| 1. |
- Ho, Joshua W. K., et al.
(författare)
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Comparative analysis of metazoan chromatin organization
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 512:7515, s. 449-U507
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Tidskriftsartikel (refereegranskat)abstract
- Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms(1-3). Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths(4,5). To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.
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| 2. |
- Sartono, Erliyani, et al.
(författare)
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Oral Polio Vaccine Influences the Immune Response to BCG Vaccination. A Natural Experiment
- 2010
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Oral polio vaccine (OPV) is recommended to be given at birth together with BCG vaccine. While we were conducting two trials including low-birth-weight (LBW) and normal-birth-weight (NBW) infants in Guinea-Bissau, OPV was not available during some periods and therefore some infants did not receive OPV at birth, but only BCG. We investigated the effect of OPV given simultaneously with BCG at birth on the immune response to BCG vaccine. Methods and Findings: We compared the in vitro and the in vivo response to PPD in the infants who received OPV and BCG with that of infants who received BCG only. At age 6 weeks, the in vitro cytokine response to purified protein derivate (PPD) of M. Tuberculosis was reduced in LBW and NBW infants who had received OPV with BCG. In a pooled analysis receiving OPV with BCG at birth was associated with significantly lower IL-13 (p = 0.041) and IFN-gamma (p = 0.004) and a tendency for lower IL-10 (p = 0.054) in response to PPD. Furthermore, OPV was associated with reduced in vivo response to PPD at age 2 months, the prevalence ratio (PR) of having a PPD reaction being 0.75 (0.58-0.98), p = 0.033, and with a tendency for reduced likelihood of having a BCG scar (0.95 (0.91-1.00), p = 0.057)). Among children with a scar, OPV was associated with reduced scar size, the regression coefficient being -0.24 (-0.43-0.05), p = 0.012. Conclusions: This study is the first to address the consequences for the immune response to BCG of simultaneous administration with OPV. Worryingly, the results indicate that the common practice in low-income countries of administering OPV together with BCG at birth may down-regulate the response to BCG vaccine.
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| 3. |
- Mussbacher, G., et al.
(författare)
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The Relevance of Model-Driven Engineering Thirty years from Now
- 2014
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. ; 8767, s. 183-200
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Tidskriftsartikel (refereegranskat)abstract
- Although model-driven engineering (MDE) is now an established approach for developing complex software systems, it has not been universally adopted by the software industry. In order to better understand the reasons for this, as well as to identify future opportunities for MDE, we carried out a week-long design thinking experiment with 15 MDE experts. Participants were facilitated to identify the biggest problems with current MDE technologies, to identify grand challenges for society in the near future, and to identify ways that MDE could help to address these challenges. The outcome is a reflection of the current strengths of MDE, an outlook of the most pressing challenges for society at large over the next three decades, and an analysis of key future MDE research opportunities.
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| 4. |
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| 5. |
- Sundberg, Cecilia, et al.
(författare)
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Characterisation of source-separated household waste intended for composting
- 2011
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Ingår i: Bioresource Technology. - : Elsevier. - 0960-8524 .- 1873-2976. ; 102:3, s. 2859-2867
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale composting of source-separated household waste has expanded in recent years in the Nordic countries. One problem can be low pH at the start of the process. Incoming biowaste at four composting plants was characterised chemically, physically and microbiologically. The pH of food waste ranged from 4.7 to 6.1 and organic acid concentration from 24 to 81mmolkg -1. The bacterial diversity in the waste samples was high, with all samples dominated by Gammaproteobacteria, particularly Pseudomonas and Enterobacteria (Escherichia coli, Klebsiella, Enterobacter). Lactic acid bacteria were also numerically important and are known to negatively affect the composting process because the lactic acid they produce lowers the pH, inhibiting other bacteria. The bacterial groups needed for efficient composting, i.e. Bacillales and Actinobacteria, were present in appreciable amounts. The results indicated that start-up problems in the composting process can be prevented by recycling bulk material and compost.
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| 6. |
- Sundberg, Cecilia, et al.
(författare)
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Effects of pH and microbial composition on odour in food waste composting
- 2013
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Ingår i: Waste Management. - : Elsevier. - 0956-053X .- 1879-2456. ; 33:1, s. 204-211
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Tidskriftsartikel (refereegranskat)abstract
- A major problem for composting plants is odour emission. Slow decomposition during prolonged low-pH conditions is a frequent process problem in food waste composting. The aim was to investigate correlations between low pH, odour and microbial composition during food waste composting. Samples from laboratory composting experiments and two large scale composting plants were analysed for odour by olfactometry, as well as physico-chemical and microbial composition. There was large variation in odour, and samples clustered in two groups, one with low odour and high pH (above 6.5), the other with high odour and low pH (below 6.0). The low-odour samples were significantly drier, had lower nitrate and TVOC concentrations and no detectable organic acids. Samples of both groups were dominated by Bacillales or Actinobacteria, organisms which are often indicative of well-functioning composting processes, but the high-odour group DNA sequences were similar to those of anaerobic or facultatively anaerobic species, not to typical thermophilic composting species. High-odour samples also contained Lactobacteria and Clostridia, known to produce odorous substances. A proposed odour reduction strategy is to rapidly overcome the low pH phase, through high initial aeration rates and the use of additives such as recycled compost.
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