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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.

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  • Holopainen, Mika Antero (2016)
  • Holopainen, Mika; Viitala, Eeva Liisa Marjatta (2015)
  • Antchev, G.; Aspell, P.; Atanassov, I.; Avati,; Baechler, J.; Barrera, C. Baldenegro; Berardi, V.; Berretti, M.; Bossini, E.; Bottigli, U.; Bozzo, M.; Bruce, R.; Burkhardt, H.; Cafagna, F. S.; Catanesi, M. G.; Csanad, M.; Csorgo, T.; Deile, M.; De Leonardis, F.; D'Orazio, A.; Doubek, M.; Druzhkin, D.; Eggert, K.; Eremin,; Ferro, F.; Fiergolski, A.; Garcia, F.; Morales, H. Garcia; Georgiev,; Giani, S.; Grzanka, L.; Hammerbauer, J.; Heino, J.; Helander, P.; Isidori, T.; Ivanchenko,; Janda, M.; Karev, A.; Kavspar, J.; Kopal, J.; Kundrat,; Lami, S.; Latino, G.; Lauhakangas, R.; Linhart, R.; Naaranoja, T.; Oljemark, F.; Österberg, K.; Saarikko, H.; Welti, J. (2019)
    The TOTEM experiment at the LHC has performed the first measurement at root s = 13 TeV of the rho parameter, the real to imaginary ratio of the nuclear elastic scattering amplitude at t = 0, obtaining the following results: rho = 0.09 +/- 0.01 and rho = 0.10 +/- 0.01, depending on different physics assumptions and mathematical modelling. The unprecedented precision of the rho measurement, combined with the TOTEM total cross-section measurements in an energy range larger than 10 TeV (from 2.76 to 13 TeV), has implied the exclusion of all the models classified and published by COMPETE. The rho results obtained by TOTEM are compatible with the predictions, from other theoretical models both in the Regge-like framework and in the QCD framework, of a crossing-odd colourless 3-gluon compound state exchange in the t-channel of the proton-proton elastic scattering. On the contrary, if shown that the crossing-odd 3-gluon compound state t-channel exchange is not of importance for the description of elastic scattering, the rho value determined by TOTEM would represent a first evidence of a slowing down of the total cross-section growth at higher energies. The very low-vertical bar t vertical bar reach allowed also to determine the absolute normalisation using the Coulomb amplitude for the first time at the LHC and obtain a new total proton-proton cross-section measurement sigma(tot) = (110.3 +/- 3.5) mb, completely independent from the previous TOTEM determination. Combining the two TOTEM results yields sigma(tot) = (110.5 +/- 2.4) mb.
  • Haapasalo, Karita; Meri, Seppo (2019)
    The functions of pentraxins, like C-reactive protein (CRP), serum amyloid protein P (SAP) and pentraxin-3 (PTX3), are to coordinate spatially and temporally targeted clearance of injured tissue components, to protect against infections and to regulate related inflammation together with the complement system. For this, pentraxins have a dual relationship with the complement system. Initially, after a focused binding to their targets, e.g., exposed phospholipids or cholesterol in the injured tissue area, or microbial components, the pentraxins activate complement by binding its first component C1q. However, the emerging inflammation needs to be limited to the target area. Therefore, pentraxins inhibit complement at the C3b stage to prevent excessive damage. The complement inhibitory functions of pentraxins are based on their ability to interact with complement inhibitors C4bp or factor H (FH). C4bp binds to SAP, while FH binds to both CRP and PTX3. FH promotes opsonophagocytosis through inactivation of C3b to iC3b, and inhibits AP activity thus preventing formation of the C5a anaphylatoxin and the complement membrane attack complex (MAC). Monitoring CRP levels gives important clinical information about the extent of tissue damage and severity of infections. CRP is a valuable marker for distinguishing bacterial infections from viral infections. Disturbances in the functions and interactions of pentraxins and complement are also involved in a number of human diseases. This review will summarize what is currently known about the FH family proteins and pentraxins that interact with FH. Furthermore, we will discuss diseases, where interactions between these molecules may play a role.
  • Kaltiala-Heino, Riittakerttu; Lindberg, Nina; Fröjd, Sari; Haravuori, Henna; Marttunen, Mauri (2019)
    Purpose: To explore whether sexual harassment experiences are more common among adolescents reporting romantic and erotic interests in the same sex and both sexes, when sociodemographic and mental health confounding are controlled for, and whether the associations are similar in both sexes and in different phases of adolescence. Methods: A cross-sectional survey among a nationally representative dataset of 25,147 boys and 25,257 girls in comprehensive school, and 33,231 boys and 36,765 girls in upper secondary education. Self-reports of experiences of sexual harassment, and emotional (depression) and behavioral (delinquency) symptoms were used. Results: All associations between sexual minority status and harassment diminished clearly when mental disorder dimensions were controlled for. In the comprehensive school sample (mean age 15.4 years), sexual harassment experiences were 4-7-fold more common among boys, and 1.5-3-fold among girls, with same-sex/both-sexes interest, compared to those interested exclusively in the opposite sex. In the upper secondary education sample (mean age 17.4 years), among boys, sexual harassment was reported 3-6-fold more commonly by those not exclusively heterosexually interested. Among older girls, a slight increase in sexual harassment experiences was seen among those interested in both sexes. Conclusions: Sexual harassment experiences are associated with sexual minority status, particularly among boys. Confounding by mental disorders needs to be accounted for when studying sexual minority status and sexual harassment.
  • Kerola, Tuomas; Eranti, Antti; Aro, Aapo L.; Haukilahti, M. Anette; Holkeri, Arttu; Junttila, M. Juhani; Kenttä, Tuomas V.; Rissanen, Harri; Vittinghoff, Eric; Knekt, Paul; Heliövaara, Markku; Huikuri, Heikki V.; Marcus, Gregory M. (2019)
    IMPORTANCE Pacemaker implantations as a treatment for atrioventricular (AV) block are increasing worldwide. Prevention strategies for AV block are lacking because modifiable risk factors have not yet been identified. OBJECTIVE To identify risk factors for AV block in community-dwelling individuals. DESIGN, SETTING, AND PARTICIPANTS In this population-based cohort study, data from the Mini-Finland Health Survey, conducted from January 1, 1978, to December 31, 1980, were used to examine demographics, comorbidities, habits, and laboratory and electrocardiographic (ECG) measurements as potential risk factors for incident AV block. Data were ascertained during follow-up from January 1, 1987, through December 31, 2011, using a nationwide registry. A total of 6146 community-dwelling individuals were included in the analysis performed from January 15 through April 3, 2018. MAIN OUTCOMES AND MEASURES Incidence of AV block (hospitalization for second-or third-degree AV block). RESULTS Among the 6146 participants (3449 [56.1%] women; mean [SD] age, 49.2 [12.9] years), 529 (8.6%) had ECG evidence of conduction disease and 58 (0.9%) experienced a hospitalization with AV block. Older age (hazard ratio [HR] per 5-year increment, 1.34; 95% CI, 1.16-1.54; P CONCLUSIONS AND RELEVANCE In this analysis of data from a population-based cohort study, suboptimal blood pressure and fasting glucose level were associated with AV block. These results suggest that a large proportion of AV blocks are assocated with these risk factors, even after adjusting for other major adverse coronary events.
  • Jitta, Aditya; Klami, Arto (AAAI Press, 2018)
    Classical model-based partitional clustering algorithms, such as k-means or mixture of Gaussians, provide only loose and indirect control over the size of the resulting clusters. In this work, we present a family of probabilistic clustering models that can be steered towards clusters of desired size by providing a prior distribution over the possible sizes, allowing the analyst to fine-tune exploratory analysis or to produce clusters of suitable size for future down-stream processing. Our formulation supports arbitrary multimodal prior distributions, generalizing the previous work on clustering algorithms searching for clusters of equal size or algorithms designed for the microclustering task of finding small clusters. We provide practical methods for solving the problem, using integer programming for making the cluster assignments, and demonstrate that we can also automatically infer the number of clusters.
  • Previti, Alessandro; Mencía, Carlos; Järvisalo, Matti Juhani; Marques-Silva, Joao (AAAI Press, 2018)
    Proceedings of the AAAI Conference on Artificial Intelligence
  • Tabassum, Rubina; Rämö, Joel T.; Ripatti, Pietari; Koskela, Jukka T.; Kurki, Mitja; Karjalainen, Juha; Palta, Priit; Hassan, Shabbeer; Nunez-Fontarnau, Javier; Kiiskinen, Tuomo T. J.; Söderlund, Sanni; Matikainen, Niina; Laivuori, Hannele; Havulinna, Aki S.; Pirinen, Matti; Jalanko, Anu; Kaprio, Jaakko; Donner, Kati; Kaunisto, Mari; Mars, Nina; Dada, Alexander; Shcherban, Anastasia; Ganna, Andrea; Lehisto, Arto; Kilpeläinen, Elina; Brein, Georg; Awaisa, Ghazal; Harju, Jarmo; Pärn, Kalle; Parolo, Pietro Della Briotta; Kajanne, Risto; Lemmelä, Susanna; Sipilä, Timo P.; Sipilä, Tuomas; Lyhs, Ulrike; Llorens, Vincent; Niiranen, Teemu; Kristiansson, Kati; Jiménez, Manuel González; Perola, Markus; Hiekkalinna, Tero; Mattsson, Hannele; Laiho, Päivi; Soini, Sirpa; Lehtonen, Anne; Pulkki, Kari; Heikkinen, Sami; Laukkanen, Jari; Laaksonen, Reijo; Ritari, Jarmo; Partanen, Jukka; Hyvärinen, Kati; Auro, Kirsi; Pitkänen, Kimmo; Mäkelä, Tomi; Loukola, Anu; Joensuu, Heikki; Sinisalo, Juha; Eklund, Kari; Aaltonen, Lauri; Färkkilä, Martti; Carpen, Olli; Kauppi, Paula; Tienari, Pentti; Ollila, Terhi; Tuomi, Tiinamaija; Meretoja, Tuomo; Pitkäranta, Anne; Turunen, Joni; Hannula-Jouppi, Katariina; Pikkarainen, Sampsa; Seitsonen, Sanna; Koskinen, Miika; Palomäki, Antti; Voutilainen, Markku; Kettunen, Johannes; Pelkonen, Margit; Julkunen, Valtteri; Lehtonen, Heli; Parkkinen, Jaakko; Linden, Kari; Jussila, Airi; Laitinen, Tarja; Palin, Kimmo; Jauhiainen, Matti; Daly, Mark J.; Palotie, Aarno; Taskinen, Marja-Riitta; Ripatti, Samuli (2019)
    Understanding genetic architecture of plasma lipidome could provide better insights into lipid metabolism and its link to cardiovascular diseases (CVDs). Here, we perform genome-wide association analyses of 141 lipid species (n = 2,181 individuals), followed by phenome-wide scans with 25 CVD related phenotypes (n = 511,700 individuals). We identify 35 lipid-species-associated loci (P 
  • Jang, Jieun; Cho, Eun-Jung; Hwang, Yunji; Weiderpass, Elisabete; Ahn, Choonghyun; Choi, Jeoungbin; Chang, Soung-Hoon; Shin, Hai-Rim; Lim, Min Kyung; Yoo, Keun-Young; Park, Sue K. (2019)
    Purpose Few studies investigated roles of body mass index (BMI) on gastric cancer (GC) risk according to Helicobacter pylori infection status. This study was conducted to evaluate associations between BMI and GC risk with consideration of H. pylori infection information. Materials and Methods We performed a case-cohort study (n=2,458) that consists of a subcohort (n=2,193 including 67 GC incident cases) randomly selected from the Korean Multicenter Cancer Cohort (KMCC) and 265 incident GC cases outside of the subcohort. H. pylori infection was assessed using an immunoblot assay. GC risk according to BMI was evaluated by calculating hazard ratios (HRs) and their 95% confidence intervals (95% CIs) using weighted Cox hazard regression model. Results Increased GC risk in lower BMI group (= 25 kg/m(2)) showed non-significantly increased GC risk (HR, 10.82; 95% CI, 1.25 to 93.60 and HR, 11.33; 95% CI, 1.13 to 113.66, respectively). However, these U-shaped associations between BMI and GC risk were not observed in the group who had ever been infected by H. pylori. Conclusion This study suggests the U-shaped associations between BMI and GC risk, especially in subjects who had never been infected by H. pylori.
  • Claassens, Nico J.; Finger-Bou, Max; Scholten, Bart; Muis, Frederieke; de Groot, Jonas J.; de Gier, Jan-Willem; de Vos, Willem M.; van der Oost, John (2019)
    Escherichia coli has been widely used as a platform microorganism for both membrane protein production and cell factory engineering. The current methods to produce membrane proteins in this organism require the induction of target gene expression and often result in unstable, low yields. Here, we present a method combining a constitutive promoter with a library of bicistronic design (BCD) elements, which enables inducer-free, tuned translation initiation for optimal protein production. Our system mediates stable, constitutive production of bacterial membrane proteins at yields that outperform those obtained with E. coli Lemo21(DE3), the current gold standard for bacterial membrane protein production. We envisage that the continuous, fine-tunable, and high-level production of membrane proteins by our method will greatly facilitate their study and their utilization in engineering cell factories.
  • Pääkkönen, Timo; Spiliopoulos, Panagiotis; Nonappa, Dr.; Kontturi, Katri S.; Penttilä, Paavo; Viljanen, Mira; Svedström, Kirsi; Kontturi, Eero (2019)
    HCl gas hydrolysis of a bacterial cellulose (BC) aerogel followed by 2,2,6,6-tetramethylpiperidine-1-oxyl radical-mediated oxidation was used to produce hydrolyzed BC with carboxylate groups, which subsequently disintegrated into a stable dispersion of cellulose nanocrystals (CNCs). The degree of polymerization was successfully reduced from 2160 to 220 with a CNC yield of >80%.
  • Paton, Mark; Harri, Ari-Matti; Vierkens, Oliver; Savijärvi, Hannu (2019)
    As spacecraft missions return ever more data from Mars, additional tools will be required to explore and analyse these datasets efficiently. To streamline research into the atmosphere of Mars, a user-orientated modelling capability is developed that enables automatic initialisation and running of a column model. As a demonstration we utilise the modelling framework to provide additional verification for the University of Helsinki and Finnish Meteorological Institute Mars column model temperature profiles above the height of typical lander meteorological measurements, i.e. above 2 m. We utilise the framework at landing site locations that are well characterised to understand the model's applicability and to identify future opportunities for modifications to the framework. We do this by using the framework to compare the column model to temperature soundings made by the Mars Reconnaissance Orbiter. We find that the column model, without any modification, is able to reproduce the observed lapse rates and average temperatures closely in most cases except for a 20-60 K increase over the northern hemisphere mid-winter. We can reproduce this discrepancy by incorporating an adiabatic heating term into the column model. Fitting of the modified column model to the observations results in estimated maximum downward vertical wind velocities of similar to 10 cm s(-1) at altitudes of 15-20 km over the winter solstice at the VL-1 and VL-2 sites. The approach developed here may possibly provide a way to independently estimate or observe the vertical motion in the Martian atmosphere. However, even though the magnitude of the vertical wind speed appears reasonable, it is not clear at this point how much the atmospheric heating is due to other mechanisms such as advection. We have introduced new application software that can quickly find and display the requested data and can be immediately analysed using the included tools. We have demonstrated the potential of this type of software application with a glimpse into the upper atmosphere of Mars.
  • Tuomenoksa, Asta; Pajo, Kati; Klippi, Anu (2016)
    This study applies conversation analysis to compare everyday conversation samples between a person with aphasia (PWA) and a familiar communication partner (CP) before and after intensive language-action therapy (ILAT). Our analysis concentrated on collaborative repair sequences with the assumption that impairment-focused therapy would translate into a change in the nature of trouble sources, which engender collaborative repair action typical of aphasic conversation. The most frequent repair initiation technique used by the CP was candidate understandings. The function of candidate understandings changed from addressing specific trouble sources pre-ILAT to concluding longer stretches of the PWA's talk post-ILAT. Alongside with these findings, we documented a clinically significant increase in the Western Aphasia Battery's aphasia quotient post-ILAT. Our results suggest that instead of mere frequency count of conversational behaviours, examining the type and function of repair actions might provide insight into therapy-related changes in conversation following impairment-focused therapy.
  • Semenyuk, Pavel; Tiainen, Tony; Hietala, Sami; Tenhu, Heikki; Aseyev, Vladimir; Muronetz, Vladimir (2019)
    Stabilization of the enzymes under stress conditions is of special interest for modern biochemistry, bioengineering, as well as for formulation and target delivery of protein-based drugs. Aiming to achieve an efficient stabilization at elevated temperature with no influence on the enzyme under normal conditions, we studied chaperone-like activity of thermoresponsive polymers based on poly(dimethylaminoethyl methacrylate) (PDMAEMA) toward two different proteins, glyceraldehyde-3-phosphate dehydrogenase and chicken egg lysozyme. The polymers has been shown to do not interact with the folded protein at room temperature but form a complex upon heating to either protein unfolding or polymer phase transition temperature. A PDMAEMA-PEO block copolymer with a dodecyl end-group (d-PDMAEMA-PEO) as well as PDMAEMA-PEO without the dodecyl groups protected the denatured protein against aggregation in contrast to PDMAEMA homopolymer. No effect of the polymers on the enzymatic activity of the client protein was observed at room temperature. The polymers also partially protected the enzyme against inactivation at high temperature. The results provide a platform for creation of artificial chaperones with unfolded protein recognition which is a major feature of natural chaperones. (C) 2018 Elsevier B.V. All rights reserved.
  • Hyttinen, Tapani; Paolini, Gianluca (2018)
    Based on Crapo’s theory of one point extensions of combinatorial geometries, we find various classes of geometric lattices that behave very well from the point of view of stability theory. One of them, (K3, ), is ω-stable, it has a monster model and an independence calculus that satisfies all the usual properties of non-forking. On the other hand, these classes are rather unusual, e.g. in (K3, )the Smoothness Axiom fails, and so (K3, )is not an AEC.
  • Savvides, Rafael; Henelius, Andreas; Oikarinen, Emilia; Puolamäki, Kai (ACM, 2019)
    In this paper we consider the following important problem: when we explore data visually and observe patterns, how can we determine their statistical significance? Patterns observed in exploratory analysis are traditionally met with scepticism, since the hypotheses are formulated while viewing the data, rather than before doing so. In contrast to this belief, we show that it is, in fact, possible to evaluate the significance of patterns also during exploratory analysis, and that the knowledge of the analyst can be leveraged to improve statistical power by reducing the amount of simultaneous comparisons. We develop a principled framework for determining the statistical significance of visually observed patterns. Furthermore, we show how the significance of visual patterns observed during iterative data exploration can be determined. We perform an empirical investigation on real and synthetic tabular data and time series, using different test statistics and methods for generating surrogate data. We conclude that the proposed framework allows determining the significance of visual patterns during exploratory analysis.
  • Talvitie, Topi; Koivisto, Mikko (AAAI Press, 2019)

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