Browsing by Subject "CHALLENGE"

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  • Pratas, Diogo; Hosseini, Morteza; Silva, Jorge M.; Pinho, Armando J. (2019)
    The development of efficient data compressors for DNA sequences is crucial not only for reducing the storage and the bandwidth for transmission, but also for analysis purposes. In particular, the development of improved compression models directly influences the outcome of anthropological and biomedical compression-based methods. In this paper, we describe a new lossless compressor with improved compression capabilities for DNA sequences representing different domains and kingdoms. The reference-free method uses a competitive prediction model to estimate, for each symbol, the best class of models to be used before applying arithmetic encoding. There are two classes of models: weighted context models (including substitutional tolerant context models) and weighted stochastic repeat models. Both classes of models use specific sub-programs to handle inverted repeats efficiently. The results show that the proposed method attains a higher compression ratio than state-of-the-art approaches, on a balanced and diverse benchmark, using a competitive level of computational resources. An efficient implementation of the method is publicly available, under the GPLv3 license.
  • Kalliola, Satu; Malmberg, L. Pekka; Malmstrom, Kristiina; Pelkonen, Anna S.; Mäkelä, Mika J. (2019)
    Background: Recurrent wheezing in early life is transient in most children. The significance of airway hyper-responsiveness (AHR) in persistence of respiratory symptoms from infancy to early childhood is controversial. Objective: We evaluated whether AHR in wheezy infants predicts doctor-diagnosed asthma (DDA) or AHR at the age of 6 years. Methods: Sixty-one wheezy infants (age 6-24 months) were followed up to the median age of 6 years. Lung function and AHR with methacholine challenge test were assessed at infancy and 6 years. The exercise challenge test was performed at the age of 6 years. Atopy was assessed with skin prick tests. Results: At 6 years, 21 (34%) of the children had DDA. Children with DDA had higher logarithmic transformed dose-response slope (LOGDRS) to methacholine in infancy than children without DDA (0.047 vs 0.025; P = .033). Furthermore, AHR to methacholine in infancy and at 6 years were associated with each other (r = 0.324, P = .011). Children with exercise-induced bronchoconstriction (EIB) at 6 years were more reactive to methacholine in infancy than those without EIB (P = .019). Conclusion: Increased AHR in symptomatic infants was associated with increased AHR, DDA, and EIB at median the age of 6 years, suggesting early establishment of AHR. (C) 2019 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.
  • Ronnberg, Bengt; Gustafsson, Ake; Vapalahti, Olli; Emmerich, Petra; Lundkvist, Ake; Schmidt-Chanasit, Jonas; Blomberg, Jonas (2017)
    The recent spread of Zika virus (ZIKV) in the Americas and Asia necessitates an increased preparedness for improved maternal and perinatal health and blood safety. However, serological cross-reactions, especially to Dengue virus (DENV), complicate ZIKV antibody serodiagnosis. A novel "pan-Flavi" suspension multiplex immunoassay (PFSMIA) using 25 antigens, whole virus (WV), non-structural protein 1 (NS1), and envelope (E) proteins, from 7 zoonotic flaviviruses for specific detection of ZIKV and DENV IgM and IgG was developed. Patterns of antibody cross-reactivity, avidity, and kinetics were established in 104 sera from returning travelers with known ZIKV and DENV infections. PFSMIA gave IgM- and IgG-sensitivities for both viruses of 96-100%, compared to an immunofluorescence assay. Main IgM cross-reactions were to NS1, for IgG to the E and WV antigens. Infecting virus yielded reactivity to several antigens of the homologous virus, while cross-reactions tended to occur only to a single antigen from heterologous virus(es). A specificity-enhancing computer procedure took into account antibody isotype, number of antibody-reactive antigens per virus, avidity, average degree of cross-reactivity to heterologous flavivirus antigens, and reactivity changes in serial sera. It classified all 50 cases correctly. Applied to sera from 200 pregnant women and 173 blood donors from Sweden, one blood donor was found ZIKV NS1 IgM positive, and another as ZIKV NS1 IgG positive. These samples did not react with other ZIKV antigens and were thereby judged as false-positives. PFSMIA provided sensitive and specific ZIKV and DENV serology, warranting high-throughput serological surveillance and a minimized need for laborious and expensive virus neutralization assays.
  • Yohannes, Dawit A.; Freitag, Tobias L.; de Kauwe, Andrea; Kaukinen, Katri; Kurppa, Kalle; Wacklin, Pirjo; Mäki, Markku; Arstila, T. Petteri; Anderson, Robert P.; Greco, Dario; Saavalainen, Päivi (2017)
    Celiac disease (CD) patients mount an abnormal immune response to gluten. T-cell receptor (TCR) repertoires directed to some immunodominant gluten peptides have previously been described, but the global immune response to in vivo gluten exposure in CD has not been systematically investigated yet. Here, we characterized signatures associated with gluten directed immune activity and identified gluten-induced T-cell clonotypes from total blood and gut TCR repertoires in an unbiased manner using immunosequencing. CD patient total TCR repertoires showed increased overlap and substantially altered TRBV-gene usage in both blood and gut samples, and increased diversity in the gut during gluten exposure. Using differential abundance analysis, we identified gluten-induced clonotypes in each patient that were composed of a large private and an important public component. Hierarchical clustering of public clonotypes associated with dietary gluten exposure identified subsets of highly similar clonotypes, the most proliferative of which showing significant enrichment for the motif ASS[LF] R[SW][TD][DT][TE][QA][YF] in PBMC repertoires. These results show that CD-associated clonotypes can be identified and that common gluten associated immune response features can be characterized in vivo from total repertoires, with potential use in disease stratification and monitoring.
  • Hakkarainen, Heidi; Huopio, Hanna; Cederberg, Henna; Voutilainen, Raimo; Heinonen, Seppo (2018)
    Aims: Was to determine whether the birth weight of the infant predicts prediabetes (impaired fasting glucose, impaired glucose tolerance, or both) and type 2 diabetes (T2DM) during long-term follow-up of women with or without gestational diabetes mellitus (GDM). Methods: The women with or without GDM during their pregnancies in Kuopio University Hospital in 1989-2009 (n=876) were contacted and invited for an evaluation. They were stratified into two groups according to the newborn's birth weight: 10-90th percentile (appropriate-for-gestational-age; AGA) (n = 662) and >90th percentile (large-for-gestational-age; LGA) (n = 116). Glucose tolerance was investigated with an oral glucose tolerance test after a mean follow-up time of 7.3 (SD 5.1) years. Results: The incidence of T2DM was 11.8% and 0% in the women with and without GDM, respectively, after an LGA delivery. The incidence of prediabetes increased with offspring birth weight categories in the women with and without GDM: from 46.3% and 26.2% (AGA) to 52.9% and 29.2% (LGA), respectively. Conclusions: GDM women with LGA infants are at an increased risk for subsequent development of T2DM and therefore represent a target group for intervention to delay or prevent T2DM development. In contrast, an LGA delivery without GDM does not increase T2DM risk. (C) 2018 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.
  • Peiponen, Kati Susanna; Tirkkonen, Birger Taneli; Junnila, Jouni Juho Tapio; Heinonen, Mari Leena (2018)
    Background: The intracellular bacterium Lawsonia intracellularis is an important pathogen in modern swine production. The aim of this study was to investigate the effect of a live attenuated L. intracellularis vaccine (Enterisol-Ileitis (R)) on the health and production parameters of weaned and finishing pigs in a commercial Finnish 850-sow farm with diagnosed L. intracellularis infection. The herd was free from enzootic pneumonia, swine dysentery, progressive atrophic rhinitis, sarcoptic mange and salmonellosis. Four weekly groups of approximately 500 piglets were included in the study for a total of approximately 2000 piglets. Half of these piglets were vaccinated at 3 weeks of age and the other half served as controls. The study piglets were ear-tagged with individual numbers and colour-coded and were individually weighed at weaning (4 weeks), delivery to the finishing farm (12-14 weeks) and at slaughter. Mortality, symptoms of diseases and medications of the study piglets were registered in the nursery and finishing unit. Feed conversion rate was calculated for the finishing period and lean meat percentage was measured at slaughter. Results: Vaccinated piglets had a higher live weight than unvaccinated piglets at delivery to the finishing unit (+ 1.18 kg, P = 0.002) and at slaughter (+ 3.57 kg, P <0.001). The daily weight gain of vaccinated piglets was better than unvaccinated piglets in the nursery (+ 14.8 g/d, P = 0.013) and in the finishing unit (+ 30.9 g/d, P <0.001). Vaccination had no effect on feed conversion rate or lean meat percentage (P = 0.102). Altogether, 3.9 and 4.6% of the pigs were medicated for different reasons in the vaccinated and control groups, respectively. The return on investment for the vaccination was calculated to be 0.41. Conclusions: Immunisation of piglets with a live attenuated L. intracellularis vaccine resulted in higher meat yield in pig production via significantly higher live weight and average daily weight gain in a Finnish specific pathogen-free setting.
  • Koivu-Jolma, Mikko; Annila, Arto (2018)
    Mathematical epidemiology is a well-recognized discipline to model infectious diseases. It also provides guidance for public health officials to limit outbreaks. Nevertheless, epidemics take societies by surprise every now and then, for example, when the Ebola virus epidemic raged seemingly unrestrained in Western Africa. We provide insight to this capricious character of nature by describing the epidemic as a natural process, i.e., a phenomenon governed by thermodynamics. Our account, based on statistical mechanics of open systems, clarifies that it is impossible to predict accurately epidemic courses because everything depends on everything else. Nonetheless, the thermodynamic theory yields a comprehensive and analytical view of the epidemic. The tenet subsumes various processes in a scale-free manner from the molecular to the societal levels. The holistic view accentuates overarching procedures in arresting and eradicating epidemics.
  • Haapasaari, Arja; Engestrom, Yrjo; Kerosuo, Hannele (2018)
    Purpose - The purpose of this paper is to examine the generation of innovations by employees and the creation of initiative paths, and to discover which factors contribute to the implementation of an initiative. Design/methodology/approach - Based on longitudinal qualitative research, the study explores the profiles of initiative paths and the types of innovations and relationships among the generated innovations. Findings - It was found that, to become an innovation, an initiative followed different paths along which the processing and outcomes varied, as did the time needed for experimentation. The creation of initiative paths required the transformative agency of the actors involved. Power relations had an impact on the generation of initiatives and implementation of innovations. Originality/value - Innovations research has concentrated on the generation of ideas and the implementation of innovations. This study focuses on the process path along which ideas become innovations and on the role of power relations in the innovations process.
  • Grönthal, Thomas; Moodley, Arshnee; Nykäsenoja, Suvi; Junnila, Jouni; Guardabassi, Luca; Thomson, Katariina; Rantala, Merja (2014)
  • Lassmann-Klee, Paul G.; Sundblad, Britt-Marie; Malmberg, Leo P.; Sovijarvi, Anssi R. A.; Piirilä, Päivi (2020)
    Clinical testing of bronchial hyperreactivity (BHR) provides valuable information in asthma diagnostics. Nevertheless, the test results depend to a great extent on the testing procedure: test substance, apparatus and protocol. In Nordic countries, three protocols predominate in the testing field: Per Malmberg, Nieminen and Sovijarvi methods. However, knowledge of their equivalence is limited. We aimed to find equivalent provocative doses (PD) to obtain similar bronchoconstrictive responses for the three protocols. We recruited 31 patients with suspected asthma and health care workers and performed BHR testing with methacholine according to Malmberg and Nieminen methods, and with histamine according to Sovijarvi. We obtained the individual response-dose slopes for each method and predicted equivalent PD values. Applying a mixed-model, we found significant differences in the mean (standard error of mean) response-dose (forced expiratory volume in one second (FEV1)%/mg): Sovijarvi 7.2 (1.5), Nieminen 13.8 (4.2) and Malmberg 26 (7.3). We found that the earlier reported cut-point values for moderate BHR and marked BHR between the Sovijarvi (PD15) and Nieminen (PD20) methods were similar, but with the Malmberg method a significant bronchoconstrictive reaction was measured with lower PD20 values. We obtained a relationship between slope values and PD (mg) between different methods, useful in epidemiological research and clinical practice.
  • Candy, Seona; Turner, Graham; Larsen, Kirsten; Wingrove, Kate; Steenkamp, Julia; Friel, Sharon; Lawrence, Mark (2019)
    Dietary change has been suggested as a key strategy to maintain food security, improve health and reduce environmental impacts in the face of rising populations, resource scarcity and climate change impacts, particularly in developed countries. This paper presents findings from a quantitative modelling analysis of food availability and environmental implications of shifting the current average Australian dietary pattern to one of two alternative, healthy dietary patterns, the 'healthy mixed diet', with a mixture of animal and plant foods, and the 'healthy plant-based diet', with only plant foods. Both were constructed in accordance with the Australian Dietary Guideline recommendations, and four sustainability principles: Avoiding over-consumption, reducing intake of discretionary foods, reducing animal products, and reducing food waste. It was assumed that all food was provided domestically where possible, and export of foods only occurred when there was a surplus to domestic requirements. The authors compared the impacts of each dietary pattern on direct food availability, water use, land use, greenhouse gas emissions, fuel and energy use and fertiliser use. The plant-based diet had the best overall environmental and direct food availability outcomes, however had key vulnerabilities in terms of fertiliser and cropping land availability. For the agricultural sector overall, changes in diet had little effect on environmental impact due to the amount and nature of Australian exports, indicating that changes to production methods are also necessary. Likewise, changing diets had little effect on the existing environmentally intensive Australian economy, indicating that changes to other sectors are also necessary.
  • Kauppila, Tiina Kaisa; Paassilta, Marita; Kukkonen, Anna Kaarina; Kuitunen, Mikael; Pelkonen, Anna S.; Makela, Mika J. (2019)
    Background: The safety and efficacy of long-term milk oral immunotherapy (OIT) in Finnish children with persistent cow's milk allergy (CMA) were evaluated in an open-label, non-randomized study. Methods: During the 11-year study, 296 children aged 5 years or older with immunoglobulin E (IgE)-mediated CMA started milk OIT. Follow-up data were collected at three time points: the post-buildup phase, 1 year thereafter, and at the cross-sectional long-term follow-up between January 2016 and December 2017. Patients were divided according to baseline milk-specific IgE (sIgE) level and by the amount of milk consumption at the long-term follow-up. The high-dose group consumed >= 2 dL of milk daily, while the failure group consumed Results: Out of the initial study group, 244/296 (83%) patients participated in the long-term follow-up. Among these patients, 136/244 (56%) consumed >= 2 dL of milk daily. The median follow-up time was 6.5 years. Of the recorded markers and clinical factors, the baseline milk sIgE level was most associated with maintaining milk OIT (P <0.001). Respiratory symptoms in the post-buildup phase increased the risk of treatment failure (OR 3.5, 95% CI: 1.5-8.1, P = 0.003) and anaphylaxis (OR 14.3, 95% CI: 1.8-114, P = 0.01). Conclusion: More than half of the patients were able to maintain the targeted milk dose in their daily diet. Baseline milk sIgE level and reactivity during the early treatment stage strongly predicted the long-term outcome and safety of milk OIT.
  • Cebrián-Piqueras, M. A.; Filyushkina, A.; Johnson, D. N.; Lo, V. B.; López-Rodríguez, M. D.; March, H.; Oteros-Rozas, E.; Peppler-Lisbach, C.; Quintas-Soriano, C.; Raymond, C. M.; Ruiz-Mallén, I.; van Riper, C. J.; Zinngrebe, Y.; Plieninger, T. (2020)
    Context Most protected areas are managed based on objectives related to scientific ecological knowledge of species and ecosystems. However, a core principle of sustainability science is that understanding and including local ecological knowledge, perceptions of ecosystem service provision and landscape vulnerability will improve sustainability and resilience of social-ecological systems. Here, we take up these assumptions in the context of protected areas to provide insight on the effectiveness of nature protection goals, particularly in highly human-influenced landscapes. Objectives We examined how residents' ecological knowledge systems, comprised of both local and scientific, mediated the relationship between their characteristics and a set of variables that represented perceptions of ecosystem services, landscape change, human-nature relationships, and impacts. Methods We administered a face-to-face survey to local residents in the Sierra de Guadarrama protected areas, Spain. We used bi- and multi-variate analysis, including partial least squares path modeling to test our hypotheses. Results Ecological knowledge systems were highly correlated and were instrumental in predicting perceptions of water-related ecosystem services, landscape change, increasing outdoors activities, and human-nature relationships. Engagement with nature, socio-demographics, trip characteristics, and a rural-urban gradient explained a high degree of variation in ecological knowledge. Bundles of perceived ecosystem services and impacts, in relation to ecological knowledge, emerged as social representation on how residents relate to, understand, and perceive landscapes. Conclusions Our findings provide insight into the interactions between ecological knowledge systems and their role in shaping perceptions of local communities about protected areas. These results are expected to inform protected area management and landscape sustainability.
  • Kaltiainen, Janne; Lipponen, Jukka; Fugate, Mel; Vakola, Maria (2020)
    In this longitudinal field study, we examine reciprocal relationships between within-person changes in work engagement and cognitive appraisals of change (threat and challenge) across an organizational merger. Examination of these cyclical relationships provides a more accurate understanding of the complexity of employees' experience of change and a new test of spiraling work engagement and cognitive appraisals. Latent change score modeling is used to analyze 3 waves of longitudinal survey data (N = 623). Our findings showed that engagement mitigated threat appraisals and enhanced challenge appraisals through pre- and postmerger phases. A reciprocal relationship between threat appraisal and engagement was also observed, such that threat fueled decreases in engagement throughout the merger. Challenge appraisal was associated with enhanced work engagement during the first merger phase. This examination advocates managers of change to foster employees' work engagement already prior to change endeavors, along with mitigating threat appraisals throughout organizational change events. Fostering positive challenge appraisals appears to be particularly important for employees' work engagement during times of major changes. Findings suggest that upward spiral of work engagement, as postulated on the basis of the broaden-and-build theory, may be more likely to occur through engagement mitigating negative cognitions (threat) than promoting positive cognitions (challenge).
  • Kulmala, Petri; Pelkonen, Anna S.; Kuitunen, Mikael; Paassilta, Marita; Remes, Sami; Schultz, Rudiger; Dunder, Teija; Turunen, Sami; Makela, Mika J. (2018)
    Aim: This study investigated oral immunotherapy (OIT) for children aged 6-18 years with wheat allergies. Methods: Well-cooked wheat spaghetti was given to 100 children with wheat allergies every day for 17 weeks, increasing from 0.3 to 2000 mg of wheat protein, followed by three- and nine-month maintenance phases. Blood samples were taken before therapy and at follow-up visits. The study was carried out in 2009-2015 in four Finnish paediatric allergology units. Results: The children (67% male) had a mean age of 11.6 years (range 6.1-18.6), and 57 were using wheat daily 16 months after the initiation of therapy. Allergic symptoms occurred in 94/100 children: mild in 34, moderate in 36 and severe in 24. Specific immunoglobulin E (IgE) for omega-5-gliadin was significantly higher in patients who did not reach the target dose and were related to the intensity of reactions. Conclusion: The majority (57%) of children with wheat allergies could use wheat in their daily diet 16 months after the initiation of OIT, but 94/100 had adverse reactions and 60 were moderate or severe. Specific IgE to omega-5-gliadin may provide a biomarker for how much wheat can be tolerated and the intensity of the reactions to immunotherapy.