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1. Unilateral J‐cut division versus partial and subtotal removal techniques in female patients with mesh‐related urethral obstruction: Multicentric comparative study

Author

Bülent Çetinel, Göktuğ Kalender, Elif Altınay Kırlı, Aydın Yenilmez, Ömer Gülpınar, Adnan Şimşir, Gökhan Temeltaş, Alkan Çubuk, and Günay Can

Subjects
bladder outlet obstruction, de‐novo stress urinary incontinence, mesh‐related obstruction, sling excision, sling incision, surgical outcomes, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Abstract Objective To compare the functional (obstruction relieving) outcomes and complications of unilateral J‐cut division, partial and subtotal vaginal removal techniques were performed for mesh‐related urethral obstruction (MRUO) in females. Methods Patient review included demographics, a medical history and proforma with details of lower urinary tract symptoms (LUTS), physical and urodynamic findings, detailed surgical reports and follow‐up data. Variables were compared between the three groups. Results Out of 130 patients with sling revision surgery (SRS), 54 women underwent SRS for MRUO with a median follow‐up of 48 (17–96) months. Unilateral J‐cut division, partial and subtotal vaginal removal techniques were performed in 12, 31 and 11 patients with a median duration of surgery of 30 (25–34), 40 (35–56) and 60 (60–70) minutes, respectively (p = 0.001). Statistically significant increase in median maximum free urine flow rate and decrease in median post‐void residual urine volume were found after SRS in the three groups, while de novo stress urinary incontinence (SUI) developed in 10%, 44% and 60% of the patients in the unilateral J‐cut division, partial and subtotal removal groups, respectively (p = 0.007). Conclusions The unilateral J‐cut division technique was as effective as the partial and subtotal vaginal removal techniques in relieving MRUO with a shorter duration of surgery time (p = 0.001) and lower risk of de novo SUI (p = 0.007). Comparative studies with a larger number of patients are needed.

Published
2024
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3. Microencapsulation of thermochromic sytems containing fluoran dyes by poly (methyl methacrylate) wall for textile applications [Tekstil uygulamalari için fluoran boyalar I?çeren termokromik sistemlerin poli (Metil Metakrilat) duvar ile mikrokapsülasyonu]

Author

Özkayalar S., Aksoy S.A., Tözüm M.S., Alkan C., and Tokat Gaziosmanpaşa Üniversitesi

Subjects
Color change, Thermochromic microcapsule, Fluoran dye, Heat storage
Abstract

In this study, microencapsulation of thermochromic systems containing fluoran dye was aimed. For this purpose, thermochromic systems containing fluoran dye, Bisphenol A and 1-tetradecanol were microencapsulated with poly(methyl methacrylate) using emulsion polymerization method. Thermal properties and thermal stability of the microcapsules were investigated by differential scanning calorimetry (DSC) and thermal gravimetric (TG) analyzes. The thermo-regulation property of the microcapsules was tested by T-history analysis consisting of temperature sensor and data logger. The temperature-sensitive reversible discoloration properties of the microcapsules were determined by photographs taken at temperatures above and below the activation temperature. According to DSC results, microcapsules had latent heat storage in the range of 152.6-185.8 J/g. It was determined that the microcapsules, which were colored below the activation temperature, lost their color above the activation temperature and exhibited reversible color change property depending on change in temperature. From TG analysis results, it was determined that microcapsules had sufficient thermal resistance for textile applications. © Chamber of Textile Engineers.

Published
2020

5. Preparation of poly(methyl methacrylate-co-ethylene glycol dimethacrylate-co-glycidyl methacrylate) walled thermochromic microcapsules and their application to cotton fabrics

Author

Tözüm, Müyesser Selda, Alkan C., Alay Aksoy S., and Uşak Üniversitesi, Mühendislik Fakültesi, Tekstil Mühendisliği Bölümü

Subjects
emulsion polymerization, copolymers, dyes/pigments, textiles
Abstract

This study focused on fabrication of the thermochromic microcapsules and their application to the cotton fabric. In this study, thermochromic systems composed of crystal violet lactone, bisphenol A, and 1-tetradecanol were prepared and microencapsulated by emulsion polymerization method in poly(methyl methacrylate-co-ethylene glycol dimethacrylate-co-glycidyl methacrylate) wall. The microcapsules were analyzed by Fourier transform infrared spectroscopy, scanning electron microscope, transmission electron microscope, differential scanning calorimetry, and thermogravimetric analysis. Their thermoregulating property was tested by T-history test. The results revealed that microcapsules with smooth surfaces, core–shell structured, and spherical shape were successfully produced. The latent heat storage capacity of the microcapsules decreased from 202 J g?1 to 167 J g?1 when their shell/core ratio changed from 0.5/1 to 2/1. Microcapsules were adequately had sufficient thermal resistance to the temperatures they will encounter during their application to textile products and their usage. According to the UV–visible spectroscopy analysis and color measurements, the microcapsules exhibited reversible color change from blue to colorless and vice versa. Besides, the microcapsule impregnated fabric was able to absorb latent heat energy of 21.79 J g?1 at around 35 °C and had cooling effect. According to the colorimetric parameters, the fabric was at blue color at room temperature and became colorless when heated to the temperature above the melting point of thermochromic system. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 137, 48815. © 2019 Wiley Periodicals, Inc. 4602?D2?16 This study was funded by a Scientific Research Project of Suleyman Demirel University (Project no: 4602?D2?16).

Published
2019

7. Divergent origins and concerted expansion of two segmental duplications on chromosome 16

Author

Eichler, E. E., Johnson, M. E., Alkan, C., Tuzun, E., Sahinalp, C., Misceo, D., Archidiacono, N., and Rocchi, M.

Subjects
Human chromosomes -- Research, Cladistic analysis -- Research, Genomes -- Research, Genetic research, Biological sciences
Abstract

A model of rapid expansion and evolutionary turnover among the genomes of man and the great apes is supported by the evolutionary history of the two chromosome duplications. The data suggest that the two copies of genomic sequence are brought together during the chimpanzee/human divergence and are subsequently duplicated as a larger cassette within the human lineage.

Published
2001

8. A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD

Author

Renton, Ae, Majounie, E, Waite, A, Simón Sánchez, J, Rollinson, S, Gibbs, Jr, Schymick, Jc, Laaksovirta, H, van Swieten, Jc, Myllykangas, L, Kalimo, H, Paetau, A, Abramzon, Y, Remes, Am, Kaganovich, A, Scholz, Sw, Duckworth, J, Ding, J, Harmer, Dw, Hernandez, Dg, Johnson, Jo, Mok, K, Ryten, M, Trabzuni, D, Guerreiro, Rj, Orrell, Rw, Neal, J, Murray, A, Pearson, J, Jansen, Ie, Sondervan, D, Seelaar, H, Blake, D, Young, K, Halliwell, N, Callister, Jb, Toulson, G, Richardson, A, Gerhard, A, Snowden, J, Mann, D, Neary, D, Nalls, Ma, Peuralinna, T, Jansson, L, Isoviita, Vm, Kaivorinne, Al, Hölttä Vuori, M, Ikonen, E, Sulkava, R, Benatar, M, Wuu, J, Chiò, A, Restagno, G, Borghero, G, Sabatelli, M, Italsgen, Consortium, Heckerman, D, Rogaeva, E, Zinman, L, Rothstein, Jd, Sendtner, M, Drepper, C, Eichler, Ee, Alkan, C, Abdullaev, Z, Pack, Sd, Dutra, A, Pak, E, Hardy, J, Singleton, A, Williams, Nm, Heutink, P, Pickering Brown, S, Morris, Hr, Tienari, Pj, Traynor, Bj, Calvo, A, Cammarosano, S, Moglia, C, Canosa, A, Gallo, S, Brunetti, M, Ossola, I, Mora, G, Marinou, K, Papetti, L, Conte, A, Luigetti, M, La Bella, V, Spataro, R, Colletti, T, Battistini, S, Giannini, Fabio, Ricci, C, Caponnetto, C, Mancardi, G, Mandich, P, Salvi, F, Bartolomei, I, Mandrioli, J, Sola, P, Corbo, M, Lunetta, C, Penco, S, Monsurrò, Mr, Tedeschi, G, Conforti, Fl, Volanti, P, Floris, G, Cannas, A, Piras, V, Murru, Mr, Marrosu, Mg, Pugliatti, M, Ticca, A, Simone, I, Logroscino, G, Neuroscience Campus Amsterdam - Systems Biology of the Synapse, Neuroscience Campus Amsterdam - Neurodegeneration, Renton, Ae, Majounie, E, Waite, A, Simón Sánchez, J, Rollinson, S, Gibbs, Jr, Schymick, Jc, Laaksovirta, H, van Swieten, Jc, Myllykangas, L, Kalimo, H, Paetau, A, Abramzon, Y, Remes, Am, Kaganovich, A, Scholz, Sw, Duckworth, J, Ding, J, Harmer, Dw, Hernandez, Dg, Johnson, Jo, Mok, K, Ryten, M, Trabzuni, D, Guerreiro, Rj, Orrell, Rw, Neal, J, Murray, A, Pearson, J, Jansen, Ie, Sondervan, D, Seelaar, H, Blake, D, Young, K, Halliwell, N, Callister, Jb, Toulson, G, Richardson, A, Gerhard, A, Snowden, J, Mann, D, Neary, D, Nalls, Ma, Peuralinna, T, Jansson, L, Isoviita, Vm, Kaivorinne, Al, Hölttä Vuori, M, Ikonen, E, Sulkava, R, Benatar, M, Wuu, J, Chiò, A, Restagno, G, Borghero, G, Sabatelli, M, Italsgen, Consortium, Heckerman, D, Rogaeva, E, Zinman, L, Rothstein, Jd, Sendtner, M, Drepper, C, Eichler, Ee, Alkan, C, Abdullaev, Z, Pack, Sd, Dutra, A, Pak, E, Hardy, J, Singleton, A, Williams, Nm, Heutink, P, Pickering Brown, S, Morris, Hr, Tienari, Pj, COLLABORATORS: Calvo A, Traynor B. J., Cammarosano, S, Moglia, C, Canosa, A, Gallo, S, Brunetti, M, Ossola, I, Mora, G, Marinou, K, Papetti, L, Conte, A, Luigetti, M, La Bella, V, Spataro, R, Colletti, T, Battistini, S, Giannini, F, Ricci, C, Caponnetto, C, Mancardi, G, Mandich, P, Salvi, F, Bartolomei, I, Mandrioli, J, Sola, P, Corbo, M, Lunetta, C, Penco, S, Monsurro', Maria Rosaria, Tedeschi, Gioacchino, Conforti, Fl, Volanti, P, Floris, G, Cannas, A, Piras, V, Murru, Mr, Marrosu, Mg, Pugliatti, M, Ticca, A, Simone, I, Logroscino, G., Neurology, Human genetics, NCA - Systems Biology of the Synapse, and NCA - Neurodegeneration

Subjects
Male, Genotype, Neuroscience(all), Population, Biology, TARDBP, Chromosomes, 03 medical and health sciences, 0302 clinical medicine, Alleles, Amyotrophic Lateral Sclerosis, genetics, Chromosomes, Human, Pair 9, Female, Finland, Frontotemporal Dementia, genetics, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Male, Microsatellite Repeats, Pedigree, Polymorphism, Single Nucleotide, SDG 3 - Good Health and Well-being, C9orf72, Humans, genetics, Genetic Predisposition to Disease, Polymorphism, education, Alleles, Finland, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, General Neuroscience, Haplotype, Amyotrophic Lateral Sclerosis, Charged multivesicular body protein 2B, DNA Repeat Expansion, 3. Good health, Pedigree, C9orf72 Protein, Haplotypes, Frontotemporal Dementia, Female, Trinucleotide repeat expansion, 030217 neurology & neurosurgery, Pair 9, Microsatellite Repeats
Abstract

The chromosome 9p21 amyotrophic lateral sclerosis-frontotemporal dementia (ALS-FTD) locus contains one of the last major unidentified autosomal-dominant genes underlying these common neurodegenerative diseases. We have previously shown that a founder haplotype, covering the MOBKL2b, IFNK, and C9ORF72 genes, is present in the majority of cases linked to this region. Here we show that there is a large hexanucleotide (GGGGCC) repeat expansion in the first intron of C9ORF72 on the affected haplotype. This repeat expansion segregates perfectly with disease in the Finnish population, underlying 46.0% of familial ALS and 21.1% of sporadic ALS in that population. Taken together with the D90A SOD1 mutation, 87% of familial ALS in Finland is now explained by a simple monogenic cause. The repeat expansion is also present in one-third of familial ALS cases of outbred European descent, making it the most common genetic cause of these fatal neurodegenerative diseases identified to date. © 2011 Elsevier Inc.

Published
2011

9. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Author

Delaneau O., Marchini J., McVeanh G.A., Donnelly P., Lunter G., Marchini J.L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson I., Rimmer, A., Xifara, D.K., Kerasidou, A., Churchhouse, C., Altshuler, D.M., Gabriel, S.B., Lander, E.S., Gupta, N., Daly, M.J., DePristo, M.A., Banks, E., Bhatia G., Carneiro, M.O., Del Angel G., Genovese G., Handsaker, R.E., Hartl, C., McCarroll, S.A., Nemesh J.C., Poplin, R.E., Schaffner, S.F., Shakir, K., Sabeti P.C., Grossman, S.R., Tabrizi, S., Tariyal, R., Li H., Reich, D., Durbin, R.M., Hurles, M.E., Balasubramaniam, S., Burton J., Danecek P., Keane, T.M., Kolb-Kokocinski, A., McCarthy, S., Stalker J., Quail, M., Ayub Q., Chen, Y., Coffey, A.J., Colonna V., Huang, N., Jostins L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S.J., Ning, Z., Frankish, A., Harrow J., Chris, T.-S., Abecasis G.R., Kang H.M., Anderson P., Blackwell, T., Busonero F., Fuchsberger, C., Jun G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M.K., Bentley, D.R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R.K., Cox, T., Eberle, M., Murray L., Shaw, R., Chakravarti, A., Clark, A.G., Keinan, A., Rodriguez-Flores J.L., De LaVega F.M., Degenhardt J., Eichler, E.E., Flicek P., Clarke L., Leinonen, R., Smith, R.E., Zheng-Bradley X., Beal, K., Cunningham F., Herrero J., McLaren W.M., Ritchie G.R.S., Barker J., Kelman G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter I., Toneva I., Gibbs, R.A., Dinh H., Kovar, C., Lee, S., Lewis L., Muzny, D., Reid J., Wang, M., Yu F., Bainbridge, M., Challis, D., Evani, U.S., Lu J., Nagaswamy, U., Sabo, A., Wang, Y., Yu J., Fowler G., Hale W., Kalra, D., Green, E.D., Knoppers, B.M., Korbel J.O., Rausch, T., Sttz, A.M., Lee, C., Griffin L., Hsieh, C.-H., Mills, R.E., Von Grotthuss, M., Zhang, C., Shi X., Lehrach H., Sudbrak, R., Amstislavskiy V.S., Lienhard, M., Mertes F., Sultan, M., Timmermann, B., Yaspo, M.L., Herwig, S.R., Mardis, E.R., Wilson, R.K., Fulton L., Fulton, R., Weinstock G.M., Chinwalla, A., Ding L., Dooling, D., Koboldt, D.C., McLellan, M.D., Wallis J.W., Wendl, M.C., Zhang Q., Marth G.T., Garrison, E.P., Kural, D., Lee W.-P., Leong W.F., Ward, A.N., Wu J., Zhang, M., Nickerson, D.A., Alkan, C., Hormozdiari F., Ko, A., Sudmant P.H., Schmidt J.P., Davies, C.J., Gollub J., Webster, T., Wong, B., Zhan, Y., Sherry, S.T., Xiao, C., Church, D., Ananiev V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner J., Hefferon, T., Kimelman, M., Liu, C., Lopez J., Meric P., Ostapchuk, Y., Phan L., Ponomarov, S., Schneider V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang H., Wang J., Fang X., Guo X., Jian, M., Jiang H., Jin X., Li G., Li J., Li, Y., Liu X., Lu, Y., Ma X., Tai, S., Tang, M., Wang, B., Wang G., Wu H., Wu, R., Yin, Y., Zhang W., Zhao J., Zhao, M., Zheng X., Lachlan H., Fang L., Li Q., Li, Z., Lin H., Liu, B., Luo, R., Shao H., Xie, Y., Ye, C., Yu, C., Zheng H., Zhu H., Cai H., Cao H., Su, Y., Tian, Z., Yang H., Yang L., Zhu J., Cai, Z., Albrecht, M.W., Borodina, T.A., Auton, A., Yoon, S.C., Lihm J., Makarov V., Jin H., Kim W., Kim, K.C., Gottipati, S., Jones, D., Cooper, D.N., Ball, E.V., Stenson P.D., Barnes, B., Kahn, S., Ye, K., Batzer, M.A., Konkel, M.K., Walker J.A., MacArthur, D.G., Lek, M., Shriver, M.D., Bustamante, C.D., Gravel, S., Kenny, E.E., Kidd J.M., Lacroute P., Maples, B.K., Moreno-Estrada, A., Zakharia F., Henn, B., Sandoval, K., Byrnes J.K., Halperin, E., Baran, Y., Craig, D.W., Christoforides, A., Izatt, T., Kurdoglu, A.A., Sinari, S.A., Homer, N., Squire, K., Sebat J., Bafna V., Burchard, E.G., Hernandez, R.D., Gignoux, C.R., Haussler, D., Katzman, S.J., Kent W.J., Howie, B., Ruiz-Linares, A., Dermitzakis, E.T., Lappalainen, T., Devine, S.E., Maroo, A., Tallon L.J., Rosenfeld J.A., Michelson L.P., Angius, A., Cucca F., Sanna, S., Bigham, A., Jones, C., Reinier F., Lyons, R., Schlessinger, D., Awadalla P., Hodgkinson, A., Oleksyk, T.K., Martinez-Cruzado J.C., Fu, Y., Xiong, M., Jorde L., Witherspoon, D., Xing J., Browning, B.L., Hajirasouliha I., Chen, K., Albers, C.A., Gerstein, M.B., Abyzov, A., Chen J., Habegger L., Harmanci, A.O., Mu X.J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson J.J., OSullivan, C., Barnes, K.C., Gharani, N., Toji L.H., Gerry, N., Kaye J.S., Kent, A., Mathias, R., Ossorio P.N., Parker, M., Rotimi, C.N., Royal, C.D., Tishkoff, S., Via, M., Bodmer W., Bedoya G., Yang G., You, C.J., Garcia-Montero, A., Orfao, A., Dutil J., Brooks L.D., Felsenfeld, A.L., McEwen J.E., Clemm, N.C., Guyer, M.S., Peterson J.L., Duncanson, A., Dunn, M., Peltonen L., and 1000 Genomes Project Consortium

Subjects
haplotype, genetic association, genotype, General Physics and Astronomy, Genome-wide association study, genetic analysis, gene sequence, Biology, gene frequency, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, polymorphism, Gene Frequency, single nucleotide polymorphism, Humans, chromosome, human, 1000 Genomes Project, indel mutation, genome, Alleles, Genetic association, Genetics, Whole genome sequencing, Multidisciplinary, accuracy, Genome, Human, Haplotype, allele, article, reference database, General Chemistry, Microarray Analysis, chromosome 20, Haplotypes, Human genome, microarray analysis, Imputation (genetics), Algorithms, SNP array, Genome-Wide Association Study
Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved.

Published
2014

10. Great ape genetic diversity and population history

Author

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prxfcfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubxed C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, and K

Published
2013

12. An integrated map of genetic variation from 1,092 human genomes

Author

Altshuler, DM, Durbin, RM, Abecasis, GR, Bentley, DR, Chakravarti, A, Clark, AG, Donnelly, P, Eichler, EE, Flicek, P, Gabriel, SB, Gibbs, RA, Green, ED, Hurles, ME, Knoppers, BM, Korbel, JO, Lander, ES, Lee, C, Lehrach, H, Mardis, ER, Marth, GT, McVean, GA, Nickerson, DA, Schmidt, JP, Sherry, ST, Wang, J, Wilson, RK, Dinh, H, Kovar, C, Lee, S, Lewis, L, Muzny, D, Reid, J, Wang, M, Fang, X, Guo, X, Jian, M, Jiang, H, Jin, X, Li, G, Li, J, Li, Y, Li, Z, Liu, X, Lu, Y, Ma, X, Su, Z, Tai, S, Tang, M, Wang, B, Wang, G, Wu, H, Wu, R, Yin, Y, Zhang, W, Zhao, J, Zhao, M, Zheng, X, Zhou, Y, Gupta, N, Clarke, L, Leinonen, R, Smith, RE, Zheng-Bradley, X, Grocock, R, Humphray, S, James, T, Kingsbury, Z, Sudbrak, R, Albrecht, MW, Amstislavskiy, VS, Borodina, TA, Lienhard, M, Mertes, F, Sultan, M, Timmermann, B, Yaspo, M-L, Fulton, L, Fulton, R, Weinstock, GM, Balasubramaniam, S, Burton, J, Danecek, P, Keane, TM, Kolb-Kokocinski, A, McCarthy, S, Stalker, J, Quail, M, Davies, CJ, Gollub, J, Webster, T, Wong, B, Zhan, Y, Auton, A, Yu, F, Bainbridge, M, Challis, D, Evani, US, Lu, J, Nagaswamy, U, Sabo, A, Wang, Y, Yu, J, Coin, LJM, Fang, L, Li, Q, Lin, H, Liu, B, Luo, R, Qin, N, Shao, H, Xie, Y, Ye, C, Yu, C, Zhang, F, Zheng, H, Zhu, H, Garrison, EP, Kural, D, Lee, W-P, Leong, WF, Ward, AN, Wu, J, Zhang, M, Griffin, L, Hsieh, C-H, Mills, RE, Shi, X, Von Grotthuss, M, Zhang, C, Daly, MJ, DePristo, MA, Banks, E, Bhatia, G, Carneiro, MO, Del Angel, G, Genovese, G, Handsaker, RE, Hartl, C, McCarroll, SA, Nemesh, JC, Poplin, RE, Schaffner, SF, Shakir, K, Yoon, SC, Lihm, J, Makarov, V, Jin, H, Kim, W, Kim, KC, Rausch, T, Beal, K, Cunningham, F, Herrero, J, McLaren, WM, Ritchie, GRS, Gottipati, S, Keinan, A, Rodriguez-Flores, JL, Sabeti, PC, Grossman, SR, Tabrizi, S, Tariyal, R, Cooper, DN, Ball, EV, Stenson, PD, Barnes, B, Bauer, M, Cheetham, RK, Cox, T, Eberle, M, Kahn, S, Murray, L, Peden, J, Shaw, R, Ye, K, Batzer, MA, Konkel, MK, Walker, JA, MacArthur, DG, Lek, M, Herwig, R, Shriver, MD, Bustamante, CD, Byrnes, JK, De la Vega, FM, Gravel, S, Kenny, EE, Kidd, JM, Lacroute, P, Maples, BK, Moreno-Estrada, A, Zakharia, F, Halperin, E, Baran, Y, Craig, DW, Christoforides, A, Homer, N, Izatt, T, Kurdoglu, AA, Sinari, SA, Squire, K, Xiao, C, Sebat, J, Bafna, V, Burchard, EG, Hernandez, RD, Gignoux, CR, Haussler, D, Katzman, SJ, Kent, WJ, Howie, B, Ruiz-Linares, A, Dermitzakis, ET, Lappalainen, T, Devine, SE, Maroo, A, Tallon, LJ, Rosenfeld, JA, Michelson, LP, Kang, HM, Anderson, P, Angius, A, Bigham, A, Blackwell, T, Busonero, F, Cucca, F, Fuchsberger, C, Jones, C, Jun, G, Lyons, R, Maschio, A, Porcu, E, Reinier, F, Sanna, S, Schlessinger, D, Sidore, C, Tan, A, Trost, MK, Awadalla, P, Hodgkinson, A, Lunter, G, Marchini, JL, Myers, S, Churchhouse, C, Delaneau, O, Gupta-Hinch, A, Iqbal, Z, Mathieson, I, Rimmer, A, Xifara, DK, Oleksyk, TK, Fu, Y, Xiong, M, Jorde, L, Witherspoon, D, Xing, J, Browning, BL, Alkan, C, Hajirasouliha, I, Hormozdiari, F, Ko, A, Sudmant, PH, Chen, K, Chinwalla, A, Ding, L, Dooling, D, Koboldt, DC, McLellan, MD, Wallis, JW, Wendl, MC, Zhang, Q, Tyler-Smith, C, Albers, CA, Ayub, Q, Chen, Y, Coffey, AJ, Colonna, V, Huang, N, Jostins, L, Li, H, Scally, A, Walter, K, Xue, Y, Zhang, Y, Gerstein, MB, Abyzov, A, Balasubramanian, S, Chen, J, Clarke, D, Habegger, L, Harmanci, AO, Jin, M, Khurana, E, Mu, XJ, Sisu, C, Degenhardt, J, Stuetz, AM, Church, D, Michaelson, JJ, Ben, B, Lindsay, SJ, Ning, Z, Frankish, A, Harrow, J, Fowler, G, Hale, W, Kalra, D, Barker, J, Kelman, G, Kulesha, E, Radhakrishnan, R, Roa, A, Smirnov, D, Streeter, I, Toneva, I, Vaughan, B, Ananiev, V, Belaia, Z, Beloslyudtsev, D, Bouk, N, Chen, C, Cohen, R, Cook, C, Garner, J, Hefferon, T, Kimelman, M, Liu, C, Lopez, J, Meric, P, O'Sullivan, C, Ostapchuk, Y, Phan, L, Ponomarov, S, Schneider, V, Shekhtman, E, Sirotkin, K, Slotta, D, Zhang, H, Barnes, KC, Beiswanger, C, Cai, H, Cao, H, Gharani, N, Henn, B, Jones, D, Kaye, JS, Kent, A, Kerasidou, A, Mathias, R, Ossorio, PN, Parker, M, Reich, D, Rotimi, CN, Royal, CD, Sandoval, K, Su, Y, Tian, Z, Tishkoff, S, Toji, LH, Via, M, Yang, H, Yang, L, Zhu, J, Bodmer, W, Bedoya, G, Ming, CZ, Yang, G, You, CJ, Peltonen, L, Garcia-Montero, A, Orfao, A, Dutil, J, Martinez-Cruzado, JC, Brooks, LD, Felsenfeld, AL, McEwen, JE, Clemm, NC, Duncanson, A, Dunn, M, Guyer, MS, Peterson, JL, 1000 Genomes Project Consortium, Dermitzakis, Emmanouil, Universitat de Barcelona, Massachusetts Institute of Technology. Department of Biology, Altshuler, David, and Lander, Eric S.

Subjects
Natural selection, LOCI, Genome-wide association study, Evolutionary biology, Continental Population Groups/genetics, Human genetic variation, VARIANTS, Genoma humà, Binding Sites/genetics, 0302 clinical medicine, RARE, Sequence Deletion/genetics, WIDE ASSOCIATION, ddc:576.5, Copy-number variation, MUTATION, Exome sequencing, transcription factor, Conserved Sequence, Human evolution, Sequence Deletion, Genetics, RISK, 0303 health sciences, Multidisciplinary, Continental Population Groups, 1000 Genomes Project Consortium, Genetic analysis, Genomics, Polymorphism, Single Nucleotide/genetics, Research Highlight, 3. Good health, Algorithm, Multidisciplinary Sciences, Genetic Variation/genetics, Map, Science & Technology - Other Topics, Conserved Sequence/genetics, Integrated approach, General Science & Technology, Genetics, Medical, Haplotypes/genetics, Biology, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, Genetic variation, Humans, Transcription Factors/metabolism, POPULATION-STRUCTURE, 1000 Genomes Project, Polymorphism, Nucleotide Motifs, Alleles, 030304 developmental biology, COPY NUMBER VARIATION, Science & Technology, Binding Sites, Human genome, Genome, Human, Racial Groups, Genetic Variation, Genetics, Population, Haplotypes, Genome, Human/genetics, untranslated RNA, 030217 neurology & neurosurgery, Transcription Factors, Genome-Wide Association Study
Abstract

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations., National Institutes of Health (U.S.) (Grant RC2HL102925), National Institutes of Health (U.S.) (Grant U54HG3067)

Published
2012

13. A draft sequence and preliminary analysis of the Neandertal genome

Author

Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., M. Hsi-Yang, Fritz, Hansen, N.F., Durand, E.Y., Malaspinas, A.-S., Jensen, J.D., Marques-Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H.A., Good, J.M., Schultz, R., Aximu-Petri, A., Butthof, A., Höber, B., Höffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E.S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajković, D., Kućan, Z., Gušić, I., Doronichev, V.B., Golovanova, L.V., Lalueza-Fox, C., Rasilla M. De, La, Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E.E., Falush, D., Birney, E., Mullikin, J.C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., Pääbo, S., Laboratoire de mécanique des sols, structures et matériaux (MSSMat), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2010

15. Effect Of RENAL Nephrometry Score On the outcome Of Laparoscopic Partial Nephrectomy In Urologists At The Beginning Of the Learning Curve

Author

Alkan Çubuk, Ahmet Şahan, Orkunt Özkaptan, and Kasım Ertaş

Subjects
laparoscopic partial nephrectomy, complication, nephrometry score, surgeon experience, Medicine
Abstract

INTRODUCTION: Surgical experience and tumor characteristics are extremely important in laparocopic partial nephrectomy surgery (LPN). Most of the studies examining the relation of R.E.N.A.L.nephrometry score to surgical success have examined the results of experienced surgeons. In this study, we investigated the effectiveness of R.E.N.A.L. nephrometry score (RNS) in predicting complications and success for urologists who are at the beginning of the learning curve for laparoscopic partial nephrectomy. METHODS: The first 30 cases of LPN performed by a single surgeon were evaluated, retrospectively. The patients were grouped according to the RNS as low-risk and medium-high risk. Operation time, warm ischemia time and were recorded. Postoperative blood transfusion rate, hospital stay, hemogram levels and pathology results (surgical margin and tumor type) were evaluated. The comparison of perioperative values of the two groups was done by Mann-Whitney U test. RESULTS: There was no statistically significant difference between operation time, warm ischemia time, hospital stay time, and intra-operative bleeding amount (p> 0.05) between the low risk group and medium-high risk group patients. The total complication rate was 33.3%. The compliction rate for the low risk group was 27% (n = 5) (major complication 5.5% (n = 1)) and 41.6% (n = 5) for the medium-high group (major complication 8.3% (n = 1)). In comparing the two groups for complications, no significant difference was found (p = 0.46). DISCUSSION AND CONCLUSION: The R.E.N.A.L.nephrometry score does not affect the success and complication rates of urologists at the beginning of the learning curve in LPN surgery.

Published
2021
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16. Laparoscopic radical nephrectomy with inferior vena cava thrombectomy

Author

Ahmet Şahan, Orkunt Özkaptan, Alkan Çubuk, Mete Kösemen, Önder Kara, and Oktay Akça

Subjects
Kidney cancer, Laparoscopic nephrectomy, Vena cava thrombosis, Surgery, RD1-811, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Objective: To present a step-by-step video of laparoscopic radical nephrectomy and inferior vena cava (IVC) thrombectomy. Patient and surgical procedure: A 55 year-old female diagnosed with a right renal mass with inferior vena cava extension, underwent laparoscopic radical nephrectomy and IVC thrombectomy. Magnetic resonance imaging (MRI) examination revealed an approximately 9 cm mass in the right kidney, combined with a 4 cm mass extending to the right renal vein and IVC. Graded by the thrombus level system, the IVC thrombus of this patient was at level I. The patient was placed in a left decubitus position, and four laparoscopic ports were used. Results: The total duration of the surgery was 2 h and 10 min. The total IVC clamping time was 21 min. Estimated blood loss was 590 mL, and no major intraoperative or postoperative complications occurred. Time to discharge was four days. There was no complication during 12 months of follow-up. Pathological evaluation revealed clear cell renal cell carcinoma with a negative surgical margin. After 12 months of follow-up, there was no recurrence or distant metastasis. Conclusion: We believe that a laparoscopic approach should be offered to selected patients diagnosed with RCC and vena cava tumor thrombus as a minimal invasive option. Optimal patient selection, extensive laparoscopic experience, and multidisciplinary support are crucial for effective surgical treatment.

Published
2022
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18. Virus discovery in sandflies, from field studies to phylogenetic tree building: classic methods versus novel methods, what do we need to address public health impact?

Author

Bichaud, L, primary, Alkan, C, additional, Piorkowski, G, additional, Zhioua, E, additional, Bitam, I, additional, Izri, A, additional, Moin Vaziri, V, additional, Alten, B, additional, Ozbel, Y, additional, Kasap, OE, additional, De Lamballerie, X, additional, and Charrel, RN, additional

Published
2014
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20. The electronic transport properties [Co-2(L)L '(dioxane)(2)(NO3)(2)](NO3)(2) of the complex

Author

Yakuphanoglu, F, Aydogdu, Y, Gomleksiz, M, Sekerci, M, Agan, S, Alkan, C, and Kırıkkale Üniversitesi

Subjects
electrical conductivity, semiconductor, complex
Abstract

WOS: 000182126000015 The temperature dependence of the electrical conductivity, microstructure and crystal structure properties of the [Co,(L)L'(dioxane)(2)(NO3)(2)](NO3)(2) complex was investigated. The X-ray diffraction showed that the [Co,(L)L'(dioxane)(2) (NO3)(2)](NO3)(2) has a triclinic structure. Temperature dependence of the conductivity curve of the complex exhibited two conduction regions, and while increase of conductivity with temperature in the first region is of hopping conduction which takes place in localized states, the conduction in the second region is of Arrhenius-type. These conduction mechanisms are related to intermolecular and intramolecular conduction progresses. The electrical conductivity of the [Co-2(L)L'(dioxane)(2)(NO3)(2)](NO3)(2) complex was 2.57 x 10(-7) (S/cm) at room temperature with activation energy of 0.46 eV which showed semiconductivity behavior. (C) 2002 Published by Elsevier Science B.V.

Published
2003

22. Factors Affecting Outcomes of Salvage Micro Testicular Sperm Extraction Following a Failed Testicular Sperm Extraction

Author

Alkan Çubuk, Muhsin Balaban, and Orkunt Özkaptan

Subjects
azoospermia, sertoli cell-only syndrome, spermatozoa, sperm retrieval, Medicine, Medicine (General), R5-920
Abstract

Aim:To investigate the likelihood of sperm retrieval in repeated micro-testicular sperm extraction (micro-TESE) in non-obstructive azoospermia (NOA) patients.Methods:Data of 310 patients, who underwent a micro-TESE procedure at a center experienced in in vitro fertilization between January 2015 and July 2019, was evaluated retrospectively. Seventy-three patients who had a previous failed sperm retrieval procedure (33 micro-TESE, and 40 TESE) were included in the study. The patients were divided into two groups (group 1: successful, group 2: failure) according to sperm retrieval in salvage micro-TESE. The groups were compared in terms of demographic characteristics and hormonal and histological features.Results:The mean age of the patients was 36.71±8.1 (25-45) years and duration of infertility was 59.45±21.4 (22-247) months. The sperm retrieval rate in patients who underwent salvage micro-TESE was 36.99% (27/73). Sperm retrieval rates were 8/43, 8/16 and 11/14 for patients diagnosed with Sertoli Cell-only syndrome (SCOS), maturation arrest and hypospermatogenesis. The rate of patients with SCOS was significantly higher in the failure group (p

Published
2020
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23. Is Bacterial Colonization in Ureteral Double-J Stents Significant and Is It Predictable?

Author

Ahmet Şahan, Alkan Çubuk, Kasım Ertaş, Asgar Garayev, Ferhat Talibzade, Çağrı Akın Şekerci, Tuncay Toprak, and Yılören Tanıdır

Subjects
double j stent, colonization, urinalysis, stent culture, Surgery, RD1-811, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Objective:Since microscopic hematuria and pyuria can be observed in patients with a ureteral double-J (DJ) stent in place, urinalysis findings are not considered significant in terms of predicting stent-related infections. This study evaluates the presence of bacterial colonization and the value/ effectiveness of urine tests in predicting the results of DJ stent cultures.Materials and Methods:In the present prospective study, we analyzed data from patients who were treated with a DJ stent placement following endourological surgery due to ureteral stones. DJ stents were removed only after the urine cultures appeared sterile or after a period of empiric antibiotic use. The relationship between urinalysis results and stent cultures was assessed.Results:A total of 65 patients (mean age, 42.6±13.5 years; 16 females and 43 males) were evaluated. Bacterial colonization was detected in 12 (18%) DJ stent cultures with Enterococcus faecalis (n=4), extended-spectrum beta-lactamase producer (ESBL (+) Escherichia coli (n=4), Corynebacterium urealyticum (n=2), candida (n=1) and methicillin-resistant Staphylococcus aureus (n=1) growth being reported. The antibiogram results of the patients that showed colonization in their cultures demonstrated penicillin (n=4), ampicillin (n=4), tetracycline (n=3), imipenem (n=2), and linezolid (n=1) sensitivity. The rate of leukocyte esterase- and nitrite-positive patients, of those having significant number of leukocytes, and urine culturepositive patients in the groups with and without positive urine culture was 58.5%, 32%, 49%, and 7.5% vs 50%, 16.6%, 50%, and 8.5%, respectively. There were no statistically significant differences between the groups (p=>0.05). None of the study patients applied to our hospital with active infection following DJ stent removal.Conclusion:Urinalysis is insufficient in predicting catheter culture results. Based on the results of this study, we assume that stent culture for removed DJ stents is not a necessity; empirical antibiotic therapy with ampicillin-tetracycline should be started in patients with postoperative infection.

Published
2020
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24. Reporting Complications in Radical Cystoprostatectomy and Orthotopic Neobladder in Male Patients Using a Standard Reporting Methodology

Author

Orkunt Özkaptan, Alkan Çubuk, Muhsin Balaban, Cüneyd Sevinç, Osman Murat İpek, and Tahir Karadeniz

Subjects
orthotopic neobladder, postoperative complication, radical cystoprostatectomy, standard methodology., Medicine
Abstract

INTRODUCTION[|]This study aims to evaluate the 90-day complication rate and 3-month mortality after open radical cystoprostatectomy using a standardized method to report complications.[¤]METHODS[|]We retrospectively reviewed the data of 209 RC male patients operated by the same surgical team between March 2008 and December 2017 in our institution. Patients' characteristics, clinical outcome, pathological parameters and reflectors of surgical difficulty were retrospectively collected from the hospital medical record. Postoperative complications were graded according to the Clavien-Dindo classification, whereas Martin criteria were used to report complications. SPSS version 22.0 was used for the statistical analyses.[¤]RESULTS[|]A total of 239 complications developed in 143 of the 198 patients (72.2%). Thirtynine (19.7%) of these complications occurred after thirty days postoperatively. The mean operation time was 412.6+- minutes (300–485). Mean EBL was 1107+-617.3 ml (400–3600). Overall mean hospitalization time was 19.2+-7.3 days (7–30). Perioperative transfusion was given in 78.8% of the patients (n=156). Major complications (Clavien 3-5) were observed in 41 (20.7%) patients. The most common complication categories were gastrointestinal (28.8%). Ileus was the most common complication, occurring in 21.2% of the patients.[¤]DISCUSSION AND CONCLUSION[|]Our results support the consideration of a more extended follow-up period to define the morbidity of RC. The standardization of the reporting criteria for complications will allow direct comparisons between studies. The complication rates after utilizing a standard reporting methodology were higher compared to studies that do not employ such methodologies.[¤]

Published
2020
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25. Iatrogenic endometriosis following apical pelvic organ prolapse surgery: a case report

Author

Alkan Cubuk, Orkunt Ozkaptan, and Jörg Neymeyer

Subjects
Endometriosis, Pelvic organ prolapse, Laparoscopy, Hysterectomy, Medicine
Abstract

Abstract Background Iatrogenic endometriosis is the presence of endometrial glands and stroma out of the uterus following certain surgical interventions. The rate of iatrogenic endometriosis after gynecologic surgeries due to benign uterine disease is 1–2%. Laparoscopic supracervical hysterectomy is also a part of frequently used surgical treatment of apical pelvic organ prolapse, which is followed by sacrocervicopexy. However, there are no data about iatrogenic endometriosis after apical prolapse surgery in the current literature. Herein, we present a case report of a patient diagnosed with de novo endometriosis 1 year after laparoscopic supracervical hysterectomy and sacrocervicopexy. Case presentation A 46-year-old parous Slavic woman who underwent laparoscopic supracervical hysterectomy and sacrocervicopexy secondary to grade 3 symptomatic apical prolapse 1 year earlier was admitted to the same clinic with pelvic pain that had started 6 months following surgery. Deep vaginal palpation was painful. Transvaginal ultrasonography revealed an area with hypervascularization on the sacral promontory. She was scheduled for diagnostic laparoscopy. A 2 × 2-cm solid, wine-colored, hypervascular hemorrhagic lesion was seen on the sacral promontory. The lesion and the peritoneal layer behind it were totally excised. The patient was discharged on the first postoperative day, without any complications. Pathologic examination revealed foci of endometriosis comprising endometrial glands and stroma within the connective tissue, along with hemosiderin-laden macrophages. The symptoms of the patient resolved after the surgery, and no further adjuvant treatment was needed. Conclusion Although the rate of iatrogenic endometriosis is low after laparoscopic supracervical hysterectomy and sacrocervicopexy, the possibility of the occurrence of iatrogenic endometriosis should be discussed with patients who are diagnosed with apical prolapse to determine the type of surgical intervention. Iatrogenic endometriosis should be kept in mind for differential diagnosis in case of pain after laparoscopic supracervical hysterectomy and sacrocervicopexy.

Published
2020
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26. Effect of Double-J Stent Placement on Shock Wave Lithotripsy Success in the Treatment of 15-25 mm Renal Upper and Middle Calyceal Stones

Author

Akif Erbin, Alper Kafkaslı, Özgür Yazıcı, Alkan Çubuk, Sedat Çakmak, Yaşar Pazır, Ömer Sarılar, and Mehmet Fatih Akbulut

Subjects
urolithiasis, swl, double-j stent, renal upper and middle calyceal stones, Medicine, Medicine (General), R5-920
Abstract

Aim:To analyze the effect of double-J stent placement on shockwave lithotripsy (SWL) success in the treatment of relatively large (15-25 mm) upper and middle calyceal stones.Methods:A total of 167 patients who had 15-25 mm opaque upper or middle calyceal stones and scheduled for SWL were included in the study. Patients with solitary kidney, urinary system anomalies, skeletal anomalies, previous urologic surgery, severe calyceal dilatation, untreated urinary tract infection, bleeding disorder, eGFR

Published
2020
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27. Comparison of supine and prone miniaturized percutaneous nephrolithotomy in the treatment of lower pole, middle pole and renal pelvic stones: A matched pair analysis

Author

Akif Erbin, Harun Ozdemir, Murat Sahan, Metin Savun, Alkan Cubuk, Ozgur Yazici, Mehmet Fatih Akbulut, and Omer Sarilar

Subjects
Supine Position, Nephrolithotomy, Percutaneous, Pelvis, Diseases of the genitourinary system. Urology, RC870-923
Abstract

ABSTRACT Purpose We aimed to compare the outcomes of supine and prone miniaturized percutaneous nephrolithotomy (m-PNL) in the treatment of lower pole, middle pole and renal pelvic stones. Materials and Methods 54 patients who performed supine m-PNL between January 2017 and March 2018 and 498 patients who performed prone m-PNL between April 2015 and January 2018 were included in the study. Of the 498 patients, 108 matching 1: 2 in terms of age, gender, body mass index, American Association of Anesthesiology score, stone size, stone localization and hydronephrosis according to the supine m-PNL group were selected as prone m-PNL group. The patients with solitary kidney, upper pole stone, urinary system anomaly or skeletal malformation and pediatric patients (

Published
2019
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31. Impact of Prostate Needle Biopsy on Erectile Function

Author

Fatih Yanaral, Faruk Özgör, Metin Savun, Ali Ayrancı, Ufuk Çağlar, Alkan Çubuk, and Ömer Sarılar

Subjects
Biopsy, erectile dysfunction, prostate, prostate cancer, Medicine, Medicine (General), R5-920
Abstract

Aim:To evaluate the impact of transrectal ultrasonography-guided prostate needle biopsy (TRUS-Bx) on erectile function.Methods:Patients who underwent TRUS-Bx were prospectively examined. The indications for prostate biopsy were elevated prostatespecific antigen (PSA) level and/or abnormal digital rectal examination. All patients were evaluated with the 5-item version of the International Index of Erectile Function (IIEF-5) before TRUS-Bx and at one, three and six months after TRUS-Bx. Severity of erectile dysfunction (ED) was classified into five categories according to IIEF-5 scores.Results:Eighty patients were included in the study. The mean age of the patients was 64.7 years and the mean serum PSA level was 10.2 ng/mL. The mean IIEF-5 score was 16.5 prior to TRUS-Bx. Before TRUSBx, ED was reported in 61 patients and mild, mild to moderate, and moderate ED in 23 (28.8%), 21 (26.2%), and 17 (21.2%) patients, respectively. Six months after TRUS-Bx, ED was reported as mild, mild to moderate, moderate and severe in 23 (28.8%), 21 (26.3%), 16 (20%) and one (1.3%) patients, respectively. The differences between before and after prostate biopsy were statistically insignificant (p>0.05).Conclusion:TRUS-Bx does not have a permanent effect on erectile function. It seemed to be a trend toward increasing ED at 1 month and longer follow-up showed that these changes resolved back to baseline.

Published
2019
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33. Comparison of 4.8 Fr and 6 Fr ureteral stents on stent related symptoms following ureterorenoscopy: A prospective randomized controlled trial

Author

Alkan Cubuk, Fatih Yanaral, Faruk Ozgor, Metin Savun, Harun Ozdemir, Akif Erbin, Bahar Yuksel, and Omer Sarilar

Subjects
Medicine (General), R5-920
Abstract

The effects of ureteral stent diameters on ureteral stent-related symptoms were evaluated by using Turkish-validated Ureteral Stent Related Symptoms Questionnaire (USSQ). Datas on 126 patients underwent uncomplicated flexible ureterorenoscopy and 62 patients underwent uncomplicated semirigid ureteroscopy surgery without stent insertion (group 3) were collected. Patients were randomized preoperatively in a double-blind fashion to 4.8 French (group 1) and 6 French (group 2) ureteral JJ stents groups. The first follow-up visit was done at one week after surgery for all groups. Stents were removed on the third postoperative week for stented groups. The second follow-up visit was done at one week after stent removal for group 1 and group 2, and four week after surgery for group 3. Preoperative characteristics, operation time and hospitalization times were similar in both groups. Total USSQ scores were 91.9, 103.0, 44.2 at first visit and 54.3, 58.7, 28.5 at second visit in group 1, group 2, and group 3, respectively. At both first and second visits, the group 2 had significantly higher USSQ scores than the group 1 (p = 0.01 and p

Published
2018
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37. Non-invasive evaluation of obstruction after ureteroscopic stone removal: Role of renal resistive index assessment

Author

Bilal Eryildirim, Ahmet Şahan, Özlem Türkoğlu, Murat Tuncer, Övünç Kavukoğlu, Berkan Şimsek, Alkan Çubuk, and Kemal Sarica

Subjects
Ureteral obstruction, Resistive index, Renal Doppler ultrasonography, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Objectives: The aim of this study is to evaluate prediction of postoperative ureteral obstruction needing ureteral stent insertion by evaluating the resistive index (RI) values and the grade of hydronephrosis. Material and Methods: A total of 66 adult patients undergoing stentless endoscopic ureteral stone treatment (URS) between January 2018 and January 2019 were included in this prospective study. Preoperative patient and stone characteristics were noted. All patients were evaluated with renal Doppler ultrasonography study to assess degree of hydronephrosis and RI values. A renal Doppler ultrasonography was repeated at postoperative 1st, 3rd and 7th days. Changes in both RI and hydronephrosis levels before and after the procedures were noted. On the postoperative 7th day, patients were divided into two groups including obstructive and non-obstructive cases according to RI values assessed where a RI value of 0.7 was accepted as the cut-off for obstruction. The preoperative and perioperative characteristics of both groups were evaluated in a comparative manner. Results: The mean patient age was 43.6 ± 1.72 years. Significant improvements were noted in RI and grade of hydronephrosis after the operation. The grade of hydronephrosis and RI values were found to improve more significantly on postoperative 3rd day when compared to the postoperative 7th day (p < 0.01 and p < 0.01). A significant correlation was detected between the grade of hydronephrosis (>grade 2) and obstructive RI values (> 0.7) in each postoperative visits (p: 0.001). RI values (> 0.7) at postoperative seventh days were correlated with larger mean stone size, increased ureteral wall thickness, increased diameter of the ureter proximal to the stone, and longer duration of the operation. Preoperative high-grade hydronephrosis indicated obstructive RI values at postoperative seventh day (p = 0.001) Conclusion: Changes in RI values on Doppler sonography and the grade of hydronephrosis may be a guiding parameter in assessing postoperative ureteral obstruction.

Published
2020
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38. The impact of tumor invasion to muscularis mucosaevascular plexus on patient outcome in pT1 bladder urothelial carcinoma

Author

Ahmet Sahan, Fatma Gerin, Asgar Garayev, Emine Bozkurtlar, Alkan Çubuk, Orkunt Ozkaptan, Kasım Ertas, Yıloren Tanıdır, Haydar Kamil Cam, and Ilker Tınay

Subjects
T1 bladder cancer, Survival, Sub staging, Muscularis mucosae, Lamina propria depth, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Objectives: T1 bladder cancer has a wide range of tumor behavior and lamina propria invasion depth has a high potential risk of disease progression. To evaluate the patient outcome according to the tumor invasion to the muscularis mucosae-vascular plexus (MM-VP) in pT1 bladder urothelial carcinoma (BUC). Materials and methods: This study is a retrospective analysis of patients consecutively recorded from 2007 to 2013. A total of 93 patients with a history of primary pT1 BUC and complete follow-up were included. We used a pathological substaging system according to the tumor invasion regarding the MM-VP: pT1a (invasion above MM-VP) and pT1b (MM-VP invasion). We evaluated recurrence-free survival (RFS), progression- free survival (PFS), disease-specific-survival (DSS) based on this sub-staging system. Results: Pathological evaluation regarding the MM-VP invasion revealed 53 patients (57%) as pT1a BUC and 40 patients (43%) as pT1b BUC. The mean follow-up was 78.8 months. During the follow-up period; 60 patients (64.5%) had tumor recurrences, 32 patients (34.4%) had progression to invasive disease, 18 patients (19.4 %) died during follow-up related to the BUC. In 29 (54.7%) of pT1a and in 31(77.5%) of pT1b tumors, the recurrent disease was recorded during the followup period (p = 0.023). DSS rates at 5 years for pT1a and pT1b were 80.2% and 60.8%, respectively. PFS, RFS, and DSS rates were similar for pT1a/pT1b and did not reach statistical significance (p > 0.05). Conclusions: Sub-staging of pT1 BUC according to the MM-VP invasion showed a limited impact on the outcome in our patient cohort. However, the presence of pT1b disease caused a significantly higher rate of recurrence.

Published
2020
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44. Pacific symposium on biocomputing 2011

Author

Bebek, G., Chance, M., Koyuturk, M., Price, N. D., La Vega, F. M., Bustamante, C. D., Leal, S. M., James Foster, Moore, J., Bernauer, J., Flores, S., Huang, X., Shin, S., Zhou, R., Alkan, C., Capriotti, E., Hormozdiari, F., Eskin, E., Kann, M. G., Alterovitz, G., Cavalcanti, S., Wang, M., and Ramoni, M. F.

46. Synthesis, characterization and antibacterial activity of imidazole derivatives of 1,10-phenanthroline and their Cu(II), Co(II) and Ni(II) complexes

Author

Gomleksiz, M., Alkan, C., Belgin Erdem, and Kırşehir Ahi Evran Üniversitesi, Fen-Edebiyat Fakültesi, Kimya Bölümü

Subjects
antibacterial activity, 1-10-Phenanthroline, Complex, Antibacterial activity, 1,10-Phenanthroline, imidazole, complex, antibacterial activity, 1,10-Phenanthroline, Imidazole, complex, imidazole
Abstract

WOS: 000318758500013 Six new CuL1 (L-1 = 4-bromo-2-(1H-imidazo[4,5-f][1,10]phenanthroline-2-yl)phenol), CoL1, NiL1, CuL2 (L-2 = 2-(1H-imidazo[4,5-f] [1,10]phenanthroline-2-yl)-5-methoxyphenol), CoL2 and NiL2 complexes were synthesized. L-1 and L-2 ligands were prepared by the condensation of 1,10-phenanthroline-5,6-dione with 5-bromosalicylaldehyde and 2-hydroxy-4-methoxybenzaldehyde, respectively. The structures of the compounds were determined by elemental analyses, IR, UV-visible, H-1-NMR, TGA, magnetic susceptibilities and molar conductance measurements. It is observed that the synthesized complexes have tetragonal and distorted square pyramidal geometrical structures. Antibacterial activity of the ligands and their metal complexes were tested against selected bacteria by disc diffusion method. Firat University Research FoundationFirat University We are grateful to Firat University Research Foundation for the support of this research.

47. Accelerating read mapping with FastHASH

Author

Xin Hongyi, Lee Donghyuk, Hormozdiari Farhad, Yedkar Samihan, Mutlu Onur, and Alkan Can

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS. We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection. We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness.

Published
2013
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48. Genomics technologies to study structural variations in the grapevine genome

Author

Cardone Maria Francesca, Bergamini Carlo, D'Addabbo Pietro, Alkan Can, Catacchio Claudia Rita, Anaclerio Fabio, Chiatante Giorgia, Marra Annamaria, Giannuzzi Giuliana, Perniola Rocco, Ventura Mario, and Antonacci Donato

Subjects
Microbiology, QR1-502, Physiology, QP1-981, Zoology, QL1-991
Abstract

Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs) on plant genomes, few data are available on copy number variation (CNV). Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV) for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

Published
2016
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