Browsing by Subject "ENSEMBLE"

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  • Ravikumar, Balaguru; Timonen, Sanna; Alam, Zaid; Parri, Elina; Wennerberg, Krister; Aittokallio, Tero (2019)
    Owing to the intrinsic polypharmacological nature of most small-molecule kinase inhibitors, there is a need for computational models that enable systematic exploration of the chemogenomic landscape underlying druggable kinome toward more efficient kinome-profiling strategies. We implemented Virtual-KinomeProfiler, an efficient computational platform that captures distinct representations of chemical similarity space of the druggable kinome for various drug discovery endeavors. By using the computational platform, we profiled approximately 37 million compound-kinase pairs and made predictions for 151,708 compounds in terms of their repositioning and lead molecule potential, against 248 kinases simultaneously. Experimental testing with biochemical assays validated 51 of the predicted interactions, identifying 19 small-molecule inhibitors of EGFR, HCK, FLT1, and MSK1 protein kinases. The prediction model led to a 1.5-fold increase in precision and 2.8-fold decrease in false-discovery rate, when compared with traditional single-dose biochemical screening, which demonstrates its potential to drastically expedite the kinome-specific drug discovery process.
  • Jylhä, Kirsti; Laapas, Mikko; Ruosteenoja, Kimmo; Arvola, Lauri; Drebs, Achim; Kersalo, Juha; Saku, Seppo; Gregow, Hilppa; Hannula, Henna-Reetta; Pirinen, Pentti (2014)
  • Im, Ulas; Christensen, Jesper H.; Nielsen, Ole-Kenneth; Sand, Maria; Makkonen, Risto; Geels, Camilla; Anderson, Camilla; Kukkonen, Jaakko; Lopez-Aparicio, Susana; Brandt, Jørgen (2019)
    This modeling study presents the sectoral contributions of anthropogenic emissions in the four Nordic countries (Denmark, Finland, Norway and Sweden) on air pollution levels and the associated health impacts and costs over the Nordic and the Arctic regions for the year 2015. The Danish Eulerian Hemispheric Model (DEHM) has been used on a 50 km resolution over Europe in tagged mode in order to calculate the response of a 30 % reduction of each emission sector in each Nordic country individually. The emission sectors considered in the study were energy production, non-industrial/commercial heating, industry, traffic, off-road mobile sources and waste management/agriculture. In total, 28 simulations were carried out. Following the air pollution modeling, the Economic Valuation of Air Pollution (EVA) model has been used to calculate the associated premature mortality and their costs. Results showed that more than 80 % of the PM2.5 concentration was attributed to transport from outside these four countries, implying an effort outside the Nordic region in order to decrease the pollutant levels over the area. The leading emission sector in each country was found to be non-industrial combustion (contributing by more than 60 % to the total PM2.5 mass coming from the country itself), except for Sweden, where industry contributed to PM2.5 with a comparable amount to non-industrial combustion. In addition to non-industrial combustion, the next most important source categories were industry, agriculture and traffic. The main chemical constituent of PM2.5 concentrations that comes from the country itself is calculated to be organic carbon in all countries, which suggested that nonindustrial wood burning was the dominant national source of pollution in the Nordic countries. We have estimated the total number of premature mortality cases due to air pollution to be around 4000 in Denmark and Sweden and around 2000 in Finland and Norway. These premature mortality cases led to a total cost of EUR 7 billion in the selected Nordic countries. The assessment of the related premature mortality and associated cost estimates suggested that non-industrial combustion, together with industry and traffic, will be the main sectors to be targeted in emission mitigation strategies in the future.
  • Lehtinen, Aki (2018)
    Derivational robustness may increase the degree to which various pieces of evidence indirectly confirm a robust result. There are two ways in which this increase may come about. First, if one can show that a result is robust, and that the various individual models used to derive it also have other confirmed results, these other results may indirectly confirm the robust result. Confirmation derives from the fact that data not known to bear on a result are shown to be relevant when it is shown to be robust. Second, robustness may increase the degree to which the robust result is indirectly confirmed if it increases the weight with which existing evidence indirectly confirms it. This may happen when it strengthens the connection between the core and the robust result by showing that auxiliaries are not responsible for the result.
  • Ehrnsten, Eva; Norkko, Alf; Müller-Karulis, Bärbel; Gustafsson, Erik; Gustafsson, Bo G. (2020)
    Nutrient loading and climate change affect coastal ecosystems worldwide. Unravelling the combined effects of these pressures on benthic macrofauna is essential for understanding the future functioning of coastal ecosystems, as it is an important component linking the benthic and pelagic realms. In this study, we extended an existing model of benthic macrofauna coupled with a physical-biogeochemical model of the Baltic Sea to study the combined effects of changing nutrient loads and climate on biomass and metabolism of benthic macrofauna historically and in scenarios for the future. Based on a statistical comparison with a large validation dataset of measured biomasses, the model showed good or reasonable performance across the different basins and depth strata in the model area. In scenarios with decreasing nutrient loads according to the Baltic Sea Action Plan but also with continued recent loads (mean loads 2012-2014), overall macrofaunal biomass and carbon processing were projected to decrease significantly by the end of the century despite improved oxygen conditions at the seafloor. Climate change led to intensified pelagic recycling of primary production and reduced export of particulate organic carbon to the seafloor with negative effects on macrofaunal biomass. In the high nutrient load scenario, representing the highest recorded historical loads, climate change counteracted the effects of increased productivity leading to a hyperbolic response: biomass and carbon processing increased up to mid-21st century but then decreased, giving almost no net change by the end of the 21st century compared to present. The study shows that benthic responses to environmental change are nonlinear and partly decoupled from pelagic responses and indicates that benthic-pelagic coupling might be weaker in a warmer and less eutrophic sea.