Articles from TUHAT CRIS

 

Recent Submissions

  • Acharya, U. A.; Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Alfred, M.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bathe, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Black, D.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Campbell, S.; Roman, V. Canoa; Chen, C-H; Chi, C. Y.; Chiu, M.; He, X.; Kim, D. J.; Li, X.; Liu, M. X.; Novitzky, N.; Park, S.; Rak, J.; Sun, X.; Wang, X. R.; Wang, Z.; Wong, C. P.; Wu, Y.; Zou, L. (2020)
    The PHENIX experiment at the Relativistic Heavy Ion Collider has measured the differential cross section, mean transverse momentum, mean transverse momentum squared of inclusive J/psi, and cross section ratio of psi(2S) to J/psi at forward rapidity in p + p collisions at root s = 510 GeV via the dimuon decay channel. Comparison is made to inclusive J/psi cross sections measured at root s = 200 GeV and 2.76-13 TeV. The result is also compared to leading-order nonrelativistic QCD calculations coupled to a color-glass-condensate description of the low-x gluons in the proton at low transverse momentum (p(T)) and to next-to-leading order nonrelativistic QCD calculations for the rest of the p(T) range. These calculations overestimate the data at low p(T). While consistent with the data within uncertainties above approximate to 3 GeV/c, the calculations are systematically below the data. The total cross section times the branching ratio is BR d sigma(J/)(psi)(pp) / dy(1.2 <vertical bar y vertical bar <2.2,0 <p(T) <10 GeV/c) = 54.3 +/- 0.5(stat) +/- 5.5(syst) nb.
  • Kulha, Niko; Pasanen, Leena; Holmström, Lasse; Grandpre, Louis de; Gauthier, Sylvie; Kuuluvainen, Timo; Aakala, Tuomas (2020)
    Context: Changes in the structure of boreal old-growth forests are typically studied at a specific spatial scale. Consequently, little is known about forest development across different spatial scales. Objectives: We investigated how and at what spatial scales forest structure changed over several decades in three 4 km² boreal old-growth forests landscapes in northeastern Finland and two in Quebec, Canada. Methods: We used canopy cover values visually interpreted to 0.1-ha grid cells from aerial photographs taken at three time points between the years 1959 and 2011, and error distributions quantified for the interpretation. We identified the spatial scales at which canopy cover changed between the time points, and examined the credibility of changes at these scales using the error distributions in Bayesian inference. Results: Canopy cover changed at three to four spatial scales, the number of scales depending on the studied landscape and time interval. At large scales (15.4–321.7 ha), canopy cover increased in Finland during all time intervals. In Quebec, the direction of the large-scale change varied between the studied time intervals, owing to the occurrence of an insect outbreak and a consequent recovery. However, parts of these landscapes also showed canopy cover increase. Superimposed on the large-scale developments, canopy cover changed variably at smaller scales (1.3–2.8-ha and 0.1-ha). Conclusions: Our findings support the idea that the structure of boreal old-growth forests changes at discernible spatial scales. Instead of being driven by gap dynamics, the old-growth forests in the studied regions are currently reacting to large-scale drivers by an increase in canopy cover.
  • Seidl, Rupert; Honkaniemi, Juha; Aakala, Tuomas; Aleinikov, Alexey; Angelstam, Per; Bouchard, Mathieu; Boulanger, Yan; Burton, Philip J.; De Grandpre, Louis; Gauthier, Sylvie; Hansen, Winslow D.; Jepsen, Jane U.; Jogiste, Kalev; Kneeshaw, Daniel D.; Kuuluvainen, Timo; Lisitsyna, Olga; Makoto, Kobayashi; Mori, Akira S.; Pureswaran, Deepa S.; Shorohova, Ekaterina; Shubnitsina, Elena; Taylor, Anthony R.; Vladimirova, Nadezhda; Vodde, Floortje; Senf, Cornelius (2020)
    Disturbance regimes are changing in forests across the world in response to global climate change. Despite the profound impacts of disturbances on ecosystem services and biodiversity, assessments of disturbances at the global scale remain scarce. Here, we analyzed natural disturbances in boreal and temperate forest ecosystems for the period 2001-2014, aiming to 1) quantify their within- and between-biome variation and 2) compare the climate sensitivity of disturbances across biomes. We studied 103 unmanaged forest landscapes with a total land area of 28.2 x 10(6) ha, distributed across five continents. A consistent and comprehensive quantification of disturbances was derived by combining satellite-based disturbance maps with local expert knowledge of disturbance agents. We used Gaussian finite mixture models to identify clusters of landscapes with similar disturbance activity as indicated by the percent forest area disturbed as well as the size, edge density and perimeter-area-ratio of disturbed patches. The climate sensitivity of disturbances was analyzed using Bayesian generalized linear mixed effect models and a globally consistent climate dataset. Within-biome variation in natural disturbances was high in both boreal and temperate biomes, and disturbance patterns did not vary systematically with latitude or biome. The emergent clusters of disturbance activity in the boreal zone were similar to those in the temperate zone, but boreal landscapes were more likely to experience high disturbance activity than their temperate counterparts. Across both biomes high disturbance activity was particularly associated with wildfire, and was consistently linked to years with warmer and drier than average conditions. Natural disturbances are a key driver of variability in boreal and temperate forest ecosystems, with high similarity in the disturbance patterns between both biomes. The universally high climate sensitivity of disturbances across boreal and temperate ecosystems indicates that future climate change could substantially increase disturbance activity.
  • Uusitalo, Jori; Ala-Ilomaki, Jari; Lindeman, Harri; Toivio, Jenny; Siren, Matti (2020)
    Key message Rut depth in fine-grained boreal soils induced by an 8-wheeled forwarder is best predicted with soil moisture content, cumulative mass of machine passes, bulk density and thickness of the humus layer. Context Forest machines are today very heavy and will cause serious damage to soil and prevent future growth if forest operations are carried out at the wrong time of the year. Forest operations performed during the wettest season should therefore be directed at coarse-grained soils that are not as prone to soil damage. Aims The study aimed at investigating the significance of the most important soil characteristics on rutting and developing models that can be utilized in predicting rutting prior to forest operations. Methods A set of wheeling tests on two fine-grained mineral soil stands in Southern Finland were performed. The wheeling experiments were conducted in three different periods of autumn in order to get the largest possible variation in moisture content. The test drives were carried out with an 8-wheeled forwarder. Results Soil moisture content is the most important factor affecting rut depth. Rut depth of an 8-wheeled forwarder in fine-grained boreal soil is best predicted with soil moisture content, cumulative mass of machine passes, bulk density and thickness of the humus layer. Conclusion The results emphasize the importance of moisture content on the risk of rutting in fine-grained mineral soils, especially with high moisture content values when soil saturation reaches 80%. The results indicate that it is of high importance that soil type and soil wetness can be predicted prior to forest operations.
  • Vaario, Lu-Min; Asamizu, Shumpei; Sarjala, Tytti; Matsushita, Norihisa; Onaka, Hiroyasu; Xia, Yan; Kurokochi, Hiroyuki; Morinaga, Shin-Ichi; Huang, Jian; Zhang, Shijie; Lian, Chunlan (2020)
    Tricholoma matsutake is known to be the dominant fungal species in matsutake fruitbody neighboring (shiro) soil. To understand the mechanisms behind matsutake dominance, we studied the bacterial communities in matsutake dominant shiro soil and non-shiro soil, isolated the strains of Streptomyces from matsutake mycorrhizal root tips both from shiro soil and from the Pinus densiflora seedlings cultivated in shiro soil. Further, we investigated three Streptomyces spp. for their ability to inhibit fungal growth and Pinus densiflora seedling root elongation as well as two strains for their antifungal and antioxidative properties. Our results showed that Actinobacteria was the most abundant phylum in shiro soil. However, the differences in the Actinobacterial community composition (phylum or order level) between shiro and non-shiro soils were not significant, as indicated by PERMANOVA analyses. A genus belonging to Actinobacteria, Streptomyces, was present on the matsutake mycorrhizas, although in minority. The two antifungal assays revealed that the broths of three Streptomyces spp. had either inhibitory, neutral or promoting effects on the growth of different forest soil fungi as well as on the root elongation of the seedlings. The extracts of two strains, including one isolated from the P. densiflora seedlings, inhibited the growth of either pathogenic or ectomycorrhizal fungi. The effect depended on the medium used to cultivate the strains, but not the solvent used for the extraction. Two Streptomyces spp. showed antioxidant activity in one out of three assays used, in a ferric reducing antioxidant power assay. The observed properties seem to have several functions in matsutake shiro soil and they may contribute to the protection of the shiro area for T. matsutake dominance.
  • Luoto, Tomi P.; Kivila, E. Henriikka; Kotrys, Bartosz; Plociennik, Mateusz; Rantala, Marttiina; Nevalainen, Liisa (2020)
    Independent Arctic records of temperature and precipitation from the same proxy archives are rare. Nevertheless, they are important for providing detailed information on long-term climate changes and temperature-precipitation relationships in the context of large-scale atmospheric dynamics. Here, we used chironomid and cladoceran fossil assemblages to reconstruct summer air-temperature and water-level changes, during the past 400 years, in a small lake located in Finnish Lapland. Temperatures remained persistently cold over the Little Ice Age (LIA), but increased in the 20th century. After a cooler phase in the 1970s, the climate rapidly warmed to the record-high temperatures of the most recent decades. The lake-level reconstruction suggested persistently wet conditions for the LIA, followed by a dry period between similar to 1910 and 1970 CE, when the lake apparently became almost dry. Since the 1980s, the lake level has returned to a similar position as during the IAA. The temperature development was consistent with earlier records, but a significant local feature was found in the lake-level reconstruction the LIA appears to have been continuously wet, without the generally depicted dry phase during the 18th and 19th centuries. Therefore, the results suggest local precipitation patterns and enforce the concept of spatially divergent LIA conditions.
  • Molina-Flores, Baldomero; Manzano-Baena, Pablo; Coulibaly, Mamadou D. (FAO, 2020)
  • Lankoski, Jussi; Lötjönen, Sanna; Ollikainen, Markku (2020)
  • Lötjönen, Sanna; Temmes, Esa; Ollikainen, Markku (2020)
    We provide a theoretical framework and detailed bioeconomic simulations to examine privately and socially optimal dairy farm management in the presence of nutrient runoff and greenhouse gas emissions. Dairy farms produce milk by choosing herd size, diet, fertilization and land allocation between crops, as well as (discrete) manure storage and spreading technologies and the number of milking seasons. We show analytically that a critical radius emerges for the choice of land use between silage and cereal cultivation and fertilizer types (mineral and manure). Both privately and socially optimal manure application rates decrease with application distance. We characterize the optimal climate and water policy instruments for dairy farming. A detailed bioeconomic simulation model links farm management decisions with their impacts on climate and water quality. We numerically solve the social and private optima and the features of optimal climate and water policy instruments. We show that using only climate instruments provides considerable water co‐benefits, and in the same vein, the use of water quality instruments provides considerable climate co‐benefits. Climate policies lead to a reduction in herd size, as measures relating to manure management and spreading are relatively inefficient at reducing climate emissions. There is much more leeway for adapting to water policies than to climate policies, because dairy farms have multiple measures to reduce their nutrient loads.
  • Karppi, Johanna; Zhao, Hongbo; Chong, Sun-Li; Koistinen, Antti E; Tenkanen, Maija; Master, Emma (2020)
  • Wang, Linping; Saarela, Jani; Poque, Sylvain; Valkonen, Jari P. T. (2020)
    The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.
  • Chum, Haji; Hurskainen, Arvi (SALAMA - Swahili Language Manager, 2020)
    Language Resources
  • Leudet, Jerome; Christophe, Francois; Mikkonen, Tommi; Männistö, Tomi (IEEE, 2019)
    Proceedings - International Computer Software & Applications Conference
    Virtualization technologies have become common- place both in software development as well as engineering in a more general sense. Using virtualization offers other benefits than simulation and testing as a virtual environment can often be more liberally configured than the corresponding physical envi- ronment. This, in turn, introduces new possibilities for education and training, including both for humans and artificial intelligence (AI). To this end, we are developing a simulation platform AILiveSim. The platform is built on top of the Unreal Engine game development system, and it is dedicated to training and testing autonomous systems, their sensors and their algorithms in a simulated environment. In this paper, we describe the elements that we have built on top of the engine to realize a Virtual Environment (VE) useful for the design, implementation, application and analysis of autonomous systems. We present the architecture that we have put in place to transform our simulation platform from automotive specific to be domain agnostic and support two new domains of applications: autonomous ships and autonomous mining machines. We describe the important specificity of each domain in regard to simulation. In addition, we also report the challenges encountered when simulating those applications, and the decisions taken to overcome these challenges.
  • Valiev, Rashid; Hasan, Galib; Salo, Vili-Taneli; Kubecka, Jakub; Kurten, Theo (2019)
    High molecular weight "ROOR" dimers, likely formed in the gas phase through self- and cross-reactions of complex peroxy radicals (RO2), have been suggested to play a key role in forming ultrafine aerosol particles in the atmosphere. However, the molecular-level reaction mechanism producing these dimers remains unknown. Using multireference quantum chemical methods, we explore one potentially competitive pathway for ROOR' production, involving the initial formation of triplet alkoxy radical (RO) pairs, followed by extremely rapid intersystem crossings (ISC) to the singlet surface, permitting subsequent recombination to ROOR'. Using CH3OO + CH3OO as a model system, we show that the initial steps of this reaction mechanism are likely to be very fast, as the transition states for both the formation and the decomposition of the CH3O4CH3 tetroxide intermediate are far below the reactants in energy. Next, we compute ISC rates for seven different atmospherically relevant (3)(RO center dot center dot center dot R'O) complexes. The ISC rates vary significantly depending on the conformation of the complex and also exhibit strong stereoselectivity. Furthermore, the fastest ISC process is usually not between the lowest-energy triplet and singlet states but between the triplet ground state and an exited singlet state. For each studied (RO center dot center dot center dot R'O) system, at least one low-energy conformer with an ISC rate above 10(8) s(-1) can be found. This demonstrates that gas-phase dimer formation in the atmosphere very likely involves ISCs originating in relativistic quantum mechanics.
  • Radhakrishnan, Dhanya; Shanmukhan, Anju Pallipurath; Kareem, Abdul; Aiyaz, Mohammed; Varapparambathu, Vijina; Toms, Ashna; Kerstens, Merijn; Valsakumar, Devisree; Landge, Amit N.; Shaji, Anil; Mathew, Mathew K.; Sawchuk, Megan G.; Scarpella, Enrico; Krizek, Beth A.; Efroni, Idan; Mähönen, Ari Pekka; Willemsen, Viola; Scheres, Ben; Prasad, Kalika (2020)
    Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.
  • Ciragan, Annika; Backlund, Sofia M.; Mikula, Kornelia M.; Beyer, Hannes M.; Samuli Ollila, O. H.; Iwaï, Hideo (2020)
    The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical reports on language technology
    In this report I will discuss issues related to translation between two languages, using interlingua as turntable. Test languages are Swahili and Finnish, both morphologically complex and linguistically very different languages. In an earlier report (Report No. 30) I discussed the issue considering the normalised version of English as interlingua. In this report the emphasis is on the use of linguistic information of the source language in various phases of the translation process. Normally, all linguistic information is lost in the translation process. Also, when the translation from interlingua to the third language is carried out, the analyser expects that the language is clean text without linguistic tags. In this report we study the possibility of retaining the linguistic information also in the analysis of interlingua (modified English). Various tag combinations are tested.

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