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  • 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.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports on Language Technology
    The construction of a morphological analyser for English is a fairly simple operation. The language has only a few morphological features, and they can be easily described. However, listing all wordforms as separate entries in the lexicon is certainly not the optimal solution. When using finite state transducers as developing environments, it is customary to list the word stems of various POS categories into separate sub-lexicons, and the inflection suffixes (and prefixes) into other sub-lexicons. Because the comprehensive analysis system tends to expand to dimensions, which are uncomfortable, or sometimes impossible, to manage, there is strong motivation to condense the lexicon wherever possible. This report describes the method, where verbs, and words derived from them, such as adjectives and nouns, are listed as underspecified entities. In a later phase these entities are then processed into separate readings, so that the readings can be disambiguated on the basis of context. The method condenses the lexicon considerably and it is easier to maintain, when the stems are in one place.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical reports on language technology
    Free texts include also such words, which are not listed in the analysis system. Yet they need to be treated as part of the vocabulary, so that the unknown elements in text do not unnecessarily disturb the translation process. They cannot be fully treated as the known lexical items, but if we know some basic propertied of the words, we can figure out the structure of the sentence kore precisely. Traditionally, the heuristic guessing of such unknown words was done on the basis of the morphological form of the word only. In this report it is suggested that the unknown words should be treated in two phases. First, we give a tentative assignment of the word in the word-level guesser. In the second phase we test the assignment in context. The first assignment may have two or more assignment candidates, and in the second phase we test which one is the correct one in the context.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports on Language Technology
    In English writing, it is customary to merge the pronoun subject and the following auxiliary verb as a single string, pointing the abbreviated part with an apostrophe. Part of these structures can be spelled out unambiguously. However, there are structures, where the verb can be either be or have. In other structures, the verb can be will, shall, would, could, or have. The problem can be solved only on the basis of context. There are also genitive structures, which look very much the same as the verb structures. These must be kept separate and treated accordingly. The report discusses these problems.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical reports on language technology
    The report discusses such cases, where a multi-word English verb maps to a single-word or multi-word Finnish verb. Because the verbs in this group have more than one word in source language (English in this case), they must be handled as single units. This applies especially to multi-word to single-word mapping. If there are two words, for example, on the source side and target side, one could argue that they should be handled as single words. However, the word-by-word translation is often not possible even in these cases. Therefore, it is safe to handle also these cases as multi-word expressions. The isolation rules were implemented so that the second (and possibly third) member of the MWE can be immediately after the verb, is in a restricted but non-defined distance. Below we look into the problems involved in the translation of this verb group
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports on Language Technology
    The report discusses such cases, where a single-word English verb maps to a multi-word Finnish verb. Translation to Finnish includes many problems, because the multi-word solution in translation affects the inflection of the modifiers of the verb. The translation system has the default rule set for single-verb to single-verb mapping. However, in the case of single-verb to multi-verb mapping, the inflection rules are different. Therefore, these cases must be kept strictly apart from the other cases. I have collected all (more than 500) such English verbs, which have at least one such Finnish gloss, which is a multi-word verb. The verbs can be subdivided into sub-groups according to the inflection patterns, which they require. The solutions for translating each type are discussed and demonstrated.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports on Language Technology
    English compounds are normally composed of two or more consecutive words. It is also possible to form compounds using dash as a connector between words. Such constructions are difficult to handle, because they are not in the lexicon, and their interpretation must be carried out using heuristic guessing. However, it is possible to handle the members of the compound separately, and guessing can be avoided. In the Technical Report No. 57 I discussed the problem in English to Finnish machine translation. In this report I will discuss it from the viewpoint of English to Swahili machine translation. Although the basic approach in both is the same, the implementation is language-specific
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports on Language Technology
    Language is in a continuous development process, which poses a challenge to machine translation. People also tend to have their only styles of writing, which is often difficult to translate. A special problem is the so called ad hoc compounding, where the writer decides to construct such compounds, which do not exist in any dictionary. By compounds I mean here such clusters of words, which are written together, using '-' as a connecting diacritic, not the normal compounding, where members of a compound are written as separate words. In addition to ad hoc compounds, there are also established compounds using the same connecting method. This report describes the methods for handling these compounds in English to Finnish machine translation
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical Reports of Language Technology
    The description of multi-word expressions (MWE) is a necessary phase in rule-based machine translation. Because the concept MWE contains several types of word clusters, it is not self-evident how they should be described. One approach is that the isolation of multi-words is carried out after the morphological analysis, but before disambiguation. If the POS ambiguity of the language is minimal, this method is suitable, and perhaps also optimal. In case the POS ambiguity of the language is extensive, this method is hardly optimal. English belongs to this type of languages. The more optimal solution is that the isolation of MWEs is carried out in two phases. This method will be discussed and demonstrated in this report.
  • Hurskainen, Arvi (University of Helsinki, Institute for Asian and African Studies, 2020)
    Technical reports on language technology
    The report discusses Traditionally, search systems were compiled manually by collecting useful examples of a given word. The compiled works included only part of the word occurrences, and the choice of examples was subject to many kind of factors, which easily distorted the result. The advanced computational search systems give comprehensive results. They are also reliable, if the system is tailored to the subject text and the mistakes in code removed. The report compares a manually compiled system with a computational system. Results are displayed with tables.
  • Kupari, Helena (2020)
  • Kupari, Helena; Vuola, Elina (Routledge, 2019)
    Routledge Studies in Religion

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