Open access articles by University of Helsinki researchers. Contains final versions and manuscripts of research articles as well as professional publications and publications aimed at general public.

Collections in this community

Recent Submissions

  • Knaapila, Antti; Laaksonen, Oskar; Virtanen, Markus; Yang, Baoru; Lagstrom, Hanna; Sandell, Mari (2017)
    The primary dimension of odor is pleasantness, which is associated with a multitude of factors. We investigated how the pleasantness, familiarity, and identification of spice odors were associated with each other and with the use of the respective spice, overall use of herbs, and level of food neophobia. A total of 126 adults (93 women, 33 men; age 25-61 years, mean 39 years) rated the odors from 12 spices (oregano, anise, rosemary, mint, caraway, sage, thyme, cinnamon, fennel, marjoram, garlic, and clove) for pleasantness and familiarity, and completed a multiple-choice odor identification. Data on the use of specific spices, overall use of herbs, and Food Neophobia Scale score were collected using an online questionnaire. Familiar odors were mostly rated as pleasant (except garlic), whereas unfamiliar odors were rated as neutral (r = 0.63). We observed consistent and often significant trends that suggested the odor pleasantness and familiarity were positively associated with the correct odor identification, consumption of the respective spice, overall use of herbs, and food neophilia. Our results suggest that knowledge acquisition through repetitive exposure to spice odor with active attention may gradually increase the odor pleasantness within the framework set by the chemical characteristics of the aroma compound. (C) 2016 Elsevier Ltd. All rights reserved.
  • Soisalon-Soininen, Eliel; Granroth-Wilding, Mark (INCOMA, 2019)
  • Veira Canle, Daniel; Salmi, Ari Henrik; Haeggström, Edward Olof (2017)
    Propeller inspection is mandatory for safe operation of aircraft. Damage evaluation on such rotating structures requires dedicated measurement techniques. In this study efforts to create a stroboscopic technique are reported. Lamb waves were excited on a rotating blade with a Q-switched Nd:YAG laser synchronized to the sample rotation, whereas the wave amplitude was obtained by a laser Doppler vibrometer. A surface breaking notch on an aluminum sample rotating at 415 rpm was detected and sized with millimeter accuracy. The technique has potential for automatic non-contacting damage detection on rotating structures such as helicopter blades and turbines.
  • Montonen, Risto; Kassamakov, Ivan; Lehmann, Peter; Österberg, Kenneth; Haeggström, Edward (2018)
    The group refractive index is important in length calibration of Fourier domain interferometers by transparent transfer standards. We demonstrate accurate group refractive index quantification using a Fourier domain short coherence Sagnac interferometer. Because of a justified linear length calibration function, the calibration constants cancel out in the evaluation of the group refractive index, which is then obtained accurately from two uncalibrated lengths. Measurements of two standard thickness coverslips revealed group indices of 1.5426 +/- 0.0042 and 1.5434 +/- 0.0046, with accuracies quoted at the 95% confidence level. This agreed with the dispersion data of the coverslip manufacturer and therefore validates our method. Our method provides a sample specific and accurate group refractive index quantification using the same Fourier domain interferometer that is to be calibrated for the length. This reduces significantly the requirements of the calibration transfer standard. (C) 2018 Optical Society of America
  • Järvinen, Miikka; Vainikka, Tuomas; Viitala, Tapani; Bermudez, Carlos; Artigas, Roger; Nolvi, Anton; Martinez, Pol; Sandler, Niklas; Hæggström, Edward; Kassamakov, Ivan (2018)
  • Pessi, Jenni; Svanbäck, Sami; Lassila, Ilkka; Haeggstrom, Edward; Yliruusi, Jouko (2017)
    We introduce a system with a lyophilic matrix to aid dissolution studies of powders and particulate systems. This lyophilic matrix method (LM method) is based on the ability to discriminate between non-dissolved particles and the dissolved species. In the LM method the test substance is embedded in a thin lyophilic core-shell matrix. This permits rapid contact with the dissolution medium while minimizing dispersion of non-dissolved particles without presenting a substantial diffusion barrier. The method produces realistic dissolution and release results for particulate systems, especially those featuring nanoscale particles. By minimizing method-induced effects on the dissolution profile of nanopowders, the LM method overcomes shortcomings associated with current dissolution tests. (C) 2017 Elsevier B.V. All rights reserved.
  • Nolvi, Anton; Kassamakov, Ivan; Haeggström, Edward (2018)
    Mobile devices with interactive displays are ubiquitous commodities. Efficient quality control (QC) drives competitiveness. Scanning white light interferometry imaging offers a fast and nondestructive tool for QC purposes. Relying on optical compensation and image stitching, one can rapidly and cost-effectively produce sharp 3D images of a display's inner structures with a few nanometers' accuracy along the z direction. As a practical example, 3D images of a mobile device display revealed 0.92 +/- 0.02 mu m height variation in the top glass assembly. The proposed method improves quality assurance methods of display manufacturing. (c) 2017 Optical Society of America
  • Fahmi, Mustafa Kamil Mahmoud; Dafa-Alla, Dafa-Alla Mohamed; Kanninen, Markku; Luukkanen, Olavi (2018)
    National food security has been a major policy goal in Sudan since the country gained its independence in 1956. One of the fundamental reasons is to ensure the social welfare for people living in rural areas. In this study we aimed to analyse how farmers secure their food and generate income in the semi-arid Sennar state in Sudan, using two selected sites, El Dali and El Mazmum, as examples. We interviewed 281 randomly sampled household heads, of which 145 at El Dali and 136 at El Mazmum, between July and November 2011. We identified four distinct land use systems, of which three consist of monocropping and one of cultivation in agroforestry parklands. Several statistical techniques and economic analysis were applied on the study data. Our results show that, in the two areas, the highest average yields over a 10-year period for the three crops studied, sorghum, pearl millet and sesame, were achieved in agroforestry system, except for the case of sesame at El Mazmum. Economic returns for the farmers, as indicated by net present value or benefit/cost ratio, followed the same pattern. The study concludes that farmers should rely more on agroforestry to improve their food security and cash income generation. Land use and land right policies, which currently discourage farmers from growing trees on their lands, should be revised, so as to give more incentive to them to adopt ecologically and economically more sustainable land use practices.
  • Penttinen, Elina (2017)
  • Talvitie, Topi; Eggeling, Ralf; Koivisto, Mikko (2019)
    Modern exact algorithms for structure learning in Bayesian networks first compute an exact local score of every candidate parent set, and then find a network structure by combinatorial optimization so as to maximize the global score. This approach assumes that each local score can be computed fast, which can be problematic when the scarcity of the data calls for structured local models or when there are both continuous and discrete variables, for these cases have lacked efficient-to-compute local scores. To address this challenge, we introduce a local score that is based on a class of classification and regression trees. We show that under modest restrictions on the possible branchings in the tree structure, it is feasible to find a structure that maximizes a Bayes score in a range of moderate-size problem instances. In particular, this enables global optimization of the Bayesian network structure, including the local structure. In addition, we introduce a related model class that extends ordinary conditional probability tables to continuous variables by employing an adaptive discretization approach. The two model classes are compared empirically by learning Bayesian networks from benchmark real-world and synthetic data sets. We discuss the relative strengths of the model classes in terms of their structure learning capability, predictive performance, and running time. (C) 2019 The Authors. Published by Elsevier Inc.
  • Multia, Evgen; Sirén, Heli; Andersson, Karl; Samuelsson, Jörgen; Forssén, Patrik; Fornstedt, Torgny; Öörni, Katariina; Jauhiainen, Matti; Riekkola, Marja-Liisa (2017)
    Two complementary instrumental techniques were used, and the data generated was processed with advanced numerical tools to investigate the interactions between anti-human apoB-100 monoclonal antibody (anti-apoB-100 Mab) and apoB-100 containing lipoproteins. Partial Filling Affinity Capillary Electrophoresis (PF-ACE) combined with Adsorption Energy Distribution (AED) calculations provided information on the heterogeneity of the interactions without any a priori model assumptions. The AED calculations evidenced a homogenous binding site distribution for the interactions. Quartz Crystal Microbalance (QCM) studies were used to evaluate thermodynamics and kinetics of the Low-Density Lipoprotein (LDL) and anti-apoB-100 Mab interactions. High affinity and selectivity were observed, and the emerging data sets were analysed with so called Interaction Maps. In thermodynamic studies, the interaction between LDL and anti-apoB-100 Mab was found to be predominantly enthalpy driven. Both techniques were also used to study antibody interactions with Intermediate-Density (IDL) and Very Low Density (VLDL) Lipoproteins. By screening affinity constants for IDL-VLDL sample in a single injection we were able to distinguish affinity constants for both subpopulations using the numerical Interaction Map tool. (C) 2016 Elsevier Inc. All rights reserved.
  • Ahlgren, T.; Bukonte, L. (2017)
    The sink strength is an important parameter for the mean-field rate equations to simulate temporal changes in the micro-structure of materials. However, there are noteworthy discrepancies between sink strengths obtained by the Monte Carlo and analytical methods. In this study, we show the reasons for these differences. We present the equations to estimate the statistical error for sink strength calculations and show the way to determine the sink strengths for multiple traps. We develop a novel, very fast Monte Carlo method to obtain sink strengths. The results show that, in addition to the well-known sink strength dependence of the trap concentration, trap radius and the total sink strength, the sink strength also depends on the defect diffusion jump length and the total trap volume fraction. Taking these factors into account, allows us to obtain a very accurate analytic expression for the sink strength of spherical traps. (C) 2017 Elsevier B. V. All rights reserved.
  • Hiltunen, Teppo; Cairns, Johannes; Frickel, Jens; Jalasvuori, Matti; Laakso, Jouni; Kaitala, Veijo; Kuenzel, Sven; Karakoc, Emre; Becks, Lutz (2018)
    Recognizing when and how rapid evolution drives ecological change is fundamental for our understanding of almost all ecological and evolutionary processes such as community assembly, genetic diversification and the stability of communities and ecosystems. Generally, rapid evolutionary change is driven through selection on genetic variation and is affected by evolutionary constraints, such as tradeoffs and pleiotropic effects, all contributing to the overall rate of evolutionary change. Each of these processes can be influenced by the presence of multiple environmental stressors reducing a population's reproductive output. Potential consequences of multistressor selection for the occurrence and strength of the link from rapid evolution to ecological change are unclear. However, understanding these is necessary for predicting when rapid evolution might drive ecological change. Here we investigate how the presence of two stressors affects this link using experimental evolution with the bacterium Pseudomonas fluorescens and its predator Tetrahymena thermophila. We show that the combination of predation and sublethal antibiotic concentrations delays the evolution of anti-predator defence and antibiotic resistance compared with the presence of only one of the two stressors. Rapid defence evolution drives stabilization of the predator-prey dynamics but this link between evolution and ecology is weaker in the two-stressor environment, where defence evolution is slower, leading to less stable population dynamics. Tracking the molecular evolution of whole populations over time shows further that mutations in different genes are favoured under multistressor selection. Overall, we show that selection by multiple stressors can significantly alter eco-evolutionary dynamics and their predictability.
  • Coloma, Sebastian Ernesto; Gaedge, Ursula; Sivonen, Anna Kaarina; Hiltunen, Teppo Johannes (2019)
    Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0%, 5%, and 50%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0% and 5%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.
  • Scheued, Thomas; Cairns, Johannes; Becks, Lutz; Hiltunen, Teppo (2019)
    Predation is one of the key ecological mechanisms allowing species coexisence and influencing biological diversity. However, ecological processes are subject to contemporary evolutionary change, and the degree to which predation affects diversity ultimately depends on the interplay between evolution and ecology. Furthermore, ecological interactions that influence species coexistence can be altered by reciprocal coevolution especially in the case of antagonistic interactions such as predation or parasitism. Here we used an experimental evolution approach to test for the role of initial trait variation in the prey population and coevolutionary hisory of the predator in the ecological dynamics of a two-species bacterial community predated by a ciliate. We found that initial trait variation both at the bacterial and ciliate level enhanced species coexistence, and that subsequent trait evolutionary trajectories depended on the initial genetic diversity present in the population. Our findings provide further support to the notion that the ecology-centric view of diversity maintenance must be reinvestigated in light of recent findings in the field of eco-evolutionary dynamics.
  • Rask, Mikko Tapani; Mačiukaitė-Žvinienė, Saulė; Tauginienė, Loreta; Dikčius, Vytautas; Matschoss, Kaisa Johanna; Aarrevaara, Timo; d'Andrea, Luciano (Routledge - Taylor & Francis Group, 2018)
    The field of public participation is developing fast, with phenomena such as citizen science and crowdsourcing extending the resource base of research, stimulating innovation and making science more accessible to the general population. Promoting public participation means giving more weight to citizens and civil society actors in the definition of research needs and in the implementation of research and innovation. As yet, there is limited understanding of the implications of widespread use of public participation and as a result, there is a risk that it will become a burden for research and an obstacle to bridging the gap between research and society. This volume presents the findings of a three-year international study on innovative public participation. The resulting work studies the characteristics and trends of innovative public participation through a global sample of 38 case studies. It provides theoretical generalisations on the dynamics of public participation, suggestions for an evaluation framework and clear empirical examples of how public participation works in practice. Illustrated by best practice cases, the authors identify characteristics, which contribute to successful public participation. This book it aimed primarily at scholars and practitioners of public participation as well as research managers, policy makers and business actors interested in related issues. There is also a secondary market for students and scholars of European governance studies, sociology and political sciences.
  • Pulkkinen, Katja; Pekkala, Nina; Ashrafi, Roghaieh; Hamalainen, Dorrit M.; Nkembeng, Aloysius N.; Lipponen, Anssi; Hiltunen, Teppo; Valkonen, Janne K.; Taskinen, Jouni (2018)
    Understanding ecological and epidemiological factors driving pathogen evolution in contemporary time scales is a major challenge in modern health management. Pathogens that replicate outside the hosts are subject to selection imposed by ambient environmental conditions. Increased nutrient levels could increase pathogen virulence by pre-adapting for efficient use of resources upon contact to a nutrient rich host or by favouring transmission of fast-growing virulent strains. We measured changes in virulence and competition in Flavobacterium columnare, a bacterial pathogen of freshwater fish, under high and low nutrient levels. To test competition between strains in genotype mixtures, we developed a quantitative real-time PCR assay. We found that a virulent strain maintained its virulence and outcompeted less virulent strains independent of the nutrient level and resource renewal rate while a less virulent strain further lost virulence in chemostats under low nutrient level and over long-term serial culture under high nutrient level. Our results suggest that increased outside-host nutrient levels might maintain virulence in less virulent strains and increase their contribution to epidemics in aquaculture. The results highlight a need to further explore the role of resource in the outside-host environment in maintaining strain diversity and driving evolution of virulence among environmentally growing pathogens.
  • Suominen, Saara; Brauer, Verena S.; Rantala-Ylinen, Anne; Sivonen, Kaarina; Hiltunen, Teppo (2017)
    The toxicity of a harmful algal bloom is strongly determined by the relative abundance of non-toxic and toxic genotypes and might therefore be regulated by competition for growth-limiting resources. Here, we studied how the toxic Microcystis aeruginosa strain PCC 7806 and a non-toxic mutant compete for nitrogen and phosphorus under constant and pulsed nutrient supply. Our monoculture and competition experiments show that these closely related genotypes have distinct nutrient physiologies and that they differ in their ability to compete for nitrogen and phosphorus. The toxic wild type won the competition under nitrogen limitation, while the non-toxic mutant dominated under phosphorus limitation. Pulses of both nitrogen and phosphorus increased the dominance of the toxic genotype, which lead to an even faster competitive exclusion of the non-toxic genotype under nitrogen pulses and to coexistence of both genotypes under phosphorus pulses. Our findings indicate that the genotype level dynamics driven by resource competition can be an important factor in determining cyanobacterial bloom toxicity.
  • Heino, Jani; Grönroos, Mira (2017)
    It was recently suggested that beta diversity can be partitioned into contributions of single sites to overall beta diversity (LCBD) or into contributions of individual species to overall beta diversity (SCBD). We explored the relationships of LCBD and SCBD to site and species characteristics, respectively, in stream insect assemblages. We found that LCBD was mostly explained by variation in species richness, with a negative relationship being detected. SCBD was strongly related to various species characteristics, such as occupancy, abundance, niche position and niche breadth, but was only weakly related to biological traits of species. In particular, occupancy and its quadratic terms showed a very strong unimodal relationship with SCBD, suggesting that intermediate species in terms of site occupancy contribute most to beta diversity. Our findings of unravelling the contributions of sites or species to overall beta diversity are of high importance to community ecology, conservation and bioassessment using stream insect assemblages, and may bear some overall generalities to be found in other organism groups.

View more