| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
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| 4. |
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| 5. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 7. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 8. |
- 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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| 9. |
- Crowe, S., et al.
(författare)
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Near-infrared observations of outflows and young stellar objects in the massive star-forming region AFGL 5180
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 682
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Tidskriftsartikel (refereegranskat)abstract
- Context. Massive stars play important roles throughout the universe; however, their formation remains poorly understood. Observations of jets and outflows in high-mass star-forming regions, as well as surveys of young stellar object (YSO) content, can help test theoretical models of massive star formation. Aims. We aim at characterizing the massive star-forming region AFGL 5180 in the near-infrared (NIR), identifying outflows and relating these to sub-mm/mm sources, as well as surveying the overall YSO surface number density to compare to massive star formation models. Methods. Broad- and narrow-band imaging of AFGL 5180 was made in the NIR with the Large Binocular Telescope, in both seeing-limited (~0.5′) and high angular resolution (~0.09′) Adaptive Optics (AO) modes, as well as with the Hubble Space Telescope. Archival continuum data from the Atacama Millimeter/Submillimeter Array (ALMA) was also utilized. Results. At least 40 jet knots were identified via NIR emission from H2 and [FeII] tracing shocked gas. Bright jet knots outflowing from the central most massive protostar, S4 (estimated mass ~11 M⊙, via SED fitting), are detected towards the east of the source and are resolved in fine detail with the AO imaging. Additional knots are distributed throughout the field, likely indicating the presence of multiple driving sources. Sub-millimeter sources detected by ALMA are shown to be grouped in two main complexes, AFGL 5180 M and a small cluster ~15′ (0.15 pc in projection) to the south, AFGL 5180 S. From our NIR continuum images we identify YSO candidates down to masses of ~0.1 M⊙. Combined with the sub-mm sources, this yields a surface number density of such YSOs of N* ~ 103pc-2 within a projected radius of about 0.1 pc. Such a value is similar to those predicted by models of both core accretion from a turbulent clump environment and competitive accretion. The radial profile of N* is relatively flat on scales out to 0.2 pc, with only modest enhancement around the massive protostar inside 0.05 pc, which provides additional constraints on these massive star formation models. Conclusions. This study demonstrates the utility of high-resolution NIR imaging, in particular with AO, for detecting outflow activity and YSOs in distant regions. The presented images reveal the complex morphology of outflow-shocked gas within the large-scale bipolar flow of a massive protostar, as well as clear evidence for several other outflow driving sources in the region. Finally, this work presents a novel approach to compare the observed YSO surface number density from our study against different models of massive star formation.
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| 10. |
- 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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| 11. |
- Belov, Vladimir, et al.
(författare)
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Multi-site benchmark classification of major depressive disorder using machine learning on cortical and subcortical measures
- 2024
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Ingår i: Scientific Reports. - : NATURE PORTFOLIO. - 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Machine learning (ML) techniques have gained popularity in the neuroimaging field due to their potential for classifying neuropsychiatric disorders. However, the diagnostic predictive power of the existing algorithms has been limited by small sample sizes, lack of representativeness, data leakage, and/or overfitting. Here, we overcome these limitations with the largest multi-site sample size to date (N = 5365) to provide a generalizable ML classification benchmark of major depressive disorder (MDD) using shallow linear and non-linear models. Leveraging brain measures from standardized ENIGMA analysis pipelines in FreeSurfer, we were able to classify MDD versus healthy controls (HC) with a balanced accuracy of around 62%. But after harmonizing the data, e.g., using ComBat, the balanced accuracy dropped to approximately 52%. Accuracy results close to random chance levels were also observed in stratified groups according to age of onset, antidepressant use, number of episodes and sex. Future studies incorporating higher dimensional brain imaging/phenotype features, and/or using more advanced machine and deep learning methods may yield more encouraging prospects.
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| 12. |
- Fedriani, Rubén, 1991, et al.
(författare)
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The sharpest view on the high-mass star-forming region S255IR: Near infrared adaptive optics imaging of the outbursting source NIRS3
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 676
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Tidskriftsartikel (refereegranskat)abstract
- Context. Massive stars have an impact on their surroundings from early in their formation until the end of their lives. However, very little is known about their formation. Episodic accretion may play a crucial role in the process, but only a handful of observations have reported such events occurring in massive protostars. Aims. We aim to investigate the outburst event from the high-mass star-forming region S255IR where the protostar NIRS3 recently underwent an accretion outburst. We follow the evolution of this source both in photometry and morphology of its surroundings. Methods. We performed near infrared adaptive optics observations on the S255IR central region using the Large Binocular Telescope in the Ks broadband as well as the H2 and Brγ narrow-band filters with an angular resolution of 07.06, close to the diffraction limit. Results. We discovered a new near infrared knot north-east of NIRS3 that we interpret as a jet knot that was ejected during the last accretion outburst and observed in the radio regime as part of a follow-up after the outburst. We measured a mean tangential velocity for this knot of 450 ± 50 km s1. We analysed the continuum-subtracted images from H2, which traces jet-shocked emission, and Brγ, which traces scattered light from a combination of accretion activity and UV radiation from the central massive protostar. We observed a significant decrease in flux at the location of NIRS3, with K = 13.48 mag being the absolute minimum in the historic series. Conclusions. Our observations strongly suggest a scenario where the episodic accretion is followed by an episodic ejection response in the near infrared, as was seen in the earlier radio follow-up. The ~2 μm photometry from the past 30 yr suggests that NIRS3 might have undergone another outburst in the late 1980s, making it the first massive protostar with such evidence observed in the near infrared.
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| 13. |
- 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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| 14. |
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| 15. |
- Diness, Birgitte R., et al.
(författare)
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Effect of high-dose vitamin A supplementation on the immune response to Bacille Calmette-Guerin vaccines
- 2007
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Ingår i: American Journal of Clinical Nutrition. - 1938-3207. ; 86:4, s. 1152-1159
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Tidskriftsartikel (refereegranskat)abstract
- Background: Vitamin A supplementation (VAS) at birth has been associated with decreased mortality in Asia. Bacille Calmette-Guerin (BCG) vaccine is given at birth in tuberculosis-endemic countries. Previous studies suggest that VAS may influence the immune response to vaccines. Objective: Our objective was to examine whether VAS influences the immune response to simultaneously administered BCG vaccine. Design: Within a randomized trial of 50 000 IU vitamin A or placebo Given with BCG vaccine at birth in Guinea-Bissau, 27 10 infants were examined for BCG scar formation and delayed-type hypersensitivity (DTH) to purified protein derivative of Mycobacterium tuberculosis (PPD) at 2 and 6 mo of age. The ex vivo cytokine response to PPD was measured in 607 infants. Results: At 2 mo of age, 39% (43% of the boys and 34% of the girls) responded to PPD. The prevalence ratio of a measurable PPD reaction for VAS compared with placebo recipients was 0.90 (95% CI: 0.80, 1.02) for all infants. 0.81 (95% CI: 0.69, 0.95) for boys, and 1.04 (95% CI: 0.86, 1.26) for girls. At 6 mo of age, 42% of the infants responded to PPD. No difference was observed between VAS and placebo recipients. The prevalence of BCG scar was not affected by VAS. The ex vivo interferon-gamma response to PPD was increased by VAS (means ratio: 1.40: 95% CI: 1.03, 1.91). Conclusions: VAS with BCG vaccination does not appear to interfere with the long-term immune response to BCG. However, VAS temporarily altered the DTH reaction to PPD in boys at 2 mo of age, suggesting sex differences in the immunologic response to VAS Given with BCG. This trial was registered at www.clinicaltrials.gov as #NCT00168597.
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| 16. |
- Gunnarsdottir, Gudrun M., et al.
(författare)
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Validation of the Hospital Frailty Risk Score in older surgical patients : A population-based retrospective cohort study
- 2021
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Ingår i: Acta Anaesthesiologica Scandinavica. - : John Wiley & Sons. - 0001-5172 .- 1399-6576. ; 65:8, s. 1033-1042
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is a need for standardized and cost-effective identification of frailty risk. The objective was to validate the Hospital Frailty Risk Score which utilizes International Classification Diagnoses in a cohort of older surgical patients, assess the score as an independent risk factor for adverse outcomes and compare discrimination properties of the frailty risk score with other risk stratification scores.Methods: Data were analysed from all patients >= 65 years undergoing primary surgical procedures from 2006-2018. Patients were categorized based on the frailty risk score. The primary outcomes were 30-day mortality and 180-day risk of readmission.Results: Of 16 793 patients evaluated, 7480 (45%), 7605 (45%) and 1708 (10%) had a low, intermediate and high risk of frailty. There was a higher incidence of 30-day mortality for individuals with intermediate (2.9%) and high (8.3%) compared with low (1.4%) risk of frailty (P < .001 for both comparisons). Similarly, the hazard of readmission within the first 180 days was higher for intermediate (HR 1.25; 95% CI: 1.16-1.34) and high (HR 1.84; 95% CI: 1.66-2.03) compared with low (HR 1.00, P < .001 for both comparisons) risk of frailty. The hazard of long-term mortality was higher for intermediate (HR 1.70; 95% CI: 1.61-1.80) and high (HR 4.16; 95% CI: 3.84-4.49) compared with low (HR 1.00, P < .001 for both comparisons) risk of frailty. Finally, long length of primary hospitalization occurred for 9.3%, 15.0% and 27.3% of individuals with low, intermediate and high frailty risk (P < .001 for all comparisons). A model including age and ASA classification had the best discrimination for 30-day mortality (AUC 0.862; 95% CI: 0.847-0.877).Conclusion: Our findings suggest that the Hospital Frailty Risk Score might be used to screen older surgical patients for risk of frailty. While only slightly improving prediction of 30-day mortality using the ASA classification, the Hospital Frailty Risk Score can be used to independently classify older patients for the risk of important outcomes using pre-existing readily available electronic data.
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| 17. |
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| 18. |
- Martínez-Sánchez, Noelia, et al.
(författare)
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Hypothalamic AMPK-ER Stress-JNK1 Axis Mediates the Central Actions of Thyroid Hormones on Energy Balance
- 2017
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Ingår i: Cell Metabolism. - Cambridge, MA, United States : Cell Press. - 1550-4131 .- 1932-7420. ; 26:1, s. 212-229.e12
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Tidskriftsartikel (refereegranskat)abstract
- Thyroid hormones (THs) act in the brain to modulate energy balance. We show that central triiodothyronine (T3) regulates de novo lipogenesis in liver and lipid oxidation in brown adipose tissue (BAT) through the parasympathetic (PSNS) and sympathetic nervous system (SNS), respectively. Central T3 promotes hepatic lipogenesis with parallel stimulation of the thermogenic program in BAT. The action of T3 depends on AMP-activated protein kinase (AMPK)-induced regulation of two signaling pathways in the ventromedial nucleus of the hypothalamus (VMH): decreased ceramide-induced endoplasmic reticulum (ER) stress, which promotes BAT thermogenesis, and increased c-Jun N-terminal kinase (JNK) activation, which controls hepatic lipid metabolism. Of note, ablation of AMPKα1 in steroidogenic factor 1 (SF1) neurons of the VMH fully recapitulated the effect of central T3, pointing to this population in mediating the effect of central THs on metabolism. Overall, these findings uncover the underlying pathways through which central T3 modulates peripheral metabolism.
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| 19. |
- 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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| 20. |
- 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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| 21. |
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| 22. |
- Whittle, J., et al.
(författare)
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A taxonomy of tool-related issues affecting the adoption of model-driven engineering
- 2017
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Ingår i: Software and Systems Modeling. - : Springer Science and Business Media LLC. - 1619-1366 .- 1619-1374. ; 16:2, s. 313-331
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Tidskriftsartikel (refereegranskat)abstract
- Although poor tool support is often blamed for the low uptake of model-driven engineering (MDE), recent studies have shown that adoption problems are as likely to be down to social and organizational factors as with tooling issues. This article discusses the impact of tools on MDE adoption and practice and does so while placing tooling within a broader organizational context. The article revisits previous data on MDE use in industry (19 in-depth interviews with MDE practitioners) and reanalyzes that data through the specific lens of MDE tools in an attempt to identify and categorize the issues that users had with the tools they adopted. In addition, the article presents new data: 20 new interviews in two specific companies-and analyzes it through the same lens. A key contribution of the paper is a loose taxonomy of tool-related considerations, based on empirical industry data, which can be used to reflect on the tooling landscape as well as inform future research on MDE tools.
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| 23. |
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