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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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  • Deressa, Abdenna; Yli-Halla, Markku; Mohamed, Muktar (Springer Berlin Heidelberg, 2020)
    Abstract Background There is scarcity of scientific information on stocks and retention rate of soil organic carbon (SOC) among mixed farming systems in humid Western Ethiopia. The objectives of study were to determine the SOC stocks and retention rates along a 53-km long toposequence of Didessa watershed. The study was conducted in mixed farming systems (annual arable cropping, grazing, fallow, grassland, coffee agroforestry, eucalyptus agroforestry and mechanized irrigated sugarcane production) within an elevation range of 1273 to 2543 m above sea level. Results The results revealed that land use types greatly affected SOC stocks and retention rates in the upper 20 cm soil depth. The SOC stocks ranged from 9.27 to 13.5 Mg C ha−1 (0–20 cm) while the retention rates were 0.11, 0.20, 0.28, 0.31 and 1.14 Mg C ha−1 year−1 for coffee agroforestry, fallow, grazing, eucalyptus agroforestry and irrigated sugarcane production systems, respectively. Conclusion The retention rates demonstrated that the different farming systems are potential source of C sinks. The study indicated that the farming systems are efficient in sequestering SOC and their benefits can be further adopted for their economic values, social significance, restoration of degraded land, and sequestration of carbon (C) in humid tropical Western Ethiopia.
  • Vehmeijer, Florianne O L; Küpers, Leanne K; Sharp, Gemma C; Salas, Lucas A; Lent, Samantha; Jima, Dereje D; Tindula, Gwen; Reese, Sarah; Qi, Cancan; Gruzieva, Olena; Page, Christian; Rezwan, Faisal I; Melton, Philip E; Nohr, Ellen; Escaramís, Geòrgia; Rzehak, Peter; Heiskala, Anni; Gong, Tong; Tuominen, Samuli T; Gao, Lu; Ross, Jason P; Starling, Anne P; Holloway, John W; Yousefi, Paul; Aasvang, Gunn M; Beilin, Lawrence J; Bergström, Anna; Binder, Elisabeth; Chatzi, Leda; Corpeleijn, Eva; Czamara, Darina; Eskenazi, Brenda; Ewart, Susan; Ferre, Natalia; Grote, Veit; Gruszfeld, Dariusz; Håberg, Siri E; Hoyo, Cathrine; Huen, Karen; Karlsson, Robert; Kull, Inger; Langhendries, Jean-Paul; Lepeule, Johanna; Magnus, Maria C; Maguire, Rachel L; Molloy, Peter L; Monnereau, Claire; Mori, Trevor A; Oken, Emily; Räikkönen, Katri; Rifas-Shiman, Sheryl; Ruiz-Arenas, Carlos; Sebert, Sylvain; Ullemar, Vilhelmina; Verduci, Elvira; Vonk, Judith M; Xu, Cheng-jian; Yang, Ivana V; Zhang, Hongmei; Zhang, Weiming; Karmaus, Wilfried; Dabelea, Dana; Muhlhausler, Beverly S; Breton, Carrie V; Lahti, Jari; Almqvist, Catarina; Jarvelin, Marjo-Riitta; Koletzko, Berthold; Vrijheid, Martine; Sørensen, Thorkild I A; Huang, Rae-Chi; Arshad, Syed H; Nystad, Wenche; Melén, Erik; Koppelman, Gerard H; London, Stephanie J; Holland, Nina; Bustamante, Mariona; Murphy, Susan K; Hivert, Marie-France; Baccarelli, Andrea; Relton, Caroline L; Snieder, Harold; Jaddoe, Vincent W V; Felix, Janine F (BioMed Central, 2020)
    Abstract Background DNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unknown. More insight into this relationship at younger ages may have implications for future prevention of obesity and its related traits. Methods We examined whether DNA methylation in cord blood and whole blood in childhood and adolescence was associated with BMI in the age range from 2 to 18 years using both cross-sectional and longitudinal models. We performed meta-analyses of epigenome-wide association studies including up to 4133 children from 23 studies. We examined the overlap of findings reported in previous studies in children and adults with those in our analyses and calculated enrichment. Results DNA methylation at three CpGs (cg05937453, cg25212453, and cg10040131), each in a different age range, was associated with BMI at Bonferroni significance, P < 1.06 × 10−7, with a 0.96 standard deviation score (SDS) (standard error (SE) 0.17), 0.32 SDS (SE 0.06), and 0.32 BMI SDS (SE 0.06) higher BMI per 10% increase in methylation, respectively. DNA methylation at nine additional CpGs in the cross-sectional childhood model was associated with BMI at false discovery rate significance. The strength of the associations of DNA methylation at the 187 CpGs previously identified to be associated with adult BMI, increased with advancing age across childhood and adolescence in our analyses. In addition, correlation coefficients between effect estimates for those CpGs in adults and in children and adolescents also increased. Among the top findings for each age range, we observed increasing enrichment for the CpGs that were previously identified in adults (birth Penrichment = 1; childhood Penrichment = 2.00 × 10−4; adolescence Penrichment = 2.10 × 10−7). Conclusions There were only minimal associations of DNA methylation with childhood and adolescent BMI. With the advancing age of the participants across childhood and adolescence, we observed increasing overlap with altered DNA methylation loci reported in association with adult BMI. These findings may be compatible with the hypothesis that DNA methylation differences are mostly a consequence rather than a cause of obesity.
  • Aspinen, Samuli; Nordback, Panu H.; Anttila, Turkka; Stjernberg-Salmela, Susanna; Ryhänen, Jorma; Kosola, Jussi (BioMed Central, 2020)
    Abstract Background Trigger finger is a common hand disorder that limits finger range of motion and causes pain and snapping of the affected finger. Trigger finger is caused by an imbalance of the tendon sheath and the flexor tendon. The initial treatment is generally a local corticosteroid injection around the first annular (A1) pulley. However, it is not unusual that surgical release of the A1 pulley is required. Moreover, adverse events after local corticosteroid injection or operative treatment may occur. Platelet-rich plasma (PRP) has been shown to be safe and to reduce symptoms in different tendon pathologies, such as DeQuervain’s disease. However, the effects of PRP on trigger finger have not been studied. The aim of this single-center triple-blind randomized controlled trial is to study whether PRP is non-inferior to corticosteroid injection in treating trigger finger. The secondary outcome is to assess the safety and efficacy of PRP in comparison to placebo. Methods The trial is designed as a randomized, controlled, patient-, investigator-, and outcome assessor-blinded, single-center, three-armed 1:1:1 non-inferiority trial. The patients with clinical symptoms of trigger finger will be randomly assigned to treatment with PRP, corticosteroid, or normal saline injection. The primary outcome is Patient-Rated Wrist Evaluation and symptom resolution. Secondary outcomes include Quick-Disabilities of the Arm, Shoulder and Hand; pain; grip strength; finger active range of motion; and complications. Appropriate statistical methods will be applied. Discussion We present a novel RCT study design on the use of PRP for the treatment of trigger finger compared to corticosteroid and normal saline injection. The results of the trial will indicate if PRP is appropriate for the treatment of trigger finger. Trial registration ClinicalTrials.gov NCT04167098 . Registered on November 18, 2019.
  • Gershony, Liza C; Belanger, Janelle M; Hytönen, Marjo K; Lohi, Hannes; Famula, Thomas R; Oberbauer, Anita M (BioMed Central, 2020)
    Abstract Background Primary hypoadrenocorticism (or Addison’s disease, AD) is an autoimmune disease that results in destruction of the adrenal cortex and consequent adrenal insufficiency. The disease has been described in purebred and mixed breed dogs, although some breeds, including the Bearded Collie, are at increased risk for AD. Candidate gene approaches have yielded few associations that appear to be breed-specific. A single other genome-wide association study reported no significant regions of association for AD in Standard Poodles. The present study aimed to identify genomic regions of association for canine AD in Bearded Collies. Results Our study consists of the first genome-wide association analysis to identify a genome-wide significant region of association with canine AD (CFA18). Peaks of suggestive association were also noted on chromosomes 11, 16 and 29. Logistic regression analysis supported an additive effect of risk genotypes at these smaller effect loci on the probability of disease associated with carrying a risk genotype on CFA18. Potential candidate genes involved in adrenal steroidogenesis, regulation of immune responses and/or inflammation were identified within the associated regions of chromosomes 11 and 16. The gene-poor regions of chromosomes 18 and 29 may, however, harbor regulatory sequences that can modulate gene expression and contribute to disease susceptibility. Conclusion Our findings support the polygenic and complex nature of canine AD and identified a strongly associated locus on CFA18 that, when combined with three other smaller effect loci, was predictive of disease. The results offer progress in the identification of susceptibility loci for canine AD in the Bearded Collie. Further studies are needed to confirm association with the suggested candidate genes and identify actual causative mutations involved with AD susceptibility in this breed.
  • Gillin, Joel T F (2019)
    This article considers the utility of a liturgical lens for locating and analyzing religion in the public sphere. Dominant paradigms in the study of religion tend to either dissolve the religious/secular distinction or base it on overly cognitive content. Drawing on the work of James K. A. Smith, the article outlines an approach which instead locates religion in embodied practices that shape human desire. I suggest the religious/secular binary is better conceptualized as a continuum in which liturgical intensity is the primary criterion of religiosity. A liturgical continuum better articulates the contested nature of public space and the religious aspects of political life.
  • Heikkurinen, Pasi; Lozanoska, Jana; Tosi, Pierre (2019)
    Hannah Arendt's three-fold conceptualization of human activity offers a useful base for understanding the necessity of degrowth and the kinds of activities required to achieve it. The article argues that the different roles of labour, work, and action should be acknowledged and scrutinized in detail to appreciate the underpinnings of contemporary over-production and over-consumption, as well as to prompt the organization of an alternative society. While following the Arendtian analysis on the origins of meaningful political change, which emphasizes the utmost importance of 'action', the article also underscores the importance of a different conception of 'labour' through physical activity, such as community supported agriculture, and 'work' through social activity such as building off-grid energy systems. The study aligns itself with Arendt's key insight that the origin of most contemporary problems relates to the disappearance of 'action', which for her is political, but also argues that the distinction between 'paid' and 'non-paid' activity has to be carefully considered in the context of degrowth. The article concludes that non-paid activities, particularly in the form of Arendtian 'action', have great potential to contribute to the degrowth movement. Demonetized activities are important for degrowth, as monetary transactions in capitalist societies based on interest and debt tend to contribute to economic growth, which is deemed ecologically unsustainable. (C) 2018 Elsevier Ltd. All rights reserved.
  • Indukaev, Andrey (Duke University Press, 2019)
  • Maarala, Altti Ilari; Arasalo, Ossi; Valenzuela, Daniel; Heljanko, Keijo; Mäkinen, Veli (Springer International Publishing, 2020)
    Lecture Notes in Computer Science
    High-throughput sequencing (HTS) technologies have enabled rapid sequencing of genomes and large-scale genome analytics with massive data sets. Traditionally, genetic variation analyses have been based on the human reference genome assembled from a relatively small human population. However, genetic variation could be discovered more comprehensively by using a collection of genomes i.e., pan-genome as a reference. The pan-genomic references can be assembled from larger populations or a specific population under study. Moreover, exploiting the pan-genomic references with current bioinformatics tools requires efficient compression and indexing methods. To be able to leverage the accumulating genomic data, the power of distributed and parallel computing has to be harnessed for the new genome analysis pipelines. We propose a scalable distributed pipeline, PanGenSpark, for compressing and indexing pan-genomes and assembling a reference genome from the pan-genomic index. We experimentally show the scalability of the PanGenSpark with human pan-genomes in a distributed Spark cluster comprising 448 cores distributed to 26 computing nodes. Assembling a consensus genome of a pan-genome including 50 human individuals was performed in 215 min and with 500 human individuals in 1468 min. The index of 1.41 TB pan-genome was compressed into a size of 164.5 GB in our experiments.
  • Lee, Lik-Hang; Kumar, Abhishek; Pirttikangas, Susanna; Ojala, Timo (2020)
    This position paper envisions the immersive urban interfaces in our daily environments by concatenating the theoretical backgrounds of Edge Artificial Intelligence and Immersive technology. We propose a sketch framework of hybrid intelligence, with the intention of configuring "what do people care about" in immersive urban environments. We outline several research opportunities of user-centered immersive urban interfaces by considering the capability of Edge AI and AI-assisted interface designs.
  • Hoque, Mohammad Ashraful; Rao, Ashwin; Kumar, Abhishek; Ammar, Mostafa; Hui, Pan; Tarkoma, Sasu (ACM, 2020)
    We use various multimedia applications on smart devices to consume multimedia content, to communicate with our peers, and to broadcast our events live. This paper investigates the utilization of different media input/output devices, e.g., camera, microphone, and speaker, by different types of multimedia applications, and introduces the notion of multimedia context. Our measurements lead to a sensing algorithm called MediaSense, which senses the states of multiple I/O devices and identifies eleven multimedia contexts of a mobile device in real time. The algorithm distinguishes stored content playback from streaming, live broadcasting from local recording, and conversational multimedia sessions from GSM/VoLTE calls on mobile devices.
  • Pitkänen-Heikkilä, Kaarina (De Gruyter Mouton, 2020)
    Trends in Linguistics. Studies and Monographs [TiLSM], 340
  • Stepanova, P.; Srinivasan, V.; Lindholm, D.; Voutilainen, M. H. (2020)
    Huntington's disease (HD) is a neurodegenerative disorder with a progressive loss of medium spiny neurons in the striatum and aggregation of mutant huntingtin in the striatal and cortical neurons. Currently, there are no rational therapies for the treatment of the disease. Cerebral dopamine neurotrophic factor (CDNF) is an endoplasmic reticulum (ER) located protein with neurotrophic factor (NTF) properties, protecting and restoring the function of dopaminergic neurons in animal models of PD more effectively than other NTFs. CDNF is currently in phase I-II clinical trials on PD patients. Here we have studied whether CDNF has beneficial effects on striatal neurons in in vitro and in vivo models of HD. CDNF was able to protect striatal neurons from quinolinic acid (QA)-induced cell death in vitro via increasing the IRE1 alpha/XBP1 signalling pathway in the ER. A single intrastriatal CDNF injection protected against the deleterious effects of QA in a rat model of HD. CDNF improved motor coordination and decreased ataxia in QA-toxin treated rats, and stimulated the neurogenesis by increasing doublecortin (DCX)-positive and NeuN-positive cells in the striatum. These results show that CDNF positively affects striatal neuron viability reduced by QA and signifies CDNF as a promising drug candidate for the treatment of HD.
  • Grzybek, Maciej; Tolkacz, Katarzyna; Sironen, Tarja; Mäki, Sanna; Alsarraf, Mohammed; Behnke-Borowczyk, Jolanta; Biernat, Beata; Nowicka, Joanna; Vaheri, Antti; Henttonen, Heikki; Behnke, Jerzy M.; Bajer, Anna (2020)
    Simple Summary Wild rodents constitute a significant threat to public health. We tested 77 voles from northeastern Poland for the presence of antibodies to hantaviruses, arenaviruses and cowpox viruses. We report 18.2% overall seroprevalence of zoonotic viruses. Our results contribute to knowledge about the role of Polish voles as possible reservoirs of viral infections. Rodents are known to be reservoir hosts for a plethora of zoonotic viruses and therefore play a significant role in the dissemination of these pathogens. We trapped three vole species (Microtus arvalis, Alexandromys oeconomus and Microtus agrestis) in northeastern Poland, all of which are widely distributed species in Europe. Using immunofluorescence assays, we assessed serum samples for the presence of antibodies to hantaviruses, arenaviruses and cowpox viruses (CPXV). We detected antibodies against CPXV and Puumala hantavirus (PUUV), the overall seroprevalence of combined viral infections being 18.2% [10.5-29.3] and mostly attributed to CPXV. We detected only one PUUV/TULV cross-reaction in Microtus arvalis (1.3% [0.1-7.9]), but found similar levels of antibodies against CPXV in all three vole species. There were no significant differences in seroprevalence of CPXV among host species and age categories, nor between the sexes. These results contribute to our understanding of the distribution and abundance of CPXV in voles in Europe, and confirm that CPXV circulates also in Microtus and Alexandromys voles in northeastern Poland.
  • Lappi, T.; Mäntysaari, H.; Penttala, J. (2020)
    We compute a light front wave function for heavy vector mesons based on long-distance matrix elements constrained by decay width analyses in the nonrelativistic QCD framework. Our approach provides a systematic expansion of the wave function in quark velocity. The first relativistic correction included in our calculation is found to be significant and crucial for a good description of the HERA exclusive J/psi production data. When looking at cross section ratios between nuclear and proton targets, the wave function dependence does not cancel out exactly. In particular the fully nonrelativistic limit is found not to be a reliable approximation even in this ratio. The important role of the Melosh rotation to express the rest frame wave function on the light front is illustrated.
  • Muinonen, K.; Torppa, J.; Wang, X-B; Cellino, A.; Penttilä, A. (2020)
    Context. We assess statistical inversion of asteroid rotation periods, pole orientations, shapes, and phase curve parameters from photometric lightcurve observations, here sparse data from the ESA Gaia space mission (Data Release 2) or dense and sparse data from ground-based observing programs.Aims. Assuming general convex shapes, we develop inverse methods for characterizing the Bayesian a posteriori probability density of the parameters (unknowns). We consider both random and systematic uncertainties (errors) in the observations, and assign weights to the observations with the help of Bayesian a priori probability densities.Methods. For general convex shapes comprising large numbers of parameters, we developed a Markov-chain Monte Carlo sampler (MCMC) with a novel proposal probability density function based on the simulation of virtual observations giving rise to virtual least-squares solutions. We utilized these least-squares solutions to construct a proposal probability density for MCMC sampling. For inverse methods involving triaxial ellipsoids, we update the uncertainty model for the observations.Results. We demonstrate the utilization of the inverse methods for three asteroids with Gaia photometry from Data Release 2: (21) Lutetia, (26) Proserpina, and (585) Bilkis. First, we validated the convex inverse methods using the combined ground-based and Gaia data for Lutetia, arriving at rotation and shape models in agreement with those derived with the help of Rosetta space mission data. Second, we applied the convex inverse methods to Proserpina and Bilkis, illustrating the potential of the Gaia photometry for setting constraints on asteroid light scattering as a function of the phase angle (the Sun-object-observer angle). Third, with the help of triaxial ellipsoid inversion as applied to Gaia photometry only, we provide additional proof that the absolute Gaia photometry alone can yield meaningful photometric slope parameters. Fourth, for (585) Bilkis, we report, with 1-sigma uncertainties, a refined rotation period of (8.5750559 0.0000026) h, pole longitude of 320.6 degrees +/- 1.2 degrees, pole latitude of - 25.6 degrees +/- 1.7 degrees, and the first shape model and its uncertainties from convex inversion.Conclusions. We conclude that the inverse methods provide realistic uncertainty estimators for the lightcurve inversion problem and that the Gaia photometry can provide an asteroid taxonomy based on the phase curves.
  • Saarelainen, Suvi-Maria; Vähäkangas, Auli; Anttonen, Mirja Sisko (2020)
    Increasingly more older people are now being cared for in their own homes. Furthermore, it has become more common that people stay at home to receive end-of-life care. Using interpretative phenomenological analysis (IPA), we analyzed the religious experiences of older people (aged 65+). We answered these questions: What kind of religious experiences do older people have when death is approaching? What does this tell us about their religious coping? As IPA is based on the in-depth analysis of small amounts of homogenous data, we analyzed five interviews with older people who were dying. We identified three main themes. First, religious experiences are relational, that is, deeply rooted in personal relationships. Second, religious experiences are real and can provide both struggles and comfort in the last stage of life. Third, the experience of encountering one's mortality and planning for one's death was calming; while many had unclear views on the afterlife, the idea of continuing bonds after death was comforting. More open discussion on religious matters, death, and dying would be welcomed as part of home-based end-of-life care.
  • Ahlqvist, Emma; Prasad, Rashmi B.; Groop, Leif (2020)
    Type 2 diabetes (T2D) is defined by a single metabolite, glucose, but is increasingly recognized as a highly heterogeneous disease, including individuals with varying clinical characteristics, disease progression, drug response, and risk of complications. Identification of subtypes with differing risk profiles and disease etiologies at diagnosis could open up avenues for personalized medicine and allow clinical resources to be focused to the patients who would be most likely to develop diabetic complications, thereby both improving patient health and reducing costs for the health sector. More homogeneous populations also offer increased power in experimental, genetic, and clinical studies. Clinical parameters are easily available and reflect relevant disease pathways, including the effects of both genetic and environmental exposures. We used six clinical parameters (GAD autoantibodies, age at diabetes onset, HbA(1c), BMI, and measures of insulin resistance and insulin secretion) to cluster adult-onset diabetes patients into five subtypes. These subtypes have been robustly reproduced in several populations and associated with different risks of complications, comorbidities, genetics, and response to treatment. Importantly, the group with severe insulin-deficient diabetes (SIDD) had increased risk of retinopathy and neuropathy, whereas the severe insulin-resistant diabetes (SIRD) group had the highest risk for diabetic kidney disease (DKD) and fatty liver, emphasizing the importance of insulin resistance for DKD and hepatosteatosis in T2D. In conclusion, we believe that subclassification using these highly relevant parameters could provide a framework for personalized medicine in diabetes.
  • Morosan, D. E.; Palmerio, E.; Räsänen, J. E.; Kilpua, E. K. J.; Magdalenic, J.; Lynch, B. J.; Kumari, A.; Pomoell, J.; Palmroth, M. (2020)
    Context. Coronal mass ejections (CMEs) are large eruptions of magnetised plasma from the Sun that are often accompanied by solar radio bursts produced by accelerated electrons.Aims. A powerful source for accelerating electron beams are CME-driven shocks, however, there are other mechanisms capable of accelerating electrons during a CME eruption. So far, studies have relied on the traditional classification of solar radio bursts into five groups (Type I-V) based mainly on their shapes and characteristics in dynamic spectra. Here, we aim to determine the origin of moving radio bursts associated with a CME that do not fit into the present classification of the solar radio emission.Methods. By using radio imaging from the Nancay Radioheliograph, combined with observations from the Solar Dynamics Observatory, Solar and Heliospheric Observatory, and Solar Terrestrial Relations Observatory spacecraft, we investigate the moving radio bursts accompanying two subsequent CMEs on 22 May 2013. We use three-dimensional reconstructions of the two associated CME eruptions to show the possible origin of the observed radio emission.Results. We identified three moving radio bursts at unusually high altitudes in the corona that are located at the northern CME flank and move outwards synchronously with the CME. The radio bursts correspond to fine-structured emission in dynamic spectra with durations of similar to 1 s, and they may show forward or reverse frequency drifts. Since the CME expands closely following an earlier CME, a low coronal CME-CME interaction is likely responsible for the observed radio emission.Conclusions. For the first time, we report the existence of new types of short duration bursts, which are signatures of electron beams accelerated at the CME flank. Two subsequent CMEs originating from the same region and propagating in similar directions provide a complex configuration of the ambient magnetic field and favourable conditions for the creation of collapsing magnetic traps. These traps are formed if a CME-driven wave, such as a shock wave, is likely to intersect surrounding magnetic field lines twice. Electrons will thus be further accelerated at the mirror points created at these intersections and eventually escape to produce bursts of plasma emission with forward and reverse drifts.
  • Iljukov, Sergei; Kauppi, Jukka-Pekka; Uusitalo, Arja L. T.; Peltonen, Juha E.; Schumacher, Yorck O. (2020)
    The purpose of this research was to evaluate the performances of female middle- and long-distance runners before and after the implementation of a new antidoping strategy (the Athlete Biological Passport [ABP]) in a country accused of systematic doping. A retrospective analysis of the results of Russian National Championships from 2008 to 2017 was performed. The 8 best female performances for the 800-m, 1500-m, 3000-m steeplechase, 5000-m, and 10,000-m events from the semifinals and finals were analyzed. The yearly number of athletes fulfilling standard qualifications for international competitions was also evaluated. Overall, numbers of athletes banned for doping in 2008-2017 were calculated. As a result, 4 events (800, 1500, 5000 [all P
  • Klippi, Anu (Puheen ja kielen tutkimuksen yhdistys, 2020)
    Puheen ja kielen tutkimuksen yhdistyksen julkaisuja

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