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142 results on '"Alkan C"'

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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2. Virus isolation, genetic characterization and seroprevalence of Toscana virus in Algeria

Author: Alkan, C., Allal-Ikhlef, A.B., Alwassouf, S., Baklouti, A., Piorkowski, G., de Lamballerie, X., Izri, A., and Charrel, R.N.
Published: 2015
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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

4. New Insights into Centromere Organization and Evolution from the White-Cheeked Gibbon and Marmoset

Author: Cellamare, A, Catacchio, CR, Alkan, C, Giannuzzi, G, Antonacci, F, Cardone, MF, Della Valle, G, Malig, M, Rocchi, M, Eichler, EE, and Ventura, M
Published: 2009

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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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12. 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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13. Manipulating Multiple Sequence Alignments via MaM and WebMaM

Author: Alkan, C., Tuzun, E., Buard, J., Lethiec, F., Eichler, E.E., Bailey, J.A., and Sahinalp, S.C.
Published: 2005

14. 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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15. Phlebotomine sand flies on the crossroads of Anatolia: transmitted diseases and vectors

Author: Kasap Erisoz, O, primary, Belen, A, additional, Alkan, C, additional, Gunay, F, additional, Dvorak, V, additional, Ergunay, K, additional, Aydın, S, additional, Votypka, J, additional, Banuls, A-L, additional, Charrel, R, additional, Özkul, A, additional, Özbel, Y, additional, Volf, P, additional, and Alten, B, additional
Published: 2014
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16. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. Synthesis, characterization and antibacterial activity of 2-p-tolyl-1H-imidazo[4,5-f][1,10] phenanthroline and its Co(II), Ni(II) and Cu(II) complexes

Author: Gomleksiz, M., additional, Alkan, C., additional, and Erdem, B., additional
Published: 2013
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23. Sensitive and fast mapping of di-base encoded reads

Author: Hormozdiari, F., primary, Hach, F., additional, Sahinalp, S. C., additional, Eichler, E. E., additional, and Alkan, C., additional
Published: 2011
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24. Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X

Author: Nguyen, D. K., primary, Yang, F., additional, Kaul, R., additional, Alkan, C., additional, Antonellis, A., additional, Friery, K. F., additional, Zhu, B., additional, de Jong, P. J., additional, and Disteche, C. M., additional
Published: 2011
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25. 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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26. 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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27. taveRNA: a web suite for RNA algorithms and applications

Author: Aksay, C., primary, Salari, R., additional, Karakoc, E., additional, Alkan, C., additional, and Sahinalp, S. C., additional
Published: 2007
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28. Manipulating multiple sequence alignments via MaM and WebMaM

Author: Alkan, C., primary, Tuzun, E., additional, Buard, J., additional, Lethiec, F., additional, Eichler, E. E., additional, Bailey, J. A., additional, and Sahinalp, S. C., additional
Published: 2005
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29. 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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30. 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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31. 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.

32. 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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33. 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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34. Genetic history of an archaic hominin group from Denisova Cave in Siberia

Author: Heng Li, Michael P. Richards, Adrian W. Briggs, Richard E. Green, Michael V. Shunkov, Bence Viola, Eric Durand, Can Alkan, Mark Stoneking, A.P. Derevianko, Svante Pääbo, Jeffrey M. Good, Udo Stenzel, Montgomery Slatkin, Jean-Jacques Hublin, Tomislav Maricic, Janet Kelso, Tomas Marques-Bonet, Johannes Krause, Nick Patterson, Sahra Talamo, Swapan Mallick, Martin Kircher, Philip L. F. Johnson, Qiaomei Fu, Evan E. Eichler, Matthias Meyer, David Reich, Reich D., Green R.E., Kircher M., Krause J., Patterson N., Durand E.Y., Viola B., Briggs A.W., Stenzel U., Johnson P.L.F., Maricic T., Good J.M., Marques-Bonet T., Alkan C., Fu Q., Mallick S., Li H., Meyer M., Eichler E.E., Stoneking M., Richards M., Talamo S., Shunkov M.V., Derevianko A.P., Hublin J.-J., Kelso J., Slatkin M., and Paabo S.
Subjects: Gene Flow, Asia, Neanderthal, Homínids, Molecular Sequence Data, education, Population, Zoology, Archaic humans, Neanderthal genome project, DNA, Mitochondrial, Article, Finger Phalanges, biology.animal, ADN mitocondrial -- Genètica, Animals, Humans, Denisovan, Phylogeny, education.field_of_study, Genome, Multidisciplinary, biology, Animal, Fossils, Recent African origin of modern humans, Finger Phalange, Fossil, Hominidae, biology.organism_classification, Europe, Siberia, Homo sapiens, Anatomically modern human, Melanesia, Tooth, Human
Abstract: 8 páginas, 4 figuras, 1 tabla.-- Artículo Open Access.-- et al., Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans., The Presidential Innovation Fund of the Max Planck Society and the Krekeler Foundation provided financial support. M.S. was supported by a US National Institutes of Health grant (R01-GM40282). The National Science Foundation provided an International Postdoctoral Fellowship (OISE-0754461) to J.M.G., a Fellowship in Biological Informatics to P.L.F.J. and a HOMINID grant (1032255) to D.R.
Published: 2010

35. New Insights into Centromere Organization and Evolution from the White-Cheeked Gibbon and Marmoset

Author: G. Della Valle, Claudia Rita Catacchio, Can Alkan, Francesca Antonacci, Maria Francesca Cardone, Mario Ventura, Maika Malig, Mariano Rocchi, Giuliana Giannuzzi, Angelo Cellamare, Evan E. Eichler, Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, and Ventura M.
Subjects: Primates, Centromere, Sequence assembly, ALPHA-SATELLITE DNA, Genome, GIBBON AND MARMOSET GENOME, Cell Line, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, Hylobates, biology.animal, Genetics, Animals, Humans, Molecular Biology, CENTROMERE EVOLUTION, Ecology, Evolution, Behavior and Systematics, Research Articles, CENTROMERIC SEQUENCES, 030304 developmental biology, New World monkey, 0303 health sciences, biology, 030302 biochemistry & molecular biology, Marmoset, Callithrix, biology.organism_classification, Biological Evolution, body regions, chemistry, DNA
Abstract: The evolutionary history of alpha-satellite DNA, the major component of primate centromeres, is hardly defined because of the difficulty in its sequence assembly and its rapid evolution when compared with most genomic sequences. By using several approaches, we have cloned, sequenced, and characterized alpha-satellite sequences from two species representing critical nodes in the primate phylogeny: the white-cheeked gibbon, a lesser ape, and marmoset, a New World monkey. Sequence analyses demonstrate that white-cheeked gibbon and marmoset alpha-satellite sequences are formed by units of approximately 171 and approximately 342 bp, respectively, and they both lack the high-order structure found in humans and great apes. Fluorescent in situ hybridization characterization shows a broad dispersal of alpha-satellite in the white-cheeked gibbon genome including centromeric, telomeric, and chromosomal interstitial localizations. On the other hand, centromeres in marmoset appear organized in highly divergent dimers roughly of 342 bp that show a similarity between monomers much lower than previously reported dimers, thus representing an ancient dimeric structure. All these data shed light on the evolution of the centromeric sequences in Primates. Our results suggest radical differences in the structure, organization, and evolution of alpha-satellite DNA among different primate species, supporting the notion that 1) all the centromeric sequence in Primates evolved by genomic amplification, unequal crossover, and sequence homogenization using a 171 bp monomer as the basic seeding unit and 2) centromeric function is linked to relatively short repeated elements, more than higher-order structure. Moreover, our data indicate that complex higher-order repeat structures are a peculiarity of the hominid lineage, showing the more complex organization in humans.
Published: 2009

36. AutoSamp: Autoencoding k-space Sampling via Variational Information Maximization for 3D MRI.

Author: Alkan C, Mardani M, Liao C, Li Z, Vasanawala SS, and Pauly JM
Abstract: Accelerated MRI protocols routinely involve a predefined sampling pattern that undersamples the k-space. Finding an optimal pattern can enhance the reconstruction quality, however this optimization is a challenging task. To address this challenge, we introduce a novel deep learning framework, AutoSamp, based on variational information maximization that enables joint optimization of sampling pattern and reconstruction of MRI scans. We represent the encoder as a non-uniform Fast Fourier Transform that allows continuous optimization of k-space sample locations on a non-Cartesian plane, and the decoder as a deep reconstruction network. Experiments on public 3D acquired MRI datasets show improved reconstruction quality of the proposed AutoSamp method over the prevailing variable density and variable density Poisson disc sampling for both compressed sensing and deep learning reconstructions. We demonstrate that our data-driven sampling optimization method achieves 4.4dB, 2.0dB, 0.75dB, 0.7dB PSNR improvements over reconstruction with Poisson Disc masks for acceleration factors of R = 5, 10, 15, 25, respectively. Prospectively accelerated acquisitions with 3D FSE sequences using our optimized sampling patterns exhibit improved image quality and sharpness. Furthermore, we analyze the characteristics of the learned sampling patterns with respect to changes in acceleration factor, measurement noise, underlying anatomy, and coil sensitivities. We show that all these factors contribute to the optimization result by affecting the sampling density, k-space coverage and point spread functions of the learned sampling patterns.
Published: 2024
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37. Distinct Pathological Changes in Preweaning Mice Infected with Live-Attenuated Rift Valley Fever Virus Strains.

Author: Alkan C, Jurado-Cobena E, and Ikegami T
Subjects: Animals, Mice, Virulence, Female, Rift Valley fever virus pathogenicity, Rift Valley fever virus immunology, Rift Valley fever virus genetics, Rift Valley Fever virology, Rift Valley Fever pathology, Rift Valley Fever prevention & control, Rift Valley Fever immunology, Vaccines, Attenuated immunology, Vaccines, Attenuated administration & dosage, Viral Vaccines immunology, Viral Vaccines administration & dosage, Mice, Inbred C57BL, Disease Models, Animal
Abstract: Rift Valley fever (RVF) is a mosquito-borne zoonotic viral disease endemic to Africa and the Middle East. Live-attenuated RVF vaccines have been studied for both veterinary and human use due to their strong immunogenicity and cost-effective manufacturing. The live-attenuated MP-12 vaccine has been conditionally approved for veterinary use in the U.S.A., and next-generation live-attenuated RVF vaccine candidates are being actively researched. Assessing the virulence phenotype of vaccine seeds or lots is crucial for managing vaccine safety. Previously, preweaning 19-day-old outbred CD1 mice have been used to evaluate the MP-12 strain. This study aimed to characterize the relative virulence of three live-attenuated RVF vaccine strains in 19-day-old inbred C57BL/6 mice: the recombinant MP-12 (rMP-12), the RVax-1, and the ∆NSs-∆NSm-rZH501 strains. Although this mouse model did not show dose-dependent pathogenesis, mice that succumbed to the infection exhibited distinct brain pathology. Mice infected with ∆NSs-∆NSm-rZH501 showed an infiltration of inflammatory cells associated with infected neurons, and focal lesions formed around virus-infected cells. In contrast, mice infected with rMP-12 or RVax-1 showed a minimal association of inflammatory cells in the brain, yet the virus spread diffusely. The preweaning model is likely useful for evaluating host responses to attenuated RVFV strains, although further refinement may be necessary to quantitate the virulence among different RVFV strains or vaccine lots.
Published: 2024
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38. Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses.

Author: Alkan C, Brésard G, Frézal L, Richaud A, Ruaud A, Zhang G, and Félix MA
Subjects: Animals, RNA Viruses genetics, Host Specificity, RNA Virus Infections virology, Caenorhabditis genetics, Caenorhabditis virology
Abstract: Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Alkan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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39. Modeling Heartland virus disease in mice and therapeutic intervention with 4'-fluorouridine.

Author: Westover JB, Jung KH, Alkan C, Boardman KM, Van Wettere AJ, Martens C, Rojas I, Hicks P, Thomas AJ, Saindane MT, Bluemling GR, Mao S, Kolykhalov AA, Natchus MG, Bates P, Painter GR, Ikegami T, and Gowen BB
Subjects: Animals, Humans, Mice, Ticks, United States, Bunyaviridae, Bunyaviridae Infections drug therapy, Uracil Nucleotides therapeutic use
Abstract: Heartland virus (HRTV) is an emerging tick-borne bandavirus that causes a febrile illness of varying severity in humans, with cases reported in eastern and midwestern regions of the United States. No vaccines or approved therapies are available to prevent or treat HRTV disease. Here, we describe the genetic changes, natural history of disease, and pathogenesis of a mouse-adapted HRTV (MA-HRTV) that is uniformly lethal in 7- to 8-week-old AG129 mice at low challenge doses. We used this model to assess the efficacy of the ribonucleoside analog, 4'-fluorouridine (EIDD-2749), and showed that once-daily oral treatment with 3 mg/kg of drug, initiated after the onset of disease, protects mice against lethal MA-HRTV challenge and reduces viral loads in blood and tissues. Our findings provide insights into HRTV virulence and pathogenesis and support further development of EIDD-2749 as a therapeutic intervention for HRTV disease., Importance: More than 60 cases of HRTV disease spanning 14 states have been reported to the United States Centers for Disease Control and Prevention. The expanding range of the Lone Star tick that transmits HRTV, the growing population of at-risk persons living in geographic areas where the tick is abundant, and the lack of antiviral treatments or vaccines raise significant public health concerns. Here, we report the development of a new small-animal model of lethal HRTV disease to gain insight into HRTV pathogenesis and the application of this model for the preclinical development of a promising new antiviral drug candidate, EIDD-2749. Our findings shed light on how the virus causes disease and support the continued development of EIDD-2749 as a therapeutic for severe cases of HRTV infection., Competing Interests: G.R.B. and G.R.P. are coinventors on patent WO 2019/1736002 covering the composition of matter and use of EIDD-2749 and its analogs as an antiviral treatment. All other authors declare that they have no competing interests.
Published: 2024
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40. Computer-Selected Antiviral Compounds: Assessing In Vitro Efficacies against Rift Valley Fever Virus.

Author: Alkan C, O'Brien T, Kenyon V, and Ikegami T
Subjects: Chlorocebus aethiops, Humans, Animals, Artificial Intelligence, Vero Cells, Computers, RNA, Viral, Antiviral Agents pharmacology, Rift Valley fever virus, Phlebovirus
Abstract: Rift Valley fever is a zoonotic viral disease transmitted by mosquitoes, impacting both humans and livestock. Currently, there are no approved vaccines or antiviral treatments for humans. This study aimed to evaluate the in vitro efficacy of chemical compounds targeting the Gc fusion mechanism. These compounds were identified through virtual screening of millions of commercially available small molecules using a structure-based artificial intelligence bioactivity predictor. In our experiments, a pretreatment with small molecule compounds revealed that 3 out of 94 selected compounds effectively inhibited the replication of the Rift Valley fever virus MP-12 strain in Vero cells. As anticipated, these compounds did not impede viral RNA replication when administered three hours after infection. However, significant inhibition of viral RNA replication occurred upon viral entry when cells were pretreated with these small molecules. Furthermore, these compounds exhibited significant inhibition against Arumowot virus, another phlebovirus, while showing no antiviral effects on tick-borne bandaviruses. Our study validates AI-based virtual high throughput screening as a rational approach for identifying effective antiviral candidates for Rift Valley fever virus and other bunyaviruses.
Published: 2024
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41. ECOLE: Learning to call copy number variants on whole exome sequencing data.

Author: Mandiracioglu B, Ozden F, Kaynar G, Yilmaz MA, Alkan C, and Cicek AE
Subjects: Humans, Exome Sequencing, Algorithms, Exons, High-Throughput Nucleotide Sequencing methods, DNA Copy Number Variations, Exome genetics
Abstract: Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES) data has been a long sought-after goal for use in clinics. This was not possible despite recent improvements in performance because algorithms mostly suffer from low precision and even lower recall on expert-curated gold standard call sets. Here, we present a deep learning-based somatic and germline CNV caller for WES data, named ECOLE. Based on a variant of the transformer architecture, the model learns to call CNVs per exon, using high-confidence calls made on matched WGS samples. We further train and fine-tune the model with a small set of expert calls via transfer learning. We show that ECOLE achieves high performance on human expert labelled data for the first time with 68.7% precision and 49.6% recall. This corresponds to precision and recall improvements of 18.7% and 30.8% over the next best-performing methods, respectively. We also show that the same fine-tuning strategy using tumor samples enables ECOLE to detect RT-qPCR-validated variations in bladder cancer samples without the need for a control sample. ECOLE is available at https://github.com/ciceklab/ECOLE ., (© 2024. The Author(s).)
Published: 2024
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42. Advancements in Rift Valley fever vaccines: a historical overview and prospects for next generation candidates.

Author: Alkan C, Jurado-Cobena E, and Ikegami T
Abstract: Rift Valley fever (RVF) is a zoonotic viral disease transmitted by mosquitoes and causes abortion storms, fetal malformations, and newborn animal deaths in livestock ruminants. In humans, RVF can manifest as hemorrhagic fever, encephalitis, or retinitis. Outbreaks of RVF have been occurring in Africa since the early 20th century and continue to pose a threat to both humans and animals in various regions such as Africa, Madagascar, the Comoros, Saudi Arabia, and Yemen. The development of RVF vaccines is crucial in preventing mortality and morbidity and reducing the spread of the virus. While several veterinary vaccines have been licensed in endemic countries, there are currently no licensed RVF vaccines for human use. This review provides an overview of the existing RVF vaccines, as well as potential candidates for future studies on RVF vaccine development, including next-generation vaccines that show promise in combating the disease in both humans and animals., (© 2023. The Author(s).)
Published: 2023
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43. Identification of protein-protein interaction bridges for multiple sclerosis.

Author: Yazıcı G, Kurt Vatandaslar B, Aydin Canturk I, Aydinli FI, Arici Duz O, Karakoc E, Kerman BE, and Alkan C
Subjects: Humans, Leukocytes, Mononuclear, Oligodendroglia physiology, Neurons, Myelin Sheath, Multiple Sclerosis
Abstract: Motivation: Identifying and prioritizing disease-related proteins is an important scientific problem to develop proper treatments. Network science has become an important discipline to prioritize such proteins. Multiple sclerosis, an autoimmune disease for which there is still no cure, is characterized by a damaging process called demyelination. Demyelination is the destruction of myelin, a structure facilitating fast transmission of neuron impulses, and oligodendrocytes, the cells producing myelin, by immune cells. Identifying the proteins that have special features on the network formed by the proteins of oligodendrocyte and immune cells can reveal useful information about the disease., Results: We investigated the most significant protein pairs that we define as bridges among the proteins providing the interaction between the two cells in demyelination, in the networks formed by the oligodendrocyte and each type of two immune cells (i.e. macrophage and T-cell) using network analysis techniques and integer programming. The reason, we investigated these specialized hubs was that a problem related to these proteins might impose a bigger damage in the system. We showed that 61%-100% of the proteins our model detected, depending on parameterization, have already been associated with multiple sclerosis. We further observed the mRNA expression levels of several proteins we prioritized significantly decreased in human peripheral blood mononuclear cells of multiple sclerosis patients. We therefore present a model, BriFin, which can be used for analyzing processes where interactions of two cell types play an important role., Availability and Implementation: BriFin is available at https://github.com/BilkentCompGen/brifin., (© The Author(s) 2023. Published by Oxford University Press.)
Published: 2023
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44. Deep Learning-Based Reconstruction for Cardiac MRI: A Review.

Author: Oscanoa JA, Middione MJ, Alkan C, Yurt M, Loecher M, Vasanawala SS, and Ennis DB
Abstract: Cardiac magnetic resonance (CMR) is an essential clinical tool for the assessment of cardiovascular disease. Deep learning (DL) has recently revolutionized the field through image reconstruction techniques that allow unprecedented data undersampling rates. These fast acquisitions have the potential to considerably impact the diagnosis and treatment of cardiovascular disease. Herein, we provide a comprehensive review of DL-based reconstruction methods for CMR. We place special emphasis on state-of-the-art unrolled networks, which are heavily based on a conventional image reconstruction framework. We review the main DL-based methods and connect them to the relevant conventional reconstruction theory. Next, we review several methods developed to tackle specific challenges that arise from the characteristics of CMR data. Then, we focus on DL-based methods developed for specific CMR applications, including flow imaging, late gadolinium enhancement, and quantitative tissue characterization. Finally, we discuss the pitfalls and future outlook of DL-based reconstructions in CMR, focusing on the robustness, interpretability, clinical deployment, and potential for new methods.
Published: 2023
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45. BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.

Author: Firtina C, Park J, Alser M, Kim JS, Cali DS, Shahroodi T, Ghiasi NM, Singh G, Kanellopoulos K, Alkan C, and Mutlu O
Abstract: Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND , the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the same hash value for similar sets, and (ii) provides the proper mechanisms for using seeds as sets with the SimHash technique to find fuzzy seed matches efficiently. We show the benefits of BLEND when used in read overlapping and read mapping. For read overlapping, BLEND is faster by 2.4×-83.9× (on average 19.3×), has a lower memory footprint by 0.9×-14.1× (on average 3.8×), and finds higher quality overlaps leading to accurate de novo assemblies than the state-of-the-art tool, minimap2. For read mapping, BLEND is faster by 0.8×-4.1× (on average 1.7×) than minimap2. Source code is available at https://github.com/CMU-SAFARI/BLEND., (© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
Published: 2023
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46. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.

Author: Söylev A, Çokoglu SS, Koptekin D, Alkan C, and Somel M
Subjects: Humans, Genotype, Genome, Human genetics, Genetics, Population, Polymorphism, Single Nucleotide genetics, DNA Copy Number Variations genetics, Genomics methods
Abstract: To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Söylev et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2022
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47. FastRemap: a tool for quickly remapping reads between genome assemblies.

Author: Kim JS, Firtina C, Cavlak MB, Senol Cali D, Alkan C, and Mutlu O
Subjects: Sequence Analysis, DNA methods, Genomics methods, Genome, High-Throughput Nucleotide Sequencing methods, Software
Abstract: Motivation: A genome read dataset can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly used CrossMap tool. With the explosion of available genomic datasets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis., Results: We provide FastRemap, a fast and efficient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.82× speedup (6.47×, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap., Availability and Implementation: FastRemap is written in C++. Source code and user manual are freely available at: github.com/CMU-SAFARI/FastRemap. Docker image available at: https://hub.docker.com/r/alkanlab/fastremap. Also available in Bioconda at: https://anaconda.org/bioconda/fastremap-bio., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Published: 2022
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48. Evaluations of rationally designed rift valley fever vaccine candidate RVax-1 in mosquito and rodent models.

Author: Ikegami T, Jurado-Cobena E, Alkan C, Smith JK, Zhang L, Kalveram B, Juelich TL, Esterly AT, Bhaskar JR, Thangamani S, and Freiberg AN
Abstract: Rift Valley fever (RVF) is a mosquito-borne zoonosis endemic to Africa and the Arabian Peninsula, which causes large outbreaks among humans and ruminants. Single dose vaccinations using live-attenuated RVF virus (RVFV) support effective prevention of viral spread in endemic countries. Due to the segmented nature of RVFV genomic RNA, segments of vaccine strain-derived genomic RNA could be incorporated into wild-type RVFV within co-infected mosquitoes or animals. Rationally designed vaccine candidate RVax-1 displays protective epitopes fully identical to the previously characterized MP-12 vaccine. Additionally, all genome segments of RVax-1 contribute to the attenuation phenotype, which prevents the formation of pathogenic reassortant strains. This study demonstrated that RVax-1 cannot replicate efficiently in orally fed Aedes aegypti mosquitoes, while retaining strong immunogenicity and protective efficacy in an inbred mouse model, which were indistinguishable from the MP-12 vaccine. These findings support further development of RVax-1 as the next generation MP-12-based vaccine for prevention of Rift Valley fever in humans and animals., (© 2022. The Author(s).)
Published: 2022
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49. Author Correction: Comparative and demographic analysis of orang-utan genomes.

Author: Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, RoyChoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, and Wilson RK
Published: 2022
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50. Polishing copy number variant calls on exome sequencing data via deep learning.

Author: Özden F, Alkan C, and Çiçek AE
Subjects: Algorithms, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing methods, Reproducibility of Results, Exome Sequencing, Deep Learning, Exome
Abstract: Accurate and efficient detection of copy number variants (CNVs) is of critical importance owing to their significant association with complex genetic diseases. Although algorithms that use whole-genome sequencing (WGS) data provide stable results with mostly valid statistical assumptions, copy number detection on whole-exome sequencing (WES) data shows comparatively lower accuracy. This is unfortunate as WES data are cost-efficient, compact, and relatively ubiquitous. The bottleneck is primarily due to the noncontiguous nature of the targeted capture: biases in targeted genomic hybridization, GC content, targeting probes, and sample batching during sequencing. Here, we present a novel deep learning model, DECoNT , which uses the matched WES and WGS data, and learns to correct the copy number variations reported by any off-the-shelf WES-based germline CNV caller. We train DECoNT on the 1000 Genomes Project data, and we show that we can efficiently triple the duplication call precision and double the deletion call precision of the state-of-the-art algorithms. We also show that our model consistently improves the performance independent of (1) sequencing technology, (2) exome capture kit, and (3) CNV caller. Using DECoNT as a universal exome CNV call polisher has the potential to improve the reliability of germline CNV detection on WES data sets., (© 2022 Özden et al.; Published by Cold Spring Harbor Laboratory Press.)
Published: 2022
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