Browsing by Subject "EMERGENCE"

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  • Hosoya, Haruo; Hyvärinen, Aapo (2017)
    Experimental studies have revealed evidence of both parts-based and holistic representations of objects and faces in the primate visual system. However, it is still a mystery how such seemingly contradictory types of processing can coexist within a single system. Here, we propose a novel theory called mixture of sparse coding models, inspired by the formation of category-specific subregions in the inferotemporal (IT) cortex. We developed a hierarchical network that constructed a mixture of two sparse coding submodels on top of a simple Gabor analysis. The submodels were each trained with face or non-face object images, which resulted in separate representations of facial parts and object parts. Importantly, evoked neural activities were modeled by Bayesian inference, which had a top-down explaining-away effect that enabled recognition of an individual part to depend strongly on the category of the whole input. We show that this explaining-away effect was indeed crucial for the units in the face submodel to exhibit significant selectivity to face images over object images in a similar way to actual face-selective neurons in the macaque IT cortex. Furthermore, the model explained, qualitatively and quantitatively, several tuning properties to facial features found in the middle patch of face processing in IT as documented by Freiwald, Tsao, and Livingstone (2009). These included, in particular, tuning to only a small number of facial features that were often related to geometrically large parts like face outline and hair, preference and anti-preference of extreme facial features (e.g., very large/small inter-eye distance), and reduction of the gain of feature tuning for partial face stimuli compared to whole face stimuli. Thus, we hypothesize that the coding principle of facial features in the middle patch of face processing in the macaque IT cortex may be closely related to mixture of sparse coding models.
  • McGarvey, Alison C.; Rybtsov, Stanislav; Souilhol, Celine; Tamagno, Sara; Rice, Ritva; Hills, David; Godwin, Duncan; Rice, David; Tomlinson, Simon R.; Medvinsky, Alexander (2017)
    In the developing embryo, hematopoietic stem cells (HSCs) emerge from the aorta-gonad-mesonephros (AGM) region, but the molecular regulation of this process is poorly understood. Recently, the progression from E9.5 to E10.5 and polarity along the dorso-ventral axis have been identified as clear demarcations of the supportive HSC niche. To identify novel secreted regulators of HSC maturation, we performed RNA sequencing over these spatiotemporal transitions in the AGM region and supportive OP9 cell line. Screening several proteins through an ex vivo reaggregate culture system, we identify BMP ER as a novel positive regulator of HSC development. We demonstrate that BMP ER is associated with BMP signaling inhibition, but is transcriptionally induced by BMP4, suggesting that BMP ER contributes to the precise control of BMP activity within the AGM region, enabling the maturation of HSCs within a BMP-negative environment. These findings and the availability of our transcriptional data through an accessible interface should provide insight into the maintenance and potential derivation of HSCs in culture.
  • Becker, Daniel J.; Hall, Richard J.; Forbes, Kristian M.; Plowright, Raina K.; Altizer, Sonia (2018)
  • Toppinen, M.; Perdomo, Maria; Palo, J. U.; Simmonds, P.; Lycett, S. J.; Soderlund-Venermo, M.; Sajantila, A.; Hedman, K. (2015)
    DNA in human skeletal remains represents an important historical source of host genomic information and potentially of infecting viruses. However, little is known about viral persistence in bone. We searched ca. 70-year-old long bones of putative Finnish casualties from World War II for parvovirus B19 (B19V) DNA, and found a remarkable prevalence of 45%. The viral sequences were exclusively of genotypes 2 (n = 41), which disappeared from circulation in 1970's, or genotype 3 (n = 2), which has never been reported in Northern Europe. Based on mitochondrial and Y-chromosome profiling, the two individuals carrying B19V genotype 3 were likely from the Soviet Red Army. The most recent common ancestor for all genotypes was estimated at early 1800s. This work demonstrates the forms of B19V that circulated in the first half of the 20th century and provides the first evidence of the suitability of bone for exploration of DNA viruses.
  • Virtanen, Jenni; Smura, Teemu; Aaltonen, Kirsi; Moisander-Jylhä, Anna-Maria; Knuuttila, Anna; Vapalahti, Olli; Sironen, Tarja (2019)
    Aleutian mink disease virus (AMDV) is the causative agent of Aleutian disease (AD), which affects mink of all genotypes and also infects other mustelids such as ferrets, martens and badgers. Previous studies have investigated diversity in Finnish AMDV strains, but these studies have been restricted to small parts of the virus genome, and mostly from newly infected farms and free-ranging mustelids. Here, we investigated the diversity and evolution of Finnish AMDV strains by sequencing the complete coding sequences of 31 strains from mink originating from farms differing in their virus history, as well as from free-ranging mink. The data set was supplemented with partial genomes obtained from 26 strains. The sequences demonstrate that the Finnish AMDV strains have considerable diversity, and that the virus has been introduced to Finland in multiple events. Frequent recombination events were observed, as well as variation in the evolutionary rate in different parts of the genome and between different branches of the phylogenetic tree. Mink in the wild carry viruses with high intra-host diversity and are occasionally even co-infected by two different strains, suggesting that free-ranging mink tolerate chronic infections for extended periods of time. These findings highlight the need for further sampling to understand the mechanisms playing a role in the evolution and pathogenesis of AMDV.
  • Sannino, Annalisa; Engeström, Yrjö H M (2017)
    Formative interventions and the specific method of the Change Laboratory (CL) are presented as examples of intervention research that generates actionable and societally impactful knowledge. In contrast with stabilization knowledge that fixates phenomena into static categories, actionable knowledge is understood here as collaborative and generative possibility knowledge intertwined with transformative action. The article asks what can be learned from the different ways the epistemological principles behind formative interventions are implemented in different CLs. Three CL interventions are analyzed. The analysis is summarized with the help of a grid covering the key characteristics of formative interventions: contradictions, conflicts of motives, double stimulation, zone of proximal development, germ cells and emerging concepts. Comparison of the three cases shows that understanding the specific historical stage of the development of contradictions in a given organization is of foundational importance. In transformations induced by CLs, contradiction and conflict may be seen as acute push and the future-oriented concept as gradually emerging pull, with the change actions of the local practitioners in the middle. Constructing a germ cell and eventually an expanded concrete concept based on it are the most demanding challenges for CL interventions.
  • McNally, Alan; Oren, Yaara; Kelly, Darren; Pascoe, Ben; Dunn, Steven; Sreecharan, Tristan; Vehkala, Minna; Välimäki, Niko; Prentice, Michael B.; Ashour, Amgad; Avram, Oren; Pupko, Tal; Dobrindt, Ulrich; Literak, Ivan; Guenther, Sebastian; Schaufler, Katharina; Wieler, Lothar H.; Zong Zhiyong,; Sheppard, Samuel K.; McInerney, James O.; Corander, Jukka (2016)
    The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
  • Smith, Martine M.; Batorowicz, Beata; Sandberg, Annika Dahlgren; Murray, Janice; Stadskleiv, Kristine; van Balkom, Hans; Neuvonen, Kirsi; von Tetzchner, Stephen (2018)
    Narratives are a pervasive form of discourse and a rich source for exploring a range of language and cognitive skills. The limited research base to date suggests that narratives generated using aided communication may be structurally simple, and that features of cohesion and reference may be lacking. This study reports on the analysis of narratives generated in interactions involving aided communication in response to short, silent, video vignettes depicting events with unintended or unexpected consequences. Two measures were applied to the data: the Narrative Scoring Scheme and the Narrative Analysis Profile. A total of 15 participants who used aided communication interacted with three different communication partners (peers, parents, professionals) relaying narratives about three video events. Their narratives were evaluated with reference to narratives of 15 peers with typical development in response to the same short videos and to the narratives that were interpreted by their communication partners. Overall, the narratives generated using aided communication were shorter and less complete than those of the speaking peers, but they incorporated many similar elements. Topic maintenance and inclusion of scene-setting elements were consistent strengths. Communication partners offered rich interpretations of aided narratives. Relative to the aided narratives, these interpreted narratives were typically structurally more complete and cohesive and many incorporated more elaborated semantic content. The data reinforce the robust value of narratives in interaction and their potential for showcasing language and communication achievements in aided communication.
  • Sannino, A.; Engeström, Y. (2018)
    The article presents central ideas and future challenges of cultural-historical activity theory, focusing specifically on the work of the so-called Helsinki school of activity theory. We first introduce the revolutionary roots of the theory in the works of Marx and Vygotsky, and the evolution of the unit of analysis through different generations of activity theory. We then discuss the foundational role of historicity and dialectics in activity theory. We identify two central epistemological-methodological principles that guide activity-theoretical studies, namely the principle of double stimulation and the principle of ascending from the abstract to the concrete. These principles lead us to emphasize formative interventions as a powerful way to conduct societally impactful activity-theoretical research. We conclude by pointing out some major challenges facing activity theory in the 21st century.
  • Pietikainen, Risto; Nordling, Stig; Jokiranta, Sakari; Saari, Seppo; Heikkinen, Petra; Gardiner, Chris; Kerttula, Anne-Marie; Kantanen, Tiina; Nikanorova, Anna; Laaksonen, Sauli; Lavikainen, Antti; Oksanen, Antti (2017)
    Background: The spread of vector-borne diseases to new regions has become a global threat due to climate change, increasing traffic, and movement of people and animals. Dirofilaria repens, the canine subcutaneous filarioid nematode, has expanded its distribution range northward during the last decades. The northernmost European locations, where the parasite life-cycle has been confirmed, are Estonia and the Novgorod Region in Russia. Results: Herein, we describe an autochthonous D. repens infection in a Finnish woman. We also present two cases of D. repens infection in imported dogs indicating the life-cycle in the Russian Vyborg and St Petersburg areas, close to the Finnish border. Conclusions: The most obvious limiting factor of the northern distribution of D. repens is the summer temperature, due to the temperature-dependent development of larvae in vectors. With continuing climate change, further spread of D. repens in Fennoscandia can be expected.
  • Poelman, Randy; Schuffenecker, Isabelle; Van Leer-Buter, Coretta; Josset, Laurence; Niesters, Hubert G. M.; Lina, Bruno; Vuorinen, Tytti; ESCV-ECDC EV-D68 Study Grp; Lappalainen, Maija; Jääskeläinen, Anne; Smura, Teemu (2015)
    Background: In August and September 2014, unexpected clusters of enterovirus-D68 (EV-D68) infections associated with severe respiratory disease emerged from North-America. In September, the European Centre for Disease Prevention and Control (ECDC) asked European countries to strengthen respiratory sample screening for enterovirus detection and typing in cases with severe respiratory presentations. Objectives: To provide a detailed picture of EV-D68 epidemiology in Europe by conducting a retrospective and prospective laboratory analysis of clinical specimens. Study design: An initiative supported by the European Society for Clinical Virology (ESCV) and ECDC was launched to screen for EV-D68 in respiratory specimens between July 1st and December 1st 2014 in Europe and to sequence the VP1 region of detected viruses for phylogenetic analytic purposes. Results: Forty-two institutes, representing 51 laboratories from 17 European countries, analyzed 17,248 specimens yielding 389 EV-D68 positive samples (2.26%) in 14 countries. The proportion of positive samples ranged between 0 and 25% per country. These infections resulted primarily in mild respiratory disease, mainly detected in young children presenting with wheezing and in immuno-compromised adults. The viruses detected in Europe are genetically very similar to those of the North-American epidemic and the majority (83%) could be assigned to clade B. Except for 3 acute flaccid paralysis (AFP) cases, one death and limited ICU admissions, no severe cases were reported. Conclusions: The European study showed that EV-D68 circulated in Europe during summer and fall of 2014 with a moderate disease burden and different pathogenic profile compared to the North-American epidemic. (C) 2015 The Authors. Published by Elsevier B.V.
  • Jakava-Viljanen, Miia; Tiina, Nokireki; Sironen, Tarja; Vapalahti, Olli; Sihvonen, Liisa; Anita, Huovilainen (2015)
    Among other Lyssaviruses, Daubenton's and pond-bat-related European bat lyssavirus type 2 (EBLV-2) can cause human rabies. To investigate the diversity and evolutionary trends of EBLV-2, complete genome sequences of two Finnish isolates were analysed. One originated from a human case in 1985, and the other originated from a bat in 2009. The overall nucleotide and deduced amino acid sequence identity of the two Finnish isolates were high, as well as the similarity to fully sequenced EBLV-2 strains originating from the UK and the Netherlands. In phylogenetic analysis, the EBLV-2 strains formed a monophyletic group that was separate from other bat-type lyssaviruses, with significant support. EBLV-2 shared the most recent common ancestry with Bokeloh bat lyssavirus (BBLV) and Khujan virus (KHUV). EBLV-2 showed limited diversity compared to RABV and appears to be well adapted to its host bat species. The slow tempo of viral evolution was evident in the estimations of divergence times for EBLV-2: the current diversity was estimated to have built up during the last 2000 years, and EBLV-2 diverged from KHUV about 8000 years ago. In a phylogenetic tree of partial N gene sequences, the Finnish EBLV-2 strains clustered with strains from Central Europe, supporting the hypothesis that EBLV-2 circulating in Finland might have a Central European origin. The Finnish EBLV-2 strains and a Swiss strain were estimated to have diverged from other EBLV-2 strains during the last 1000 years, and the two Finnish strains appear to have evolved from a common ancestor during the last 200 years.
  • Engeström, Yrjö; Sannino, Annalisa (2021)
    The article outlines four generations of theorizing and research on work and learning within the Finnish school of activity theory. The main focus of the paper is on the evolution of the unit of analysis through the four generations, from mediated action to a collective activity system, to multiple-interconnected activity systems, and most recently to heterogenous work coalitions aimed at resolving wicked societal problems. We examine how learning and agency are conceptualized in each generation, and what kinds of interventions are conducted in the projects presented as examples of the four generations. We conclude that the four generations of activity-theoretical studies of work and learning continue to co-exist. To meet the challenges of work in today's world, activity theory must seriously engage in the development of its fourth generation, building on ideas and instruments developed by the preceding generations.
  • Nystuen, Kristin O.; Sundsdal, Kristine; Opedal, Øystein H.; Holien, Håkon; Strimbeck, G. Richard; Graae, Bente J. (2019)
    Abstract Questions How do mat thickness, physical structure and allelopathic properties of terricolous mat-forming lichens affect recruitment of vascular plants in dwarf-shrub and lichen heath vegetation?. Location The mountains of Dovrefjell, central Norway. Methods In autumn, seeds of ten vascular plant species were collected and sown in a common garden experiment with mats of six lichen species and bare-soil controls as experimental treatments. We recorded growing season soil temperature and moisture, and seedling recruitment and growth after one year. The effect of lichen secondary compounds on germination was tested in a growth chamber experiment and compared to the lichen-plant interactions detected under field conditions. Results The lichen mats buffered extreme soil temperatures and soil drying in dry weather, with soils below the thickest mats (Cladonia stellaris and C. rangiferina) experiencing the lowest temperature fluctuations. Seedling recruitment and seedling growth in the field and seed germination in the lab were species-specific. Seedling recruitment rates were overall higher within lichen mats than on bare soil, but the c. 6.5 cm thick mats of C. stellaris reduced recruitment of many species. The lab experiment suggested no overall strong effect of lichen allelopathy on seed germination, and effects on seed germination were only moderately correlated with the lichen-plant interactions observed for seedling recruitment in the field. Conclusions In harsh environments like alpine dwarf-shrub and lichen heaths, the presence of lichens and the resulting amelioration of the microclimate seems more important for vascular plant recruitment than are allelopathic effects often reported in lab experiments. We might therefore expect most terricolous lichens, depending on the plant species in focus, to facilitate rather than hamper the early stages of plant recruitment into lichen-dominated arctic-alpine heath vegetation. This article is protected by copyright. All rights reserved.
  • NoroNet; van Beek, Janko; Al-Hello, Haider; Maunula, Leena (2018)
    Background The development of a vaccine for norovirus requires a detailed understanding of global genetic diversity of noroviruses. We analysed their epidemiology and diversity using surveillance data from the NoroNet network. Methods We included genetic sequences of norovirus specimens obtained from outbreak investigations and sporadic gastroenteritis cases between 2005 and 2016 in Europe, Asia, Oceania, and Africa. We genotyped norovirus sequences and analysed sequences that overlapped at open reading frame (ORF) 1 and ORF2. Additionally, we assessed the sampling date and country of origin of the first reported sequence to assess when and where novel drift variants originated. Findings We analysed 16 635 norovirus sequences submitted between Jan 1, 2005, to Nov 17, 2016, of which 1372 (8.2%) sequences belonged to genotype GI, 15 256 (91.7%) to GII, and seven ( Interpretation Continuous changes in the global norovirus genetic diversity highlight the need for sustained global norovirus surveillance, including assessment of possible immune escape and evolution by recombination, to provide a full overview of norovirus epidemiology for future vaccine policy decisions.
  • Patomäki, Heikki (2020)
    The question I raise is whether the basic features of mind, social categories, and society are unchanging or changing. Some understandings of ontology would seem to suggest that social ontology is a branch of metaphysics. However, as the history of concepts such as metaphysical and ontology indicate, our concepts and knowledge are historical. It is widely held that society is concept‐ and activity‐dependent. I examine critically two strands of social ontology in terms of their answers to this problematic: (1) John Searle’s theory of the construction of social reality and (2) critical realist theory of mind and society as interlaced emergent layers of reality. Apart from emergence in natural systems, there is also emergence beyond nature as consciousness, agency and society cannot be completely explained in terms of biological realities; but how and when did this emergence occur? We need an account of the emergent order of language, reflectively conscious mind, and institutions not only for its own sake, but also because the process whereby new objects and properties emerge may be on‐going, path‐dependent, diverse, and open‐ended. The main argument is that the object of study of social theorists is geo‐historically specific, liable to diversity within any given world‐historical epoch, and open to further changes and new forms of emergence in the future.
  • Colclough, Abigail; Corander, Jukka; Sheppard, Samuel K.; Bayliss, Sion C.; Vos, Michiel (2019)
    Bacteria interact with a multitude of other organisms, many of which produce antimicrobials. Selection for resistance to these antimicrobials has the potential to result in resistance to clinical antibiotics when active compounds target the same bacterial pathways. The possibility of such cross-resistance between natural antimicrobials and antibiotics has to our knowledge received very little attention. The antimicrobial activity of extracts from seaweeds, known to be prolific producers of antimicrobials, is here tested against Staphylococcus aureus isolates with varied clinical antibiotic resistance profiles. An overall effect consistent with cross-resistance is demonstrated, with multidrug-resistant S. aureus strains being on average more resistant to seaweed extracts. This pattern could potentially indicate that evolution of resistance to antimicrobials in the natural environment could lead to resistance against clinical antibiotics. However, patterns of antimicrobial activity of individual seaweed extracts vary considerably and include collateral sensitivity, where increased resistance to a particular antibiotic is associated with decreased resistance to a particular seaweed extract. Our correlation-based methods allow the identification of antimicrobial extracts bearing most promise for downstream active compound identification and pharmacological testing.
  • Batista, Romina; Olsson, Urban; Andermann, Tobias; Aleixo, Alexandre; Ribas, Camila Cherem; Antonelli, Alexandre (2020)
    To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescentphylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to thePalaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.
  • Moradigaravand, Danesh; Palm, Martin; Farewell, Anne; Mustonen, Ville; Warringer, Jonas; Parts, Leopold (2018)
    The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The detection of antibiotic resistance is typically made by measuring a few known determinants previously identified from genome sequencing, and thus requires the prior knowledge of its biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average accuracy of 0.91 on held-out data (range 0.81-0.97). While the best models most frequently employed gene content, an average accuracy score of 0.79 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and significantly improved prediction only for two antibiotics, including ciprofloxacin. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data can be informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.
  • Smura, Teemu; Blomqvist, Soile; Vuorinen, Tytti; Ivanova, Olga; Samoilovich, Elena; Al-Hello, Haider; Savolainen-Kopra, Carita; Hovi, Tapani; Roivainen, Merja (2014)