20 results on '"Yaman U"'
Search Results
2. Genetic variability associated withOAS1expression in myeloid cells increases the risk of Alzheimer’s disease and severe COVID-19 outcomes
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Juan A. Botía, Thomas M. Piers, Magusali N, Jennifer M. Pocock, Panichnantakul P, Yaman U, Keeley J. Brookes, Maryam Shoai, Graham Ac, Sala Frigerio C, Sevinc Bayram, Mina Ryten, Escott-Price, Kevin Morgan, Regina H. Reynolds, Eftychia Bellou, Dervis A. Salih, John Hardy, Tamar Guetta-Baranes, and Sokolova D
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Innate immune system ,Microglia ,Disease ,Biology ,medicine.disease ,medicine.anatomical_structure ,Interferon ,Immunology ,medicine ,Tumor necrosis factor alpha ,Alzheimer's disease ,Gene ,medicine.drug ,Genetic association - Abstract
Genome-wide association studies of late-onset Alzheimer’s disease (AD) have highlighted the importance of variants associated with genes expressed by the innate immune system in determining risk for AD. Recently, we and others have shown that genes associated with variants that confer risk for AD are significantly enriched in transcriptional networks expressed by amyloid-responsive microglia. This allowed us to predict new risk genes for AD, including the interferon-responsive oligoadenylate synthetase 1 (OAS1). However, the function ofOAS1within microglia and its genetic pathway are not known. Using genotyping from 1,313 individuals with sporadic AD and 1,234 control individuals, we confirm that theOAS1variant, rs1131454, is associated with increased risk for AD and decreasedOAS1expression. Moreover, we note that the same locus was recently associated with critical illness in response to COVID-19, linking variants that are associated with AD and a severe response to COVID-19. By analysing single-cell RNA-sequencing (scRNA-seq) data of isolated microglia fromAPPNL-G-Fknock-in and wild-type C57BL/6J mice, we identify a transcriptional network that is significantly upregulated with age and amyloid deposition, and contains the mouse orthologueOas1a, providing evidence thatOas1aplays an age-dependent function in the innate immune system. We identify a similar interferon-related transcriptional network containingOAS1by analysing scRNA-seq data from human microglia isolated from individuals with AD. Finally, using human iPSC-derived microglial cells (h-iPSC-Mg), we see thatOAS1is required to limit the pro-inflammatory response of microglia. When stimulated with interferon-gamma (IFN-γ), we note that cells with lowerOAS1expression show an exaggerated pro-inflammatory response, with increased expression and secretion of TNF-α. Collectively, our data support a link between genetic risk for AD and susceptibility to critical illness with COVID-19 centred onOAS1and interferon signalling, a finding with potential implications for future treatments of both AD and COVID-19, and the development of biomarkers to track disease progression.
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- 2021
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3. The toxic effects of Aroclor 1254 on rat testis and modulatory effect of selenium status
- Author
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Erkekoglu, P., primary, Zeybek, N.D., additional, Balci, A., additional, Yıldıztekin, K.G., additional, Yaman, U., additional, Asci, A., additional, Kizilgun, M., additional, Edebal, O.H., additional, and Gumusel, B. Kocer, additional
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- 2016
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4. Direct command generation for CNC machinery based on data compression techniques
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Yaman, U., primary and Dolen, M., additional
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- 2013
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5. A new hardware-in-the-loop simulator for CNC machine applications
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Usenmez, S., primary, Mutlu, B. R., additional, Yaman, U., additional, Kilic, E., additional, Dolen, M., additional, and Koku, A. B., additional
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- 2013
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6. Direct command generation methods for servo-motor drives
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Yaman, U., primary, Mutlu, B. R., additional, Dolen, M., additional, and Koku, A. B., additional
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- 2009
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7. Performance evaluation of different real-time motion controller topologies implemented on a FPGA
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Mutlu, B. R., primary, Yaman, U., additional, Dolen, M., additional, and Koku, A. B., additional
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- 2009
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8. Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference
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Benjamin Hawks, Javier Duarte, Nicholas J. Fraser, Alessandro Pappalardo, Nhan Tran, and Yaman Umuroglu
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pruning ,quantization ,neural networks ,generalizability ,regularization ,batch normalization ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.
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- 2021
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9. Evaluation of compression algorithms for motion command generation.
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Yaman, U. and Dolen, M.
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- 2011
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10. A novel command generation method with variable feedrate utilizing FGPA for motor drives.
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Yaman, U., Dolen, M., and Koku, A.B.
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- 2010
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11. Prepubertal phthalate exposure can cause histopathological alterations, DNA methylation and histone acetylation changes in rat brain.
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Koc S, Erdogmus E, Bozdemir O, Ozkan-Vardar D, Yaman U, Erkekoglu P, Zeybek ND, and Kocer-Gumusel B
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- Animals, Male, Rats, Acetylation drug effects, Diethylhexyl Phthalate toxicity, Epigenesis, Genetic drug effects, Phthalic Acids toxicity, Rats, Sprague-Dawley, DNA Methylation drug effects, Brain drug effects, Brain pathology, Brain metabolism, Histones metabolism, Oxidative Stress drug effects
- Abstract
Di-2-(ethylhexyl)phthalate (DEHP) is a phthalate derivative used extensively in a wide range of materials, such as medical devices, toys, cosmetics, and personal care products. Many mechanisms, including epigenetics, may be involved in the effects of phthalates on brain development. In this study, Sprague-Dawley male rats were obtained 21-23 days after their birth (post-weaning) and were exposed to DEHP during the prepubertal period with low-dose DEHP (DEHP-L, 30 mg/kg/day) and high-dose DEHP (DEHP-H, 60 mg/kg/day, 37 days) until the end of adolescence (PND 60). The rats in the study groups were sacrificed during adulthood, and histopathological changes, epigenetic changes, and oxidative stress parameters were evaluated in brain tissues. Histopathological findings indicating the presence of deterioration in brain tissue morphology were obtained, more prominently in the DEHP-H group. Examining the hippocampus under the light microscope, pyramidal neuron loss was detected only in CA1 of the DEHP-L group, while in DEHP-H rats, pyramidal neuron losses were detected in the CA1, CA2, and CA3 regions. No significant change was observed in brain lipid peroxidation levels with DEHP compared to control. Significant increases in total glutathione (GSH) in both dose groups were considered to be an adaptive response to DEHP-induced oxidative stress. The decrease in DNA methylation in the brain, although not statistically significant, and the increase in histone modification showed that exposure to DEHP may cause epigenetic changes in the brain and these epigenetic changes may also take place as one of the mechanisms underlying the damage observed in the brain. The results suggest that DEHP exposure during early development may have a significant effect on brain development., Competing Interests: Declaration of conflicting interestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
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- 2025
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12. Microglia contribute to the production of the amyloidogenic ABri peptide in familial British dementia.
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Arber C, Casey JM, Crawford S, Rambarack N, Yaman U, Wiethoff S, Augustin E, Piers TM, Price M, Rostagno A, Ghiso J, Lewis PA, Revesz T, Hardy J, Pocock JM, Houlden H, Schott JM, Salih DA, Lashley T, and Wray S
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- Humans, Animals, Mice, Adaptor Proteins, Signal Transducing genetics, Adaptor Proteins, Signal Transducing metabolism, Neurons metabolism, Neurons pathology, Brain metabolism, Brain pathology, Amyloid beta-Peptides metabolism, Microglia metabolism, Microglia pathology, Induced Pluripotent Stem Cells metabolism, Dementia metabolism, Dementia pathology, Dementia genetics
- Abstract
Mutations in ITM2B cause familial British, Danish, Chinese, and Korean dementias. In familial British dementia (FBD), a mutation in the stop codon of the ITM2B gene (also known as BRI2) causes a C-terminal cleavage fragment of the ITM2B/BRI2 protein to be extended by 11 amino acids. This fragment, termed amyloid-Bri (ABri), is highly insoluble and forms extracellular plaques in the brain. ABri plaques are accompanied by tau pathology, neuronal cell death and progressive dementia, with striking parallels to the aetiology and pathogenesis of Alzheimer's disease. The molecular mechanisms underpinning FBD are ill-defined. Using patient-derived induced pluripotent stem cells, we show that expression of ITM2B/BRI2 is 34-fold higher in microglia than neurons and 15-fold higher in microglia compared with astrocytes. This cell-specific enrichment is supported by expression data from both mouse and human brain tissue. ITM2B/BRI2 protein levels are higher in iPSC-microglia compared with neurons and astrocytes. The ABri peptide was detected in patient iPSC-derived microglial lysates and conditioned media but was undetectable in patient-derived neurons and control microglia. The pathological examination of post-mortem tissue supports the presence of ABri in microglia that are in proximity to pre-amyloid deposits. Finally, gene co-expression analysis supports a role for ITM2B/BRI2 in disease-associated microglial responses. These data demonstrate that microglia are major contributors to the production of amyloid forming peptides in FBD, potentially acting as instigators of neurodegeneration. Additionally, these data also suggest ITM2B/BRI2 may be part of a microglial response to disease, motivating further investigations of its role in microglial activation. These data have implications for our understanding of the role of microglia and the innate immune response in the pathogenesis of FBD and other neurodegenerative dementias including Alzheimer's disease., Competing Interests: Declarations Conflict of interest The authors declare no competing interests., (© 2024. The Author(s).)
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- 2024
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13. Chromosome X-wide association study in case control studies of pathologically confirmed Alzheimer's disease in a European population.
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Simmonds E, Leonenko G, Yaman U, Bellou E, Myers A, Morgan K, Brookes K, Hardy J, Salih D, and Escott-Price V
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- Humans, Male, Female, Case-Control Studies, Aged, White People genetics, Genetic Predisposition to Disease, Aged, 80 and over, DEAD-box RNA Helicases genetics, Interleukin-1 Receptor Accessory Protein genetics, Alzheimer Disease genetics, Genome-Wide Association Study, Chromosomes, Human, X genetics, Polymorphism, Single Nucleotide
- Abstract
Although there are several genome-wide association studies available which highlight genetic variants associated with Alzheimer's disease (AD), often the X chromosome is excluded from the analysis. We conducted an X-chromosome-wide association study (XWAS) in three independent studies with a pathologically confirmed phenotype (total 1970 cases and 1113 controls). The XWAS was performed in males and females separately, and these results were then meta-analysed. Four suggestively associated genes were identified which may be of potential interest for further study in AD, these are DDX53 (rs12006935, OR = 0.52, p = 6.9e-05), IL1RAPL1 (rs6628450, OR = 0.36, p = 4.2e-05; rs137983810, OR = 0.52, p = 0.0003), TBX22 (rs5913102, OR = 0.74, p = 0.0003) and SH3BGRL (rs186553004, OR = 0.35, p = 0.0005; rs113157993, OR = 0.52, p = 0.0003), which replicate across at least two studies. The SNP rs5913102 in TBX22 achieves chromosome-wide significance in meta-analysed data. DDX53 shows highest expression in astrocytes, IL1RAPL1 is most highly expressed in oligodendrocytes and neurons and SH3BGRL is most highly expressed in microglia. We have also identified SNPs in the NXF5 gene at chromosome-wide significance in females (rs5944989, OR = 0.62, p = 1.1e-05) but not in males (p = 0.83). The discovery of relevant AD associated genes on the X chromosome may identify AD risk differences and similarities based on sex and lead to the development of sex-stratified therapeutics., (© 2024. The Author(s).)
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- 2024
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14. Microplastic pollution in aquatic ecosystem: A review of existing policies and regulations.
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Khan MT, Rashid S, Yaman U, Khalid SA, Kamal A, Ahmad M, Akther N, Kashem MA, Hossain MF, and Rashid W
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- Environmental Policy, Plastics analysis, Environmental Pollution legislation & jurisprudence, Microplastics analysis, Ecosystem, Environmental Monitoring, Water Pollutants, Chemical analysis
- Abstract
Environmental pollution due to plastic waste is a global challenge causing adverse impacts on the ecosystem and public health. Microplastic (MP) originates at the upstream processes such as industrial and household activities; however, their existence is affecting the downstream environment. Even though many governments and non-government organizations have taken technological and regulatory steps, these current efforts and strategies are insufficient to prevent the MP release in the environment. Thus, a multidisciplinary global approach is required, which must prioritize the reducing of plastic inputs to the environment. To regulate MP levels in the environment, worldwide reformative and preventive strategies are required because the issue is not limited to a single nation or region. In relation to marine plastic waste, a number of multilateral agreements and measures exist at global level. Several regulatory measures have been examined by regulatory bodies with the intention of safeguarding the environment from excessive MP contamination. However, neither of the frameworks in place is specifically made to stop the increased MP pollution in the environment. Therefore, this review focused on the preventive measures taken by the government and non-government organizations for MP control through legislations. The study also critically discussed MP-related policies aiming to increase the viability and efficiency of implementing future plastic management. This review is expected to provide the basic guidelines for formulating MP standards in the environment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
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- 2024
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15. Mechanical Behaviour of Photopolymer Cell-Size Graded Triply Periodic Minimal Surface Structures at Different Deformation Rates.
- Author
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Yılmaz YE, Novak N, Al-Ketan O, Erten HI, Yaman U, Mauko A, Borovinsek M, Ulbin M, Vesenjak M, and Ren Z
- Abstract
This study investigates how varying cell size affects the mechanical behaviour of photopolymer Triply Periodic Minimal Surfaces (TPMS) under different deformation rates. Diamond, Gyroid, and Primitive TPMS structures with spatially graded cell sizes were tested. Quasi-static experiments measured boundary forces, representing material behaviour, inertia, and deformation mechanisms. Separate studies explored the base material's behaviour and its response to strain rate, revealing a strength increase with rising strain rate. Ten compression tests identified a critical strain rate of 0.7 s
-1 for "Grey Pro" material, indicating a shift in failure susceptibility. X-ray tomography, camera recording, and image correlation techniques observed cell connectivity and non-uniform deformation in TPMS structures. Regions exceeding the critical rate fractured earlier. In Primitive structures, stiffness differences caused collapse after densification of smaller cells at lower rates. The study found increasing collapse initiation stress, plateau stress, densification strain, and specific energy absorption with higher deformation rates below the critical rate for all TPMS structures. However, cell-size graded Primitive structures showed a significant reduction in plateau and specific energy absorption at a 500 mm/min rate.- Published
- 2024
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16. The effect of intercultural sensitivity and ethnocentrism on health tourism awareness level in nurses: Analysis with machine learning approach.
- Author
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Yıldız M, Aydin MA, Gökçay G, Kizilarslan V, and Yaman U
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- Humans, Cross-Sectional Studies, Communication, Turkey, Medical Tourism
- Abstract
Purpose: In this study, the effects of intercultural sensitivity and ethnocentrism on health tourism awareness levels in nurses were examined., Design and Methods: This quantitative cross-sectional study was conducted in Turkey between November 2022 and March 2023. Intercultural sensitivity scale, ethnocentrism scale, and health tourism awareness scale were used to collect the data. R programming language 4.1.3, G*Power 3.1 and SPSS-22 program were used in the analysis of the study., Results: This study was conducted with 386 nurses. Intercultural sensitivity has a positive and significant effect on health tourism awareness levels (β = 0.141; t(384) = 2.784, p = 0.006). Ethnocentrism has a positive and significant effect on health tourism awareness levels (β = 0.184; t(384) = 3.659, p = 0.001). Random Forest regression was found to be the best performing algorithm among the machine learning algorithms for predicting the Health Tourism Awareness variable. Looking at the contributions of the variables to the model, according to the SHAP value (Shapley Additive Explanations), it was seen that the most important variable that should be in the model to predict the health tourism awareness variable is the ethnocentrism variable., Conclusion: It was determined that as the level of intercultural sensitivity and ethnocentrism of nurses increased, their awareness of health tourism increased. Longitudinal studies on health tourism awareness in nurses are recommended., Competing Interests: Declaration of competing interest The author(s) declared no potential conflicts of interest concerning the research, authorship, and/or publication of this article., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
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17. Microglia produce the amyloidogenic ABri peptide in familial British dementia.
- Author
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Arber C, Casey JM, Crawford S, Rambarack N, Yaman U, Wiethoff S, Augustin E, Piers TM, Rostagno A, Ghiso J, Lewis PA, Revesz T, Hardy J, Pocock JM, Houlden H, Schott JM, Salih DA, Lashley T, and Wray S
- Abstract
Mutations in ITM2B cause familial British, Danish, Chinese and Korean dementias. In familial British dementia (FBD) a mutation in the stop codon of the ITM2B gene (also known as BRI2 ) causes a C-terminal cleavage fragment of the ITM2B/BRI2 protein to be extended by 11 amino acids. This fragment, termed amyloid-Bri (ABri), is highly insoluble and forms extracellular plaques in the brain. ABri plaques are accompanied by tau pathology, neuronal cell death and progressive dementia, with striking parallels to the aetiology and pathogenesis of Alzheimer's disease. The molecular mechanisms underpinning FBD are ill-defined. Using patient-derived induced pluripotent stem cells, we show that expression of ITM2B/BRI2 is 34-fold higher in microglia than neurons, and 15-fold higher in microglia compared with astrocytes. This cell-specific enrichment is supported by expression data from both mouse and human brain tissue. ITM2B/BRI2 protein levels are higher in iPSC-microglia compared with neurons and astrocytes. Consequently, the ABri peptide was detected in patient iPSC-derived microglial lysates and conditioned media but was undetectable in patient-derived neurons and control microglia. Pathological examination of post-mortem tissue support ABri expression in microglia that are in proximity to pre-amyloid deposits. Finally, gene co-expression analysis supports a role for ITM2B/BRI2 in disease-associated microglial responses. These data demonstrate that microglia are the major contributors to the production of amyloid forming peptides in FBD, potentially acting as instigators of neurodegeneration. Additionally, these data also suggest ITM2B/BRI2 may be part of a microglial response to disease, motivating further investigations of its role in microglial activation. This has implications for our understanding of the role of microglia and the innate immune response in the pathogenesis of FBD and other neurodegenerative dementias including Alzheimer's disease.
- Published
- 2023
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18. Embedding Information into or onto Additively Manufactured Parts: A Review of QR Codes, Steganography and Watermarking Methods.
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Usama M and Yaman U
- Abstract
The paper gives a detailed review of the approaches adopted for embedding information into/onto additively manufactured parts. The primary purpose of this paper is to review all the techniques adopted for embedding information, highlight notable trends and improvements in these works, and provide design and manufacturing pipelines to realize most of these works. It classifies these approaches into four different categories and summarizes the works carried out in each field. It also compares all the results in textual and tabular forms and then gives a detailed conclusion of the best works in terms of application and effectiveness. The four categories discussed are 3D QR codes, 3D watermarking, steganography and nonclassified methods. Lastly, it discusses the future extensions and potential improvements in the field of embedding information, while exploring manufacturing technologies.
- Published
- 2022
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19. A genetic link between risk for Alzheimer's disease and severe COVID-19 outcomes via the OAS1 gene.
- Author
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Magusali N, Graham AC, Piers TM, Panichnantakul P, Yaman U, Shoai M, Reynolds RH, Botia JA, Brookes KJ, Guetta-Baranes T, Bellou E, Bayram S, Sokolova D, Ryten M, Sala Frigerio C, Escott-Price V, Morgan K, Pocock JM, Hardy J, and Salih DA
- Subjects
- Adolescent, Aged, Aged, 80 and over, Alzheimer Disease diagnosis, Alzheimer Disease epidemiology, COVID-19 diagnosis, COVID-19 epidemiology, Cells, Cultured, Female, Gene Regulatory Networks genetics, Genetic Predisposition to Disease epidemiology, Humans, Induced Pluripotent Stem Cells physiology, Male, Middle Aged, Polymorphism, Single Nucleotide genetics, Young Adult, 2',5'-Oligoadenylate Synthetase genetics, Alzheimer Disease genetics, COVID-19 genetics, Genetic Linkage genetics, Genetic Predisposition to Disease genetics, Patient Acuity
- Abstract
Recently, we reported oligoadenylate synthetase 1 (OAS1) contributed to the risk of Alzheimer's disease, by its enrichment in transcriptional networks expressed by microglia. However, the function of OAS1 within microglia was not known. Using genotyping from 1313 individuals with sporadic Alzheimer's disease and 1234 control individuals, we confirm the OAS1 variant, rs1131454, is associated with increased risk for Alzheimer's disease. The same OAS1 locus has been recently associated with severe coronavirus disease 2019 (COVID-19) outcomes, linking risk for both diseases. The single nucleotide polymorphisms rs1131454(A) and rs4766676(T) are associated with Alzheimer's disease, and rs10735079(A) and rs6489867(T) are associated with severe COVID-19, where the risk alleles are linked with decreased OAS1 expression. Analysing single-cell RNA-sequencing data of myeloid cells from Alzheimer's disease and COVID-19 patients, we identify co-expression networks containing interferon (IFN)-responsive genes, including OAS1, which are significantly upregulated with age and both diseases. In human induced pluripotent stem cell-derived microglia with lowered OAS1 expression, we show exaggerated production of TNF-α with IFN-γ stimulation, indicating OAS1 is required to limit the pro-inflammatory response of myeloid cells. Collectively, our data support a link between genetic risk for Alzheimer's disease and susceptibility to critical illness with COVID-19 centred on OAS1, a finding with potential implications for future treatments of Alzheimer's disease and COVID-19, and development of biomarkers to track disease progression., (© The Author(s) (2021). Published by Oxford University Press on behalf of the Guarantors of Brain.)
- Published
- 2021
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20. TPH1 A218 allele is associated with suicidal behavior in Turkish population.
- Author
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Beden O, Senol E, Atay S, Ak H, Altintoprak AE, Kiyan GS, Petin B, Yaman U, and Aydin HH
- Subjects
- Adolescent, Adult, Aged, Female, Genotype, Humans, Male, Middle Aged, Turkey, Young Adult, Genetic Predisposition to Disease, Polymorphism, Genetic genetics, Suicide, Attempted, Tryptophan Hydroxylase genetics
- Abstract
Background: Serotonergic dysfunction is implicated in depression, psychiatric disorders and suicidal behaviors. The first and rate-limiting step in the synthesis of serotonin is catalyzed by tryptophan hydroxylase (TPH) which is encoded by TPH1 and THP2 genes. Genetic association studies have revealed contradictory results about the effect of the TPH1 A218C (rs1800532) polymorphism on suicidal behavior in different populations., Material and Method: In this study, we investigated A218C polymorphism in 109 suicide attempters and 98 healthy controls. Socio-demographic characteristics of participants were obtained through questionnaire. DNA was extracted from peripheral blood and genotyping was performed by Real Time PCR. Fisher's exact test was used to evaluate the significance of the difference among the independent variables. Hardy-Weinberg equilibrium was tested using Pearson's goodness-of-fit chi-squared test., Results: The frequency of A allele was significantly higher in suicide attempters than controls (46.33% vs. 35.71%, p=0.0357). However, there were no differences in genotype frequencies of this locus between participants having attempted suicide and controls (p>0.05). Among males, frequencies of CC genotype and C allele were found to be significantly higher in controls (p=0.0125, p=0.0298). With regard to the female subjects and female controls, no significant association was detected between suicidal behavior and genotype/allele frequencies (p>0.05)., Conclusion: Our results provide evidence that A allele of TPH1 A218C polymorphism may be associated with suicidal behavior in Turkish population., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2016
- Full Text
- View/download PDF
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