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The Contribution of Fluorine .

Molecular imaging and radionuclide therapy

Budak E, Çok G, Akgün A.
PMID: 29889029
Mol Imaging Radionucl Ther. 2018 Jun 07;27(2):73-80. doi: 10.4274/mirt.53315.

OBJECTIVE: Lung cancer is the most common cause of cancer-related death throughout the world, and the correct choice of treatment based on early diagnosis and staging increases the chance of survival. The present study aims to investigate the contribution...

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Budak E, Çok G, Akgün A. Flor 18F-FDG PET/BT’nin Akciğer Kanseri Tanı, Evreleme ve Tedavi Planlamasına Katkısı. The Contribution of Fluorine . Mol Imaging Radionucl Ther. 2018;27(2):73-80doi: 10.4274/mirt.53315.
Budak, E., Çok, G., & Akgün, A. (2018). Flor 18F-FDG PET/BT’nin Akciğer Kanseri Tanı, Evreleme ve Tedavi Planlamasına Katkısı. The Contribution of Fluorine . Molecular imaging and radionuclide therapy, 27(2), 73-80. https://doi.org/10.4274/mirt.53315
Budak, Emine, et al. "Flor 18F-FDG PET/BT’nin Akciğer Kanseri Tanı, Evreleme ve Tedavi Planlamasına Katkısı." The Contribution of Fluorine . Molecular imaging and radionuclide therapy vol. 27,2 (2018): 73-80. doi: https://doi.org/10.4274/mirt.53315
Budak E, Çok G, Akgün A. Flor 18F-FDG PET/BT’nin Akciğer Kanseri Tanı, Evreleme ve Tedavi Planlamasına Katkısı. The Contribution of Fluorine . Mol Imaging Radionucl Ther. 2018 Jun 07;27(2):73-80. doi: 10.4274/mirt.53315. PMID: 29889029; PMCID: PMC5996604.
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First Report of Charcoal Rot Caused by Macrophomina phaseolina in Sunflower in Turkey.

Plant disease

Mahmoud A, Budak H.
PMID: 30743418
Plant Dis. 2011 Feb;95(2):223. doi: 10.1094/PDIS-09-10-0631.

Charcoal rot symptoms were observed on 2-month-old oilseed sunflower plants (Helianthus annuus L.) in the Eskişehir Province of Turkey in June 2009. The disease was observed in 70% of the fields surveyed and incidence ranged from 10 to 50%....

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Mahmoud A, Budak H. First Report of Charcoal Rot Caused by Macrophomina phaseolina in Sunflower in Turkey. Plant Dis. 2011;95(2):223doi: 10.1094/PDIS-09-10-0631.
Mahmoud, A., & Budak, H. (2011). First Report of Charcoal Rot Caused by Macrophomina phaseolina in Sunflower in Turkey. Plant disease, 95(2), 223. https://doi.org/10.1094/PDIS-09-10-0631
Mahmoud, A, and Budak, H. "First Report of Charcoal Rot Caused by Macrophomina phaseolina in Sunflower in Turkey." Plant disease vol. 95,2 (2011): 223. doi: https://doi.org/10.1094/PDIS-09-10-0631
Mahmoud A, Budak H. First Report of Charcoal Rot Caused by Macrophomina phaseolina in Sunflower in Turkey. Plant Dis. 2011 Feb;95(2):223. doi: 10.1094/PDIS-09-10-0631. PMID: 30743418.
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Exserohilum monoceras, Newly Reported on Late Watergrass in Turkey.

Plant disease

Erper I, Mennan H, Budak U, Kaya Altop E.
PMID: 30743365
Plant Dis. 2011 Apr;95(4):497. doi: 10.1094/PDIS-12-10-0867.

Echinochloa species are major weeds in rice-cropping systems and are among the most noxious weeds in the world. Throughout the world, Echinochloa oryzicola Vasing, (late watergrass) is one of the most important and serious weed species of this genus....

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Erper I, Mennan H, Budak U, et al. Exserohilum monoceras, Newly Reported on Late Watergrass in Turkey. Plant Dis. 2011;95(4):497doi: 10.1094/PDIS-12-10-0867.
Erper, I., Mennan, H., Budak, U., & Kaya Altop, E. (2011). Exserohilum monoceras, Newly Reported on Late Watergrass in Turkey. Plant disease, 95(4), 497. https://doi.org/10.1094/PDIS-12-10-0867
Erper, I, et al. "Exserohilum monoceras, Newly Reported on Late Watergrass in Turkey." Plant disease vol. 95,4 (2011): 497. doi: https://doi.org/10.1094/PDIS-12-10-0867
Erper I, Mennan H, Budak U, Kaya Altop E. Exserohilum monoceras, Newly Reported on Late Watergrass in Turkey. Plant Dis. 2011 Apr;95(4):497. doi: 10.1094/PDIS-12-10-0867. PMID: 30743365.
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Transfer learning based histopathologic image classification for breast cancer detection.

Health information science and systems

Deniz E, Şengür A, Kadiroğlu Z, Guo Y, Bajaj V, Budak Ü.
PMID: 30279988
Health Inf Sci Syst. 2018 Sep 28;6(1):18. doi: 10.1007/s13755-018-0057-x. eCollection 2018 Dec.

Breast cancer is one of the leading cancer type among women in worldwide. Many breast cancer patients die every year due to the late diagnosis and treatment. Thus, in recent years, early breast cancer detection systems based on patient's...

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Deniz E, Şengür A, Kadiroğlu Z, et al. Transfer learning based histopathologic image classification for breast cancer detection. Health Inf Sci Syst. 2018;6(1):18doi: 10.1007/s13755-018-0057-x.
Deniz, E., Şengür, A., Kadiroğlu, Z., Guo, Y., Bajaj, V., & Budak, �. �. (2018). Transfer learning based histopathologic image classification for breast cancer detection. Health information science and systems, 6(1), 18. https://doi.org/10.1007/s13755-018-0057-x
Deniz, Erkan, et al. "Transfer learning based histopathologic image classification for breast cancer detection." Health information science and systems vol. 6,1 (2018): 18. doi: https://doi.org/10.1007/s13755-018-0057-x
Deniz E, Şengür A, Kadiroğlu Z, Guo Y, Bajaj V, Budak Ü. Transfer learning based histopathologic image classification for breast cancer detection. Health Inf Sci Syst. 2018 Sep 28;6(1):18. doi: 10.1007/s13755-018-0057-x. eCollection 2018 Dec. PMID: 30279988; PMCID: PMC6162199.
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Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells.

Frontiers in genetics

Bodak M, Yu J, Ciaudo C.
PMID: 30619491
Front Genet. 2018 Dec 20;9:683. doi: 10.3389/fgene.2018.00683. eCollection 2018.

No abstract available.

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Bodak M, Yu J, Ciaudo C. Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells. Front Genet. 2018;9:683doi: 10.3389/fgene.2018.00683.
Bodak, M., Yu, J., & Ciaudo, C. (2018). Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells. Frontiers in genetics, 9683. https://doi.org/10.3389/fgene.2018.00683
Bodak, Maxime, et al. "Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells." Frontiers in genetics vol. 9 (2018): 683. doi: https://doi.org/10.3389/fgene.2018.00683
Bodak M, Yu J, Ciaudo C. Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells. Front Genet. 2018 Dec 20;9:683. doi: 10.3389/fgene.2018.00683. eCollection 2018. PMID: 30619491; PMCID: PMC6306448.
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Plant Small Non-coding RNAs and Their Roles in Biotic Stresses.

Frontiers in plant science

Brant EJ, Budak H.
PMID: 30079074
Front Plant Sci. 2018 Jul 20;9:1038. doi: 10.3389/fpls.2018.01038. eCollection 2018.

Non-coding RNAs (ncRNAs) have emerged as critical components of gene regulatory networks across a plethora of plant species. In particular, the 20-30 nucleotide small ncRNAs (sRNAs) play important roles in mediating both developmental processes and responses to biotic stresses....

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Brant EJ, Budak H. Plant Small Non-coding RNAs and Their Roles in Biotic Stresses. Front Plant Sci. 2018;9:1038doi: 10.3389/fpls.2018.01038.
Brant, E. J., & Budak, H. (2018). Plant Small Non-coding RNAs and Their Roles in Biotic Stresses. Frontiers in plant science, 91038. https://doi.org/10.3389/fpls.2018.01038
Brant, Eleanor J, and Budak, Hikmet. "Plant Small Non-coding RNAs and Their Roles in Biotic Stresses." Frontiers in plant science vol. 9 (2018): 1038. doi: https://doi.org/10.3389/fpls.2018.01038
Brant EJ, Budak H. Plant Small Non-coding RNAs and Their Roles in Biotic Stresses. Front Plant Sci. 2018 Jul 20;9:1038. doi: 10.3389/fpls.2018.01038. eCollection 2018. PMID: 30079074; PMCID: PMC6062887.
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Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.

Nature methods

Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C.
PMID: 34862503
Nat Methods. 2021 Dec;18(12):1489-1495. doi: 10.1038/s41592-021-01315-z. Epub 2021 Dec 03.

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the...

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Rigano A, Ehmsen S, Öztürk SU, et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021;18(12):1489-1495doi: 10.1038/s41592-021-01315-z.
Rigano, A., Ehmsen, S., Öztürk, S. U., Ryan, J., Balashov, A., Hammer, M., Kirli, K., Boehm, U., Brown, C. M., Bellve, K., Chambers, J. J., Cosolo, A., Coleman, R. A., Faklaris, O., Fogarty, K. E., Guilbert, T., Hamacher, A. B., Itano, M. S., Keeley, D. P., Kunis, S., Lacoste, J., Laude, A., Ma, W. Y., Marcello, M., Montero-Llopis, P., Nelson, G., Nitschke, R., Pimentel, J. A., Weidtkamp-Peters, S., Park, P. J., Alver, B. H., Grunwald, D., & Strambio-De-Castillia, C. (2021). Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nature methods, 18(12), 1489-1495. https://doi.org/10.1038/s41592-021-01315-z
Rigano, Alessandro, et al. "Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications." Nature methods vol. 18,12 (2021): 1489-1495. doi: https://doi.org/10.1038/s41592-021-01315-z
Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021 Dec;18(12):1489-1495. doi: 10.1038/s41592-021-01315-z. Epub 2021 Dec 03. PMID: 34862503.
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A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly.

The Journal of comparative neurology

Schön M, Nosanova A, Jacob C, Kraus JM, Kestler HA, Mayer B, Feldengut S, Amunts K, Del Tredici K, Boeckers TM, Braak H.
PMID: 34402535
J Comp Neurol. 2021 Aug 17; doi: 10.1002/cne.25233. Epub 2021 Aug 17.

The entorhinal cortex (EC) is the main interface between the sensory association areas of the neocortex and the hippocampus. It is crucial for the evaluation and processing of sensory data for long-term memory consolidation and shows damage in many...

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Schön M, Nosanova A, Jacob C, et al. A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly. J Comp Neurol. 2021;doi: 10.1002/cne.25233.
Schön, M., Nosanova, A., Jacob, C., Kraus, J. M., Kestler, H. A., Mayer, B., Feldengut, S., Amunts, K., Del Tredici, K., Boeckers, T. M., & Braak, H. (2021). A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly. The Journal of comparative neurology, . https://doi.org/10.1002/cne.25233
Schön, Michael, et al. "A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly." The Journal of comparative neurology vol. (2021). doi: https://doi.org/10.1002/cne.25233
Schön M, Nosanova A, Jacob C, Kraus JM, Kestler HA, Mayer B, Feldengut S, Amunts K, Del Tredici K, Boeckers TM, Braak H. A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly. J Comp Neurol. 2021 Aug 17; doi: 10.1002/cne.25233. Epub 2021 Aug 17. PMID: 34402535.
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Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.

Nature methods

Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C.
PMID: 34862503
Nat Methods. 2021 Dec;18(12):1489-1495. doi: 10.1038/s41592-021-01315-z. Epub 2021 Dec 03.

For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the...

Cite
Rigano A, Ehmsen S, Öztürk SU, et al. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021;18(12):1489-1495doi: 10.1038/s41592-021-01315-z.
Rigano, A., Ehmsen, S., Öztürk, S. U., Ryan, J., Balashov, A., Hammer, M., Kirli, K., Boehm, U., Brown, C. M., Bellve, K., Chambers, J. J., Cosolo, A., Coleman, R. A., Faklaris, O., Fogarty, K. E., Guilbert, T., Hamacher, A. B., Itano, M. S., Keeley, D. P., Kunis, S., Lacoste, J., Laude, A., Ma, W. Y., Marcello, M., Montero-Llopis, P., Nelson, G., Nitschke, R., Pimentel, J. A., Weidtkamp-Peters, S., Park, P. J., Alver, B. H., Grunwald, D., & Strambio-De-Castillia, C. (2021). Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nature methods, 18(12), 1489-1495. https://doi.org/10.1038/s41592-021-01315-z
Rigano, Alessandro, et al. "Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications." Nature methods vol. 18,12 (2021): 1489-1495. doi: https://doi.org/10.1038/s41592-021-01315-z
Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods. 2021 Dec;18(12):1489-1495. doi: 10.1038/s41592-021-01315-z. Epub 2021 Dec 03. PMID: 34862503.
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The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes.

Scientific reports

Budak Ö, Bostancı MS, Tuna A, Toprak V, Çakiroğlu H, Gök K.
PMID: 34907217
Sci Rep. 2021 Dec 14;11(1):23922. doi: 10.1038/s41598-021-03177-z.

This study aimed to evaluate the effects of propofol and dexmedetomidine over different timescales on the IVF outcomes for transvaginal oocyte retrieval (TVOR). Twenty-four rats included in the study were divided into two main groups and three subgroups were...

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Budak Ö, Bostancı MS, Tuna A, et al. The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes. Sci Rep. 2021;11(1):23922doi: 10.1038/s41598-021-03177-z.
Budak, �. �., Bostancı, M. S., Tuna, A., Toprak, V., Çakiroğlu, H., & Gök, K. (2021). The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes. Scientific reports, 11(1), 23922. https://doi.org/10.1038/s41598-021-03177-z
Budak, Özcan, et al. "The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes." Scientific reports vol. 11,1 (2021): 23922. doi: https://doi.org/10.1038/s41598-021-03177-z
Budak Ö, Bostancı MS, Tuna A, Toprak V, Çakiroğlu H, Gök K. The effect of Propofol versus Dexmedetomidine as anesthetic agents for oocyte pick-up on in vitro fertilization (IVF) outcomes. Sci Rep. 2021 Dec 14;11(1):23922. doi: 10.1038/s41598-021-03177-z. PMID: 34907217; PMCID: PMC8671473.
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Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation.

G3 (Bethesda, Md.)

Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J.
PMID: 34515796
G3 (Bethesda). 2021 Dec 08;11(12). doi: 10.1093/g3journal/jkab325.

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further...

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Wang L, Zhu T, Rodriguez JC, et al. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda). 2021;11(12)doi: 10.1093/g3journal/jkab325.
Wang, L., Zhu, T., Rodriguez, J. C., Deal, K. R., Dubcovsky, J., McGuire, P. E., Lux, T., Spannagl, M., Mayer, K. F. X., Baldrich, P., Meyers, B. C., Huo, N., Gu, Y. Q., Zhou, H., Devos, K. M., Bennetzen, J. L., Unver, T., Budak, H., Gulick, P. J., Galiba, G., Kalapos, B., Nelson, D. R., Li, P., You, F. M., Luo, M. C., & Dvorak, J. (2021). Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda, Md.), 11(12), . https://doi.org/10.1093/g3journal/jkab325
Wang, Le, et al. "Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation." G3 (Bethesda, Md.) vol. 11,12 (2021). doi: https://doi.org/10.1093/g3journal/jkab325
Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 (Bethesda). 2021 Dec 08;11(12). doi: 10.1093/g3journal/jkab325. PMID: 34515796; PMCID: PMC8664484.
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Isolation and Characterization of Phages Active against .

Viruses

Jończyk-Matysiak E, Owczarek B, Popiela E, Świtała-Jeleń K, Migdał P, Cieślik M, Łodej N, Kula D, Neuberg J, Hodyra-Stefaniak K, Kaszowska M, Orwat F, Bagińska N, Mucha A, Belter A, Skupińska M, Bubak B, Fortuna W, Letkiewicz S, Chorbiński P, Weber-Dąbrowska B, Roman A, Górski A.
PMID: 34201873
Viruses. 2021 Jun 23;13(7). doi: 10.3390/v13071217.

The aim of this study was the isolation and characterization, including the phage effect on honeybees in laboratory conditions, of phages active against

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Jończyk-Matysiak E, Owczarek B, Popiela E, et al. Isolation and Characterization of Phages Active against . Viruses. 2021;13(7)doi: 10.3390/v13071217.
Jończyk-Matysiak, E., Owczarek, B., Popiela, E., Świtała-Jeleń, K., Migdał, P., Cieślik, M., Łodej, N., Kula, D., Neuberg, J., Hodyra-Stefaniak, K., Kaszowska, M., Orwat, F., Bagińska, N., Mucha, A., Belter, A., Skupińska, M., Bubak, B., Fortuna, W., Letkiewicz, S., Chorbiński, P., Weber-Dąbrowska, B., Roman, A., & Górski, A. (2021). Isolation and Characterization of Phages Active against . Viruses, 13(7), . https://doi.org/10.3390/v13071217
Jończyk-Matysiak, Ewa, et al. "Isolation and Characterization of Phages Active against ." Viruses vol. 13,7 (2021). doi: https://doi.org/10.3390/v13071217
Jończyk-Matysiak E, Owczarek B, Popiela E, Świtała-Jeleń K, Migdał P, Cieślik M, Łodej N, Kula D, Neuberg J, Hodyra-Stefaniak K, Kaszowska M, Orwat F, Bagińska N, Mucha A, Belter A, Skupińska M, Bubak B, Fortuna W, Letkiewicz S, Chorbiński P, Weber-Dąbrowska B, Roman A, Górski A. Isolation and Characterization of Phages Active against . Viruses. 2021 Jun 23;13(7). doi: 10.3390/v13071217. PMID: 34201873; PMCID: PMC8310151.
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