Porous Ti5Al2.5Fe alloy was successfully fabricated using the spark plasma sintering technique. E... more Porous Ti5Al2.5Fe alloy was successfully fabricated using the spark plasma sintering technique. Experiments were performed within a temperature range of between 750 and 850 o C. The microstructure, compression and biocompatibility properties of the porous samples were investigated. Sintered samples were immersed for different times in a simulated body fluid with elemental concentrations comparable to those of human blood plasma. Porous sample was also implanted in fibroblast culture for biocompatibility evaluation. The compressive strength of the porous samples was found to be mainly dependent on sintering temperature, and the porous compacts exhibiting good biocompatibility properties.
In this study, the development of the yolk nucleus in cytoplasm of previtellogenic oocytes was ex... more In this study, the development of the yolk nucleus in cytoplasm of previtellogenic oocytes was examined by light microscopy during oogenesis in trout, Oncorhynchus mykiss. We determined that oocytes 20-30 μm in diameter have much basophilic (electron dense) cytoplasm and an area of fl occulent appearance begins to emerge around the nucleus. The yolk nucleus was first recognized within this area as a few fragments dense granular thread. These fragments were observed gradually increase in number and length until they assemble into a spherical mass. When oocytes develop to greater than 107 μm in diameter, the yolk nucleus was dispersed throughout the cytoplasm and the cytoplasm was observed more homogenous.
Playtesting is a lifecycle phase in game development wherein the completeness and smooth progress... more Playtesting is a lifecycle phase in game development wherein the completeness and smooth progress of planned content are verified before release of a new game. Although studies on playtesting in Match 3 games have attempted to utilize Monte Carlo tree search (MCTS) and convolutional neural networks (CNNs), the applicability of these methods are limited because the associated training is timeconsuming and data collection is difficult. To address this problem, game playtesting was performed via learning based on strategic play in Match 3 games. Five strategic plays were defined in the Match 3 game under consideration and game playtesting was performed for each situation via reinforcement learning. The proposed agent performed within a 5% margin of human performance on the most complex mission in the experiment. We demonstrate that it is possible for the level designer to measure the difficulty of the level via playtesting various missions. This study also provides level testing standards for several types of missions in Match 3 games.
Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populati... more Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2DE MALDI TOF/TOF MS. Results: Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) w...
... Columnaris disease generally begins as an external infection on the skin, fins, gills, or ora... more ... Columnaris disease generally begins as an external infection on the skin, fins, gills, or oral cavity [6]. On the skin and fins, lesions are characterized by dull, grayish-white or yellow erosive lesions that can progress to deep ulcers in the underlying muscle. ...
This paper describes various aspects of previtellogenic oocyte growth in sharpsnout seabream, Dip... more This paper describes various aspects of previtellogenic oocyte growth in sharpsnout seabream, Diplodus puntazzo , is an important marine culture fish species in the Mediterranean. The ultrastructural characteristics of nuclear morphology, nuclear-cytoplasmic ratio and the starting of the follicle envelope formation were described in detail. These cells do not significantly differ from those of the other teleost species. The ultrastructural aspects provide new information on the reproductive biology of Sparidae.
A novel implant coating material containing graphene oxide (GO) and collagen (COL), and hydroxyap... more A novel implant coating material containing graphene oxide (GO) and collagen (COL), and hydroxyapatite (HA) was fabricated with the aid of tannic acid by electrodeposition. The surface of Ti16Nb alloy was subjected to anodic oxidation, and then HA-GO coating was applied to Ti16Nb surface by cathodic method. Then, COL was deposited on the surface of the HA-GO coating by the biomimetic method. HA, HA-GO, HA-GO-COL coatings on the surface of the Ti16Nb alloy have increased the corrosion resistance by the formation of a barrier layer on the surface. For HA-GO-COL coating, the highest corrosion resistance is obtained due to the compactness and homogeneity of the coating structure. The contact angle of the bare Ti16Nb is approximately 65°, while the contact angle of the coated samples is close to 0°. Herein, the increased surface wettability is important for cell adhesion. The surface roughness of the uncoated Ti16Nb alloy was between 1 and 3 μm, while the surface roughness of the coated surfaces was measured between 20 and 110 μm. The contact between the bone and the implant has been improved. Graphene oxide-containing coatings have improved the antibacterial properties compared to the GO-free coating using S. aureus. The hardness and elastic modulus of the coatings were measured by the nanoindentation test, and the addition of GO and collagen to the HA coating resulted in an increase in strength. The addition of GO to the HA coating reduced the viability of 3 T3 fibroblast cells, whereas the addition of collagen to HA-GO coat increased the cell adhesion and viability.
Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common... more Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA-DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391...
The present study is conducted to determine the potential mechanisms of Boron compounds, boric ac... more The present study is conducted to determine the potential mechanisms of Boron compounds, boric acid (BA) and borax (BX), on genotoxicity of zebrafish Danio rerio for 24, 48, 72 and 96-hours acute exposure (level:1, 4, 16, 64 mg/l BA and BX) in semi-static bioassay experiment. For that purpose, peripheral erythrocytes were drawn from caudal vein and Comet assay was applied to assess genotoxicity. Acute (96 hours) exposure and high concentrations of boric acid and borax increases % tail DNA and Olive tail moment. Genotoxicity was found for BA as concentration-dependent and BX as concentration and time dependent manner. In general, significant effects (P < 0,05) on both concentrations and exposure times were observed in experimental groups. DNA damage was highest at 96 h and 24 h for all BX and BA concentrations, respectively in peripheral blood of D. rerio. For the first time, our study demonstrates the effect of waterborne BA and BX exposure on genotoxicity at the molecular level,...
Journal of the Mechanical Behavior of Biomedical Materials, 2015
The research investigated the effect of Zr, Nb and Ti additions on mechanical, electrochemical pr... more The research investigated the effect of Zr, Nb and Ti additions on mechanical, electrochemical properties and biocompatibility of injection molded 316L stainless steel. Addition of elemental powder is promoted to get high performance of sintered 316L stainless steels. The amount of additive powder plays a role in determining the sintered microstructure and all properties. In this study, 316L stainless steel powders used with the elemental Zr, Nb and Ti powders. A feedstock containing 62.5wt% powders loading was molded at different injection molded temperature. The binders were completely removed from molded components by solvent and thermal debinding at different temperatures. The debinded samples were sintered at 1350°C for 60min. Mechanical, electrochemical property and biocompatibility of the sintered samples were performed mechanical, electrochemical, SBF immersion tests and cell culture experiments. Results of study showed that sintered 316L and 316L with additives samples exhibited high corrosion properties and biocompatibility in a physiological environment.
Titanium and Titanium alloys exhibits properties that are excellent for various bio-applications.... more Titanium and Titanium alloys exhibits properties that are excellent for various bio-applications. Metal injection molding is a processing route that offers reduction in costs, with the added advantage of near net-shape components. Different physical properties of Titanium alloy powders, shaped and processed via injection molding can achieve high complexity of part geometry with mechanical and bioactivity properties, similar or superior to wrought material. This study describes that the effect of particle morphology on the microstructural, mechanical and biocompatibility properties of injection molded Ti-6Al-4V (Ti64) alloy powder for biomaterials applications. Ti64 powders irregular and spherical in shape were injection molded with wax based binder. Binder debinding was performed in solvent and thermal method. After debinding the samples were sintered under high vacuum. Metallographic studies were determined to densification and the corresponding microstructural changes. Sintered sa...
Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populati... more Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS. Results: Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) were unique in 2-D LC and 2-DE, respectively. COG groupings and subcellular localizations were similar between our data set and proteins predicted from the whole genome. Twenty eight pathways were significantly represented in our dataset (P < 0.05). Conclusion: Results from this study provide experimental evidence for many proteins that were predicted from the F. columnare genome annotation, and they should accelerate functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.
Porous Ti5Al2.5Fe alloy was successfully fabricated using the spark plasma sintering technique. E... more Porous Ti5Al2.5Fe alloy was successfully fabricated using the spark plasma sintering technique. Experiments were performed within a temperature range of between 750 and 850 o C. The microstructure, compression and biocompatibility properties of the porous samples were investigated. Sintered samples were immersed for different times in a simulated body fluid with elemental concentrations comparable to those of human blood plasma. Porous sample was also implanted in fibroblast culture for biocompatibility evaluation. The compressive strength of the porous samples was found to be mainly dependent on sintering temperature, and the porous compacts exhibiting good biocompatibility properties.
In this study, the development of the yolk nucleus in cytoplasm of previtellogenic oocytes was ex... more In this study, the development of the yolk nucleus in cytoplasm of previtellogenic oocytes was examined by light microscopy during oogenesis in trout, Oncorhynchus mykiss. We determined that oocytes 20-30 μm in diameter have much basophilic (electron dense) cytoplasm and an area of fl occulent appearance begins to emerge around the nucleus. The yolk nucleus was first recognized within this area as a few fragments dense granular thread. These fragments were observed gradually increase in number and length until they assemble into a spherical mass. When oocytes develop to greater than 107 μm in diameter, the yolk nucleus was dispersed throughout the cytoplasm and the cytoplasm was observed more homogenous.
Playtesting is a lifecycle phase in game development wherein the completeness and smooth progress... more Playtesting is a lifecycle phase in game development wherein the completeness and smooth progress of planned content are verified before release of a new game. Although studies on playtesting in Match 3 games have attempted to utilize Monte Carlo tree search (MCTS) and convolutional neural networks (CNNs), the applicability of these methods are limited because the associated training is timeconsuming and data collection is difficult. To address this problem, game playtesting was performed via learning based on strategic play in Match 3 games. Five strategic plays were defined in the Match 3 game under consideration and game playtesting was performed for each situation via reinforcement learning. The proposed agent performed within a 5% margin of human performance on the most complex mission in the experiment. We demonstrate that it is possible for the level designer to measure the difficulty of the level via playtesting various missions. This study also provides level testing standards for several types of missions in Match 3 games.
Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populati... more Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2DE MALDI TOF/TOF MS. Results: Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) w...
... Columnaris disease generally begins as an external infection on the skin, fins, gills, or ora... more ... Columnaris disease generally begins as an external infection on the skin, fins, gills, or oral cavity [6]. On the skin and fins, lesions are characterized by dull, grayish-white or yellow erosive lesions that can progress to deep ulcers in the underlying muscle. ...
This paper describes various aspects of previtellogenic oocyte growth in sharpsnout seabream, Dip... more This paper describes various aspects of previtellogenic oocyte growth in sharpsnout seabream, Diplodus puntazzo , is an important marine culture fish species in the Mediterranean. The ultrastructural characteristics of nuclear morphology, nuclear-cytoplasmic ratio and the starting of the follicle envelope formation were described in detail. These cells do not significantly differ from those of the other teleost species. The ultrastructural aspects provide new information on the reproductive biology of Sparidae.
A novel implant coating material containing graphene oxide (GO) and collagen (COL), and hydroxyap... more A novel implant coating material containing graphene oxide (GO) and collagen (COL), and hydroxyapatite (HA) was fabricated with the aid of tannic acid by electrodeposition. The surface of Ti16Nb alloy was subjected to anodic oxidation, and then HA-GO coating was applied to Ti16Nb surface by cathodic method. Then, COL was deposited on the surface of the HA-GO coating by the biomimetic method. HA, HA-GO, HA-GO-COL coatings on the surface of the Ti16Nb alloy have increased the corrosion resistance by the formation of a barrier layer on the surface. For HA-GO-COL coating, the highest corrosion resistance is obtained due to the compactness and homogeneity of the coating structure. The contact angle of the bare Ti16Nb is approximately 65°, while the contact angle of the coated samples is close to 0°. Herein, the increased surface wettability is important for cell adhesion. The surface roughness of the uncoated Ti16Nb alloy was between 1 and 3 μm, while the surface roughness of the coated surfaces was measured between 20 and 110 μm. The contact between the bone and the implant has been improved. Graphene oxide-containing coatings have improved the antibacterial properties compared to the GO-free coating using S. aureus. The hardness and elastic modulus of the coatings were measured by the nanoindentation test, and the addition of GO and collagen to the HA coating resulted in an increase in strength. The addition of GO to the HA coating reduced the viability of 3 T3 fibroblast cells, whereas the addition of collagen to HA-GO coat increased the cell adhesion and viability.
Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common... more Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA-DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391...
The present study is conducted to determine the potential mechanisms of Boron compounds, boric ac... more The present study is conducted to determine the potential mechanisms of Boron compounds, boric acid (BA) and borax (BX), on genotoxicity of zebrafish Danio rerio for 24, 48, 72 and 96-hours acute exposure (level:1, 4, 16, 64 mg/l BA and BX) in semi-static bioassay experiment. For that purpose, peripheral erythrocytes were drawn from caudal vein and Comet assay was applied to assess genotoxicity. Acute (96 hours) exposure and high concentrations of boric acid and borax increases % tail DNA and Olive tail moment. Genotoxicity was found for BA as concentration-dependent and BX as concentration and time dependent manner. In general, significant effects (P < 0,05) on both concentrations and exposure times were observed in experimental groups. DNA damage was highest at 96 h and 24 h for all BX and BA concentrations, respectively in peripheral blood of D. rerio. For the first time, our study demonstrates the effect of waterborne BA and BX exposure on genotoxicity at the molecular level,...
Journal of the Mechanical Behavior of Biomedical Materials, 2015
The research investigated the effect of Zr, Nb and Ti additions on mechanical, electrochemical pr... more The research investigated the effect of Zr, Nb and Ti additions on mechanical, electrochemical properties and biocompatibility of injection molded 316L stainless steel. Addition of elemental powder is promoted to get high performance of sintered 316L stainless steels. The amount of additive powder plays a role in determining the sintered microstructure and all properties. In this study, 316L stainless steel powders used with the elemental Zr, Nb and Ti powders. A feedstock containing 62.5wt% powders loading was molded at different injection molded temperature. The binders were completely removed from molded components by solvent and thermal debinding at different temperatures. The debinded samples were sintered at 1350°C for 60min. Mechanical, electrochemical property and biocompatibility of the sintered samples were performed mechanical, electrochemical, SBF immersion tests and cell culture experiments. Results of study showed that sintered 316L and 316L with additives samples exhibited high corrosion properties and biocompatibility in a physiological environment.
Titanium and Titanium alloys exhibits properties that are excellent for various bio-applications.... more Titanium and Titanium alloys exhibits properties that are excellent for various bio-applications. Metal injection molding is a processing route that offers reduction in costs, with the added advantage of near net-shape components. Different physical properties of Titanium alloy powders, shaped and processed via injection molding can achieve high complexity of part geometry with mechanical and bioactivity properties, similar or superior to wrought material. This study describes that the effect of particle morphology on the microstructural, mechanical and biocompatibility properties of injection molded Ti-6Al-4V (Ti64) alloy powder for biomaterials applications. Ti64 powders irregular and spherical in shape were injection molded with wax based binder. Binder debinding was performed in solvent and thermal method. After debinding the samples were sintered under high vacuum. Metallographic studies were determined to densification and the corresponding microstructural changes. Sintered sa...
Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populati... more Background: Flavobacterium columnare causes columnaris disease in cultured and wild fish populations worldwide. Columnaris is the second most prevalent bacterial disease of commercial channel catfish industry in the United States. Despite its economic importance, little is known about the expressed proteins and virulence mechanisms of F. columnare. Here, we report the first high throughput proteomic analysis of F. columnare using 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS. Results: Proteins identified in this study and predicted from the draft F. columnare genome were clustered into functional groups using clusters of orthologous groups (COGs), and their subcellular locations were predicted. Possible functional relations among the identified proteins were determined using pathway analysis. The total number of unique F. columnare proteins identified using both 2-D LC and 2-DE approaches was 621, of which 10.95% (68) were identified by both methods, while 77.29% (480) and 11.76% (73) were unique in 2-D LC and 2-DE, respectively. COG groupings and subcellular localizations were similar between our data set and proteins predicted from the whole genome. Twenty eight pathways were significantly represented in our dataset (P < 0.05). Conclusion: Results from this study provide experimental evidence for many proteins that were predicted from the F. columnare genome annotation, and they should accelerate functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.
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Papers by Nagihan Gulsoy