Articles from TUHAT CRIS


Kokoelma sisältää TUHAT-tutkimustietojäjestelmän kautta tallennetut Open Access-artikkelit.

Helsingin yliopiston tutkijat voivat rinnakkaistallentaa tutkimusjulkaisujansa HELDAan liittämällä kokotekstin julkaisuun TUHAT-tutkimustietojärjestelmässä. (Toimintaohje tutkijalle)

This collection contains Open Access articles deposited from the University of Helsinki TUHAT CRIS

Recent Submissions

  • Kulmala, Liisa; Read, Jesse; Nöjd, Pekka; Rathgeber, Cyrille B.K.; Cuny, Henri E.; Hollmén, Jaakko; Mäkinen, Harri (Elsevier Scientific Publ. Co, 2017)
    Even though studies monitoring the phenology and seasonal dynamics of the wood formation have accumulated for several conifer species across the Northern Hemisphere, the environmental control of tracheid production and differentiation is still fragmentary. With microcore and environmental data from six stands in Finland and France, we built auto-calibrated data-driven black box models for analyzing the most important factors controlling the tracheid production and maturation in Scots pine stem. In the best models, estimation was accurate to within a fraction of a tracheid per week. We compared the relative results of models built using different predictors, and found that the rate of tracheid production was partly regular but current and previous air temperature had influence on the sites in the middle of the temperature range and photosynthetic production in the coldest ones. The rate of mature cell production was more difficult to relate to the predictors but recent photosynthetic production was included in all successful models.
  • Prozorov, Sergei (SAGE, 2017)
    The publication of The Use of Bodies, the final volume in Giorgio Agamben’s Homo Sacer series, makes it possible to take stock of Agamben’s project as a whole. Having started with a powerful critique of the biopolitical sovereignty as the essence of modern politics, Agamben concludes his project with an affirmative vision of inoperative politics of form-of-life, in which life is not negated or sacrificed to the privileged form it must attain, but rather remains inseparable from the form that does nothing but express it. The article begins by reconstituting the non-relational logic that Agamben develops in order to render inoperative the existing apparatuses of ontology, ethics and politics. We then address the dimension of lifestyle as a new key domain of Agamben’s work, in which biopolitics may be recast in an affirmative key of form-of-life. While Agamben is better known for sceptical and scornful statements about contemporary liberal democracies, we shall argue that his affirmative biopolitics, characterized by destituent power, resonates with Claude Lefort’s understanding of democracy as structured around the ontological void and epistemic indeterminacy. In the conclusion we question the viability of this biopolitical democracy, focusing on Agamben’s example of the Nocturnal Council in Plato’s Laws.
  • Nurmi, Johanna; Hagger, Martin; Haukkala, Ari; Araújo-Soares, Vera; Hankonen, Nelli (Human Kinetics, 2016)
  • Shetty, Sudarshan A.; Hugenholtz, Floor; Lahti, Leo; Smidt, Hauke; de Vos, Willem M. (Oxford University Press, 2017)
    High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella-and Bacteroides-dominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.
  • Parkkonen, Olavi; Nieminen, Mikko Tapani; Vesterinen, Paula; Tervahartiala, Taina; Perola, Markus; Salomaa, Veikko; Jousilahti, Pekka; Sorsa, Timo; Pussinen, Pirkko; Sinisalo, Juha-Pekka (PUBLIC LIBRARY OF SCIENCE, 2017)
    Background Matrix metalloproteinase 8 (MMP-8) is the most potent type-I collagen protease. Such collagen mainly constitutes the transient fibrosis in takotsubo cardiomyopathy (TTC) endomyocardial biopsies. High MMP-8 and tissue-inhibitor of matrix metalloproteinase-1 (TIMP-1) levels are implicated in acute coronary syndrome (ACS). We compared MMP-8 and TIM P-1 levels in consecutive TTC and ACS patients, and their association to TTC severity. Methods and results In 45 acute serum samples of TTC, 2072 ACS and 1000 controls, TI MP-1 differed between ACS 146.7ng/mL (115.0-186.3) (median (interquartile range)), TTC 115.7 (94.3-137.7) and controls 80.9 (73.2-90.4), (p Conclusions Even with other differing factors considered, TIMP-1 differentiated TTC from ACS better than TnT. In TTC, the low MMP-8/TIM P-1 molar ratio may reflect decreased proteolysis and increased transient fibrosis, perhaps in part explaining the left-ventricle impairment.
  • Cammarota, Giovanni; Ianiro, Gianluca; Tilg, Herbert; Rajilic-Stojanovic, Mirjana; Kump, Patrizia; Satokari, Reetta; Sokol, Harry; Arkkila, Perttu; Pintus, Cristina; Hart, Ailsa; Segal, Jonathan; Aloi, Marina; Masucci, Luca; Molinaro, Antonio; Scaldaferri, Franco; Gasbarrini, Giovanni; Lopez-Sanroman, Antonio; Link, Alexander; De Groot, Pieter; de Vos, Willem M.; Hoegenauer, Christoph; Malfertheiner, Peter; Mattila, Eero; Milosavljevic, Tomica; Nieuwdorp, Max; Sanguinetti, Maurizio; Simren, Magnus; Gasbarrini, Antonio; European FMT Working Grp (BMJ PUBLISHING GROUP, 2017)
    Faecal microbiota transplantation (FMT) is an important therapeutic option for Clostridium difficile infection. Promising findings suggest that FMT may play a role also in the management of other disorders associated with the alteration of gut microbiota. Although the health community is assessing FMT with renewed interest and patients are becoming more aware, there are technical and logistical issues in establishing such a non-standardised treatment into the clinical practice with safety and proper governance. In view of this, an evidence-based recommendation is needed to drive the practical implementation of FMT. In this European Consensus Conference, 28 experts from 10 countries collaborated, in separate working groups and through an evidence-based process, to provide statements on the following key issues: FMT indications; donor selection; preparation of faecal material; clinical management and faecal delivery and basic requirements for implementing an FMT centre. Statements developed by each working group were evaluated and voted by all members, first through an electronic Delphi process, and then in a plenary consensus conference. The recommendations were released according to best available evidence, in order to act as guidance for physicians who plan to implement FMT, aiming at supporting the broad availability of the procedure, discussing other issues relevant to FMT and promoting future clinical research in the area of gut microbiota manipulation. This consensus report strongly recommends the implementation of FMT centres for the treatment of C. difficile infection as well as traces the guidelines of technicality, regulatory, administrative and laboratory requirements.
  • Nagy, Szabolcs; Polgar, Peter J.; Andersson, Magnus; Kovacs, Andras (Akadémiai Kiadó, 2016)
    The aim of the present study was to test the FXCycle PI/RNase kit for routine DNA analyses in order to detect breeding bulls and/or insemination doses carrying cytogenetic aberrations. In a series of experiments we first established basic DNA histogram parameters of cytogenetically healthy breeding bulls by measuring the intraspecific genome size variation of three animals, then we compared the histogram profiles of bulls carrying cytogenetic defects to the baseline values. With the exception of one case the test was able to identify bulls with cytogenetic defects. Therefore, we conclude that the assay could be incorporated into the laboratory routine where flow cytometry is applied for semen quality control.
  • Deckers, Pieterjan; Lewis, Michael; Thomas, Suzie (De Gruyter Open, 2016)
    Since the Valletta Convention (1992), the debate concerning non-professional archaeological metal-detecting in Europe has been conducted largely at the level of individual legislations. Papers in this Topical Issue take stock of current knowledge of and attitudes towards metal-detecting across Europe; its nature and impact as well as the policies and approaches that arise from it within professional archaeology and heritage management. With this collection of papers, the editors aim to stimulate a more unified debate and, ultimately, a common understanding of ethics and best practices in relation to metal-detecting that transcends national and jurisdictional boundaries in Europe.
  • Kaatrakoski, Heli; Lahikainen, Johanna (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2016)
    Change, transformation, the reassessment of services and professional capabilities are key concepts in the language of academic libraries today. We suggest that two intertwined rationales - technical development and the marketisation of the public sector along with a customer approach - are driving the change that is challenging academic libraries to rethink their work and services. In this article, we first discuss embedded librarianship and knotworking in libraries as participatory approaches to the arrangement of academic library work and services. Second, we presented the findings of the Knotworking project and its follow-up interviews and suggest knotworking as a method with which librarians can collaboratively analyse their own work and develop services with researchers and thus respond to changing working environments. Third, we discuss changes in the work identity of librarians. (C) 2016 Elsevier Inc. All rights reserved.
  • Lahtinen, Anu (Kasvatuksen Historian Tutkimusverkosto / Suomen Kouluhistoriallinen Seura, 2016)
  • Skwark, Marcin J.; Croucher, Nicholas J.; Puranen, Santeri; Chewapreecha, Claire; Pesonen, Maiju; Xu, Ying Ying; Turner, Paul; Harris, Simon R.; Beres, Stephen B.; Musser, James M.; Parkhill, Julian; Bentley, Stephen D.; Aurell, Erik; Corander, Jukka (PUBLIC LIBRARY OF SCIENCE, 2017)
    Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus). For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS) data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein- protein interactions, or genes whose product activities contribute to the same phenotype. This discovery approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work.
  • Uitto, Anna; Saloranta, Seppo (MDPI AG, 2017)
    Sustainability education (SE) is included in school curricula to integrate the principles, values, and practices of sustainable development (SD) into all education. This study investigates lower secondary school subject teachers as educators for sustainability. A survey was used to study the perceptions of 442 subject teachers from 49 schools in Finland. There were significant differences between the subject teachers’ perceptions of their SE competence, and the frequency with which they used different dimensions of SE (ecological, economic, social, well-being, cultural) in their teaching varied. Teachers’ age had a small effect, but gender, school, and its residential location were nonsignificant factors. Teachers could be roughly classified into three different subgroups according to their perceptions of the role of SE in their teaching; those who considered three SE dimensions rather often and used holistic sustainability approaches in their teaching (biology, geography, history); those who considered two or three dimensions often but were not active in holistic teaching (mother tongue, religion, visual arts, crafts, music, physical and health education, and home economics) and those who used one SE dimension or consider only one holistic approach in their teaching (mathematics, physics, chemistry and language). Subject teachers’ awareness of their SE competence is important to encourage them to plan and implement discipline-based and interdisciplinary SE in their teaching. The specific SE expertise of subject teachers should be taken into account in teacher training and education.
  • Levrini, Olivia; De Ambrosis, Anna; Hemmer, Sabine; Laherto, Antti Mikko Petteri; Malgieri, Massimiliano; Pantano, Ornella; Tasquier, Giulia (Institute of Physics Publishing, 2016)
    This paper focuses on results of an interview based survey of first-year university physics students, carried out within the EU Horizons in Physics Education (HOPE) project ( 94 interviews conducted in 13 universities have been analyzed to investigate the factors that inspire young people to study physics. In particular, the main motivational factor, which was proven to consist of personal interest and curiosity, was unfolded into different categories and detailed interest profiles were produced. The results are arguably useful to help academic curriculum developers and teaching personnel in physics departments to provide guidance to students in developing and focusing their interest towards specific sub-fields and/or to design targeted recruitment and outreach initiatives.
  • Korrensalo, Aino; Alekseychik, Pavel; Hajek, Tomas; Rinne, Janne; Vesala, Timo; Mehtätalo, Lauri; Mammarella, Ivan; Tuittila, Eeva-Stiina (COPERNICUS GESELLSCHAFT MBH, 2017)
    In boreal bogs plant species are low in number, but they differ greatly in their growth forms and photosynthetic properties. We assessed how ecosystem carbon (C) sink dynamics were affected by seasonal variations in the photosynthetic rate and leaf area of different species. Photosynthetic properties (light response parameters), leaf area development and areal cover (abundance) of the species were used to quantify species-specific net and gross photosynthesis rates (P-N and P-G, respectively), which were summed to express ecosystem-level P-N and P-G. The ecosystem-level P-G was compared with a gross primary production (GPP) estimate derived from eddy covariance (EC) measurements. Species areal cover, rather than differences in photosynthetic properties, determined the species with the highest P-G of both vascular plants and Sphagna. Species-specific contributions to the ecosystem P-G varied over the growing season, which, in turn, determined the seasonal variation in ecosystem P-G. The upscaled growing season P-G estimate, 230 gCm (-2), agreed well with the GPP estimated by the EC (243 gCm (-2)). Sphagna were superior to vascular plants in ecosystemlevel P-G throughout the growing season but had a lower P-N. P-N results indicated that areal cover of the species, together with their differences in photosynthetic parameters, shape the ecosystem-level C balance. Species with low areal cover but high photosynthetic efficiency appear to be potentially important for the ecosystem C sink. Results imply that func-tional diversity, i. e., the presence of plant groups with different seasonal timing and efficiency of photosynthesis, may increase the stability of C sinks of boreal bogs.
  • Hellen, Heidi; Schallhart, Simon; Praplan, Arnaud P.; Petäjä, Tuukka; Hakola, Hannele (COPERNICUS GESELLSCHAFT MBH, 2017)
    An in situ method for studying gas-phase C-2-C-7 monocarboxylic volatile organic acids (VOAs) in ambient air was developed and evaluated. Samples were collected directly into the cold trap of the thermal desorption unit (TD) and analysed in situ using a gas chromatograph (GC) coupled to a mass spectrometer (MS). A polyethylene glycol column was used for separating the acids. The method was validated in the laboratory and tested on the ambient air of a boreal forest in June 2015. Recoveries of VOAs from fluorinated ethylene propylene (FEP) and heated stainless steel inlets ranged from 83 to 123 %. Different VOAs were fully desorbed from the cold trap and well separated in the chromatograms. Detection limits varied between 1 and 130 pptv and total uncertainty of the method at mean ambient mixing ratios was between 16 and 76 %. All straight chain VOAs except heptanoic acid in the ambient air measurements were found with mixing ratios above the detection limits. The highest mixing ratios were found for acetic acid and the highest relative variations for hexanoic acid. In addition, mixing ratios of acetic and propanoic acids measured by the novel GC-MS method were compared with proton-mass-transfer time-off-light mass spectrometer (PTR-TOFMS) data. Both instruments showed similar variations, but differences in the mixing ratio levels were significant.