Search

Your search keyword '"Tanskanen, P."' showing total 697 results
Start Over Author "Tanskanen, P."
697 results on '"Tanskanen, P."'

5. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Published
2024
Full Text
View/download PDF

8. Comparing 1-year GUMICS-4 simulations of the Terrestrial Magnetosphere with Cluster Measurements

Author

Facsko, Gabor, Sibeck, David, Honkonen, Ilja, Bor, Jozsef, Perez, German Farinas, Timar, Aniko, Shprits, Yuri, Peitso, Pyry, Degener, Laura, Tanskanen, Eija, Anekallu, Chandrasekhar Reddy, Szalai, Sandor, Kis, Arpad, Wesztergom, Viktor, Madar, Akos, Biro, Nikolett, Koban, Gergely, Illyes, Andras, Kovacs, Peter, Dalya, Zsuzsanna, and Lkhagvadorj, Munkhjargal

Subjects
Physics - Space Physics
Abstract

We compare the predictions of the GUMICS$-$4 global magnetohydrodynamic model for the interaction of the solar wind with the Earth's magnetosphere with Cluster~SC3 measurements for over one year, from January 29, 2002, to February 2, 2003. In particular, we compare model predictions with the north/south component of the magnetic field ($B_{z}$) seen by the magnetometer, the component of the velocity along the Sun-Earth line ($V_{x}$), and the plasma density as determined from a top hat plasma spectrometer and the spacecraft's potential from the electric field instrument. We select intervals in the solar wind, the magnetosheath, and the magnetosphere where these instruments provided good-quality data, and the model correctly predicted the region in which the spacecraft is located. We determine the location of the bow shock, the magnetopause, and the neutral sheet from the spacecraft measurements and compare these locations to those predicted by the simulation. The GUMICS$-$4 model agrees well with the measurements in the solar wind however its accuracy is worse in the magnetosheath. The simulation results are not realistic in the magnetosphere. The bow shock location is predicted well, however, the magnetopause location is less accurate. The neutral sheet positions are located quite accurately thanks to the special solar wind conditions when the $B_{y}$ component of the interplanetary magnetic field is small., Comment: submitted to the AGU Space Weather, 51 pages, 19 figures, 8 tables

Published
2023
Full Text
View/download PDF

10. Deep reinforced learning enables solving rich discrete-choice life cycle models to analyze social security reforms

Author

Tanskanen, Antti J.

Subjects
Economics - General Economics, Computer Science - Machine Learning
Abstract

Discrete-choice life cycle models of labor supply can be used to estimate how social security reforms influence employment rate. In a life cycle model, optimal employment choices during the life course of an individual must be solved. Mostly, life cycle models have been solved with dynamic programming, which is not feasible when the state space is large, as often is the case in a realistic life cycle model. Solving a complex life cycle model requires the use of approximate methods, such as reinforced learning algorithms. We compare how well a deep reinforced learning algorithm ACKTR and dynamic programming solve a relatively simple life cycle model. To analyze results, we use a selection of statistics and also compare the resulting optimal employment choices at various states. The statistics demonstrate that ACKTR yields almost as good results as dynamic programming. Qualitatively, dynamic programming yields more spiked aggregate employment profiles than ACKTR. The results obtained with ACKTR provide a good, yet not perfect, approximation to the results of dynamic programming. In addition to the baseline case, we analyze two social security reforms: (1) an increase of retirement age, and (2) universal basic income. Our results suggest that reinforced learning algorithms can be of significant value in developing social security reforms.

Published
2020

12. Differences in the solar cycle variability of simple and complex active regions during 1996-2018

Author

Nikbakhsh, Shabnam, Tanskanen, Eija, Käpylä, Maarit, and Hackman, Thomas

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

Aims. Our aim is to examine the solar cycle variability of magnetically simple and complex active region. Methods. We studied simple ($\alpha$ and $\beta$) and complex ($\beta\gamma$ and $\beta\gamma\delta$) active regions based on the Mount Wilson magnetic classification by applying our newly developed daily approach. We analyzed the daily number of the simple active regions (SARs) and compared that to the abundance of the complex active regions (CARs) over the entire solar cycle 23 and cycle 24 until December 2018. Results. We show that CARs evolve differently over the solar cycle from SARs. The time evolution of SARs and CARs on different hemispheres also shows differences, even though on average their latitudinal distributions are shown to be similar. The time evolution of SARs closely follows that of the sunspot number, and their maximum abundance was observed to occur during the early maximum phase, while that of the CARs was seen roughly two years later. We furthermore found that the peak of CARs was reached before the latitudinal width of the activity band starts to decease. Conclusions. Our results suggest that the active region formation process is a competition between the large-scale dynamo (LSD) and the small-scale dynamo (SSD) near the surface, the former varying cyclically and the latter being independent of the solar cycle. During solar maximum, LSD is dominant, giving a preference to SARs, while during the declining phase the relative role of SSD increases. Therefore, a preference for CARs is seen due to the influence of the SSD on the emerging flux., Comment: 9 pages, 10 figures, A&A journal

Published
2019
Full Text
View/download PDF

16. The giant diploid faba genome unlocks variation in a global protein crop

Author

Jayakodi, Murukarthick, Golicz, Agnieszka A., Kreplak, Jonathan, Fechete, Lavinia I., Angra, Deepti, Bednář, Petr, Bornhofen, Elesandro, Zhang, Hailin, Boussageon, Raphaël, Kaur, Sukhjiwan, Cheung, Kwok, Čížková, Jana, Gundlach, Heidrun, Hallab, Asis, Imbert, Baptiste, Keeble-Gagnère, Gabriel, Koblížková, Andrea, Kobrlová, Lucie, Krejčí, Petra, Mouritzen, Troels W., Neumann, Pavel, Nadzieja, Marcin, Nielsen, Linda Kærgaard, Novák, Petr, Orabi, Jihad, Padmarasu, Sudharsan, Robertson-Shersby-Harvie, Tom, Robledillo, Laura Ávila, Schiemann, Andrea, Tanskanen, Jaakko, Törönen, Petri, Warsame, Ahmed O., Wittenberg, Alexander H. J., Himmelbach, Axel, Aubert, Grégoire, Courty, Pierre-Emmanuel, Doležel, Jaroslav, Holm, Liisa U., Janss, Luc L., Khazaei, Hamid, Macas, Jiří, Mascher, Martin, Smýkal, Petr, Snowdon, Rod J., Stein, Nils, Stoddard, Frederick L., Stougaard, Jens, Tayeh, Nadim, Torres, Ana M., Usadel, Björn, Schubert, Ingo, O’Sullivan, Donal Martin, Schulman, Alan H., and Andersen, Stig Uggerhøj

Published
2023
Full Text
View/download PDF

17. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
Full Text
View/download PDF

18. The genome of cowpea (Vigna unguiculata [L.] Walp.)

Author

Lonardi, Stefano, Muñoz‐Amatriaín, María, Liang, Qihua, Shu, Shengqiang, Wanamaker, Steve I, Lo, Sassoum, Tanskanen, Jaakko, Schulman, Alan H, Zhu, Tingting, Luo, Ming‐Cheng, Alhakami, Hind, Ounit, Rachid, Hasan, Abid Md, Verdier, Jerome, Roberts, Philip A, Santos, Jansen RP, Ndeve, Arsenio, Doležel, Jaroslav, Vrána, Jan, Hokin, Samuel A, Farmer, Andrew D, Cannon, Steven B, and Close, Timothy J

Subjects
Genetics, Biotechnology, Chromosome Mapping, Chromosomes, Plant, DNA, Plant, Genes, Plant, Genome Size, Genome, Plant, Phaseolus, Retroelements, Sequence Analysis, DNA, Synteny, Vigna, chromosomal inversion, cowpea, domestication, genome annotation, genome evolution, genome size, next-generation sequencing, legumes, Phaseolus vulgaris, repetitive elements, Vigna unguiculata, Phaseolus vulgaris, Vigna unguiculata, Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany
Abstract

Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

Published
2019

20. Repurposing Semaglutide and Liraglutide for Alcohol Use Disorder.

Author

Lähteenvuo, Markku, Tiihonen, Jari, Solismaa, Anssi, Tanskanen, Antti, Mittendorfer-Rutz, Ellenor, and Taipale, Heidi

Subjects
ALCOHOLISM, GLUCAGON-like peptide-1 receptor, GLUCAGON-like peptide-1 agonists, TYPE 2 diabetes, INPATIENT care
Abstract

This cohort study examines nationwide registry data for Swedish residents with a diagnosis of alcohol use disorder to determine whether hospitalization risk for an individual is decreased during periods of GLP-1 agonist use vs periods of nonuse. Key Points: Question: Are glucagon-like peptide-1 receptor (GLP-1) agonists effective in the treatment of alcohol use disorder? Findings: This cohort study with a median follow-up time of more than 8 years indicates that individuals are at markedly lower risk of alcohol-related hospitalizations and hospitalizations due to somatic reasons when using GLP-1 agonists, especially semaglutide, as compared with times they are not using them. Meaning: GLP-1 agonists, especially semaglutide, offer promise as a novel treatment to reduce alcohol consumption and to prevent development of alcohol-related outcomes, but randomized clinical trials are needed to verify these initial findings. Importance: Preliminary studies suggest that glucagon-like peptide-1 receptor (GLP-1) agonists, used to treat type 2 diabetes and obesity, may decrease alcohol consumption. Objective: To test whether the risk of hospitalization due to alcohol use disorder (AUD) is decreased during the use of GLP-1 agonists compared with periods of nonuse for the same individual. Design, Setting, and Participants: This cohort study was an observational study conducted nationwide in Sweden using data from January 2006 to December 2023. The population-based cohort was identified from registers of inpatient care, specialized outpatient care, sickness absence, and disability pension. Participants were all residents aged 16 to 64 years who had a diagnosis of AUD. Exposures: The primary exposure was use of individual GLP-1 agonists (compared with nonuse of GLP-1 agonists), and the secondary exposure was medications with indication for AUD. Main Outcomes and Measures: The primary outcome was AUD hospitalization analyzed in a Cox regression within-individual model. Secondary outcomes were any substance use disorder (SUD)–related hospitalization, somatic hospitalization, and suicide attempt. Results: The cohort included 227 866 individuals with AUD; 144 714 (63.5%) were male and 83 154 (36.5%) were female, with a mean (SD) age of 40.0 (15.7) years. Median (IQR) follow-up time was 8.8 (4.0-13.3) years. A total of 133 210 individuals (58.5%) experienced AUD hospitalization. Semaglutide (4321 users) was associated with the lowest risk (AUD: adjusted hazard ratio [aHR], 0.64; 95% CI, 0.50-0.83; any SUD: aHR, 0.68; 95% CI, 0.54-0.85) and use of liraglutide (2509 users) with the second lowest risk (AUD: aHR, 0.72; 95% CI, 0.57-0.92; any SUD: aHR, 0.78; 95% CI, 0.64-0.97) of both AUD and SUD hospitalization. Use of any AUD medication was associated with a modestly decreased risk (aHR, 0.98; 95% CI, 0.96-1.00). Semaglutide (aHR, 0.78; 95% CI, 0.68-0.90) and liraglutide (aHR, 0.79; 95% CI, 0.69-0.91) use were also associated with decreased risk of somatic hospitalizations but not associated with suicide attempts (semaglutide: aHR, 0.55; 95% CI, 0.23-1.30; liraglutide: aHR, 1.08; 95% CI, 0.55-2.15). Conclusions and Relevance: Among patients with AUD and comorbid obesity/type 2 diabetes, the use of semaglutide and liraglutide were associated with a substantially decreased risk of hospitalization due to AUD. This risk was lower than that of officially approved AUD medications. Semaglutide and liraglutide may be effective in the treatment of AUD, and clinical trials are urgently needed to confirm these findings. [ABSTRACT FROM AUTHOR]

Published
2025
Full Text
View/download PDF

23. One year in the Earth's magnetosphere: A global MHD simulation and spacecraft measurements

Author

Facsko, G., Honkonen, I., Zivkovic, T., Palin, L., Kallio, E., Agren, K., Opgenoorth, H., Tanskanen, E. I., and Milan, S. E.

Subjects
Physics - Space Physics
Abstract

The response of the Earth's magnetosphere to changing solar wind conditions are studied with a 3D Magnetohydrodynamic (MHD) model. One full year (155 Cluster orbits) of the Earth's magnetosphere is simulated using Grand Unified Magnetosphere Ionosphere Coupling simulation (GUMICS-4) magnetohydrodynamic code. Real solar wind measurements are given to the code as input to create the longest lasting global magnetohydrodynamics simulation to date. The applicability of the results of the simulation depends critically on the input parameters used in the model. Therefore, the validity and the variance of the OMNIWeb data is first investigated thoroughly using Cluster measurement close to the bow shock. The OMNIWeb and the Cluster data were found to correlate very well before the bow shock. The solar wind magnetic field and plasma parameters are not changed significantly from the $L_1$ Lagrange point to the foreshock, therefore the OMNIWeb data is appropriate input to the GUMICS-4. The Cluster SC3 footprints are determined by magnetic field mapping from the simulation results and the Tsyganenko (T96) model in order to compare two methods. The determined footprints are in rather good agreement with the T96. However, it was found that the footprints agree better in the northern hemisphere than the southern one during quiet conditions. If the By is not zero, the agreement of the GUMICS-4 and T96 footprint is worse in longitude in the southern hemisphere. Overall, the study implies that a 3D MHD model can increase our insight of the response of the magnetosphere to solar wind conditions., Comment: Accepted for publication in Space Weather, http://onlinelibrary.wiley.com/doi/10.1002/2015SW001355/full

Published
2016
Full Text
View/download PDF

24. Random selection of factors preserves the correlation structure in a linear factor model to a high degree

Author

Tanskanen, Antti J., Lukkarinen, Jani, and Vatanen, Kari

Subjects
Quantitative Finance - Statistical Finance, Quantitative Finance - Computational Finance, Quantitative Finance - Risk Management
Abstract

In a very high-dimensional vector space, two randomly-chosen vectors are almost orthogonal with high probability. Starting from this observation, we develop a statistical factor model, the random factor model, in which factors are chosen at random based on the random projection method. Randomness of factors has the consequence that covariance matrix is well preserved in a linear factor representation. It also enables derivation of probabilistic bounds for the accuracy of the random factor representation of time-series, their cross-correlations and covariances. As an application, we analyze reproduction of time-series and their cross-correlation coefficients in the well-diversified Russell 3,000 equity index., Comment: 27 pages, 7 figures, ver 2: includes major revision of the abstract, introduction and discussion, ver 3: title changed to match the final published version (available as an open access file following the DOI link)

Published
2016
Full Text
View/download PDF

28. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Author

Beier, Sebastian, Himmelbach, Axel, Colmsee, Christian, Zhang, Xiao-Qi, Barrero, Roberto A, Zhang, Qisen, Li, Lin, Bayer, Micha, Bolser, Daniel, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Sampath, Dharanya, Heavens, Darren, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K, Tan, Cong, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A, Bellgard, Matthew I, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Langridge, Peter, Muehlbauer, Gary J, Kersey, Paul, Clark, Matthew D, Caccamo, Mario, Schulman, Alan H, Platzer, Matthias, Close, Timothy J, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Li, Chengdao, Waugh, Robbie, Scholz, Uwe, Stein, Nils, and Mascher, Martin

Subjects
Hordeum, Chromosome Mapping, Sequence Analysis, Genome, Plant, Genome, Plant
Abstract

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Published
2017

29. A chromosome conformation capture ordered sequence of the barley genome

Author

Mascher, Martin, Gundlach, Heidrun, Himmelbach, Axel, Beier, Sebastian, Twardziok, Sven O, Wicker, Thomas, Radchuk, Volodymyr, Dockter, Christoph, Hedley, Pete E, Russell, Joanne, Bayer, Micha, Ramsay, Luke, Liu, Hui, Haberer, Georg, Zhang, Xiao-Qi, Zhang, Qisen, Barrero, Roberto A, Li, Lin, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Bolser, Daniel, Colmsee, Christian, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Chailyan, Anna, Sampath, Dharanya, Heavens, Darren, Clissold, Leah, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K, Tan, Cong, Wang, Penghao, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A, Bellgard, Matthew I, Borisjuk, Ljudmilla, Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Kersey, Paul, Langridge, Peter, Muehlbauer, Gary J, Clark, Matthew D, Caccamo, Mario, Schulman, Alan H, Mayer, Klaus FX, Platzer, Matthias, Close, Timothy J, Scholz, Uwe, Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Spannagl, Manuel, Li, Chengdao, Waugh, Robbie, and Stein, Nils

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Cell Nucleus, Centromere, Chromatin, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Genetic Variation, Genome, Plant, Genomics, Haplotypes, Hordeum, Meiosis, Repetitive Sequences, Nucleic Acid, Seeds, General Science & Technology
Abstract

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

Published
2017

30. Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
Full Text
View/download PDF

31. Pneumonia Risk, Antipsychotic Dosing, and Anticholinergic Burden in Schizophrenia.

Author

Luykx, Jurjen J., Correll, Christoph U., Manu, Peter, Tanskanen, Antti, Hasan, Alkomiet, Tiihonen, Jari, and Taipale, Heidi

Subjects
PROPORTIONAL hazards models, HOSPITAL admission & discharge, PEOPLE with schizophrenia, ANTIPSYCHOTIC agents, INPATIENT care
Abstract

This cohort study examines the risk of pneumonia associated with the use of antipsychotics in patients with schizophrenia. Key Points: Question: What antipsychotics are associated with pneumonia, which is the fourth leading cause of death in patients with schizophrenia? Findings: In this cohort study of 61 889 people with schizophrenia, antipsychotics with high anticholinergic burden were associated with an increased incidence of pneumonia. Significantly higher risks were detected for clozapine (≥180 mg/d), quetiapine (≥440 mg/d), and olanzapine (≥11 mg/d). Meaning: Findings of this study suggest that in patients with schizophrenia, pneumonia is associated with the use of specific antipsychotics, setting the stage for personalized prevention strategies to decrease the incidence of this life-threatening condition in patients with schizophrenia. Importance: Antipsychotic drugs (particularly clozapine) have been associated with pneumonia in observational studies. Despite studies of the associations between antipsychotic use and incident pneumonia, it remains unclear to what degree antipsychotic use is associated with increased risk of pneumonia, whether dose-response associations exist, and what agents are specifically associated with incident pneumonia. Objective: To estimate pneumonia risk associated with specific antipsychotics and examine whether polytherapy, dosing, and receptor binding properties are associated with pneumonia in patients with schizophrenia. Design, Setting, and Participants: This cohort study identified patients with schizophrenia or schizoaffective disorder (hereafter, schizophrenia) aged 16 years or older from nationwide Finnish registers from 1972 to 2014. Data on diagnoses, inpatient care, and specialized outpatient care were obtained from the Hospital Discharge Register. Information on outpatient medication dispensing was obtained from the Prescription Register. Study follow-up was from 1996 to 2017. Data were analyzed from November 4, 2022, to December 5, 2023. Exposures: Use of specific antipsychotic monotherapies; antipsychotics modeled by dosage as low (<0.6 of the World Health Organization defined daily dose [DDD] per day), medium (0.6 to <1.1 DDDs per day), or high dose (≥1.1 DDDs per day); antipsychotic polypharmacy; and antipsychotics categorized according to their anticholinergic burden as low, medium, and high. Main Outcomes and Measures: The primary outcome was hospitalization for incident pneumonia. Pneumonia risk was analyzed using adjusted, within-individual Cox proportional hazards regression models, with no antipsychotic use as the reference. Results: The study included 61 889 persons with schizophrenia (mean [SD] age, 46.2 [16.0] years; 31 104 men [50.3%]). During 22 years of follow-up, 8917 patients (14.4%) had 1 or more hospitalizations for pneumonia and 1137 (12.8%) died within 30 days of admission. Compared with no antipsychotic use, any antipsychotic use overall was not associated with pneumonia (adjusted hazard ratio [AHR], 1.12; 95% CI, 0.99-1.26). Monotherapy use was associated with increased pneumonia risk compared with no antipsychotic use (AHR, 1.15 [95% CI, 1.02-1.30]; P =.03) in a dose-dependent manner, but polytherapy use was not. When categorized by anticholinergic burden, only the use of antipsychotics with a high anticholinergic burden was associated with pneumonia (AHR, 1.26 [95% CI, 1.10-1.45]; P <.001). Of specific drugs, high-dose quetiapine (AHR, 1.78 [95% CI, 1.22-2.60]; P =.003), high- and medium-dose clozapine (AHR, 1.44 [95% CI, 1.22-1.71]; P <.001 and AHR, 1.43 [95% CI, 1.18-1.74]; P <.001, respectively), and high-dose olanzapine (AHR, 1.29 [95% CI, 1.05-1.58]; P =.02) were associated with increased pneumonia risk. Conclusions and Relevance: Results of this cohort study suggest that in patients with schizophrenia, antipsychotic agents associated with pneumonia include not only clozapine (at dosages ≥180 mg/d) but also quetiapine (≥440 mg/d) and olanzapine (≥11 mg/d). Moreover, monotherapy antipsychotics and antipsychotics with high anticholinergic burden are associated with increased pneumonia risk in a dose-dependent manner. These findings call for prevention strategies aimed at patients with schizophrenia requiring high-risk antipsychotics. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

33. Selective metal deposition at graphene line defects by atomic layer deposition

Author

Kim, Kwanpyo, Lee, Han-Bo-Ram, Johnson, Richard W., Tanskanen, Jukka T., Liu, Nan, Kim, Myung-Gil, Pang, Changhyun, Ahn, Chiyui, Bent, Stacey F., and Bao, Zhenan

Subjects
Condensed Matter - Materials Science
Abstract

One-dimensional defects in graphene have strong influence on its physical properties, such as electrical charge transport and mechanical strength. With enhanced chemical reactivity, such defects may also allow us to selectively functionalize the material and systematically tune the properties of graphene. Here we demonstrate the selective deposition of metal at chemical vapour deposited graphene's line defects, notably grain boundaries, by atomic layer deposition. Atomic layer deposition allows us to deposit Pt predominantly on graphene's grain boundaries, folds, and cracks due to the enhanced chemical reactivity of these line defects, which is directly confirmed by transmission electron microscopy imaging. The selective functionalization of graphene defect sites, together with the nanowire morphology of deposited Pt, yields a superior platform for sensing applications. Using Pt-graphene hybrid structures, we demonstrate high-performance hydrogen gas sensors at room temperatures and show its advantages over other evaporative Pt deposition methods, in which Pt decorates graphene surface non-selectively., Comment: 27 pages, 6 main figures

Published
2014
Full Text
View/download PDF

34. How to formulate membrane potential in a spatially homogeneous myocyte model?

Author

Tanskanen, A. J., Tanskanen, E. I., Greenstein, J. L., and Winslow, R. L.

Subjects
Quantitative Biology - Cell Behavior
Abstract

Membrane potential in a mathematical model of a cardiac myocyte can be formulated in different ways. Assuming a spatially homogeneous myocyte that is strictly charge-conservative and electroneutral as a whole, two methods will be compared: (1) the differential formulation dV/dt=-I/C_m of membrane potential used traditionally; and (2) the capacitor formulation, where membrane potential is defined algebraically by the capacitor equation V=Q/C_m. We examine the relationship between the formulations, assumptions under which each formulation is consistent, and show that the capacitor formulation provides a transparent, physically realistic formulation of membrane potential, whereas use of the differential formulation may introduce unintended and undesirable behavior, such as monotonic drift of concentrations. We prove that the drift of concentrations in the differential formulation arises as a compensation for failure to assign all currents in concentrations. As an example of these considerations, we present an electroneutral, explicitly charge-conservative formulation of Winslow et al. model (1999), and extend it to describe membrane potentials between intracellular compartments., Comment: 18 pages, 4 figures

Published
2005

39. Defining Competences for Future Geography Students in Relation to Low Carbon Societies

Author

Feliu, Jaume, Inkeroinen, Paula, Markuszewska, Iwona, Tanskanen, Minna, Nuss, Sergi, and Vila-Subirós, Josep

Abstract

This paper presents the results of an analysis of the most important skills and competences that will be important in the coming years for future geographers involved in assessing and managing low-carbon societies. The analysed information was extracted from a questionnaire answered by professionals working in low-carbon management in three European countries (Finland, Poland and Catalonia, Spain). From the results, we have identified not only the most requisite abilities and skills, but also differences between countries on a European scale. Among the findings, we would highlight the general agreement that "soft skills", as opposed to "hard skills", are critical for future professionals addressing policies in relation to low carbon societies.

Published
2019
Full Text
View/download PDF

44. Multigenerational Effects on Children's Cognitive and Socioemotional Outcomes: A Within-Child Investigation

Author

Tanskanen, Antti O. and Danielsbacka, Mirkka

Abstract

Associations between grandparental investment and child outcomes were investigated using three waves of a longitudinal British Millennium Cohort Study that included children between the ages of 9 months and 5 years (n = 24,614 person-observations from 13,744 children). Grandparental investment was measured by parent--grandparent contact frequency and grandparental financial support. Child cognitive development was measured using the British Ability Scale and socioemotional outcomes using the Strength and Difficulties Questionnaire. Grandparental investment was associated with improved cognitive and socioemotional outcomes among children. However, these associations occurred because of between-person effects and did not exist in within-person analyses that compared the same children over time. The results are discussed in terms of their contribution to multigenerational relationships research.

Published
2018
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results