Browsing by Subject "SYSTEMS"

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  • Gatta, Viviana; Tomašič, Tihomir; Ilaš, Janez; Zidar, Nace; Peterlin Mašič, Lucija; Barančoková, Michaela; Frlan, Rok; Anderluh, Marko; Kikelj, Danijel; Tammela, Päivi (2020)
    Quorum sensing (QS), a bacterial communication strategy, has been recognized as one of the control mechanisms of virulence in bacteria. Thus, targeting QS offers an interesting opportunity to impair bacterial pathogenicity and develop antivirulence agents. Aiming to enhance the discovery of QS inhibitors, we developed a bioreporter Escherichia coli JW5505 pET-Plsrlux and set up a cell-based assay for identifying inhibitors of autoinducer-2 (AI-2)-mediated QS. A comparative study on the performance of target- versus cell-based assays was performed, and 91 compounds selected with the potential to target the ATP binding pocket of LsrK, a key enzyme in AI-2 processing, were tested in an LsrK inhibition assay, providing 36 hits. The same set of compounds was tested by the AI-2-mediated QS interference assay, resulting in 24 active compounds. Among those, six were also found to be active against LsrK, whereas 18 might target other components of the pathway. Thus, this AI-2-mediated QS interference cell-based assay is an effective tool for complementing target-based assays, yet also stands as an independent assay for primary screening.
  • Ottka, Claudia; Vapalahti, Katariina; Puurunen, Jenni; Vahtera, Laura; Lohi, Hannes (2021)
    Background Metabolomics has been proven to be an invaluable research tool by providing comprehensive insight into systemic metabolism. However, the lack of scalable and quantitative methods with known reference intervals (RIs) and documented reproducibility has prevented the use of metabolomics in the clinical setting. Objective The objective of this study was to validate the developed quantitative nuclear magnetic resonance (NMR) spectroscopy-based metabolomics platform for canine serum and plasma samples and determine optimal sample handling conditions for its use. Methods Altogether, 8247 canine samples were analyzed using a Bruker's 500 MHz NMR spectrometer. Using statistical approaches derived from international guidelines, we studied method precision, measurand stability in various long- and short-term storage conditions, as well as the effect of prolonged contact with red blood cells (RBCs), and differences among blood collection tubes. We also screened interferences with lipemia, hemolysis, and bilirubinemia. The results were compared against routine clinical chemistry methods, and RIs were defined for all measurands. Results We determined RIs for 123 measurands, most of which were previously unpublished. The reproducibility of the results of the NMR platform appeared generally outstanding, and the integrity of the results can be ensured by following standard blood drawing and processing guidelines. Conclusions Owing to the advantages of quantitative results, high reproducibility, and scalability, this canine metabolomics platform holds great potential for numerous clinical and research applications to improve canine health and well-being.
  • Baumeister, Dorothea; Järvisalo, Matti; Neugebauer, Daniel; Niskanen, Andreas; Rothe, Jörg (2021)
    A Abstract argumentation frameworks (AFs), originally proposed by Dung, constitute a central formal model for the study of computational aspects of argumentation in AI. Credulous and skeptical acceptance of arguments in a given AF are well-studied problems both in terms of theoretical analysis-especially computational complexity-and the development of practical decision procedures for the problems. However, AFs make the assumption that all attacks between arguments are certain (i.e., present attacks are known to exist, and missing attacks are known to not exist), which can in various settings be a restrictive assumption. A generalization of AFs to incomplete AFs was recently proposed as a formalism that allows the representation of both uncertain attacks and uncertain arguments in AFs. In this article, we explore the impact of allowing for modeling such uncertainties in AFs on the computational complexity of natural generalizations of acceptance problems to incomplete AFs under various central AF semantics. Complementing the complexity-theoretic analysis, we also develop the first practical decision procedures for all of the NP-hard variants of acceptance in incomplete AFs. In terms of complexity analysis, we establish a full complexity landscape, showing that depending on the variant of acceptance and property/semantics, the complexity of acceptance in incomplete AFs ranges from polynomial-time decidable to completeness for Sigma(p)(3). In terms of algorithms, we show through an extensive empirical evaluation that an implementation of the proposed decision procedures, based on boolean satisfiability (SAT) solving, is effective in deciding variants of acceptance under uncertainties. We also establish conditions for what type of atomic changes are guaranteed to be redundant from the perspective of preserving extensions of completions of incomplete AFs, and show that the results allow for considerably improving the empirical efficiency of the proposed SAT-based counterexample-guided abstraction refinement algorithms for acceptance in incomplete AFs for problem variants with complexity beyond NP. (C) 2021 The Authors. Published by Elsevier B.V.
  • Palojoki, Sari; Makela, Matti; Lehtonen, Lasse; Saranto, Kaija (2017)
    The aim of this study was to analyse electronic health record-related patient safety incidents in the patient safety incident reporting database in fully digital hospitals in Finland. We compare Finnish data to similar international data and discuss their content with regard to the literature. We analysed the types of electronic health record-related patient safety incidents that occurred at 23 hospitals during a 2-year period. A procedure of taxonomy mapping served to allow comparisons. This study represents a rare examination of patient safety risks in a fully digital environment. The proportion of electronic health record-related incidents was markedly higher in our study than in previous studies with similar data. Human-computer interaction problems were the most frequently reported. The results show the possibility of error arising from the complex interaction between clinicians and computers.
  • Polvi, J.; Heinola, K.; Nordlund, K. (2016)
    N-2 gas is routinely used as a seeding species in fusion plasma to control the amount of power emitted from the plasma by radiation to the tungsten walls of an ITER-like divertor. Nitrogen atoms interact with the plasma-facing materials beryllium and tungsten, and form chemical bonds with the wall surfaces, as well as with plasma hydrogen isotopes, thus raising a special interest in W-N and N-H interactions in the fusion community. In this work we describe the development of an analytical interatomic potential for W-N interactions and benchmark the potential against DFT calculation results for N defects in tungsten.
  • Haaranen, Mia; Scuppa, Giulia; Tambalo, Stefano; Järvi, Vilja; Bertozzi, Sine M.; Armirotti, Andrea; Sommer, Wolfgang H.; Bifone, Angelo; Hyytiä, Petri (2020)
    The anterior insular cortex plays a key role in the representation of interoceptive effects of drug and natural rewards and their integration with attention, executive function, and emotions, making it a potential target region for intervention to control appetitive behaviors. Here, we investigated the effects of chemogenetic stimulation or inhibition of the anterior insula on alcohol and sucrose consumption. Excitatory or inhibitory designer receptors (DREADDs) were expressed in the anterior insula of alcohol-preferring rats by means of adenovirus-mediated gene transfer. Rats had access to either alcohol or sucrose solution during intermittent sessions. To characterize the brain network recruited by chemogenetic insula stimulation we measured brain-wide activation patterns using pharmacological magnetic resonance imaging (phMRI) and c-Fos immunohistochemistry. Anterior insula stimulation by the excitatory Gq-DREADDs significantly attenuated both alcohol and sucrose consumption, whereas the inhibitory Gi-DREADDs had no effects. In contrast, anterior insula stimulation failed to alter locomotor activity or deprivation-induced water drinking. phMRI and c-Fos immunohistochemistry revealed downstream activation of the posterior insula and medial prefrontal cortex, as well as of the mediodorsal thalamus and amygdala. Our results show the critical role of the anterior insula in regulating reward-directed behavior and delineate an insula-centered functional network associated with the effects of insula stimulation. From a translational perspective, our data demonstrate the therapeutic potential of circuit-based interventions and suggest that potentiation of insula excitability with neuromodulatory methods, such as repetitive transcranial magnetic stimulation (rTMS), could be useful in the treatment of alcohol use disorders.
  • Niemi, Riitta; Vilar, Maria J; Dohoo, I.R.; Hovinen, Mari; Simojoki, Heli; Rajala-Schultz, Päivi Johanna (2020)
    Antibiotic dry cow therapy (DCT) is an important part of most mastitis control programs. Updating DCT recommendations is an ongoing topic due to the global problem of antimicrobial resistance. Finland, along with other Nordic countries, has implemented selective DCT for decades. Our study analyzed Dairy Herd Improvement (DHI) information from 241 Finnish farmers who participated in a survey about their drying-off practices. The aim was to evaluate herd-level associations between milk somatic cell count (SCC), milk production, and various antimicrobial DCT approaches both cross-sectionally in 2016 and longitudinally in 2012 - 2016. The three DCT approaches in the study were selective, blanket, and no DCT use. An additional aim was to evaluate whether dynamic changes occurred in herd-average SCC and annual milk production over five years, and whether these potential changes differed between different DCT approaches. The method for the longitudinal analyses was growth modeling with random coefficient models. Differences in SCC and milk production between farms with different DCT approaches were minor. Regardless of the farm's DCT approach, annual milk production increased over the years, while average SCC was reasonably constant. The variability in SCC and milk production across all DCT groups was low between years, and most of the variability was between farms. Compared to other milking systems, farms with automatic milking system (AMS) had higher SCC, and in 2016 higher milk production. The results of this study suggest that it is possible to maintain low herd-average SCC and good milk production when using selective DCT and following the guidelines for prudent antimicrobial use. Average SCC and milk production varied across the herds, suggesting that advice on DCT practices should be herd-specific. The methodology of growth modeling using random coefficient models was applicable in analyzing longitudinal data, in which the time frame was relatively short and the number of herds was limited.
  • Bogacheva, Mariia; Egorova, Anna; Slita, Anna; Maretina, Marianna; Baranov, Vladislav; Kiselev, Anton (2017)
    The major barriers for intracellular DNA transportation by cationic polymers are their toxicity, poor endosomal escape and inefficient nuclear uptake. Therefore, we designed novel modular peptide-based carriers modified with SV40 nuclear localization signal (NLS). Core peptide consists of arginine, histidine and cysteine residues for DNA condensation, endosomal escape promotion and interpeptide cross-linking, respectively. We investigated three polyplexes with different NLS content (10 mol%, 50 mol% and 90 mol% of SV40 NLS) as vectors for intranuclear DNA delivery. All carriers tested were able to condense DNA, to protect it from DNAase I and were not toxic to the cells. We observed that cell cycle arrest by hydroxyurea did not affect transfection efficacy of NLS-modified carriers which we confirmed using quantitative confocal microscopy analysis. Overall, peptide carrier modified with 90 mol% of SV40 NLS provided efficient transfection and nuclear uptake in non-dividing cells. Thus, incorporation of NLS into arginine-rich cross-linking peptides is an adequate approach to the development of efficient intranuclear gene delivery vehicles. (C) 2017 Elsevier Ltd. All rights reserved.
  • Paatela, Teemu; Vasara, Anna; Nurmi, Heikki; Kautiainen, Hannu; Kiviranta, Ilkka (2020)
    The International Cartilage Repair Society (ICRS) score and the Oswestry Arthroscopic Score (OAS) have been validated to evaluate repair tissue quality. However, the performance of these scores has not been studied in typical patients undergoing cartilage repair and who have lesions of varying sizes. In this study, we compared the performance of the ICRS and the OAS scores and analyzed the effect of lesion characteristics on the performance of these two scores. Cartilage repair quality was assessed in a total of 104 arthroscopic observations of cartilage repair sites of the knee in 62 patients after autologous chondrocyte implantation. Two observers scored the repair areas independently with the ICRS and the OAS scores. The performance of both scores was evaluated according to internal consistency and inter-rater reliability and correlation between the scores. The frequency and proportion of disagreements were analyzed according to the repair site area and the given score. The correlation between the scores was good (r = 0.91, 95% confidence interval [CI]: 0.87-0.94). Both scores showed moderate internal consistency and inter-rater reliability. Cronbach's alpha was 0.88 (95% CI: 0.80-0.92) for the ICRS score and 0.79 (95% CI: 0.70-0.86) for the OAS score. The intraclass correlation coefficient was 0.89 (95% CI: 0.84-0.92) for the ICRS and 0.81 (95% CI: 0.74-0.87) for the OAS scores. The frequency and proportion of disagreements were higher in larger repair sites. In arthroscopic use, both ICRS and OAS scores perform similarly, however, their reliability deteriorates as the lesion size increases. (c) 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res
  • Cattaneo, Marco; Giorgi, Gian Luca; Maniscalco, Sabrina; Paraoanu, Gheorghe Sorin; Zambrini, Roberta (2021)
    A common environment acting on a pair of qubits gives rise to a plethora of different phenomena, such as the generation of qubit-qubit entanglement, quantum synchronization, and subradiance. Here, time-independent figures of merit for entanglement generation, quantum synchronization, and subradiance are defined, and an extensive analytical and numerical study of their dependence on model parameters is performed. A recently proposed measure of the collectiveness of the dynamics driven by the bath is also addressed, and it is found that it almost perfectly witnesses the behavior of entanglement generation. The results show that synchronization and subradiance can be employed as reliable local signatures of an entangling common-bath in a general scenario. Finally, an experimental implementation of the model based on two transmon qubits capacitively coupled to a common resistor is proposed, which provides a versatile quantum simulation platform of the open system in any regime.
  • Halliday, Fletcher W.; Rohr, Jason R.; Laine, Anna-Liisa (2020)
    The dilution effect predicts increasing biodiversity to reduce the risk of infection, but the generality of this effect remains unresolved. Because biodiversity loss generates predictable changes in host community competence, we hypothesised that biodiversity loss might drive the dilution effect. We tested this hypothesis by reanalysing four previously published meta-analyses that came to contradictory conclusions regarding generality of the dilution effect. In the context of biodiversity loss, our analyses revealed a unifying pattern: dilution effects were inconsistently observed for natural biodiversity gradients, but were commonly observed for biodiversity gradients generated by disturbances causing losses of biodiversity. Incorporating biodiversity loss into tests of generality of the dilution effect further indicated that scale-dependency may strengthen the dilution effect only when biodiversity gradients are driven by biodiversity loss. Together, these results help to resolve one of the most contentious issues in disease ecology: the generality of the dilution effect.
  • Pale, Ville; Nikkonen, Taru; Vapaavuori, Jaana; Kostiainen, Mauri; Kavakka, Jari; Selin, Jorma; Tittonen, Ilkka; Helaja, Juho (2013)
  • Hardisty, Alex R.; Bacall, Finn; Beard, Niall; Balcazar-Vargas, Maria-Paula; Balech, Bachir; Barcza, Zoltan; Bourlat, Sarah J.; De Giovanni, Renato; de Jong, Yde; De Leo, Francesca; Dobor, Laura; Donvito, Giacinto; Fellows, Donal; Guerra, Antonio Fernandez; Ferreira, Nuno; Fetyukova, Yuliya; Fosso, Bruno; Giddy, Jonathan; Goble, Carole; Guentsch, Anton; Haines, Robert; Ernst, Vera Hernandez; Hettling, Hannes; Hidy, Dora; Horvath, Ferenc; Ittzes, Dora; Ittzes, Peter; Jones, Andrew; Kottmann, Renzo; Kulawik, Robert; Leidenberger, Sonja; Lyytikäinen-Saarenmaa, Paivi; Mathew, Cherian; Morrison, Norman; Nenadic, Aleksandra; de la Hidalga, Abraham Nieva; Obst, Matthias; Oostermeijer, Gerard; Paymal, Elisabeth; Pesole, Graziano; Pinto, Salvatore; Poigne, Axel; Fernandez, Francisco Quevedo; Santamaria, Monica; Saarenmaa, Hannu; Sipos, Gergely; Sylla, Karl-Heinz; Tähtinen, Marko; Vicario, Saverio; Vos, Rutger Aldo; Williams, Alan R.; Yilmaz, Pelin (2016)
    Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on- line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
  • Kindler, Oliver; Pulkkinen, Otto; Cherstvy, Andrey G.; Metzler, Ralf (2019)
    Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called "autoinducers") and themselves sense the autoinducer concentration in their vicinity. Once-due to increased local cell density inside a "cluster" of the growing colony-the concentration of autoinducers exceeds a threshold value, cells in this clusters get "induced" into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
  • Hamalainen, Liisa; Rowland, Hannah M.; Mappes, Johanna; Thorogood, Rose (2017)
    Video playback is becoming a common method for manipulating social stimuli in experiments. Parid tits are one of the most commonly studied groups of wild birds. However, it is not yet clear if tits respond to video playback or how their behavioural responses should be measured. Behaviours may also differ depending on what they observe demonstrators encountering. Here we present blue tits (Cyanistes caeruleus) videos of demonstrators discovering palatable or aversive prey (injected with bitter-tasting Bitrex) from coloured feeding cups. First we quantify variation in demonstrators' responses to the prey items: aversive prey provoked high rates of beak wiping and head shaking. We then show that focal blue tits respond differently to the presence of a demonstrator on a video screen, depending on whether demonstrators discover palatable or aversive prey. Focal birds faced the video screen more during aversive prey presentations, and made more head turns. Regardless of prey type, focal birds also hopped more frequently during the presence of a demonstrator (compared to a control video of a different coloured feeding cup in an empty cage). Finally, we tested if demonstrators' behaviour affected focal birds' food preferences by giving individuals a choice to forage from the same cup as a demonstrator, or from the cup in the control video. We found that only half of the individuals made their choice in accordance to social information in the videos, i.e., their foraging choices were not different from random. Individuals that chose in accordance with a demonstrator, however, made their choice faster than individuals that chose an alternative cup. Together, our results suggest that video playback can provide social cues to blue tits, but individuals vary greatly in how they use this information in their foraging decisions.
  • Waldén, Pirjetta; Ollikainen, Markku; Kahiluoto, Helena (2020)
    The impact of carbon revenue on the profitability of agroforestry systems in comparison to monocultures is unexplored in regard to Sub-Saharan Africa. This study creates a multivariate model to evaluate the impact of carbon revenue on the profitability of agroforestry relative to the dominant monocultures in Ethiopia by using stylized plots. Yields and carbon stock changes of eight agroforestry systems were modeled based on data from agroforestry plots in the Ethiopian Central Rift Valley. According to our model, agroforestry was, on average, four times more profitable than the main monoculture systems (wheat, barley, maize, teff, sorghum, sugarcane and lentil) even when carbon revenues were excluded, primarily due to the higher prices of fruit produce. Carbon revenues were estimated using a plausible carbon price ranging from US$8/tCO2e to $40/tCO2e and carbon sequestration rates of 0.59 to 17.2 Mg C ha−1 year−1. The possibility of receiving carbon revenue increased the profitability of agroforestry by 0.5% when using the lowest utilized carbon price and carbon sequestration rate, by 20% when using the carbon price of $20 and the average carbon sequestration rate, and by 70% when using the highest price and highest sequestration rate of carbon. On average, carbon revenue increased the profitability of agroforestry by 150% in comparison to monoculture farming. We conclude that carbon income may have significant potential to motivate smallholders to convert to agroforestry when there is a proper management system, a sufficiently high carbon price and effective institutional support to mitigate the transition and transaction costs.
  • Clavert, Maria; Löfström, Erika; Niemi, Hannele; Nevgi, Anne (2018)
    In the face of organizational transformations, academics are given a role as informal ‘change agents’ in their discipline-specific communities of practice (DCoP). Simultaneous participation in pedagogically oriented communities of practice (PCoP) enables them to promote pedagogical development through brokering at community interfaces. This empirical study explores academics’ experiences of acting as informal change agents at the interfaces of DCoP and PCoP during an organizational transition phase of three years. The longitudinal data were collected with interviews of 13 academics from the fields of science and technology. The findings reveal a variety of pedagogical development activities related to shared meanings, practices, identities, and ways of belonging. The activities are aligned with the organizational transition process and enabled by collegial support. The findings indicate that lack of supportive formal leadership may terminate the informal development activities. The resulting model of change agency provides a novel approach to pedagogical development in higher education.
  • Vainio, Annukka; Varho, Vilja; Tapio, Petri; Pulkka, Anna; Paloniemi, Riikka (2019)
    Achieving a sustainable energy transition is crucial for mitigating climate change. Citizens' acceptance of the transition is important for it to succeed. We explored citizens' images of the future energy forms and energy system in Finland, and the drivers of a sustainable energy transition. The data gathered with an online questionnaire targeting an adult population 17–75 years of age (N = 1012) were analysed with exploratory factor analysis and multiple linear regression. Four dimensions of future energy forms were identified: next-generation renewables, fossil energy, bioenergy, and established renewable vs. nuclear energy. Four dimensions of the future energy system were also identified: renewing the energy market, domestic power, small-scale producers, and consumer awareness. Five transition drivers were likewise identified: mainstreaming renewable energy, international actors, individual actions, changing values and economy, and emancipatory change. Mainstreaming renewable energy emerged as the key driver of transition, followed by individual actions. Generally, the sustainable energy transition was strongly supported by citizens' images, but different socio-economic groups preferred somewhat different images. Thus, the diversity of consumers' and citizens’ roles in the transition needs to be acknowledged and encouraged in legitimate national energy policies.
  • Mäkelä, Valtteri; Wahlström, Ronny; Holopainen-Mantila, Ulla; Kilpeläinen, Ilkka; King, Alistair W. T. (2018)
    Herein, we describe a new method of assessing the kinetics of dissolution of single fibers by dissolution under limited dissolving conditions. The dissolution is followed by optical microscopy under limited dissolving conditions. Videos of the dissolution were processed in Image) to yield kinetics for dissolution, based on the disappearance of pixels associated with intact fibers. Data processing was performed using the Python language, utilizing available scientific libraries. The methods of processing the data include clustering of the single fiber data, identifying clusters associated with different fiber types, producing average dissolution traces and also extraction of practical parameters, such as, time taken to dissolve 25, SO, 75, 95, and 99.5% of the clustered fibers. In addition to these simple parameters, exponential fitting was also performed yielding rate constants for fiber dissolution. Fits for sample and cluster averages were variable, although demonstrating first-order kinetics for dissolution overall. To illustrate this process, two reference pulps (a bleached softwood kraft pulp and a bleached hardwood pre hydrolysis kraft pulp) and their cellulase-treated versions were analyzed. As expected, differences in the kinetics and dissolution mechanisms between these samples were observed. Our initial interpretations are presented, based on the combined mechanistic observations and single fiber dissolution kinetics for these different samples. While the dissolution mechanisms observed were similar to those published previously, the more direct link of mechanistic information with the kinetics improve our understanding of cell wall structure and pre-treatments, toward improved processability.