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23 results on '"Przyborowski, Mateusz"'

1. Schema matching using Gaussian mixture models with Wasserstein distance

Author

Przyborowski, Mateusz, Pabiś, Mateusz, Janusz, Andrzej, and Ślęzak, Dominik

Subjects
Computer Science - Machine Learning, Computer Science - Databases, Statistics - Machine Learning
Abstract

Gaussian mixture models find their place as a powerful tool, mostly in the clustering problem, but with proper preparation also in feature extraction, pattern recognition, image segmentation and in general machine learning. When faced with the problem of schema matching, different mixture models computed on different pieces of data can maintain crucial information about the structure of the dataset. In order to measure or compare results from mixture models, the Wasserstein distance can be very useful, however it is not easy to calculate for mixture distributions. In this paper we derive one of possible approximations for the Wasserstein distance between Gaussian mixture models and reduce it to linear problem. Furthermore, application examples concerning real world data are shown.

Published
2021

2. Clustering Methods for Adaptive e-Commerce User Interfaces

Author

Wasilewski, Adam, Przyborowski, Mateusz, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Campagner, Andrea, editor, Urs Lenz, Oliver, editor, Xia, Shuyin, editor, Ślęzak, Dominik, editor, Wąs, Jarosław, editor, and Yao, JingTao, editor

Published
2023
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3. An Improved RNA Extraction Protocol for Rye Grain Full-Length Transcriptome Sequencing.

Author

Jazowska, Justyna, Przyborowski, Mateusz, Wojciechowski, Marek, and Groszyk, Jolanta

Abstract

RNA quality and integrity are critical for many studies in plant molecular biology. However, extracting high-quality RNA from cereal grains is challenging due to the presence of polysaccharides, polyphenols, and other compounds that bind or coprecipitate with RNA particles. To address this, we introduced an initial purification step into the Tri Reagent Solution protocol, which effectively eliminated starch and other contaminants. The performance of this modified protocol was then compared with five other RNA extraction methods, including those based on Tri Reagent Solution and the Direct-zol RNA Miniprep Plus Kit. Introducing our method modification prior to homogenization with Tri Reagent Solution successfully yielded total RNA with both high quality (RIN values ranging from 9.50 to 9.70) and high efficiency, making it suitable for both mRNA extraction using the Dynabeads mRNA Purification Kit and library preparation for transcriptome sequencing by long-read methods, such as Oxford Nanopore Technologies. The protocol was successfully applied to total RNA extraction from rye grains at 14 and 21 days after pollination. This study demonstrates that improving the Tri Reagent Solution protocol through initial purification enables the extraction of high-quality RNA from rye grains. [ABSTRACT FROM AUTHOR]

Published
2024
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6. 4th Conference of Cereal Biotechnology and Breeding jointly organized by EUCARPIA Cereal Section November 6–9, 2017 • Budapest, Hungary : BOOK OF ABSTRACTS

Author

Consortium INEW, PPP Barley Consortium, Börner, Andreas, Nagel, Manuela, Tarawneh, Rasha, Arif, Mian Abdur Rehman, Agacka-Mołdoch, Monika, Börner, Mariann, Lohwasser, Ulrike, Rieweach, David, Wieb, Janine, Altmann, Thomas, Góralska, Magdalena, Lenarczyk-Puri, Natalia, Podgórska, Katarzyna, Berdzik, Marcin, Stojałowski, Stefan, Myśków, Beata, Kiss, Tibor, Veisz, Ottó, Karsai, Ildikó, Martín, Antonio, Rasmussen, Søren K., Legzdina, Linda, Fan, Weiyao, Tikhenko, Natalia, Rutten, Twan, Senula, Angelika, Rubtsova, Myroslava, Keller, E. R. Joachim, Vitányi, Beáta, Nagy, Katalin, Fekete, Anna Katalin, Dudás, Brigitta, Lantos, Csaba, Pauk, János, Jenes, Barnabás, Yu, Bianyun, Zhang, Wentao, Gao, Peng, Sidebottom, Christine, Lokuruge, Prabhath, Polley, Brittany, Clarke, Carling, Sharpe, Andrew, Knox, Ron, Cuthbert, Richard, Ruan, Yuefeng, Pozniak, Curtis J., Fobert, Pierre, Dziurka, Kinga, Noga, Angelika, Marcińska, Izabela, Czyczyło-Mysza, Ilona, Warchoł, Marzena, Kapłoniak, Kamila, Warzecha, Tomasz, Sutkowska, Agnieszka, Werwińska, Krystyna, Nita, Zygmunt, Skrzypek, Edyta, Fradgley, Nick, Bentley, Alison, Gardner, Keith, Howell, Phil, Mackay, Ian, Scott, Mike, Mott, Richard, Cockram, James, Galani, Saddia, Sahar, Shagufta, Musharraf, Syed Ghulam, Azhar, Abid, Ferjaoui, Sahbi, Bouslimi, Chadha, Udupa, Sripada M., Hamza, Sonia, Mariana, Ittu, Ciuca, Matilda, Marinciu, Cristina, Cristina, Daniel, Turcu, Alina, Mandea, Vasile, Ittu, Gheorghe, Jabłoński, Bartosz, Onyśk, Agnieszka, Wyszyńska, Renata, Boczkowska, Maja, Przyborowski, Mateusz, Gasparis, Sebastian, Orczyk, Wacław, Nadolska-Orczyk, Anna, Bińkowski, Jan, Kubiś, Jakub, Pogorzelska, Katarzyna, Pellny, Till K, Bolibok-Brągoszewska, Hanna, Idziak-Helmcke, Dominika, Rojek, Magdalena, Hosiawa-Barańska, Marta, Tsai, Hsin-Yuan, Cericola, Fabio, Edriss, Vahid, Andersen, Jeppe, Orabi, Jihad, Jensen, Jens, Jahoor, Ahmed, Janss, Luc, Jensen, Just, Lawrenson, Tom, Hayta, Sadiye, Smedley, Mark, Hinchliffe, Alison, Harwood, Wendy, Gimenez, Guillermo G., Barakate, Abdellah, Russell, Joanne, Stephens, Jennifer, Lampugnani, Edwin R., Doblin, Monika S., Fincher, Geoffrey B., Burton, Rachel A., Waugh, Robbie, Tucker, Matthew, Houston, Kelly, Jouanin, Aurelie, Leigh, Fiona, Wallington, Emma, Schaart, Jan, Smulders, Marinus J.M., Kała, Maciej, Kim, Sung-Yong, Brueggeman, Robert, Åhman, Inger, Zhu, Li-Hua, Bouchet, Sophie, Lemarié, Stéphane, Fugeray-Scarbel, Aline, Auzanneau, Jérôme, Charmet, Gilles, Ali, Ahmad, Mastrangelo, Anna Maria, De Vita, Pasquale, Laido, Giovanni, Marone, Daniale, Arshad, Muhammad, Naqvi, S.M. Sawlan, Sher, Hassan, Rasheed, Awais, Kazi, Abdul Mujeeb, Oakey, Helena, Bayer, Micha, Macaulay, Malcolm, Byrt, Caitlin, Gilliham, Matthew, Salt, David E, István, Monostori, Fruzsina, Szira, Alessandro, Tondelli, Tamás, Árendás, Krisztián, Gierczik, Luigi, Cattivelli, Gábor, Galiba, Attila, Vágújfalvi, Bakuma, Alla, Chebotar, Galyna, Filimonov, Vadim, Kyrylyuk, Tetyana, Chebotar, Sabina, Kristensen, Peter Skov, Andersen, Jeppe Reitan, Guzmán, Carlos, Schurr, Ulrich, Pieruschka, Roland, Neumann, Kerstin, Zhao, Yusheng, Dhanagond, Sidram, Reif, Jochen C., Graner, Andreas, Raymaekers, Dries, Taylor, Mike, Åhman, Inger M., Crespo-Herrera, Leonardo A., Kobiljski, Borislav, Mladenović, Gojko, Jestrović, Zorica, Jancsó, Mihály, Ács, Katalin, Bóna, Lajos, Purgel, Szandra, Békés, Ferenc, Schwember, A.R., Matus, I., Sharma, Dew Kumari, Rosenqvist, Eva, Carl-Otto-Ottosen, Torp, Anna Maria, Andersen, Sven Bode, El-Haddoury, Jamal, Henkrar, Fatima, Grana, Zahra, Nyiraguhirwa, Solange, Gyawali, Sanjaya, Verma, Ramesh, Ouabbou, Hassan, Ibriz, Mohammed, Iraqi, Driss, Forgeois, Paul, Grausgruber, Heinrich, Cuendet, Catherine, Dell’Avo, Franca, Koppel, Reine, Weyermann, Verena, Mikó, Péter, Vida, Gyula, Rakszegi, Marianna, Lafferty, Julia, Lorentz, Bruno, Longin, Carl Friedrich Horst, Megyeri, Mária, Kaskarbayev, Zheksenbay, Zhloba, Ludmila, Kiyas, Aldabergen, Kunanbayev, Kairat, Churkina, Galina, Zueva, Nataliya, Cattivelli, Luigi, Guerra, Davide, Tondelli, Alessandro, Bustos-Korts, D., Rizza, Fulvia, Bretani, Gianluca, Ferrandi, Chiara, Lazzari, Barbara, Rossini, Laura, Ozkan, Hakan, Molnar-Lang, Marta, van Eeuwijk, Fred, Dawson, Ian K, Fricano, Agostino, Azad, Md. Abul Kalam, Kamruzzaman, Md., Yasmine, Fahmina, Islam, Mirza Mofazzal, Jankuloski, Ljupcho, Christopher, John (Jack), Anzooman, Monia, Menzies, Neal, Dalal, Ram, Dang, Yash, Novák, Aliz, Boldizsár, Ákos, Gierczik, Krisztián, Mohamed, Ahres, Ádám, Éva, Bognár, László Kozma, Vágújfalvi, Attila, Båga, Monica, Chibbar, Ravindra, Galiba, Gábor, Gottwald, Sven, Bhandari, Dhaka Ram, Wang, Qing, Li, Bin, Römpp, Andreas, Friedt, Wolfgang, Spengler, Bernhard, Jäger, Katalin, Sáfrán, Eszter, Fábián, Attila, Deák, Csilla, Papp, István, Barnabás, Beáta, Mesterhazy, Akos, Varga, Mónika, Bartók, Tibor, Lehoczki-Krjak, Szabolcs, Toth, Beata, Miloud, Hafsi, Pál, Magda, Szalai, Gabriella, Janda, Tibor, Molnár, István, Lovegrove, Alison, Darkó, Éva, Farkas, András, Láng, László, Bedő, Zoltán, Doležel, Jaroslav, Molnár-Láng, Márta, Shewry, Peter, Tiryakioğlu, Murat, Sakallı, Abdulla, Alloudane, Rajae, El Mourabit, Nourdin, Barrijal, Said, Bengtsson, Therése, Manninen, Outi, Bulatova, Kulpash, Mazkirat, Shynar, Babissekova, Dilyara, Aytimbetova, Klara, Goncharova, Anastasiya, Lavrinenko, Yuriy, Bazaliy, Galyna, Cope, Jonathan, Norton, Gareth, George, Timothy, Newton, Adrian, Császár, Orsolya, Lajos, Károly, Szalai, Márk, Dziurka, Michał, Dashkevich, Svetlana, Utebayev, Maral, Chilimova, Irina, Babkenov, Adilchan, Akhmetova, Galiya, Chaimae, Senhaji, Khadija, Ahansal, Rabha, Abdelwahd, Allal, Douira, Driss, Iraqi, Gracz, Joanna, Karłowski, Wojciech, Kuczyński, Jakub, Tyczewska, Agata, Haberle, Jan, Svoboda, Pavel, Neumannová, Adéla, Kurešová, Gabriela, Raimanová, Ivana, Holková, Ludmila, Solařová, Eva, Bradáčová, Marta, Smutná, Pavlína, Horčička, P., Pospíšilová, V., Veškrna, O., Bížova, I., Chrpova, J., Sumíková, T., Ittu, Mariana, Marinciu, Cristina Mihaela, Voica, Maria, Banateanu, Cecilia, Mayer, Marianna, Karsai, Idikó, Mirosavljević, Milan, Momčilović, Vojislava, Mikić, Sanja, Trkulja, Dragana, Denčić, Srbislav, Jocković, Bojan, Aćin, Vladimir, Pržulj, Novo, Nakhoda, Babak, Mohammadi-Nejad, Ghasem, Mardi, Mohsen, Amini, Ashkboos, Tabatabaei, Mohammad-Taghi, Parsayev, Evgeniy, Filippova, Nadezhda, Permana, Hadian, Ishii, Kazuo, Murata, Kazumasa, Yamada, Tetsuya, Kanekatsu, Motoki, Prokesova, Lenka, Smutna, Pavlina, Holkova, Ludmila, Rukavitsina, Irina, Suleimenov, Mechlis, Yerpasheva, Dana, Shtefan, Galina, Ivanova, Galina, Ferderer, Ella, Kalapos, Balázs, Ahres, Mohamed, Székely, András, Gulyás, Zsolt, Kovács, Kristóf, Jones, Huw D, Dalmay, Tamás, Soltész, Alexandra, Trávníčková, Martina, Chrpová, Jana, Martinek, Petr, Hnilička, František, Żywicki, Marek, Twardowski, Tomasz, Végh, Balázs, Marček, Tihana, Wiśniewska, Halina, Kwiatek, Michał, Majka, Maciej, Gawłowska, Magdalena, Korbas, Marek, Danielewicz, Jakub, Belter, Jolanta, Bilgrami, Sayedeh Saba, Sichani, Jalal Sabouri, Zandi, Peiman, Zhunusbayeva, Zhazira, Omirbekova, Nargul, Zhussupova, Aizhan, Mursalieva, Valentina, Nam, Svetlana, Żur, Iwona, Surówka, Ewa, Dubas, Ewa, Nowicka, Anna, Krzewska, Monika, Hura, Tomasz, Rapacz, Marcin, Wójcik-Jagła, Magdalena, Ostrowska, Agnieszka, Malaga, Sabina, Janowiak, Franciszek, Pellny, Till, Patil, Archana, Freeman, Jackie, Plummer, Amy, Hess, Linde, Phillips, Andy, Berry, Simon, Mitchell, Rowan, Larkin, Philip, Tanner, Gregory, Colgrave, Michelle, Blundell, Malcolm, Howitt, Crispin, Morita, Naofumi, Van Hung, Pham, Cegiełko, Małgorzata, Kiecana, Irena, Mielniczuk, Elżbieta, Pastucha, Alina, Perkowski, Juliusz, Áy, Zoltán, Czirle, Csaba, Palágyi, András, Mihály, Róbert, Vermeulen, Philippe, Suman, Michele, Pierna, Juan Antonio Fernández, and Baeten, Vincent

Published
2017

16. MOESM3 of A simple and efficient CRISPR/Cas9 platform for induction of single and multiple, heritable mutations in barley (Hordeum vulgare L.)

Author

Gasparis, Sebastian, Kała, Maciej, Przyborowski, Mateusz, Łyżnik, Leszek, Wacław Orczyk, and Nadolska-Orczyk, Anna

Abstract

Additional file 3: Figure S4. Sequence alignment of the HvCKX1 gene fragments cloned from selected T1 plants. Target sequence is marked in yellow and PAM motif in light blue; deletions are indicated by dashes.

Published
2018
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20. Efficient CRISPR/Cas9 based system for genome editing in barley (Hordeum vulgare L.).

Author

Gasparis, Sebastian, Przyborowski, Mateusz, Kała, Maciej, Orczyk, Wacław, and Nadolska-Orczyk, Anna

Subjects
CRISPRS, GENOME editing, BARLEY breeding
Abstract

Since its demonstration in 2012, CRISPR/Cas9 system has been applied as a break-through technology for precise genome editing in a broad range of organisms. The main advantages of this system are among others, the technical simplicity, easy multiplex gene targeting by single construct and the ability to cleave methylated DNA. The Cas9 nuclease can also be re-engineered or inactivated and used for other genetic engineering approaches, such as gene expression regulation or for labeling of specific chromosomal regions in vivo. In this study we demonstrate the simple and efficient CRISPR/Cas9-mediated genome editing system for barley in which the target sequence is cloned into Gateway compatible vector for stable Agrobacterium-mediated transformation. To introduce site-directed mutations we chose two different barley genes, HvCKX1 and Nud, both determining important agronomical traits. HvCKX1gene is a member of the CKX gene family encoding oxidase/ dehydrogenase enzymes which metabolize cytokinins in plants and control developmental processes. Nud gene is a member of the gene family of ethylene-response transcription factor ERF. Mutations in this gene result in a phenotype with naked (hulless) caryopses. The crucial role of CKX genes in plant development and the possibility of direct detection of phenotypic changes in plants modified by site-directed mutagenesis of Nud gene were two main reasons for choosing these genes. Immature embryos of barley were transformed with vectors containing codon-optimized gene of nuclease Cas9 and single guided RNA sequence (sgRNA) targeting either HvCKX1 or Nud gene under wheat U6 RNA promoter. Induced mutations were detected by restriction analysis of amplified fragments of both genes. 71 transgenic plants were obtained after transformation with CRISPR/Cas9 construct for HvCKX1 gene and 28 transgenic plants for Nud gene. The mutation frequency was 66% and 64% of HvCKX1 and Nud genes respectively. In part of the plants the sequences carrying mutations were cloned and sequenced. Single nucleotide deletions or insertions were the most frequent types of mutations however, larger deletions (up to 10 bp) were also detected. Moreover, in most of the plants with altered Nud gene, the naked caryopses with non-adherent hulls were observed. Our results show that the CRISPR/ Cas9 technology is a simple and powerful tool for breeding improvement of crop plants. [ABSTRACT FROM AUTHOR]

Published
2017
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21. Knockout of the HvCKX1 or HvCKX3 Gene in Barley (Hordeum vulgare L.) by RNA-Guided Cas9 Nuclease Affects the Regulation of Cytokinin Metabolism and Root Morphology.

Author

Gasparis, Sebastian, Przyborowski, Mateusz, Kała, Maciej, and Nadolska-Orczyk, Anna

Subjects
*CYTOKININS, *BARLEY, *METABOLIC regulation, *CROP yields, *GRAIN yields, *MORPHOLOGY
Abstract

Barley is among four of the most important cereal crops with respect to global production. Increasing barley yields to desired levels can be achieved by the genetic manipulation of cytokinin content. Cytokinins are plant hormones that regulate many developmental processes and have a strong influence on grain yield. Cytokinin homeostasis is regulated by members of several multigene families. CKX genes encode the cytokinin oxidase/dehydrogenase enzyme, which catalyzes the irreversible degradation of cytokinin. Several recent studies have demonstrated that the RNAi-based silencing of CKX genes leads to increased grain yields in some crop species. To assess the possibility of increasing the grain yield of barley by knocking out CKX genes, we used an RNA-guided Cas9 system to generate ckx1 and ckx3 mutant lines with knockout mutations in the HvCKX1 and HvCKX3 genes, respectively. Homozygous, transgene-free mutant lines were subsequently selected and analyzed. A significant decrease in CKX enzyme activity was observed in the spikes of the ckx1 lines, while in the ckx3 lines, the activity remained at a similar level to that in the control plants. Despite these differences, no changes in grain yield were observed in either mutant line. In turn, differences in CKX activity in the roots between the ckx1 and ckx3 mutants were reflected via root morphology. The decreased CKX activity in the ckx1 lines corresponded to greater root length, increased surface area, and greater numbers of root hairs, while the increased CKX activity in the ckx3 mutants gave the opposite results. RNA-seq analysis of the spike and root transcriptomes revealed an altered regulation of genes controlling cytokinin metabolism and signaling, as well as other genes that are important during seed development, such as those that encode nutrient transporters. The observed changes suggest that the knockout of a single CKX gene in barley may be not sufficient for disrupting cytokinin homeostasis or increasing grain yields. [ABSTRACT FROM AUTHOR]

Published
2019
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23. Do TaCKX1 and TaCKX2 genes regulate wheat productivity?

Author

Jabłoński, Bartosz, Onyśk, Agnieszka, Wyszyńska, Renata, Boczkowska, Maja, Przyborowski, Mateusz, Gasparis, Sebastian, Orczyk, Wacław, and Nadolska-Orczyk, Anna

Subjects
CYTOKININS, WHEAT genetics, WHEAT breeding
Abstract

Multigene family of CKX genes encode cytokinin dehydrogenase proteins (CKX), which regulate cytokinin content in developing plants and substantially influence their development. The detailed biological function of most of the TaCKX genes in wheat is not known. The goal of this research is to characterize their functions and to select those, which might regulate yield-related traits in wheat. In our earlier research we showed that regulation patterns and expression level of HvCKX genes of barley indicated their roles in growth and reproductive development (Zalewski et al. 2010, 2012, 2014). Therefore the first step was to analyze expression pattern of 10 TaCKX genes in different tissues and organs of developing plants of 3 cultivars of wheat. Two genes: TaCKX1 and TaCKX2 showed high level of expression in developing kernels 0 DAP (days after pollination), 7 DAP and 14 DAP and were selected for further research and functional analysis. The selected genes were transcriptionally silenced in two wheat cultivars Kontesa and Ostka. This was achieved by Agrobacterium-mediated integration of RNAi silencing cassette. The relative expression of TaCKX1 and TaCKX2 in kernels 7 DAP and 14 DAP of selected transgenic lines was significantly decreased. In several lines decreased expression of the tested genes correlated with decreased activity of the CKX enzyme. The analysis of chlorophyll content in flag leaves and evaluation of selected phenotype traits in silenced T1 lines will be presented and discussed. [ABSTRACT FROM AUTHOR]

Published
2017
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