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1. Technology and Performance Benchmarks of IQM's 20-Qubit Quantum Computer

Author

Abdurakhimov, Leonid, Adam, Janos, Ahmad, Hasnain, Ahonen, Olli, Algaba, Manuel, Alonso, Guillermo, Bergholm, Ville, Beriwal, Rohit, Beuerle, Matthias, Bockstiegel, Clinton, Calzona, Alessio, Chan, Chun Fai, Cucurachi, Daniele, Dahl, Saga, Davletkaliyev, Rakhim, Fedorets, Olexiy, Frieiro, Alejandro Gomez, Gao, Zheming, Guldmyr, Johan, Guthrie, Andrew, Hassel, Juha, Heimonen, Hermanni, Heinsoo, Johannes, Hiltunen, Tuukka, Holland, Keiran, Hotari, Juho, Hsu, Hao, Huhtala, Antti, Hyyppä, Eric, Hämäläinen, Aleksi, Ikonen, Joni, Inel, Sinan, Janzso, David, Jaakkola, Teemu, Jenei, Mate, Jolin, Shan, Juliusson, Kristinn, Jussila, Jaakko, Khalid, Shabeeb, Kim, Seung-Goo, Koistinen, Miikka, Kokkoniemi, Roope, Komlev, Anton, Ockeloen-Korppi, Caspar, Koskinen, Otto, Kotilahti, Janne, Kuisma, Toivo, Kukushkin, Vladimir, Kumpulainen, Kari, Kuronen, Ilari, Kylmälä, Joonas, Lamponen, Niclas, Lamprich, Julia, Landra, Alessandro, Leib, Martin, Li, Tianyi, Liebermann, Per, Lintunen, Aleksi, Liu, Wei, Luus, Jürgen, Marxer, Fabian, de Griend, Arianne Meijer-van, Mitra, Kunal, Moqadam, Jalil Khatibi, Mrożek, Jakub, Mäkynen, Henrikki, Mäntylä, Janne, Naaranoja, Tiina, Nappi, Francesco, Niemi, Janne, Ortega, Lucas, Palma, Mario, Papič, Miha, Partanen, Matti, Penttilä, Jari, Plyushch, Alexander, Qiu, Wei, Rath, Aniket, Repo, Kari, Riipinen, Tomi, Ritvas, Jussi, Romero, Pedro Figueroa, Ruoho, Jarkko, Räbinä, Jukka, Saarinen, Sampo, Sagar, Indrajeet, Sargsyan, Hayk, Sarsby, Matthew, Savola, Niko, Savytskyi, Mykhailo, Selinmaa, Ville, Smirnov, Pavel, Suárez, Marco Marín, Sundström, Linus, Słupińska, Sandra, Takala, Eelis, Takmakov, Ivan, Tarasinski, Brian, Thapa, Manish, Tiainen, Jukka, Tosto, Francesca, Tuorila, Jani, Valenzuela, Carlos, Vasey, David, Vehmaanperä, Edwin, Vepsäläinen, Antti, Vienamo, Aapo, Vesanen, Panu, Välimaa, Alpo, Wesdorp, Jaap, Wurz, Nicola, Wybo, Elisabeth, Yang, Lily, and Yurtalan, Ali

Subjects
Quantum Physics
Abstract

Quantum computing has tremendous potential to overcome some of the fundamental limitations present in classical information processing. Yet, today's technological limitations in the quality and scaling prevent exploiting its full potential. Quantum computing based on superconducting quantum processing units (QPUs) is among the most promising approaches towards practical quantum advantage. In this article the basic technological approach of IQM Quantum Computers is described covering both the QPU and the rest of the full-stack quantum computer. In particular, the focus is on a 20-qubit quantum computer featuring the Garnet QPU and its architecture, which we will scale up to 150 qubits. We also present QPU and system-level benchmarks, including a median 2-qubit gate fidelity of 99.5% and genuinely entangling all 20 qubits in a Greenberger-Horne-Zeilinger (GHZ) state.

Published
2024

6. Testosterone levels at diagnosis: A key predictor of overall survival among patients with prostate cancer

Author

Ilkka Jussila, Juha P. Ahtiainen, Eija K. Laakkonen, Pirjo Käkelä, Maisa Parviainen, Heikki Pohjolainen, Jarno Aaltonen, Ninamaria Onni, Koskimaa Mikko, Teemu J. Murtola, Heini Huhtala, and Heikki Seikkula

Subjects
mortality risk, prostate cancer, prostate cancer prognosis, prostate cancer survival, survival, testosterone, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Abstract Background and Objective The exact relationship between testosterone levels at diagnosis and prostate cancer (PCa) prognosis remains inadequately explored. The objective was to determine whether serum testosterone levels at the time of PCa diagnosis are associated with overall survival. Patients and Methods The study cohort involved 2544 PCa patients, divided into three groups; normal (>10.4 nmol/L), grey zone (8.0–10.4 nmol/L) and low (2.0–8.0 nmol/L) serum testosterone groups. Survival outcomes were analysed using Kaplan–Meier curves and Cox regression models. Results The analysis revealed an increased risk of death among patients with low testosterone levels compared to those with normal levels in uni‐ (HR = 1.67, 95% CI: 1.37–2.05, p

Published
2025
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7. Design Factory -- Supporting Technology Students' Learning of General Competences through University-Industry Collaboration

Author

Lahdenperä, Juulia, Jussila, Jari, Järvenpää, Anne-Mari, and Postareff, Liisa

Abstract

Many studies emphasise the need for supporting higher education students to develop general competences. In this study, we report on the first cycle of a designbased research project conducted in the Design Factory context. The aim of the project is to understand how general competences can be integrated into course modules and within university-industry collaboration in a successful way. In this study, we report on a theoretical problem analysis and describe the design solution, namely the Design Factory implementation. We then move on to an empirical problem analysis and investigate how students reported developing general competences in the implementation. When discussing the implications for further developing the design solution, we conclude that communication has a vital role in university-industry collaboration; it is essential in clarifying the multilevel learning opportunities (e.g., the subject content, development of general competences) for students, and in aligning industry interests with educational learning objectives. We also reflect on the first development cycle as a whole and provide implications for refining the design process. Finally, we draw conclusions from the whole DBR project and provide a new theoretical perspective (cf. Edelson, 2002), namely design-based education in the co-creation contexts, that can be utilised when investigating the development of general competences in the Design Factory context.

Published
2022

8. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.

Author

Zhu, Chenxu, Chen, Jiawen, Xie, Liangqi, Hafner, Antonina, Mishra, Shreya, Wang, Duan, Strambio-De-Castillia, Caterina, Boettiger, Alistair, Ren, Bing, Li, Yun, Hu, Ming, Lee, Lindsay, Yu, Hongyu, Jia, Bojing, and Jussila, Adam

Subjects
Animals, Mice, Chromatin, In Situ Hybridization, Fluorescence, DNA
Abstract

Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .

Published
2023

9. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH.

Author

Jia, Bojing, Kern, Colin, Zhu, Quan, Ren, Bing, and Jussila, Adam

Subjects
Animals, Mice, Chromatin, In Situ Hybridization, Fluorescence, Chromosomes, DNA, Polymers
Abstract

Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.

Published
2023

14. World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens

Author

Mihaela C. Ion, Caitlin C. Bloomer, Tudor I. Bărăscu, Francisco J. Oficialdegui, Nathaniel F. Shoobs, Bronwyn W. Williams, Kevin Scheers, Miguel Clavero, Frédéric Grandjean, Marc Collas, Thomas Baudry, Zachary Loughman, Jeremy J. Wright, Timo J. Ruokonen, Christoph Chucholl, Simone Guareschi, Bram Koese, Zsombor M. Banyai, James Hodson, Margo Hurt, Katrin Kaldre, Boris Lipták, James W. Fetzner, Tommaso Cancellario, András Weiperth, Jạnis Birzaks, Teodora Trichkova, Milcho Todorov, Maksims Balalaikins, Bogna Griffin, Olga N. Petko, Ada Acevedo-Alonso, Guillermo D’Elía, Karolina Śliwińska, Anatoly Alekhnovich, Henry Choong, Josie South, Nick Whiterod, Katarina Zorić, Peter Haase, Ismael Soto, Daniel J. Brady, Phillip J. Haubrock, Pedro J. Torres, Denis Şadrin, Pavel Vlach, Cüneyt Kaya, Sang Woo Jung, Jin-Young Kim, Xavier H.C. Vermeersch, Maciej Bonk, Radu Guiaşu, Muzaffer M. Harlioğlu, Jane Devlin, Irmak Kurtul, Dagmara Błońska, Pieter Boets, Hossein Masigol, Paul R. Cabe, Japo Jussila, Trude Vrålstad, David V. Beresford, Scott M. Reid, Jiří Patoka, David A. Strand, Ali S. Tarkan, Frédérique Steen, Thomas Abeel, Matthew Harwood, Samuel Auer, Sandor Kelly, Ioannis A. Giantsis, Rafał Maciaszek, Maria V. Alvanou, Önder Aksu, David M. Hayes, Tadashi Kawai, Elena Tricarico, Adroit Chakandinakira, Zanethia C. Barnett, Ştefan G. Kudor, Andreea E. Beda, Lucian Vîlcea, Alexandru E. Mizeranschi, Marian Neagul, Anton Licz, Andra D. Cotoarbă, Adam Petrusek, Antonín Kouba, Christopher A. Taylor, and Lucian Pârvulescu

Subjects
Aphanomyces astaci, Endangered species, Invasive species, Open data, Astacidae, Cambaridae, Medicine, Biology (General), QH301-705.5
Abstract

Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.

Published
2024
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15. How far has research into disruptive innovations in the field of sustainability come to date?

Author

Ahmadov Tarlan, Durst Susanne, Eriksson Taina, Jussila Maria, and Saaristo Aino

Subjects
Disruptive innovation, Sustainability, Innovation, Sustainable development, Critical review, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

The term ‘disruptive innovation’ has been on everyone's lips for some years now, both in theory and in practice. This type of innovation is considered promising when it comes to the transition to sustainability. Based on a critical literature review comprising 121 academic articles, this study provides a systematic overview of the state of research on disruptive innovation for sustainability over 20 years. This overview makes it possible to determine whether and how an accumulation of knowledge has taken place in this area. The study reports on the selected theories, methods and definitions of the core concepts used. A thematic analysis was conducted that identified five broad themes, namely business models, people skills, supply chains, product/service development and transformations/transitions. In addition, the evolution of thematic areas over time is presented. The results indicate that there is a significant need for greater knowledge accumulation. This paper proposes concrete directions for future research to come closer to this goal.

Published
2024
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16. A Scintillation Arc Survey of 22 Pulsars with Low to Moderate Dispersion Measures

Author

Stinebring, Dan R., Rickett, Barney J., Minter, Anthony H., Hill, Alex S., Jussila, Adam P., Mathis, Lele, McLaughlin, Maura A., Ocker, Stella Koch, and Ransom, Scott M.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies
Abstract

Context: By providing information about the location of scattering material along the line of sight (LoS) to pulsars, scintillation arcs are a powerful tool for exploring the distribution of ionized material in the interstellar medium. Here, we present observations that probe the ionized ISM on scales of $\sim$~0.001 -- 30~au. Aims: We have surveyed pulsars for scintillation arcs in a relatively unbiased sample with DM < 100 pc cm-3. We present multi-frequency observations of 22 low to moderate DM pulsars. Many of the 54 observations were also observed at another frequency within a few days. Methods: For all observations we present dynamic spectra, autocorrelation functions, and secondary spectra. We analyze these data products to obtain scintillation bandwidths, pulse broadening times, and arc curvatures. Results: We detect definite or probable scintillation arcs in 19 of the 22 pulsars and 34 of the 54 observations, showing that scintillation arcs are a prevalent phenomenon. The arcs are better defined in low DM pulsars. We show that well-defined arcs do not directly imply anisotropy of scattering. Only the presence of reverse arclets and a deep valley along the delay axis, which occurs in about 20\% of the pulsars in the sample, indicates substantial anisotropy of scattering. Conclusions: The survey demonstrates substantial patchiness of the ionized ISM on both au size scales transverse to the line of sight and on $\sim$~100~pc scales along it. We see little evidence for distributed scattering along most lines of sight in the survey., Comment: 34 pages, 5 tables, 12 figures. In addition, there are two figure sets, one with 54 .png files in it and one with 22 .png files in it. These are included in the /anc directory

Published
2022
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18. Quantifying wetness variability in aapa mires with Sentinel‐2: towards improved monitoring of an EU priority habitat

Author

Tytti Jussila, Risto K. Heikkinen, Saku Anttila, Kaisu Aapala, Mikko Kervinen, Juha Aalto, and Petteri Vihervaara

Subjects
Boreal fen, drought impacts, ecosystem monitoring, image classification, satellite remote sensing, surface moisture, Technology, Ecology, QH540-549.5
Abstract

Abstract Aapa mires are waterlogged northern peatland ecosystems characterized by a patterned surface structure where water‐filled depressions (‘flarks’) alternate with drier hummock strings. As one of the EU Habitat Directive priority habitats, aapa mires are important for biodiversity and carbon cycling, harbouring several red‐listed species and supporting unique species communities. Due to their sensitivity to hydrological disturbances, reliable, up‐to‐date and systematic information on the hydrological condition and responses of mires is crucial and required for multiple purposes ranging from carbon exchange modelling to EU Habitats Directive reporting and conservation and ecosystem restoration planning. Here, we demonstrate the usability of Sentinel‐2 satellite data in a semi‐automatic cloud‐based approach to retrieve large‐scale information on aapa mire hydrological variability. Two satellite‐derived metrics, soil moisture index and the extent of water‐saturated surfaces based on pixel‐wise classification, are used to quantify monthly and interannual wetness variation between 2017 and 2020 across Natura 2000 aapa mires in Finland, including responses to the extreme drought of 2018. The results revealed high temporal variability in wetness, particularly in the southern parts of the aapa mire zone and generally in the late summer months interannually. Observations from the drought summer showed that one third of usually year‐round wet flark surfaces may be exposed to drying during climatic extremes. Responses varied between sites and regions, implicating the significance of environmental factors for drought resistance: some sites maintained high levels of moisture, whereas others lost wet surfaces completely. Our study provides the first comprehensive national‐level representation of seasonal and interannual wetness variability and drought‐sensitivity of pristine aapa mire sites. The approach and methods used here can be directly upscaled outside protected areas and to other EU countries. Thus, they provide a means for harmonized, systematic large‐scale monitoring of this priority habitat, as well as valuable information for other applications supporting peatland conservation and research.

Published
2024
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20. A Comprehensive Analysis of Speech Disfluencies in Autistic Young Adults and Control Young Adults: Group Differences in Typical, Stuttering-Like, and Atypical Disfluencies

Author

Pirinen, Veera, Loukusa, Soile, Dindar, Katja, Mäkinen, Leena, Hurtig, Tuula, Jussila, Katja, Mattila, Marja-Leena, and Eggers, Kurt

Abstract

Purpose: The purpose of this study was to examine the nature of speech disfluencies in autistic young adults and controls by using a wide-range disfluency classification of typical disfluencies (TD; i.e., filled pauses, revisions, abandoned utterances, and multisyllable word and phrase repetitions), stuttering-like disfluencies (SLD; i.e., sound and syllable repetitions, monosyllable word repetitions, prolongations, blocks, and broken words), and atypical disfluencies (AD; i.e., word-final prolongations and repetitions and atypical insertions). Method: Thirty-two autistic young adults and 35 controls completed a narrative telling task based on socially complex events. Frequencies of total disfluencies, TD, SLD, AD and stuttering severity were compared between groups. Results: The overall frequency of disfluencies was significantly higher in the autistic group and significant between-group differences were found for all disfluency categories. The autistic group produced significantly more revisions, filled pauses, and abandoned utterances, and each subtype of SLD and AD than the control group. In total, approximately every fourth autistic participants scored at least a very mild severity of stuttering, and every fifth produced more than three SLD per 100 syllables. Conclusions: Disfluent speech can be challenging for effective communication. This study revealed that the speech of autistic young adults was highly more disfluent than that of the controls. The findings provide information on speech disfluency characteristics in autistic young adults and highlight the importance of evaluating speech disfluency with a wide-range disfluency classification in autistic persons in order to understand their role in overall communication. The results of this study offer tools for SLPs to evaluate and understand the nature of disfluencies in autistic persons.

Published
2023
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21. Non-Linguistic Comprehension, Social Inference and Empathizing Skills in Autistic Young Adults, Young Adults with Autistic Traits and Control Young Adults: Group Differences and Interrelatedness of Skills

Author

Loukusa, Soile, Gabbatore, Ilaria, Kotila, Aija R., Dindar, Katja, Mäkinen, Leena, Leinonen, Eeva, Mämmelä, Laura, Bosco, Francesca M., Jussila, Katja, Ebeling, Hanna, Hurtig, Tuula M., and Mattila, Marja-Leena

Abstract

Background: Despite increasing knowledge of social communication skills of autistic people, the interrelatedness of different skills such as non-linguistic comprehension, social inference and empathizing skills is not much known about. A better understanding of the complex interplay between different domains of social communication helps us to develop assessment protocols for individuals with social communication difficulties. Aims: To compare the performances of autistic young adults, young adults with autistic traits identified in childhood and control young adults in social communication tasks measuring non-linguistic comprehension, social inference and empathizing skills. In addition, to examine associations between the different social communication measures. Methods & Procedures: Autistic young adults (n = 34), young adults with autistic traits (n = 19) and control young adults (n = 36) completed the extra- and paralinguistic scales of the Assessment Battery for Communication (ABaCo), the Faux Pas Recognition Test, Social-Pragmatic Questions (SoPra) and the Empathy Quotient (EQ). Outcomes & Results: Group differences were found in the performance in the ABaCo, SoPra and EQ scores. Compared with the control young adults, autistic young adults scored lower. The performance of the young adults in the autistic traits group fell in between the other two groups. There were no group differences in the Faux Pas Recognition Test. The variability within the groups was large in all measurements. In the control group, there was a significant correlation between EQ and SoPra scores and between the Faux Pas and SoPra scores. In the autistic group, a significant correlation was found between Faux Pas and SoPra scores. Also, other patterns were observed but these were not statistically significant. Conclusions & Implications: The young adults with autistic traits fell in between the control and autistic young adults, highlighting the presence of the continuum in the terms of features of social communication. The results support other current research that suggests that theory of mind and other social communication skills may not be universally or widely impaired in all autistic individuals without cognitive deficits. Although all tasks examined social communication skills, only a small number of significant correlations were found between test scores. This highlights that clinical conclusions about a person's social communication should be based on the outcomes of different types of methods measuring different aspects of social communication. It is clear that the interrelatedness of different social communication skills needs further research.

Published
2023
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23. Global Consensus Recommendations on Improving the Safety of Chronic Total Occlusion Interventions

Author

Rafeh, Nidal Abi, Agostoni, Pierfrancesco, Alaswad, Khaldoon, Araya, Mario, Avran, Alexandre, Ayoub, Mohamed, Azzalini, Lorenzo, Babunashvili, Avtandil M., Bayani, Baktash, Behnes, Michael, Bhindi, Ravinay, Boudou, Nicolas, Boukhris, Marouane, Bozinovic, Nenad Z., Bryniarski, Leszek, Bufe, Alexander, Buller, Christopher E., Burke, M. Nicholas, Buettner, Heinz Joachim, Cardoso, Pedro, Carlino, Mauro, Chan, Chi-Kin, Chen, Jiyan, Christiansen, Evald Hoej, Colombo, Antonio, Croce, Kevin, Damas de los Santos, Felix, de Martini, Tony, Dens, Joseph, di Mario, Carlo, Doshi, Darshan, Dou, Kefei, Egred, Mohaned, Elbarouni, Basem, ElGuindy, Ahmed M., Escaned, Javier, Furkalo, Sergey, Gagnor, Andrea, Galassi, Alfredo R., Garbo, Roberto, L.Gasparini, Gabriele, Ge, Junbo, Ge, Lei, Goel, Pravin Kumar, Goktekin, Omer, Gonzalo, Nieves, Gorgulu, Sevket, Grancini, Luca, Hall, Allison B., Hanratty, Colm, Harb, Stefan, Harding, Scott A., Hatem, Raja, Hellig, Farrel, Henriques, Jose P.S., Hildick-Smith, David, Hill, Jonathan M., Hoye, Angela, Jaber, Wissam, Jaffer, Farouc A., Jang, Yangsoo, Jussila, Risto, Kalnins, Artis, Kalra, Sanjog, Kandzari, David E., Kao, Hsien-Li, Karmpaliotis, Dimitri, Kassem, Hussien Heshmat, Kearney, Kathleen E., Kerrigan, Jimmy, Khatri, Jaikirshan, Khelimskii, Dmitri, Kirtane, Ajay J., Knaapen, Paul, Kornowski, Ran, Krestyaninov, Oleg, Kumar, V. Ganesh, Kumar, Prathap, Lamelas, Pablo Manuel, Lee, Seung-Whan, Lefevre, Thierry, Leibundgut, Gregor, Leung, Raymond, Leung, Sum-Kin, Li, Yu, Li, Yue, Lim, Soo-Teik, Lo, Sidney, Lombardi, William, Maran, Anbukarasi, McEntegart, Margaret, Moses, Jeffrey, Munawar, Muhammad, Nagamatsu, Wataru, Navarro, Andres, Ngo, Hung M., Nicholson, William, Oksnes, Anja, Olivecrona, Goran K., Padilla, Lucio, Patel, Mitul, Pershad, Ashish, Postu, Marin, Pyxaras, Stylianos, Qian, Jie, Quadros, Alexandre, Hanna Quesada, Franklin Leonardo, Råmunddal, Truls, Rao, Vithala Suryaprakasa, Rathore, Sudhir, Reifart, Nicolaus, Riley, Robert F., Rinfret, Stephane, Saghatelyan, Meruzhan, Santiago, Ricardo, Seth, Ashok, Sianos, Georgios, Smith, Elliot, Spaedy, Anthony, Spratt, James, Stone, Gregg W., Strange, Julian W., Tammam, Khalid O., Thompson, Craig A., Toma, Aurel, Tremmel, Jennifer A., Ungi, Imre, Vadalà, Giuseppe, Vo, Minh, Vu, Vu Hoang, Walsh, Simon, Weilenmann, Daniel, Werner, Gerald S., Wojcik, Jaroslaw, Wollmuth, Jason, Wu, Chiung-Jen, Xu, Bo, Yamane, Masahisa, Ybarra, Luiz F., Yeh, Robert W., Zambakides, Chris, Zhang, Qi, Wu, Eugene B., Kalyanasundaram, Arun, Brilakis, Emmanouil S., Mashayekhi, Kambis, and Tsuchikane, Etsuo

Published
2024
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25. Thrombosis risk in single- and double-heterozygous carriers of factor V Leiden and prothrombin G20210A in FinnGen and the UK Biobank

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Viollet, Coralie, Petrovski, Slavé, Chen, Chia-Yen, John, Sally, Okafo, George, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Pendergrass, Rion, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Vlahiotis, Anna, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Waterworth, Dawn, O´Donnell, Chris, Renaud, Nicole, Mäkelä, Tomi P., Kaprio, Jaakko, Ruddock, Minna, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Kristiansson, Kati, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Ding, Zhihao, Jung, Marc, Tuoken, Hanati, Biswas, Shameek, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Obeidat, Ma´en, Chung, Jonathan, Zierer, Jonas, Niemi, Mari, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Runz, Heiko, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Laitinen, Tarja, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Paul, Dirk, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Rivas, Manuel, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Cooper, Helen, Öller, Denise, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Ryu, Justine, Rämö, Joel T., Jurgens, Sean J., Sanna-Cherchi, Simone, Bauer, Kenneth A., Haj, Amelia, Choi, Seung Hoan, Ellinor, Patrick T., and Bendapudi, Pavan K.

Published
2024
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27. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Petrovski, Slavé, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Yang, Robert, ODonnell, Chris, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Rivas, Manuel, Waterworth, Dawn, Renaud, Nicole, Obeidat, Maen, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Viollet, Coralie, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Als, Thomas Damm, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Kristiansson, Kati, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Cooper, Helen, Öller, Denise, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Pärn, Kalle, Kals, Mart, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Youssef, Omar, Zidi-Mouaffak, Yossra H.S., and Tamlander, Max

Published
2024
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28. Diagnostic performance of short noncontrast biparametric 3-T MRI for tonsillar infections: comparison with a full protocol including contrast-enhanced sequences

Author

Jari-Pekka Vierula, Janne Nurminen, Ville Jussila, Mikko Nyman, Jaakko Heikkinen, Bernd Pape, Kaarlo Sorvettula, Kimmo Mattila, and Jussi Hirvonen

Subjects
Emergency medicine, Magnetic resonance imaging, Observer variation, Peritonsillar abscess, Tonsillitis, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract

Abstract Background We investigated whether a short, 5-min magnetic resonance imaging (MRI) protocol consisting of only axial T2-weighted and diffusion-weighted imaging (DWI) sequences can discriminate between tonsillar infections, peritonsillar abscesses and deeply extending abscesses in a retrospective, blinded, multireader setting. Methods We included patients sent by emergency physicians with suspected pharyngotonsillar infections who underwent emergency neck 3-T MRI from April 1 2013 to December 31 2018. Three radiologists (with 10−16 years of experience) reviewed the images for abscesses and their extension into deep neck spaces. Data were reviewed first using only axial T2-weighted Dixon images and DWI (short protocol) and second including other sequences and contrast-enhanced T1-weighted Dixon images (full protocol). Diagnostic accuracy, interobserver agreement, and reader confidence were measured. Surgical findings and clinical course served as standard of reference. Results The final sample consisted of 52 patients: 13 acute tonsillitis with no abscesses, 19 peritonsillar abscesses, and 20 deeply extending abscesses. Using the short protocol, diagnostic accuracy for abscesses across all readers was good-to-excellent: sensitivity 0.93 (95% confidence interval 0.87−0.97), specificity 0.85 (0.70−0.93), accuracy 0.91 (0.85−0.95). Using the full protocol, respective values were 0.98 (0.93−1.00), 0.85 (0.70−0.93), and 0.95 (0.90−0.97), not significantly different compared with the short protocol. Similar trends were seen with detecting deep extension. Interobserver agreement was similar between protocols. However, readers had higher confidence in diagnosing abscesses using the full protocol. Conclusions Short MRI protocol showed good-to-excellent accuracy for tonsillar abscesses. Contrast-enhanced images improved reader confidence but did not affect diagnostic accuracy or interobserver agreement. Relevance statement Short protocol consisting only of T2-weighted Dixon and DWI sequences can accurately image tonsillar abscesses, which may improve feasibility of emergency neck MRI. Key points • The short 3-T MRI protocol (T2-weighted images and DWI) was faster (5 min) than the full protocol including T1-weighted contrast-enhanced images (24 min). • The short 3-T MRI protocol showed good diagnostic accuracy for pharyngotonsillar abscesses. • Contrast-enhanced sequences improved reader confidence but did not impact diagnostic accuracy or interobserver agreement. Graphical Abstract

Published
2023
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29. TWINGEN: protocol for an observational clinical biobank recall and biomarker cohort study to identify Finnish individuals with high risk of Alzheimer’s disease

Author

Tommi Vasankari, Henri Vähä-Ypyä, Oskari Heikinheimo, Athena Matakidou, Jaakko Kaprio, Eero Vuoksimaa, Ying Wu, Kai Kaarniranta, Peeter Karihtala, Wei Zhou, Caroline Fox, Sanna-Kaisa Herukka, Sarah Smith, Apinya Lertratanakul, Katri Kaukinen, Johannes Kettunen, Minna Männikkö, Eeva Sliz, Markus Perola, Veikko Salomaa, Hilkka Soininen, Ilkka Kalliala, Mika Kähönen, Hao Chen, Andrey Loboda, Laure Morin-Papunen, Terhi Piltonen, Anders Mälarstig, Jason Miller, Jussi Hernesniemi, Henrike Heyne, Sirkku Peltonen, Daniel Gordin, Masahiro Kanai, Benjamin Challis, Juha Sinisalo, David Rice, Fredrik Åberg, Aarno Palotie, Samuli Ripatti, Oili Kaipiainen-Seppänen, Aki Havulinna, Satu Strausz, Tuomo Kiiskinen, Sanni Ruotsalainen, Jukka Koskela, Tuula Palotie, Mark Daly, Howard Jacob, Heiko Runz, Sally John, Robert Plenge, Mark McCarthy, Julie Hunkapiller, Dawn Waterworth, Petri Virolainen, Terhi Kilpi, Jukka Partanen, Anne Pitkäranta, Veli-Matti Kosma, Outi Tuovila, Raimo Pakkanen, Shameek Biswas, Xinli Hu, Johanna Schleutker, Mikko Arvas, Olli Carpen, Reetta Hinttala, Arto Mannermaa, Valtteri Julkunen, Anne Remes, Reetta Kälviäinen, Mikko Hiltunen, Jukka Peltola, Pentti Tienari, Juha Rinne, Adam Ziemann, Jeffrey Waring, Nizar Smaoui, Anne Lehtonen, Susan Eaton, Sanni Lahdenperä, Natalie Bowers, Edmond Teng, Fanli Xu, David Pulford, Martti Färkkilä, Sampsa Pikkarainen, Airi Jussila, Timo Blomster, Mikko Kiviniemi, Markku Voutilainen, Fedik Rahimov, Joseph Maranville, Tim Lu, Kirsi Kalpala, Melissa Miller, Linda McCarthy, Kari Eklund, Antti Palomäki, Pia Isomäki, Laura Pirilä, Johanna Huhtakangas, Marla Hochfeld, Nan Bing, Jorge Esparza Gordillo, Nina Mars, Tarja Laitinen, Margit Pelkonen, Paula Kauppi, Hannu Kankaanranta, Terttu Harju, Hubert Chen, Teemu Niiranen, Kaj Metsärinne, Marja-Riitta Taskinen, Tiinamaija Tuomi, Jari Laukkanen, Audrey Chu, Jaakko Parkkinen, Heikki Joensuu, Tuomo Meretoja, Lauri Aaltonen, Annika Auranen, Päivi Auvinen, Klaus Elenius, Relja Popovic, Bridget Riley-Gillis, Jennifer Schutzman, Heli Lehtonen, Stefan McDonough, Diptee Kulkarni, Terhi Ollila, Hannu Uusitalo, Erich Strauss, Kaisa Tasanen, Laura Huilaja, Katariina Hannula-Jouppi, Teea Salmi, Leena Koulu, David Choy, Anu Jalanko, Risto Kajanne, Mari Kaunisto, Chia-Yen Chen, Robert Yang, Kirsi Auro, Clement Chatelain, Mitja Kurki, Juha Karjalainen, Kimmo Palin, Priit Palta, Susanna Lemmelä, Manuel Rivas, Arto Lehisto, Andrea Ganna, Vincent Llorens, Kati Kristiansson, Kati Hyvärinen, Jarmo Ritari, Katri Pylkäs, Minna Karjalainen, Tuomo Mantere, Eeva Kangasniemi, Sami Heikkinen, Eija Laakkonen, Anu Loukola, Päivi Laiho, Tuuli Sistonen, Essi Kaiharju, Markku Laukkanen, Elina Järvensivu, Sini Lähteenmäki, Lotta Männikkö, Regis Wong, Hannele Mattsson, Tero Hiekkalinna, Kati Donner, Kalle Pärn, Elina Kilpeläinen, Hannele Laivuori, Harri Siirtola, Sirpa Soini, Teijo Kuopio, Ioanna Tachmazidou, Katja Kivinen, Pekka Nieminen, Adam Platt, Sanna Toppila-Salmi, Antti Mäkitie, Elmo Saarentaus, Kristiina Aittomäki, Elisabeth Widen, Marja Vääräsmäki, Erkki Isometsä, Laura Addis, Mika Helminen, Taneli Raivio, Mart Kals, Majd Mouded, Hanna Ollila, Vuokko Anttonen, Tarja Kokkola, Robert Graham, Amanda Elliott, Ali Abbasi, Bridget Riley-Gills, Dirk Paul, Katherine Klinger, Deepak Raipal, Antti Hakanen, Raisa Serpi, Johanna Mäkelä, Mengzhen Liu, Neha Raghavan, Adriana Huertas-Vazquez, Nicole Renaud, Roosa Kallionpää, John Eicher, Minna Raivio, Juulia Partanen, Riitta Lahesmaa, Glenda Lassi, Joanna Betts, Rajashree Mishra, Felix Vaura, Joel Rämö, Mary Pat Reeve, Johanna Mattson, Sauli Vuoti, Esa Pitkänen, Joni A Turunen, Stephanie Loomis, Pirkko Pussinen, Aino Salminen, Tuula Salo, Ulla Palotie, Maria Siponen, Liisa Suominen, Päivi Mäntylä, Ulvi Gursoy, Kirsi Sipilä, Venla Kurra, Laura Kotaniemi-Talonen, Outi Uimari, Taru Tukiainen, Niko Välimäki, Janet Kumar, Juha Mehtonen, Shabbeer Hassan, Pietro Della Briotta Parolo, Mutaamba Maasha, Javier Garcia-Tabuenca, Jiwoo Lee, Kristin Tsuo, Nina Pitkänen, Eero Punkka, Huei-Yi Shen, Mervi Aavikko, L. Elisa Lahtela, Timo P. Sipilä, Awaisa Ghazal, Sami Koskelainen, Teemu Paajanen, Shuang Luo, Javier Gracia-Tabuenca, Tiina Luukkaala, Iida Vähätalo, Marco Hautalahti, Tom Southerington, Paula Iso-Markku, Jaana Suvisaari, Zhihao Ding, Qingqin S Li, Amy Hart, Perttu Terho, Alessandro Porello, Anastasia Kytölä, Antti Aarnisalo, Aoxing Liu, Argyro Bizaki-Vallaskangas, Auli Toivola, Debby Ngo, Dermot Reilly, Ekaterina Khramtsova, Elisa Rahikkala, Eric Green, Eveliina Salminen, Fabiana Farias, George Okafo, Heidi Silven, Heli Salminen-Mankonen, Henna Palin, Iiris Hovatta, Jaakko Tyrmi, Jae-Hoon Sul, Jenni Aittokallio, Jyrki Pitkänen, Karen He, Katriina Aalto-Setälä, Maarit Niinimäki, Malla-Maria Linna, Marc Jung, Margaret G. Ehm, Marianna Niemi, Meijian Guan, Mike Mendelson, Minna Brunfeldt, Natalia Pujol, Nathan Lawless, Oluwaseun Alexander Dada, Rigbe Weldatsadik, Riikka Arffman, Rion Pendergrass, Sahar Mozaffari, Samuel Lessard, Sanna Siltanen, Shanmukha Sampath Padmanabhuni, Simonne Longerich, Susanna Savukoski, Thomas Damm Als, Timo Hiltunen, Tomi P. Mäkelä, Triin Laisk, Tytti Willberg, Varpu Jokimaa, Aija Kyttälä, Toni T Saari, Aino Aaltonen, Sari Aaltonen, Sari Kärkkäinen, Hilkka Liedes, Miina Ollikainen, Teemu Palviainen, Ilona Ruotsalainen, Mia Urjansson, Markus M Forsberg, Jaakko Lähteenmäki, Pia Nyberg, Jani Tikkanen, Mari E. Niemi, and Rodos Rodosthenous

Subjects
Medicine
Abstract

Introduction A better understanding of the earliest stages of Alzheimer’s disease (AD) could expedite the development or administration of treatments. Large population biobanks hold the promise to identify individuals at an elevated risk of AD and related dementias based on health registry information. Here, we establish the protocol for an observational clinical recall and biomarker study called TWINGEN with the aim to identify individuals at high risk of AD by assessing cognition, health and AD-related biomarkers. Suitable candidates were identified and invited to participate in the new study among THL Biobank donors according to TWINGEN study criteria.Methods and analysis A multi-centre study (n=800) to obtain blood-based biomarkers, telephone-administered and web-based memory and cognitive parameters, questionnaire information on lifestyle, health and psychological factors, and accelerometer data for measures of physical activity, sedentary behaviour and sleep. A subcohort is being asked to participate in an in-person neuropsychological assessment (n=200) and wear an Oura ring (n=50). All participants in the TWINGEN study have genome-wide genotyping data and up to 48 years of follow-up data from the population-based older Finnish Twin Cohort (FTC) study of the University of Helsinki. The data collected in TWINGEN will be returned to THL Biobank from where it can later be requested for other biobank studies such as FinnGen that supported TWINGEN.Ethics and dissemination This recall study consists of FTC/THL Biobank/FinnGen participants whose data were acquired in accordance with the Finnish Biobank Act. The recruitment protocols followed the biobank protocols approved by Finnish Medicines Agency. The TWINGEN study plan was approved by the Ethics Committee of Hospital District of Helsinki and Uusimaa (number 16831/2022). THL Biobank approved the research plan with the permission no: THLBB2022_83.

Published
2024
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30. Unlocking success: key elements of sustainable business models in the wooden multistory building sector

Author

Emil Nagy, Jaakko Jussila, Liina Häyrinen, Katja Lähtinen, Cecilia Mark-Herbert, Ritva Toivonen, Anne Toppinen, and Anders Roos

Subjects
business strategy, co-creation of value, sustainability transition, sustainable business model, timber construction, Economic theory. Demography, HB1-3840
Abstract

Few studies have investigated the processes and strategic interactions among the Wooden Multistory Construction (WMC) industry actors, its customers, and local policymakers. Further insights into this field are needed for a sustainability transition in the construction sector. This study aims to explain WMC’s corporate sustainability strategies for co-creation with customers and municipalities. This was based on interviews with key informants in the sector and WMC actors using three case studies in Sweden. Our interviews focused on business processes, interactions with users and municipalities, sustainability, and innovation in the WMC market. The findings reflect the notion of a slow transition in the Swedish WMC market toward using more wood as a bearing structure, which is supported by the competitive advantages and climate performance of wood. The three case studies indicated that the corporate focus is currently placed on incremental improvements in operations, price competitiveness, and successful project management. However, in contexts where wood construction is seen as a unique advantage, collaborations between the construction industry and end users have developed and served as novel platforms for WMC market development. The study concludes that WMCl growth hinges on the industry’s housing offerings prioritizing quality, affordability, and swift construction.

Published
2024
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33. CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Author

Huang, Hui, Zhu, Quan, Jussila, Adam, Han, Yuanyuan, Bintu, Bogdan, Kern, Colin, Conte, Mattia, Zhang, Yanxiao, Bianco, Simona, Chiariello, Andrea M, Yu, Miao, Hu, Rong, Tastemel, Melodi, Juric, Ivan, Hu, Ming, Nicodemi, Mario, Zhuang, Xiaowei, and Ren, Bing

Subjects
Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Binding Sites, CCCTC-Binding Factor, Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Insulator Elements, Mice, Mouse Embryonic Stem Cells, Promoter Regions, Genetic, Protein Binding, Transcription, Genetic, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

Published
2021

34. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

Author

Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li, and Ming Hu

Subjects
Science
Abstract

Abstract Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .

Published
2023
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38. Vertical profiles of volatile organic compounds and fine particles in atmospheric air by using an aerial drone with miniaturized samplers and portable devices

Author

E. D. Pusfitasari, J. Ruiz-Jimenez, A. Tiusanen, M. Suuronen, J. Haataja, Y. Wu, J. Kangasluoma, K. Luoma, T. Petäjä, M. Jussila, K. Hartonen, and M.-L. Riekkola

Subjects
Physics, QC1-999, Chemistry, QD1-999
Abstract

The increase in volatile organic compound (VOC) emissions released into the atmosphere is one of the main threats to human health and climate. VOCs can adversely affect human life through their contribution to air pollution directly and indirectly by reacting via several mechanisms in the air to form secondary organic aerosols. In this study, an aerial drone equipped with miniaturized air-sampling systems including up to four solid-phase microextraction (SPME) Arrows and four in-tube extraction (ITEX) samplers for the collection of VOCs, along with portable devices for the real-time measurement of black carbon (BC) and total particle numbers at high altitudes was exploited. In total, 135 air samples were collected under optimal sampling conditions from 4 to 14 October 2021 at the boreal forest SMEAR II station, Finland. A total of 48 different VOCs, including nitrogen-containing compounds, alcohols, aldehydes, ketones, organic acids, and hydrocarbons, were detected at different altitudes from 50 to 400 m above ground level with concentrations of up to 6898 ng m−3 in the gas phase and 8613 ng m−3 in the particle phase. Clear differences in VOC distributions were seen in samples collected from different altitudes, depending on the VOC sources. It was also possible to collect aerosol particles by the filter accessory attached on the ITEX sampling system, and five dicarboxylic acids were quantified with concentrations of 0.43 to 10.9 µg m−3. BC and total particle number measurements provided similar diurnal patterns, indicating their correlation. For spatial distribution, BC concentrations were increased at higher altitudes, being 2278 ng m−3 at 100 m and 3909 ng m−3 at 400 m. The measurements aboard the drone provided insights into horizontal and vertical variability in BC and aerosol number concentrations above the boreal forest.

Published
2023
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39. The public health impact of poor sleep on severe COVID-19, influenza and upper respiratory infections

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Petrovski, Slavé, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Yang, Robert, O´Donnell, Chris, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Rivas, Manuel, Waterworth, Dawn, Renaud, Nicole, Obeidat, Ma´en, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Viollet, Coralie, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Als, Thomas Damm, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Kristiansson, Kati, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Pärn, Kalle, Kals, Mart, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Jones, Samuel E., Maisha, Fahrisa I., Strausz, Satu J., Lammi, Vilma, Cade, Brian E., Tervi, Anniina, Helaakoski, Viola, Broberg, Martin E., Lane, Jacqueline M., Redline, Susan, Saxena, Richa, and Ollila, Hanna M.

Published
2023
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40. Developing students’ transversal skills: A case study of an international product development project

Author

Jari Jussila, Milla Räty, and Sanna-Maaria Siintoharju

Subjects
21st-century skills, Design Factory, Transversal skills, Product development, Technology (General), T1-995, Technological innovations. Automation, HD45-45.2
Abstract

One of the biggest challenges faced by higher education is the development of students’ transversal skills. With the aim of uncovering practices that support the development of students’ transversal skills, this case study investigates the students’ perceptions of transversal skills development in an international product development project organised by inno.space Design Factory Mannheim and HAMK Design Factory. The interviews to survey the students’ expectations early in the course and during the end of the course, point out the importance of physical learning environments, student mobility and interdisciplinary teams for transversal skills development.

Published
2023
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42. Optical harmonic generation in monolayer group-VI transition metal dichalcogenides

Author

Autere, Anton, Jussila, Henri, Marini, Andrea, Saavedra, J. R. M., Dai, Yunyun, Saynatjoki, Antti, Karvonen, Lasse, Yang, He, Amirsolaimani, Babak, Norwood, Robert A., Peyghambarian, Nasser, Lipsanen, Harri, Kieu, Khanh, de Abajo, Francisco J. Garcia, and Sun, Zhipei

Subjects
Physics - Optics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Monolayer transition metal dichalcogenides (TMDs) exhibit high nonlinear optical (NLO) susceptibilities. Experiments on MoS$_2$ have indeed revealed very large second-order ($\chi^{(2)}$) and third-order ($\chi^{(3)}$) optical susceptibilities. However, third harmonic generation results of other layered TMDs has not been reported. Furthermore, the reported $\chi^{(2)}$ and $\chi^{(3)}$ of MoS$_2$ vary by several orders of magnitude, and a reliable quantitative comparison of optical nonlinearities across different TMDs has remained elusive. Here, we investigate second- and third-harmonic generation, and three-photon photoluminescence in TMDs. Specifically, we present an experimental study of $\chi^{(2)}$, and $\chi^{(3)}$ of four common TMD materials (\ce{MoS2}, \ce{MoSe2}, \ce{WS2} and \ce{WSe2}) by placing different TMD flakes in close proximity to each other on a common substrate, allowing their NLO properties to be accurately obtained from a single measurement. $\chi^{(2)}$ and $\chi^{(3)}$ of the four monolayer TMDs have been compared, indicating that they exhibit distinct NLO responses. We further present theoretical simulations of these susceptibilities in qualitative agreement with the measurements. Our comparative studies of the NLO responses of different two-dimensional layered materials allow us to select the best candidates for atomic-scale nonlinear photonic applications, such as frequency conversion and all-optical signal processing., Comment: 7 pages, 5 figures, To be appeared in Physical Review B

Published
2018
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45. List of contributors

Author

Abi Rafeh, Nidal, primary, Agostoni, Pierfrancesco, additional, Akyuz, Sukru, additional, Alaswad, Khaldoon, additional, Ali, Ziad A., additional, Allana, Salman S., additional, Alraies, Chadi, additional, Araya, Mario, additional, Avran, Alexandre, additional, Azzalini, Lorenzo, additional, Babunashvili, Avtandil, additional, Banerjee, Subhash, additional, Bangalore, Sripal, additional, Bayani, Baktash, additional, Behnes, Michael, additional, Bhindi, Ravinay, additional, Boudou, Nicolas, additional, Božinović, Nenad Ž., additional, Bryniarski, Leszek, additional, Bufe, Alexander, additional, Buller, Christopher E., additional, Burke, M. Nicholas, additional, Cardoso, Pedro Pinto, additional, Carlino, Mauro, additional, Cavalcante, Joao L., additional, Chami, Tarek, additional, Chandwaney, Raj H., additional, Charitakis, Konstantinos, additional, Cheng, Victor Y., additional, Choi, James W., additional, Christiansen, Evald Høj, additional, Chugh, Yashasvi, additional, Colombo, Antonio, additional, Cosgrove, Claudia, additional, Croce, Kevin, additional, Daggubati, Ramesh, additional, Damas de los Santos, Félix, additional, Dautov, Rustem, additional, Davies, Rhian E., additional, de Martini, Tony, additional, Denktas, Ali E., additional, Dens, Joseph, additional, di Mario, Carlo, additional, Diletti, Roberto, additional, Dimitriadis, Zisis, additional, Doshi, Darshan, additional, Doshi, Parag, additional, Dou, Kefei, additional, Egred, Mohaned, additional, Elbarouni, Basem, additional, ElGuindy, Ahmed M., additional, Elhadidy, Amr, additional, Ellis, Stephen, additional, Escaned, Javier, additional, Fasseas, Panayotis, additional, Forouzandeh, Farshad, additional, Furkalo, Sergey, additional, Gagnor, Andrea, additional, Galassi, Alfredo R., additional, Gallino, Robert, additional, Garbo, Roberto, additional, Garcia, Santiago, additional, Gasparini, Gabriele, additional, Ge, Junbo, additional, Ge, Lei, additional, Goel, Pravin Kumar, additional, Goktekin, Omer, additional, Gonzalo, Nieves, additional, Gorgulu, Sevket, additional, Grancini, Luca, additional, Grantham, J. Aaron, additional, Guddeti, Raviteja, additional, Haddad, Elias V., additional, Hall, Allison B., additional, Hall, Jack J., additional, Halligan, Sean, additional, Hanna Quesada, Franklin Leonardo, additional, Hanratty, Colm, additional, Harb, Stefan, additional, Harding, Scott A., additional, Hatem, Raja, additional, Hildick-Smith, David, additional, Hill, Jonathan M., additional, Hirai, Taishi, additional, Iannaccone, Mario, additional, Jaber, Wissam, additional, Jaffer, Farouc A., additional, Jang, Yangsoo, additional, Jefferson, Brian K., additional, Jeremias, Allen, additional, Jussila, Risto, additional, Kakouros, Nikolaos, additional, Kalnins, Artis, additional, Kalra, Sanjog, additional, Kalyanasundaram, Arun, additional, Kandzari, David E., additional, Kao, Hsien-Li, additional, Karacsonyi, Judit, additional, Karmpaliotis, Dimitri, additional, Kassem, Hussien Heshmat, additional, Kearney, Kathleen, additional, Kerrigan, Jimmy, additional, Khatri, Jaikirshan, additional, Khelimskii, Dmitrii, additional, Kirtane, Ajay J., additional, Knaapen, Paul, additional, Kostantinis, Spyridon, additional, Koutouzis, Michalis, additional, Kovacic, Mihajlo, additional, Krestyaninov, Oleg, additional, Kumar, A.V. Ganesh, additional, Kumar N., Prathap, additional, Kunkel, Katherine J., additional, Lamelas, Pablo Manuel, additional, Lee, Seung-Whan, additional, Lefevre, Thierry, additional, Leibundgut, Gregor, additional, Lembo, Nicholas J., additional, Leon, Martin, additional, Lesser, John R., additional, Leung, Raymond, additional, Lim, Soo-Teik, additional, Lo, Sidney Tsz Ho, additional, Lombardi, William, additional, Luna, Michael, additional, Mahmud, Ehtisham, additional, Mahowald, Madeline K., additional, Maran, Anbukarasi, additional, Marmagkiolis, Konstantinos, additional, Martins Filho, Evandro, additional, Mashayekhi, Kambis, additional, McEntegart, Margaret B., additional, Megaly, Michael, additional, Meraj, Perwaiz, additional, Michalis, Lampros, additional, Milkas, Anastasios N., additional, Mogabgab, Owen, additional, Moses, Jeffrey, additional, Munawar, Muhammad, additional, Murad, Bilal, additional, Nap, Alexander, additional, Navarro, Andres, additional, Nicholson, William J., additional, Øksnes, Anja, additional, Olivecrona, Göran, additional, Omer, Mohamed A., additional, Oreglia, Jacopo Andrea, additional, Padilla, Lucio, additional, Patel, Mitul P., additional, Patel, Rajan A.G., additional, Patel, Taral, additional, Pershad, Ashish, additional, Pinto, Duane, additional, Poommipanit, Paul, additional, Postu, Marin, additional, Potluri, Srini, additional, Pyxaras, Stylianos, additional, Quadros, Alexandre Schaan de, additional, Ragosta, Michael, additional, Rao, Sunil V., additional, Rao, Vithala Surya Prakasa, additional, Rathore, Sudhir, additional, Reifart, Joerg, additional, Rempakos, Athanasios, additional, Rier, Jeremy, additional, Riley, Robert, additional, Rinfret, Stéphane, additional, Russo, Juan J., additional, Saghatelyan, Meruzhan, additional, Sandhu, Gurpreet S., additional, Sandoval, Yader, additional, Santiago, Ricardo, additional, Sapontis, James, additional, Shah, Alpesh, additional, Shlofmitz, Evan, additional, Shunk, Kendrick A., additional, Sianos, George, additional, Simsek, Bahadir, additional, Smith, Elliot J., additional, Spaedy, Anthony, additional, Spratt, James, additional, Strange, Julian W., additional, Strauss, Bradley, additional, Tajti, Péter, additional, Tamez, Hector, additional, Tammam, Khalid O., additional, Thompson, Craig A., additional, Toma, Aurel, additional, Toma, Catalin, additional, Tsiafoutis, Ioannis, additional, Tsuchikane, Etsuo, additional, Ungi, Imre, additional, Uretsky, Barry F., additional, Vlachojannis, Georgios J., additional, Vo, Minh Nhat, additional, Vu, Hoang Vu, additional, Walsh, Simon, additional, Weilenmann, Daniel, additional, Werner, Gerald, additional, Wójcik, Jarosław, additional, Wollmuth, Jason, additional, Wu, Eugene B., additional, Wyman, R. Michael, additional, Xenogiannis, Iosif, additional, Xu, Bo, additional, Yamane, Masahisa, additional, Ybarra, Luiz F., additional, and Yeh, Robert W., additional

Published
2023
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47. Risk of Midlife Stroke After Adverse Pregnancy Outcomes: The FinnGen Study

Author

Miller, Eliza C., Kauko, Anni, Tom, Sarah E., Laivuori, Hannele, Niiranen, Teemu, Bello, Natalie A., Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Matakidou, Athena, Platt, Adam, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Hunkapiller, Julie, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Fox, Caroline, Mälarstig, Anders, Klinger, Katherine, Raipal, Deepak, Green, Eric, Graham, Robert, Yang, Robert, Donnell, Chris O´, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Runz, Heiko, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Hunkapiller, Julie, Ehm, Margaret G., Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Mälarstig, Anders, Hu, Xinli, Klinger, Katherine, Graham, Robert, Green, Eric, Mozaffari, Sahar, Waterworth, Dawn, Renaud, Nicole, Obeidat, Ma´en, Ripatti, Samuli, Schleutker, Johanna, Perola, Markus, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Laukkanen, Jari, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Runz, Heiko, Lahdenperä, Sanni, Biswas, Shameek, Hunkapiller, Julie, Bowers, Natalie, Teng, Edmond, Pendergrass, Rion, Xu, Fanli, Pulford, David, Auro, Kirsi, Addis, Laura, Eicher, John, Li, Qingqin S, He, Karen, Khramtsova, Ekaterina, Raghavan, Neha, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Daly, Mark, Abbasi, Ali, Waring, Jeffrey, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Lu, Tim, Bowers, Natalie, Pendergrass, Rion, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Hu, Xinli, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Abbasi, Ali, Waring, Jeffrey, Rahimov, Fedik, Lertratanakul, Apinya, Smaoui, Nizar, Lehtonen, Anne, Hochfeld, Marla, Bowers, Natalie, Pendergrass, Rion, Esparza Gordillo, Jorge, Auro, Kirsi, Waterworth, Dawn, Farias, Fabiana, Kalpala, Kirsi, Bing, Nan, Hu, Xinli, Laitinen, Tarja, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Smaoui, Nizar, Lassi, Glenda, Eaton, Susan, Chen, Hubert, Pendergrass, Rion, Bowers, Natalie, Betts, Joanna, Auro, Kirsi, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Kähönen, Mika, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Laukkanen, Jari, Elliott, Amanda, Pat Reeve, Mary, Ruotsalainen, Sanni, Challis, Benjamin, Paul, Dirk, Hunkapiller, Julie, Bowers, Natalie, Pendergrass, Rion, Chu, Audrey, Auro, Kirsi, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Miller, Melissa, Meretoja, Tuomo, Joensuu, Heikki, Carpén, Olli, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Elenius, Päivi Auvinen Klaus, Schleutker, Johanna, Pitkänen, Esa, Mars, Nina, Daly, Mark, Popovic, Relja, Waring, Jeffrey, Riley-Gillis, Bridget, Lehtonen, Anne, Schutzman, Jennifer, Hunkapiller, Julie, Bowers, Natalie, Pendergrass, Rion, Kulkarni, Diptee, Auro, Kirsi, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A, Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Pitkänen, Esa, Liu, Mengzhen, Runz, Heiko, Loomis, Stephanie, Strauss, Erich, Bowers, Natalie, Chen, Hao, Pendergrass, Rion, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Choy, David, Pendergrass, Rion, Waterworth, Dawn, Kalpala, Kirsi, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Pendergrass, Rion, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Kettunen, Johannes, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Pat Reeve, Mary, Daly, Mark, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Liu, Mengzhen, Riley-Gillis, Bridget, Pendergrass, Rion, Kumar, Janet, Auro, Kirsi, Hovatta, Iiris, Chen, Chia-Yen, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Damm Als, Thomas, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Salminen, Eveliina, Rahikkala, Elisa, Kettunen, Johannes, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Ripatti, Samuli, Daly, Mark, Karjalainen, Juha, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della, Pietro, Parolo, Briotta, Zhou, Wei, Maasha, Mutaamba, Hassan, Shabbeer, Lemmelä, Susanna, Rivas, Manuel, Niemi, Mari E., Palotie, Aarno, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Tukiainen, Taru, Pat Reeve, Mary, Heyne, Henrike, Mars, Nina, Rämö, Joel, Saarentaus, Elmo, Ollila, Hanna, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Elliott, Amanda, Kristiansson, Kati, Arvas, Mikko, Hyvärinen, Kati, Ritari, Jarmo, Carpén, Olli, Kettunen, Johannes, Pylkäs, Katri, Sliz, Eeva, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Mannermaa, Arto, Laakkonen, Eija, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Terho, Perttu, Soini, Sirpa, Partanen, Jukka, Punkka, Eero, Serpi, Raisa, Siltanen, Sanna, Kosma, Veli-Matti, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Palin, Henna, Linna, Malla-Maria, Kurki, Mitja, Karjalainen, Juha, Della, Pietro, Parolo, Briotta, Lehisto, Arto, Mehtonen, Juha, Zhou, Wei, Kanai, Masahiro, Maasha, Mutaamba, Havulinna, Aki, Lemmelä, Susanna, Kiiskinen, Tuomo, Elisa Lahtela, L., Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Alexander Dada, Oluwaseun, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Ruotsalainen, Sanni, Donner, Kati, Sipilä, Timo P., Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Kristiansson, Kati, Lemmelä, Susanna, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Palta, Priit, Pärn, Kalle, Kals, Mart, Luo, Shuang, Laitinen, Tarja, Pat Reeve, Mary, Sampath Padmanabhuni, Shanmukha, Niemi, Marianna, Siirtola, Harri, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Pitkänen, Jyrki, Hautalahti, Marco, Mäkelä, Johanna, Smith, Sarah, and Southerington, Tom

Published
2023
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48. Live imaging and conditional disruption of native PCP activity using endogenously tagged zebrafish sfGFP-Vangl2

Author

Maria Jussila, Curtis W. Boswell, Nigel W. Griffiths, Patrick G. Pumputis, and Brian Ciruna

Subjects
Science
Abstract

Planar cell polarity (PCP) is critical for tissue-wide coordination and successful development. Here Jussila et al. generate a GFP-Vangl2 fusion for live imaging and discover a surprising directionality to the intercellular propagation of cell polarity, and ultimately link PCP defects with idiopathic scoliosis.

Published
2022
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49. Dataset of the de novo assembly and annotation of the marbled crayfish and the noble crayfish hepatopancreas transcriptomes

Author

Ljudevit Luka Boštjančić, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklós Bálint, Klaus Schwenk, Odile Lecompte, and Kathrin Theissinger

Subjects
Freshwater crayfish, Astacus astacus, Procambarus virginalis, Crayfish plague, RNA sequencing, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Objectives Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037 ), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z ) Data description In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.

Published
2022
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50. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence

Author

Ljudevit Luka Boštjančić, Caterina Francesconi, Christelle Rutz, Lucien Hoffbeck, Laetitia Poidevin, Arnaud Kress, Japo Jussila, Jenny Makkonen, Barbara Feldmeyer, Miklós Bálint, Klaus Schwenk, Odile Lecompte, and Kathrin Theissinger

Subjects
Crayfish plague, Astacus astacus, Invertebrate immune mechanisms, Innate immune system, Procambarus virginalis, Differential gene expression, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host’s molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. Results We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. Conclusions We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.

Published
2022
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