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1. BASE TTS: Lessons from building a billion-parameter Text-to-Speech model on 100K hours of data

Author

Łajszczak, Mateusz, Cámbara, Guillermo, Li, Yang, Beyhan, Fatih, van Korlaar, Arent, Yang, Fan, Joly, Arnaud, Martín-Cortinas, Álvaro, Abbas, Ammar, Michalski, Adam, Moinet, Alexis, Karlapati, Sri, Muszyńska, Ewa, Guo, Haohan, Putrycz, Bartosz, Gambino, Soledad López, Yoo, Kayeon, Sokolova, Elena, and Drugman, Thomas

Subjects
Computer Science - Machine Learning, Computer Science - Computation and Language, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

We introduce a text-to-speech (TTS) model called BASE TTS, which stands for $\textbf{B}$ig $\textbf{A}$daptive $\textbf{S}$treamable TTS with $\textbf{E}$mergent abilities. BASE TTS is the largest TTS model to-date, trained on 100K hours of public domain speech data, achieving a new state-of-the-art in speech naturalness. It deploys a 1-billion-parameter autoregressive Transformer that converts raw texts into discrete codes ("speechcodes") followed by a convolution-based decoder which converts these speechcodes into waveforms in an incremental, streamable manner. Further, our speechcodes are built using a novel speech tokenization technique that features speaker ID disentanglement and compression with byte-pair encoding. Echoing the widely-reported "emergent abilities" of large language models when trained on increasing volume of data, we show that BASE TTS variants built with 10K+ hours and 500M+ parameters begin to demonstrate natural prosody on textually complex sentences. We design and share a specialized dataset to measure these emergent abilities for text-to-speech. We showcase state-of-the-art naturalness of BASE TTS by evaluating against baselines that include publicly available large-scale text-to-speech systems: YourTTS, Bark and TortoiseTTS. Audio samples generated by the model can be heard at https://amazon-ltts-paper.com/., Comment: v1.1 (fixed typos)

Published
2024

2. Student Voice in Distance Foreign Language Course Design and its Practical Implications in Higher Education

Author

Barbara Muszynska and Cristina A. Huertas-Abril

Abstract

The purpose of this research is to analyze whether university students would be willing to engage in distance foreign language (FL) course design, and if the knowledge of their preferences could be used to present guidelines for course designers. Student engagement is seen as crucial to graduates' achievement in HE, especially in online courses, yet there are no studies examining student voice in distance FL course design or curriculum delivery in the context of HE in Poland and very few international ones. The study identified five dimensions and feedback as the basic constructs to analyze students' preferences about learning design of distance foreign language courses. The research study design is quantitative with descriptive and correlational methods. Data were gathered from HE students (n = 626) studying in Poland. The results show statistically significant differences regarding students' gender, age, and academic level. The findings suggest that the learning paths in a FL distance course in HE should be created by taking into account the language skills students want to practice, gender identity, educational stage, learning communities, and age. The latter can influence students' willingness to co-design the course, the course content, and the type of interactions.

Published
2023

3. The Role of eTwinning Tools in Social and Curriculum Integration Using Multimodal Communication

Author

Huertas-Abril, Cristina A. and Muszynska, Barbara

Abstract

Research shows that learning tools play an important role in social interactions in curriculum integration. Online social integration and interactive modality have been identified as two success factors for online learning from the students' perspective. There is little research on students' perceptions on the use of eTwinning in higher education (HE), and the use of eTwinning tools with the focus on creating a collaborative online learning environment in HE has not been explored to this date. Yet, it may have practical implications for curricular development. Therefore, the aim of the study was to learn whether eTwinning tools can play an important role in social and online curriculum integration in HE. This qualitative study aims at comparing undergraduate students' perceptions from two universities (UCO, Spain, and ULS, Poland) regarding the development of multimodal communication and telecollaborative learning. Key findings emerging from the study suggest the use of eTwinning tools enabled multimodal communication between students and the development of new social practices and social learning strategies between them. A new understanding of eTwinning tools in curriculum integration in high education was raised, and new knowledge developed, which may lead to a higher quality of teaching and learning.

Published
2022

7. Effects of Playing the Video Game 'Her Story' on Multiple Dimensions of Creativity in EFL Writing -- An International Replication Study

Author

Huertas-Abril, Cristina A. and Muszynska, Barbara

Abstract

This international replication study demonstrates how playing a video game is related to multiple dimensions of creativity in foreign language writing. In this research project, university students were asked to interact with a commercial murder mystery video game, "Her Story," and produce a piece of creative writing, which was a replication with a new data collection of the original study by Lee (2019). The reason for using this digital game was to provide an authentic learning opportunity for students and analyze whether digital game-based learning facilitates creativity in EFL writing. This replication, involving 25 university students from Poland and 25 university students from Spain, is a media transfer study based on the students transforming one media format (video game) into another (writing). The results demonstrate that the use of a video game with an ambiguous storyline prompts discovery (specific curiosity) and could be the determining factor for producing original, quality ideas in writing even when holding a negative view of one's creativity. The findings also indicate that the choice of genre and a viewpoint in writing may influence the level of elaboration in the texts produced by students.

Published
2023
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8. Expressive, Variable, and Controllable Duration Modelling in TTS

Author

Abbas, Ammar, Merritt, Thomas, Moinet, Alexis, Karlapati, Sri, Muszynska, Ewa, Slangen, Simon, Gatti, Elia, and Drugman, Thomas

Subjects
Electrical Engineering and Systems Science - Audio and Speech Processing, Computer Science - Sound
Abstract

Duration modelling has become an important research problem once more with the rise of non-attention neural text-to-speech systems. The current approaches largely fall back to relying on previous statistical parametric speech synthesis technology for duration prediction, which poorly models the expressiveness and variability in speech. In this paper, we propose two alternate approaches to improve duration modelling. First, we propose a duration model conditioned on phrasing that improves the predicted durations and provides better modelling of pauses. We show that the duration model conditioned on phrasing improves the naturalness of speech over our baseline duration model. Second, we also propose a multi-speaker duration model called Cauliflow, that uses normalising flows to predict durations that better match the complex target duration distribution. Cauliflow performs on par with our other proposed duration model in terms of naturalness, whilst providing variable durations for the same prompt and variable levels of expressiveness. Lastly, we propose to condition Cauliflow on parameters that provide an intuitive control of the pacing and pausing in the synthesised speech in a novel way., Comment: Accepted to be published in the Proceedings of InterSpeech 2022

Published
2022

10. Retrospective comparative analysis of two medical evacuation systems for Ukrainian patients affected by war

Author

Adyrov, Mykhaylo V, Alanbousi, Inna, Alexander, Sarah Weeks, Apel, Anna, Avula, Meghana, Bal, Wioletta Anna, Balwierz, Walentyna Aniela, Basset-Salom, Luisa, Bastardo Blanco, Daniel, Bauer, Karolina Jadwiga, Bayazitov, Ildar T, Berlanga, Pablo, Bhakta, Nickhill Hitesh, Bieniek, Katarzyna Anna, Bien, Ewa Iwona, Blackwood, Christopher Andrew, Blair, Sally Jane, Bodak, Khrystyna Ihorivna, Bordeianu, Irina, Bouffet, Eric Eric, Braganca, Joao Maria, Bucurenci, Mihaela Silvia, Budny, Elżbieta Beata, Budzyn, Andrii, Bumgardner, Christopher Carl, Burditt, Raina Nichole, Burnside Clapp, Victoria, Bykov, Viacheslav Valeriyovych, Cañete, Adela, Carnelli, Monica, Cela, Elena, Cepowska, Zuzanna, Chaber, Radoslaw, Cherner-Drieux, Anna, Chubata, Mariya, Clough, Heidi M, Czauderna, Piotr Stefan, Czernicka - Siwecka, Jolanta, Czyzewski, Krzysztof, Dalle, Jean-Hugues, Dashchakovska, Olha, de Koning, Linda A, Dembowska-Baginska, Bozenna Malgorzata, Derwich, Katarzyna, Dirksen, Uta, Dommett, Rachel, Dorosh, Olha Ihorivna, dos Reis Farinha, Nuno Jorge, Drabko, Katarzyna Anna, Dragomir, Monica Desiree, Dutkiewicz, Malgorzata, Dworzak, Michael, Dyma, Sergii Vitaliiovych, Earl, Julian, Eggert, Angelika, English, Martin William, Farren, Becky S, Fedyk, Nataliia Yuriina, Fernández-Teijeiro, Ana, Ferneza, Severyn Romanovych, Foster, Whitney Baer, Fox Irwin, Leeanna Elizabeth, Gałązkowski, Robert Maciej, Ganieva, Galyna, Garanzha, Vasylyna Andriivna, Gelman, Marina S, Godzinski, Jan Krzysztof, Goeres, Anne Françoise, Golban, Rodica, Graetz, Dylan Elizabeth, Greiner, Jeanette, Griksaitis, Michael J, Gupta, Sumit, Hampel, Michal Andrzej, Hastings, Sara Grace, Heenen, Delphine Liliane, Hill, Marcela C, Holiuk, Ihor, Holter, Wolfgang, Hough, Rachael Emma, Hutnik, Lukasz Marek, Irga-Jaworska, Ninela, Istomin, Oleksandr Andriyovych, Ignatova, Anna, Janczar, Szymon Lech, Kacharian, Arman, Kalwak, Krzysztof, Karolczyk, Grażyna Małgorzata, Karpenko, Nataliia Mikolaivna, Katsubo, Halyna Oleksandrivna, Kattamis, Antonis, Kazanowska, Bernarda Jadwiga, Kentsis, Alex, Ketteler, Petra, Kienesberger, Anita, Kiselev, Roman, Kizyma, Zoryana Petrivna, Kliuchkivska, Khrystyna, Klymniuk, Hryhorii Ivanovych, Kolenova, Alexandra, Kolodrubiec, Julia, Kostiuk, Yuliia, Kowalik, Tomasz, Kozlova, Olena Igorivna, Kozubenko, Vladyslav, Kraal, Kathelijne, Kramar, Tetyana Oleksandrivna, Krawczuk-Rybak, Maryna Maryna, Kulemzina, Irina, Kurkowska, Paulina, Kuzyk, Andriy S., Ladenstein, Ruth Lydia, Laguna, Pawel Jozef, Lassaletta, Alvaro, Lehmberg, Kai, Leontieva, Oksana, Liashenko, Serhii, Loizou, Loizos G., Lucchetta, Sonia Anna, Lupo, Matthew William, Lysytsia, Lesya, Lysytsia, Oleksandr, Machnik, Katarzyna Anna, Massimino, Maura, Mainland, Jeff A, Matczak, Katarzyna, Matysiak, Michal Jacek, Mayeur, Pierre, Miller, Beth Anne, Minervina, Anastasia A, Mishkova, Volha, Mizia-Malarz, Agnieszka Joanna, Morales La Madrid, Andres, Moreira, Daniel C, Moreno, Lucas, Moskvin, Vadim P, Mukkada, Sheena Teresa, Muszyńska-Rosłan, Katarzyna Maria, Mykychak, Iryna Volodymyrivna, Niemeyer, Charlotte, Nelson, Akoya Janae', Nogovitsyna, Yuliya, Ociepa, Tomasz, Oltolini, Stefano, Onipko, Nataliia, Pappas, Andrew, Patel, Amit B, Patrahau, Alina Alina, Pauley, Jennifer L., Pavlenko, Yehor Mikhailovich, Pavlovych, Andrij Oleksandrovych, Peregud-Pogorzelski, Jarosław Władyslaw, Perek-Polnik, Marta, Pérez, Vanesa, Pérez-Martínez, Antonio, Pikman, Yana, Pitozzi, Graziano Pitozzi, Portugal, Rui Gentil, Posternak, Victoria Vita, Pleshkan, Viktoriya, Prete, Arcangelo, Pritchard-Jones, Kathy, Raciborska, Anna, Radaelli, Alessandra, Reeves, Tegan Jemma, Reinhardt, Dirk, Reshetnyak, Andrey V, Rider, Andrew Jacob, Rizzari, Carmelo, Rizzi, Damiano Damiano, Rodriguez Hermosillo, Karen Gabriela, Ronenko, Olena Volodymyrivna, Rostkowska, Aneta Olga, Rudko, Liudmyla Yaroslavivna, Sakaan, Firas Mohamed, Sakhar, Nadezhda Aleksandrovna, Salman, Zeena S, Savva, Natallia N., Scaccaglia, Davide, Schaeffer, Elizabeth Hawthorne, Schneider, Carina Ursula, Scobie, Nicole, Semeniuk, Olena Volodymyrivna, Shevchyk, Roksoliana, Shuler, Ana I., Shvets, Stanislav, Sniderman, Liz, Skoczen, Szymon Pawel, Smeal, William John, Sokolowski, Igor, Sonkin, Anna Alexandra, Spolinyak, Andriy, Spota, Andrea, Sramkova, Lucie, Stepanjuk, Alla Ivanivna, Sterba, Jaroslav, Strahm, Brigitte, Styczynski, Jan, Svintsova, Olha, Synyuta, Andriy V, Szczepanski, Tomasz, Szczucinski, Pawel Kukiz, Szmyd, Bartosz Miroslaw, Tasso Cereceda, Maria, Teliuk, Alina, Tomanek, Iwona, Topping, Phoebe, Torrent, Montserrat, Trelińska, Joanna, Troyanovska, Olha Orestivna, Tsurkan, Lyudmila G., Tsymbalyuk-Voloshyn, Iryna, Tyupa, Sergiy Ihorovych, Urasinski, Tomasz Franciszek, Urbanek Dądela, Agnieszka, Vasilieva, Nataliia Jroslavivna, Vasilyeva, Aksana, Verdú-Amorós, Jaime, Vilcu-Bajurean, Natalia, Vinitsky, Leo, Vivtcharenko, Victoria, Vovk, Nelia, Volpe, Giovanni, Vorobel, Oksana Ivanivna, Wachowiak, Jacek Tadeusz, Wasiak, Marcin Slawomir, Wiedower, Lance Allan, Wobst, Natalia, Wuenschel, Lena Isolde, Wysocki, Mariusz Stanislaw, Yurieva, Marina, Zagurska, Anastasiia, Zakharenko, Stanislav S, Zakharenko, Aelita V, Zapotochna, Khrystyna, Zawitkowska, Joanna Emilia, Zecca, Marco, Mueller, Alexandra, Salek, Marta, Oszer, Aleksandra, Evseev, Dmitry, Yakimkova, Taisiya, Wlodarski, Marcin, Vinitsky, Anna, Kizyma, Roman, Pogorelyy, Mikhail, Zuber, Maria, Escalante, Juan, Lipska, Elzbieta, Fendler, Wojciech, Nowicka, Zuzanna, Szyszka, Adam, Rodriguez-Galindo, Carlos, Wise, Paul H., Agulnik, Asya, and Mlynarski, Wojciech

Published
2024
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11. Lack of cytotoxic and genotoxic effects of mPEG-silane coated iron(III) oxide nanoparticles doped with magnesium despite cellular uptake in cancerous and noncancerous lung cells

Author

Sikorska, Malgorzata, Ruzycka-Ayoush, Monika, Rios-Mondragon, Ivan, Longhin, Eleonora Marta, Meczynska-Wielgosz, Sylwia, Wojewodzka, Maria, Kowalczyk, Agata, Kasprzak, Artur, Nowakowska, Julita, Sobczak, Kamil, Muszynska, Magdalena, Cimpan, Mihaela Roxana, Runden-Pran, Elise, Shaposhnikov, Sergey, Kruszewski, Marcin, Dusinska, Maria, Nowicka, Anna M., and Grudzinski, Ireneusz P.

Published
2024
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13. RNA-seq data science: From raw data to effective interpretation

Author

Deshpande, Dhrithi, Chhugani, Karishma, Chang, Yutong, Karlsberg, Aaron, Loeffler, Caitlin, Zhang, Jinyang, Muszynska, Agata, Rotman, Jeremy, Tao, Laura, Balliu, Brunilda, Tseng, Elizabeth, Eskin, Eleazar, Zhao, Fangqing, Mohammadi, Pejman, Labaj, Pawel P, and Mangul, Serghei

Subjects
Quantitative Biology - Genomics
Abstract

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community to develop accurate and scalable computational tools. RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms. It generates enormous amounts of transcriptomic data in the form of nucleotide sequences, known as reads. RNA-seq analysis enables the probing of genes and corresponding transcripts which is essential for answering important biological questions, such as detecting novel exons, transcripts, gene expressions, and studying alternative splicing structure. However, obtaining meaningful biological signals from raw data using computational methods is challenging due to the limitations of modern sequencing technologies. The need to leverage these technological challenges have pushed the rapid development of many novel computational tools which have evolved and diversified in accordance with technological advancements, leading to the current myriad population of RNA-seq tools. Our review provides a systemic overview of RNA-seq technology and 235 available RNA-seq tools across various domains published from 2008 to 2020, discussing the interdisciplinary nature of bioinformatics involved in RNA sequencing, analysis, and software development.

Published
2020

15. Trametes betulina (L.) Pilát.; Trametes cinnabarina (Jacq.) Fr.; Trametes gibbosa (Pers.) Fr.; Trametes hirsuta (Wulfen) Lloyd; Trametes pubescens (Schumach.) Pilát; Trametes suaveolens (L.) Fr.; Trametes versicolor (L.) Lloyd - POLYPORACEAE

Author

Gafforov, Yusufjon, Rašeta, Milena, İnci, Şule, Tomšovský, Michal, Yarasheva, Manzura, Rapior, Sylvie, Wan-Mohtar, Wan Abd Al Qadr Imad, Muszyńska, Bożena, Sułkowska-Ziaja, Katarzyna, Voeks, Robert, Series Editor, Stepp, John Richard, Series Editor, Khojimatov, Olim K., editor, Gafforov, Yusufjon, editor, and Bussmann, Rainer W., editor

Published
2023
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16. Laricifomes officinalis (Vill.) Kotl. & Pouzar - FOMITOPSIDACEAE

Author

Gafforov, Yusufjon, Muszyńska, Bożena, Sułkowska-Ziaja, Katarzyna, Tomšovský, Michal, Yarasheva, Manzura, Pecoraro, Lorenzo, Mykchaylova, Oksana, Rapior, Sylvie, Voeks, Robert, Series Editor, Stepp, John Richard, Series Editor, Khojimatov, Olim K., editor, Gafforov, Yusufjon, editor, and Bussmann, Rainer W., editor

Published
2023
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19. Learning Design Preferences in LMOOCs: An International Comparative Study

Author

Huertas-Abril, Cristina A. and Muszynska, Barbara

Abstract

Massive Open Online Courses (MOOCs) have come to stay supported by the development of educational technologies, and within them, Language MOOCs (LMOOCs) are a phenomenon that has risen in expectations but also shown their limitations. This study aims at comparing students' preferences from two universities (UCO, Spain, and ULS, Poland) regarding the learning design preferences of LMOOCs and analyzing whether there are differences based on sociocultural context, gender, and educational stage. The respondents (n = 260) stated to be in favor of a balance between the constructivist and instructionist educational practices in online language courses. The findings reveal significant differences regarding LMOOCs learning and feedback design in terms of gender and sociocultural context, while no significant differences were found between undergraduate and postgraduate students. These results may be used to plan innovative and effective learning situations that suit learners' needs and preferences, which should lead to higher quality of learning and higher learner engagement and satisfaction.

Published
2022
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22. Semantic chunking

Author

Muszynska, Ewa and Copestake, Ann

Subjects
NLP, semantic chunking
Abstract

Long sentences pose a challenge for natural language processing (NLP) applications. They are associated with a complex information structure leading to increased requirements for processing resources. Although the issue is present in many areas of research, there is little uniformity in the solutions used by research communities dedicated to individual NLP applications. Different aspects of the problem are addressed by different tasks, such as sentence simplification or shallow chunking. The main contribution of this thesis is the introduction of the task of semantic chunking as a general approach to reducing the cost of processing long sentences. The goal of semantic chunking is to find semantically contained fragments of a sentence representation that can be processed independently and recombined without loss of information. We anchor its principles in established concepts of semantic theory, in particular event and situation semantics. Most of the experiments in this thesis focus on semantic chunking defined on complex semantic representations in Dependency Minimal Recursion Semantics (DMRS), but we also demonstrate that the task can be performed on sentence strings. We present three chunking models: a) rule-based proof-of-concept DMRS chunking system; b) a semi-supervised sequence labelling neural model for surface semantic chunking; c) a system capable of finding semantic chunk boundaries based on the inherent structure of DMRS graphs, generalisable in the form of descriptive templates. We show how semantic chunking can be applied within a divide-and-conquer processing paradigm, using as an example the task of realization from DMRS. The application of semantic chunking yields noticeable efficiency gains without decreasing the quality of results.

Published
2020
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30. Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo.

Author

Rolletschek, Hardy, Muszynska, Aleksandra, Schwender, Jörg, Radchuk, Volodymyr, Heinemann, Björn, Hilo, Alexander, Plutenko, Iaroslav, Keil, Peter, Ortleb, Stefan, Wagner, Steffen, Kalms, Laura, Gündel, André, Shi, Hai, Fuchs, Jörg, Szymanski, Jedrzej Jakub, Braun, Hans‐Peter, and Borisjuk, Ljudmilla

Subjects
*RAPESEED, *MAGNETIC resonance imaging, *EMBRYOLOGY, *ALLOSTERIC regulation, *STRAINS & stresses (Mechanics)
Abstract

Summary: The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear.Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling.Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response.The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation. [ABSTRACT FROM AUTHOR]

Published
2024
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35. Prevalence of risk alleles in the lysyl oxidase-like 1 gene in pseudoexfoliation glaucoma patients in India

Author

Neeru A Vallabh, Chitra Sambare, Dorota Muszynska-Lyons, Sagarika Patiyal, Aditya Kelkar, Milind Killedar, Sangeeta Malani, Medha Prabhudesai, Tejaswini Walimbe, Gareth J McKay, and Colin E Willoughby

Subjects
india, latitude, lysyl oxidase-like 1, pseudoexfoliation glaucoma, pseudo-exfoliation syndrome, snp, Ophthalmology, RE1-994
Abstract

Purpose: The purpose of this study was to genotype two previously identified SNPs (rs1048661:R141L, and rs3825942:G153D) in the lysyl oxidase-like 1 (LOXL1) gene and determine their association with pseudoexfoliation glaucoma (XFG) in patients from Pune, India. Methods: All subjects underwent detailed phenotyping, and DNA extraction was performed on blood samples by using standardized techniques. Exon 1 of the LOXL1 gene containing the SNPs (rs3825942:G153D; rs1048661:R141L) were Sanger sequenced, and the results were analyzed using sequence analysis software SeqScape 2.1.1. Results: Data were analyzed from 71 patients with XFG and 81 disease-negative, age-matched controls. There was a strong association between the G allele of rs3825942 and XFG with an odds ratio of 10.2 (CI: 3.92–26.6; P < 0.001). The G allele of rs1048661 also showed an increase in risk relative to the T allele (OR = 1.49; CI: 0.88–2.51; P = 0.13), but this was not significant. Haplotype combination frequencies were estimated for rs1048661 and rs3825942; the GG haplotype was associated with a significant increase in risk (OR = 3.91; CI: 2.27–6.73; P < 0.001). Both the GA and TG haplotypes were associated with decreased XFG risk, although the latter was not significant (GA: OR = 0.08; CI: 0.03–0.21; P < 0.001; TG: OR = 0.67; CI: 0.40–1.13; P = 0.13). Conclusion: The risk G allele in rs3852942 (G153D) is strongly associated with the development of XFG in the Western Indian population. Genetic screening strategies to identify LOXL1 risk alleles in the population can assist in case definition and early diagnosis, targeting precious resources to high-risk patients.

Published
2022
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37. The SEQC2 epigenomics quality control (EpiQC) study

Author

Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Paweł P. Łabaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B. Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, and Christopher E. Mason

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group. Results Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. Conclusions The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

Published
2021
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39. Severe toxicity free survival: physician-derived definitions of unacceptable long-term toxicities following acute lymphocytic leukaemia

Author

Attarbaschi, Andishe, Adams, Madeline R, Andres-Jensen, Liv, Bardi, Edit, Barzilai-Birenboim, Shlomit, Baust, Katja, Bhojwani, Deepa, Boesten, Tineke, Calaminus, Gabriele, Conyers, Rachel, Darlington, Anne-Sophie, de Ville, Maëlle, Escherich, Gabriele, Hagleitner, Melanie, Halsey, Christina, Harila-Saari, Arja, Hou, Jen-Yin, Huang, Ting-Huan, Hudson, Melissa, Jeha, Sima, Jenney, Meriel, Kato, Motohiro, Krawczuk-Rybak, Maryna, Kremer, Leontine, Lautem, Melchior, Liu, Hse-Che, Lopez Lopez, Elixabet, Mateos, Marion, Mlynarski, Wojciech, Möricke, Anja, Muszynska-Roslan, Katarzyna, Niinimaki, Riitta, Pieters, Rob, Piette, Caroline, Raetz, Elizabeth, Ronceray, Leila, Schmiegelow, Kjeld, Toro, Claudia, Trahair, Toby, Valsecchi, Maria Grazia, van der Sluis, Inge, van Litsenburg, Raphaële, Vrooman, Lynda, Weinreb, Sigal, Wiener, Andreas, Winick, Naomi, Yano, Michihiro, Yeh, Ting-Chi, Zapotocka, Ester, Andrés-Jensen, Liv, Hagleitner, Melanie M, van Litsenburg, Raphaele R L, Hudson, Melissa M, Kremer, Leontien, Grazia Valsecchi, Maria, and Vrooman, Lynda M

Published
2021
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41. Blood cadmium levels as a marker for early lung cancer detection

Author

Lener, Marcin R., Reszka, Edyta, Marciniak, Wojciech, Lesicka, Monika, Baszuk, Piotr, Jabłońska, Ewa, Białkowska, Katarzyna, Muszyńska, Magdalena, Pietrzak, Sandra, Derkacz, Róża, Grodzki, Tomasz, Wójcik, Janusz, Wojtyś, Małgorzata, Dębniak, Tadeusz, Cybulski, Cezary, Gronwald, Jacek, Kubisa, Bartosz, Pieróg, Jarosław, Waloszczyk, Piotr, Scott, Rodney J., Jakubowska, Anna, Narod, Steven A., and Lubiński, Jan

Published
2021
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44. Grain filling in barley relies on developmentally controlled programmed cell death

Author

Volodymyr Radchuk, Van Tran, Alexander Hilo, Aleksandra Muszynska, Andre Gündel, Steffen Wagner, Joerg Fuchs, Goetz Hensel, Stefan Ortleb, Eberhard Munz, Hardy Rolletschek, and Ljudmilla Borisjuk

Subjects
Biology (General), QH301-705.5
Abstract

Radchuk et al. report on the role of vacuolar processing enzymes (VPEs) in mediating programmed cell death (PCD) in the maternal tissues of a barley grain and influencing the delivery of assimilate to the endosperm. This study presents a means of increasing the efficiency of the grain filling process in the major cereal crop species by manipulating the timing of PCD.

Published
2021
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