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49. Elemental concentrations of atmospheric aerosols and the soil samples on the selected playgrounds in Istanbul

Author

Demir, G., Yigit, S., Huseyin Ozdemir, Borucu, G., and Saral, A.

Abstract

Considering the most of their time is in playgrounds, children are under a significant health risk in urban areas due to the exposure of high air pollution In this study, 3 different playgrounds are chosen according to their locations; one is in the city where there is highly traffic jam, the other is on the coast line of Istanbul Bosphorus, and the last one is near a high way In these playgrounds, concentrations of particulate matter (PM) fractions (PM25 and PM10) were determined in the specified periods. The elemental composition of PM were determined by measuring the concentrations of Al, K, Na, Mg, Ca, Pb, Cu, Cr, Cd, Zn, Co, Ni, and V using inductively coupled plasma-optical emission spectrometer. The correlation matrices are also developed in order to determine the relation between trace metal concentrations. The elemental concentrations and PM results showed variations between the selected playgrounds.

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