Browsing by Subject "WEB"

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  • Hepojoki, Jussi; Hepojoki, Satu; Smura, Teemu; Szirovicza, Leonora; Dervas, Eva; Prahauser, Barbara; Nufer, Lisbeth; Schraner, Elisabeth M.; Vapalahti, Olli; Kipar, Anja; Hetzel, Udo (2018)
    The family Arenaviridae comprises three genera, Mammarenavirus, Reptarenavirus and the most recently added Hartmanivirus. Arenaviruses have a bisegmented genome with ambisense coding strategy. For mammarenaviruses and reptarenaviruses the L segment encodes the Z protein (ZP) and the RNA-dependent RNA polymerase, and the S segment encodes the glycoprotein precursor and the nucleoprotein. Herein we report the full length genome and characterization of Haartman Institute snake virus-1 (HISV-1), the putative type species of hartmaniviruses. The L segment of HISV-1 lacks an open-reading frame for ZP, and our analysis of purified HISV-1 particles by SDS-PAGE and electron microscopy further support the lack of ZP. Since we originally identified HISV-1 in co-infection with a reptarenavirus, one could hypothesize that co-infecting reptarenavirus provides the ZP to complement HISV-1. However, we observed that co-infection does not markedly affect the amount of hartmanivirus or reptarenavirus RNA released from infected cells in vitro, indicating that HISV-1 does not benefit from reptarenavirus ZP. Furthermore, we succeeded in generating a pure HISV-1 isolate showing the virus to replicate without ZP. Immunofluorescence and ultrastructural studies demonstrate that, unlike reptarenaviruses, HISV-1 does not produce the intracellular inclusion bodies typical for the reptarenavirus-induced boid inclusion body disease (BIBD). While we observed HISV-1 to be slightly cytopathic for cultured boid cells, the histological and immunohistological investigation of HISV-positive snakes showed no evidence of a pathological effect. The histological analyses also revealed that hartmaniviruses, unlike reptarenaviruses, have a limited tissue tropism. By nucleic acid sequencing, de novo genome assembly, and phylogenetic analyses we identified additional four hartmanivirus species. Finally, we screened 71 individuals from a collection of snakes with BIBD by RT-PCR and found 44 to carry hartmaniviruses. These findings suggest that harmaniviruses are common in captive snake populations, but their relevance and pathogenic potential needs yet to be revealed.
  • Kiljunen, Saija; Wicklund, Anu; Skurnik, Mikael (2018)
    Escherichia phages vB_EcoM-fFiEco06 and vB_EcoM-fHoEco02 were found to have 167,076-bp and 167,064-bp genomes, respectively. They are members of genus T4virus, and they are 99.96% identical to each other. The host ranges of the phages are different, probably due to a few differences in their tail protein amino acid sequences.
  • Nurmi, Johanna; Knittle, Keegan; Ginchev, Todor; Khattak, Fida; Helf, Christopher; Zwickl, Patrick; Castellano-Tejedor, Carmina; Lusilla-Palacios, Pilar; Costa-Requena, Jose; Ravaja, Niklas; Haukkala, Ari (2020)
    Background: Most adults do not engage in sufficient physical activity to maintain good health. Smartphone apps are increasingly used to support physical activity but typically focus on tracking behaviors with no support for the complex process of behavior change. Tracking features do not engage all users, and apps could better reach their targets by engaging users in reflecting their reasons, capabilities, and opportunities to change. Motivational interviewing supports this active engagement in self-reflection and self-regulation by fostering psychological needs proposed by the self-determination theory (ie, autonomy, competence, and relatedness). However, it is unknown whether digitalized motivational interviewing in a smartphone app engages users in this process. Objective: This study aimed to describe the theory- and evidence-based development of the Precious app and to examine how digitalized motivational interviewing using a smartphone app engages users in the behavior change process. Specifically, we aimed to determine if use of the Precious app elicits change talk in participants and how they perceive autonomy support in the app. Methods: A multidisciplinary team built the Precious app to support engagement in the behavior change process. The Precious app targets reflective processes with motivational interviewing and spontaneous processes with gamified tools, and builds on the principles of self-determination theory and control theory by using 7 relational techniques and 12 behavior change techniques. The feasibility of the app was tested among 12 adults, who were asked to interact with the prototype and think aloud. Semistructured interviews allowed participants to extend their statements. Participants’ interactions with the app were video recorded, transcribed, and analyzed with deductive thematic analysis to identify the theoretical themes related to autonomy support and change talk. Results: Participants valued the autonomy supportive features in the Precious app (eg, freedom to pursue personally relevant goals and receive tailored feedback). We identified the following five themes based on the theory-based theme autonomy support: valuing the chance to choose, concern about lack of autonomy, expecting controlling features, autonomous goals, and autonomy supportive feedback. The motivational interviewing features actively engaged participants in reflecting their outcome goals and reasons for activity, producing several types of change talk and very little sustain talk. The types of change talk identified were desire, need, reasons, ability, commitment, and taking steps toward change. Conclusions: The Precious app takes a unique approach to engage users in the behavior change process by targeting both reflective and spontaneous processes. It allows motivational interviewing in a mobile form, supports psychological needs with relational techniques, and targets intrinsic motivation with gamified elements. The motivational interviewing approach shows promise, but the impact of its interactive features and tailored feedback needs to be studied over time. The Precious app is undergoing testing in a series of n-of-1 randomized controlled trials. KEYWORDS health app; mHealth; human-computer interaction; prevention; service design; usability design; intrinsic motivation; reflective processes; spontaneous processes; engagement; self-determination theory; autonomous motivation; gamification; physical activity
  • Mammola, Stefano; Fontaneto, Diego; Martinez, Alejandro; Chichorro, Filipe (2021)
    Many believe that the quality of a scientific publication is as good as the science it cites. However, quantifications of how features of reference lists affect citations remain sparse. We examined seven numerical characteristics of reference lists of 50,878 research articles published in 17 ecological journals between 1997 and 2017. Over this period, significant changes occurred in reference lists' features. On average, more recent papers have longer reference lists and cite more high Impact Factor papers and fewer non-journal publications. We also show that highly cited articles across the ecological literature have longer reference lists, cite more recent and impactful references, and include more self-citations. Conversely, the proportion of 'classic' papers and non-journal publications cited, as well as the temporal span of the reference list, have no significant influence on articles' citations. From this analysis, we distill a recipe for crafting impactful reference lists, at least in ecology.
  • Venhoranta, Heli; Pausch, Hubert; Flisikowski, Krzysztof; Wurmser, Christine; Taponen, Juhani; Rautala, Helena; Kind, Alexander; Schnieke, Angelika; Fries, Ruedi; Lohi, Hannes; Andersson, Magnus (2014)
  • Faraji, Sahar; Heidari, Parviz; Amouei, Hoorieh; Filiz, Ertugrul; Poczai, Peter (2021)
    Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5 '-phosphosulfate-binding (5 ' PSB) regions and a 3 '-phosphate-binding (3 ' PB) motif that are essential for sulfotransferase activities. The protein-protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants' growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.
  • Splichal, Jin Michael; Oshima, Jun; Oshima, Ritsuko (2018)
    Many studies attempt to effectively support student regulation of collaboration using CSCL tools to enrich learning outcomes. However, few studies are aimed at facilitating development of students' internal scripts for regulation of collaboration. This study focuses on developing and evaluating a computer-mediated learning environment for project-based learning to facilitate student internal scripts for regulation by designing external scripts for effective reflection. Forty- eight first-year university students participated in this study as part of their curriculum. Our analyses of their internal scripts before and after PBL participation revealed that significantly more students who encountered an unfamiliar situation during collaboration constructed new regulation scripts. Moreover, in case studies, we found that students augmented their scripts for socially shared regulation when recognizing socio-cognitive challenges, whereas they augmented co-regulation and self-regulation scripts when recognizing socio-emotional challenges.
  • Kumar, Darshan; Lak, Behnam; Suntio, Taina; Vihinen, Helena; Belevich, Ilya; Viita, Tiina; Xiaonan, Liu; Vartiainen, Aki; Vartiainen, Maria; Varjosalo, Markku; Jokitalo, Eija (2021)
    The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1Nop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes.
  • Seppälä, Sini; Henriques, Sergio; Draney, Michael L.; Foord, Stefan; Gibbons, Alastair T.; Gomez, Luz A.; Kariko, Sarah; Malumbres-Olarte, Jagoba; Milne, Marc; Vink, Cor J.; Cardoso, Pedro (2018)
    Background The IUCN Red List of Threatened Species is the most widely used information source on the extinction risk of species. One of the uses of the Red List is to evaluate and monitor the state of biodiversity and a possible approach for this purpose is the Red List Index (RLI). For many taxa, mainly hyperdiverse groups, it is not possible within available resources to assess all known species. In such cases, a random sample of species might be selected for assessment and the results derived from it extrapolated for the entire group - the Sampled Red List Index (SRLI). With the current contribution and the three following papers, we intend to create the first point in time of a future spider SRLI encompassing 200 species distributed across the world. New information A sample of 200 species of spiders were randomly selected from the World Spider Catalogue, an updated global database containing all recognised species names for the group. The 200 selected species where divided taxonomically at the family level and the familes were ordered alphabetically. In this publication, we present the conservation profiles of 46 species belonging to the famillies alphabetically arranged between Agelenidae and Filistatidae, which encompassed Agelenidae, Amaurobiidae, Anyphaenidae, Araneidae, Archaeidae, Barychelidae, Clubionidae, Corinnidae, Ctenidae, Ctenizidae, Cyatholipidae, Dictynidae, Dysderidae, Eresidae and Filistatidae.
  • Zhou, Fang; Qu, Qiang; Toivonen, Hannu (2017)
    Networks often contain implicit structure. We introduce novel problems and methods that look for structure in networks, by grouping nodes into supernodes and edges to superedges, and then make this structure visible to the user in a smaller generalised network. This task of finding generalisations of nodes and edges is formulated as network Summarisation'. We propose models and algorithms for networks that have weights on edges, on nodes or on both, and study three new variants of the network summarisation problem. In edge-based weighted network summarisation, the summarised network should preserve edge weights as well as possible. A wider class of settings is considered in path-based weighted network summarisation, where the resulting summarised network should preserve longer range connectivities between nodes. Node-based weighted network summarisation in turn allows weights also on nodes and summarisation aims to preserve more information related to high weight nodes. We study theoretical properties of these problems and show them to be NP-hard. We propose a range of heuristic generalisation algorithms with different trade-offs between complexity and quality of the result. Comprehensive experiments on real data show that weighted networks can be summarised efficiently with relatively little error.
  • Dobat, Andres; Deckers, Pieterjan; Heeren, Stijn; Lewis, Michael; Thomas, Suzanne Elizabeth; Wessman, Anna Pia Frederike (2020)
    Hobby metal detecting is a controversial subject. Legal and policy approaches differ widely across national and regional contexts, and the attitudes of archaeologists and heritage professionals towards detectorists are often polarized and based on ethical or emotive arguments. We, the European Public Finds Recording Network (EPFRN), have implemented collaborative approaches towards detectorist communities in our respective contexts (Denmark, England and Wales, Finland, Flanders, and the Netherlands). Although our motivations are affected by our national circumstances, we base our work on an agreed set of goals, practices, and visions. This article presents the EPFRN's vision statement and provides insight into its underlying thoughts. We hope to create a debate on how to develop best practice approaches that acknowledge the inherent challenges of hobby metal detecting while realizing its potential.
  • Raj, Rahul; Rautio, Riitta; Pekkola, Johanna; Rahi, Melissa; Sillanpää, Mikko; Numminen, Jussi (2019)
    BACKGROUND: The Woven EndoBridge (WEB) device is a new treatment modality developed for broad-necked unruptured intracranial aneurysms (IAs) but shows potential for the treatment of ruptured IAs as well. Our aim was to describe 6-month aneurysm obliteration rates, clinical outcomes, and procedure-related complications after WEB treatment for ruptured IAs from 2 academic centers. METHODS: We conducted a retrospective observational study, including all consecutive patients treated with the WEB device (WEB single layer and single-layer sphere) for a ruptured IA causing acute subarachnoid hemorrhage between 2014 (start of use) and 2017. Primary outcome was angiographic aneurysm obliteration (Beaujon Occlusion Scale Score) rate. Secondary outcomes were early re-bleedings, complications, and patient outcome (death and modified Rankin Scale). RESULTS: A total of 33 patients with ruptured IAs were treated 0-4 days from IA rupture. Of 27 survivors, 6-month angiographic follow-up was available for 26 patients, of whom 81% showed complete occlusion. Of the 27 survivors, 24 patients (89%) had a favorable neurologic outcome at 6 months after subarachnoid hemorrhage. Two aneurysms were retreated (8% of all). There was 1 fatal procedure-related complication. No early aneurysm re-bleedings were noted. CONCLUSIONS: For anatomically suitable ruptured IAs, WEB device treatment seems to be safe and results in acceptable occlusion rates. Still, larger studies with long-term results are needed before recommendations can be made.
  • Vuong, Tung; Saastamoinen, Miamaria; Jacucci, Giulio; Ruotsalo, Tuukka (2019)
    Understanding users' search behavior has largely relied on the information available from search engine logs, which provide limited information about the contextual factors affecting users' behavior. Consequently, questions such as how users' intentions, task goals, and substances of the users' tasks affect search behavior, as well as what triggers information needs, remain largely unanswered. We report an experiment in which naturalistic information search behavior was captured by analyzing 24/7 continuous recordings of information on participants' computer screens. Written task diaries describing the participants' tasks were collected and used as real-life task contexts for further categorization. All search tasks were extracted and classified under various task categories according to users' intentions, task goals, and substances of the tasks. We investigated the effect of different task categories on three behavioral factors: search efforts, content-triggers, and application context. Our results suggest four findings: (i) Search activity is integrally associated with the users' creative processes. The content users have seen prior to searching more often triggers search, and is used as a query, within creative tasks. (ii) Searching within intellectual and creative tasks is more time-intensive, while search activity occurring as a part of daily routine tasks is associated with more frequent searching within a search task. (iii) Searching is more often induced from utility applications in tasks demanding a degree of intellectual effort. (iv) Users' leisure information-seeking activity is occurring inherently within social media services or comes from social communication platforms. The implications of our findings for information access and management systems are discussed.