Recent Submissions

  • Nygren, Anja Kaarina (2018)
    Cities in different parts of the world are going through intensive transformations based on institutional efforts to govern urban spaces and populations in the face of global environmental change and neoliberalization of governance. This essay examines inequalities and interconnectivities in urban governance and justice, drawing on a case-study of three, socially-differentiated sectors of the city of Villahermosa, Mexico, between 2011 and 2016. My analysis contributes to a multi-dimensional approach toward justice, and the cognate fields of right to the city, and segregation and inequality, that encompasses: (1) (re)distribution of residents’ exposure to risks and access to services; (2) recognition of the causes and consequences of risks and vulnerabilities; (3) fields of representation available for different residents; and (4) residents’ capabilities to recover from disasters and achieve everyday well-being within the existing urban governance and service provision structures. Instead of conceptualizing segregated cities as composed of isolated worlds, I argue that it is only possible to understand how the prevailing forms of governance produce multifaceted inequalities through a relational analysis of how residents from different parts of the city interact with the authorities and with each other. The study shows how residents’ tactics to accommodate, reconfigure and contest institutional endeavors to place them in hierarchical positions link to their differentiated ways of constructing urban space.
  • Mollerup, Filip; Aumala, Ville; Parikka, Kirsti Maria; Mathieu, Yan; Brumer, Harry; Tenkanen, Tiina Maija; Master, Emma (2019)
    Copper radical alcohol oxidases belonging to auxiliary activity family 5, subfamily 2 (AA5_2) catalyze the oxidation of galactose and galactosides, as well as aliphatic alcohols. Despite their broad applied potential, so far very few AA5_2 members have been biochemically characterized. We report the recombinant production and biochemical characterization of an AA5_2 oxidase from Penicillium rubens Wisconsin 54-1255 (PruAA5_2A), which groups within an unmapped clade phylogenetically distant from those comprising AA5_2 members characterized to date. PruAA5_2 preferentially oxidized raffinose over galactose; however, its catalytic efficiency was 6.5 times higher on glycolaldehyde dimer compared to raffinose. Deep sequence analysis of characterized AA5_2 members highlighted amino acid pairs correlated to substrate range and conserved within the family. Moreover, PruAA5_2 activity spans substrate preferences previously reported for AA5 subfamily 1 and 2 members, identifying possible functional overlap across the AA5 family.
  • Ekroos, Johan; Tiainen, Juha; Seimola, Tuomas; Herzon, Irina (2019)
    Context The current Common Agricultural Policy (CAP) of the European Union includes three greening measures, which are partly intended to benefit farmland biodiversity. However, the relative biodiversity effects of the greening measures, including joint effects of landscape context, are not well understood. Objectives We studied the effects of increasing crop diversity, proportions of production grasslands and fallows, corresponding to CAP greening measures, on open farmland bird diversity, whilst controlling for the effects of distance to forests, field edge density and proportion of built-up areas. Methods We surveyed open farmland birds using territory mapping in Southern Finland. We modelled effects of greening measures and landscape structure on farmland birds (7642 territories) using generalised linear mixed models. Results Increasing proportions of grasslands increased farmland bird species richness and diversity in open farmland, whereas increasing proportions of fallows increased bird diversity. Increasing crop diversity benefited individual species, but not species richness or diversity. Increasing field edge densities consistently increased the species richness of all farmland species, in-field nesters and non-crop nesters, as well as total farmland bird diversity. The relative effect of edge density was much stronger compared to the three greening measures. Conclusions Our results show that promoting fallows and grasslands, in particular grazed grasslands and various types of semi-natural grasslands, has the highest potential to benefit farmland bird diversity. Maintaining or increasing field edge densities, currently not supported, seems to be of even more benefit. In open farmland, with little or no field edges, fallows and grasslands are particularly beneficial.
  • Lallukka, Tea; Kerkelä, Martta; Ristikari, Tiina; Merikukka, Marko; Hiilamo, Heikki; Virtanen, Marianna; Øverland, Simon; Gissler, Mika; Halonen, Jaana I. (2019)
    Cumulative contributions of social and health-related determinants to long-term unemployment during early working life among young adults are poorly understood. Therefore, we used four cumulative indices of both parental and own social and health-related determinants of such unemployment among a cohort which comprised a complete census of children born in Finland in 1987. The cohort participants were registered in the Medical Birth Register, and they were followed-up through 2015 (N = 46 521). We calculated predicted probabilities for long-term unemployment (> 12 months) when participants were 25–28 years. Moreover, we examined whether the associations differed by unemployment at the municipal level. During the follow-up, 4.5% of women and 7.1% of men experienced long-term unemployment. All cumulative indices of parental and own social and health-related determinants predicted the probability of long-term unemployment. The greatest probabilities were observed for own social determinants, both in municipalities with high and low unemployment although the probabilities were higher in the high-unemployment municipalities. Of the individual determinants, poor school performance showed the strongest association with long-term unemployment among women (OR 6.65, 95% CI 5.21–8.55) and men (OR 3.70, 95% CI 2.96–4.67), after adjusting for other own social determinants. The results highlight the importance of life course social equality in the prevention of long-term unemployment in early adulthood.
  • Mäkelä, Jaakko Johannes; Ketoja, Elise; Kuisma, Miia T; Salo, Tapio; Yli-Halla, Markku Juhani; Kahiluoto, Helena (2019)
  • Raasmaja, Atso; Stenius, Ulla; Ghalali, Aram (2019)
    Juniper (Juniperus communis L.) is a northern coniferous plant generally used as a spice and for nutritional purposes in foods and drinks. It was previously reported that juniper extract (JE) affects p53 activity, cellular stress, and gene expression induced cell death in human neuroblastoma cells. Therefore, the effects of juniper on p53 and Akt signaling was examined further in A549 lung, 22RV1 and DU145 prostate, and HepG2 liver cancer cells using Western blot, confocal microscopy, and MTT analysis. We found that juniper simultaneously decreased cell viability, activated the p53 pathway, and inactivated the PI3K/Akt pathway. The p53 activation was associated with increased nuclear p53 level. Akt was dephosphorylated, and its inactivation was associated with increased levels of PHLPP1 and PHLPP2 phosphatases. Parallel increases of PARP suggest that JE decreased cell viability by activating cell death. In addition, JE potentiated the effects of gemcitabine and 5-fluorouracil anticancer drugs. Thus, JE can activate cell death in different cancer cell lines through p53 and Akt pathways.
  • Kemppainen, Antti; Smirnov, Stanislav (2019)
    In this article we show the convergence of a loop ensemble of interfaces in the FK Ising model at criticality, as the lattice mesh tends to zero, to a unique conformally invariant scaling limit. The discrete loop ensemble is described by a canonical tree glued from the interfaces, which then is shown to converge to a tree of branching SLEs. The loop ensemble contains unboundedly many loops and hence our result describes the joint law of infinitely many loops in terms of SLE type processes, and the result gives the full scaling limit of the FK Ising model in the sense of random geometry of the interfaces. Some other results in this article are convergence of the exploration process of the loop ensemble (or the branch of the exploration tree) to SLE(κ,κ−6), κ=16/3, and convergence of a generalization of this process for 4 marked points to SLE[κ,Z], κ=16/3, where Z refers to a partition function. The latter SLE process is a process that can't be written as a SLE(κ,ρ1,ρ2,…) process, which are the most commonly considered generalizations of SLEs.
  • Hannula, Miika (2019)
    The computational properties of modal and propositional dependence logics have been extensively studied over the past few years, starting from a result by Sevenster showing NEXPTIME-completeness of the satisfiability problem for modal dependence logic. Thus far, however, the validity and entailment properties of these logics have remained mostly unaddressed. This paper provides a comprehensive classification of the complexity of validity and entailment in various modal and propositional dependence logics. The logics examined are obtained by extending the standard modal and propositional logics with notions of dependence, independence, and inclusion in the team semantics context. In particular, we address the question of the complexity of validity in modal dependence logic. By showing that it is NEXPTIME-complete we refute an earlier conjecture proposing a higher complexity for the problem.
  • Vidilaseris, Keni; Kiriazis, Alexandros; Turku, Ainoleena; Khattab, Ayman Abdelnaby Shaaban; Johansson, Niklas G; Leino, Teppo Olavi; Kiuru, Paula Sinikka; Boije af Gennäs, Per Gustav; Meri, Seppo Kalevi; Yli-Kauhaluoma, Jari Tapani; Xhaard, Henri Guillaume Michel; Goldman, Adrian (2019)
    Membrane-bound pyrophosphatases are homodimeric integral membrane proteins that hydrolyze pyrophosphate into orthophosphates, coupled to the active transport of protons or sodium ions across membranes. They are important in the life cycle of bacteria, archaea, plants, and parasitic protists, but no homologous proteins exist in vertebrates, making them a promising drug target. Here, we report the first nonphosphorus allosteric inhibitor of the thermophilic bacterium Thermotoga maritima membrane-bound pyrophosphatase and its bound structure together with the substrate analog imidodiphosphate. The unit cell contains two protein homodimers, each binding a single inhibitor dimer near the exit channel, creating a hydrophobic clamp that inhibits the movement of beta-strand 1-2 during pumping, and thus prevents the hydrophobic gate from opening. This asymmetry of inhibitor binding with respect to each homodimer provides the first clear structural demonstration of asymmetry in the catalytic cycle of membrane-bound pyrophosphatases.
  • Ylitalo, Tuomo; Finnilä, Mikko A. J.; Gahunia, Harpal K.; Karhula, Sakari S.; Suhonen, Heikki; Valkealahti, Maarit; Lehenkari, Petri; Haeggström, Edward; Pritzker, Kenneth P. H.; Saarakkala, Simo; Nieminen, Heikki J. (2019)
    One of the earliest changes in osteoarthritis (OA) is a surface discontinuity of the articular cartilage (AC), and these surface changes become gradually more complex with OA progression. We recently developed a contrast enhanced micro-computed tomography (mu CT) method for visualizing AC surface in detail. The present study aims to introduce a mu CT analysis technique to parameterize these complex AC surface features and to demonstrate the feasibility of using these parameters to quantify degenerated AC surface. Osteochondral plugs (n = 35) extracted from 19 patients undergoing joint surgery were stained with phosphotungstic acid and imaged using mu CT. The surface micro-topography of AC was analyzed with developed method. Standard root mean square roughness (R-q) was calculated as a reference, and the Area Under Curve (AUC) for receiver operating characteristic analysis was used to compare the acquired quantitative parameters with semi-quantitative visual grading of mu CT image stacks. The parameters quantifying the complex micro-topography of AC surface exhibited good sensitivity and specificity in identifying surface continuity (AUC: 0.93, [0.80 0.99]), fissures (AUC: 0.94, [0.83 0.99]) and fibrillation (AUC: 0.98, [0.88 1.0]). Standard R-q was significantly smaller compared with the complex roughness (CRq) already with mild surface changes with all surface reference parameters - continuity, fibrillation, and fissure sum. Furthermore, only CRq showed a significant difference when comparing the intact surface with lowest fissure sum score. These results indicate that the presented method for evaluating complex AC surfaces exhibit potential to identify early OA changes in superficial AC and is dynamic throughout OA progression. (c) 2019 The Authors. Journal of Orthopaedic Research (R) Published by Wiley Periodicals, Inc. on behalf of the Orthopaedic Research Society. Society. 9999:1-12, 2019.
  • Kukkala, Aija; Maiorano, Luigi; Thuiller, Wilfried; Arponen, Anni (2019)
  • Eiben, E.; Ganian, R.; Kangas, K.; Ordyniak, S. (2019)
    We consider the #P-complete problem of counting the number of linear extensions of a poset (LE is fixed-parameter intractable parameterized by the treewidth of the cover graph. This resolves an open problem recently posed in the Dagstuhl seminar on Exact Algorithms. On the positive side we show that
  • Salminen, Marja Johanna; Oliveira, E.P.; Piispa, E.J.; Smirnov, A.V.; Trindade, R.I.F. (2018)
  • Salminen, Marja Johanna; Klein, Robert; Mertanen, S. (2018)
  • COGITO-MIN Working Group; Koivisto, Emilia Anna-Liisa; Malinowski, Michal; Heinonen, Suvi; Cosma, Calin; Vaittinen, Katri; Wojdyla, Marek; Riedel, Marko; Chamarczuk, Michal (Institute of Seismology, University of Helsinki, 2018)
  • Järvinen, Juha; Piippo, Simo Vilhelmi; Silvennoinen, Sonja Eira Elina; Koivisto, Emilia Anna-Liisa; Kultti, Seija Kyllikki (Institute of Seismology, University of Helsinki, 2018)
  • Wagner, Stefan; Méndez Fernández, Daniel; Felderer, Michael; Vetrò, Antonio; Kalinowski, Marco; Wieringa, Roel; Pfahl, Dietmar; Conte, Tayana; Christiansson, Marie-Therese; Greer, Desmond; Lassenius, Casper; Männistö, Tomi; Nayebi, Maleknaz; Oivo, Markku; Penzenstadler, Birgit; Prikladnicki, Rafael; Ruhe, Guenter; Schekelmann, André; Sen, Sagar; Spínola, Rodrigo; Tuzcu, Ahmed; Luis De La Vara, Jose; Winkler, Dietmar (2019)
    Requirements Engineering (RE) has established itself as a software engineering discipline over the past decades. While researchers have been investigating the RE discipline with a plethora of empirical studies, attempts to systematically derive an empirical theory in context of the RE discipline have just recently been started. However, such a theory is needed if we are to define and motivate guidance in performing high quality RE research and practice. We aim at providing an empirical and externally valid foundation for a theory of RE practice, which helps software engineers establish effective and efficient RE processes in a problem-driven manner. We designed a survey instrument and an engineer-focused theory that was first piloted in Germany and, after making substantial modifications, has now been replicated in 10 countries worldwide. We have a theory in the form of a set of propositions inferred from our experiences and available studies, as well as the results from our pilot study in Germany. We evaluate the propositions with bootstrapped confidence intervals and derive potential explanations for the propositions. In this article, we report on the design of the family of surveys, its underlying theory, and the full results obtained from the replication studies conducted in 10 countries with participants from 228 organisations. Our results represent a substantial step forward towards developing an empirical theory of RE practice. The results reveal, for example, that there are no strong differences between organisations in different countries and regions, that interviews, facilitated meetings and prototyping are the most used elicitation techniques, that requirements are often documented textually, that traces between requirements and code or design documents are common, that requirements specifications themselves are rarely changed and that requirements engineering (process) improvement endeavours are mostly internally driven. Our study establishes a theory that can be used as starting point for many further studies for more detailed investigations. Practitioners can use the results as theory-supported guidance on selecting suitable RE methods and techniques.
  • Heinonen, Suvi; Malinowski, Michal; Gislason, Gardar; Hlousek, Felix; Buske, Stefan; Koivisto, Emilia Anna-Liisa (Institute of Seismology, University of Helsinki, 2018)
  • Väkevä, Lauri Sakari Oleksi; Koivisto, Emilia Anna-Liisa; Hillers, Gregor; Chamarczuk, Michal; Malinowski, Michal (Institute of Seismology, University of Helsinki, 2018)
  • Savijoki, Kirsi; Nyman, Tuula A.; Kainulainen, Veera; Miettinen, Ilkka; Siljamäki, Pia; Fallarero, Adyary; Sandholm, Jouko; Satokari, Reetta; Varmanen, Pekka (2019)
    Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR, and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN, and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC, and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.

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