| 26. |
- Gilbert, F., et al.
(författare)
-
Sediment reworking by the burrowing polychaete Hediste diversicolor modulated by environmental and biological factors across the temperate North Atlantic. A tribute to Gaston Desrosiers
- 2021
-
Ingår i: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 541
-
Tidskriftsartikel (refereegranskat)abstract
- Particle mixing and irrigation of the seabed by benthic fauna (bioturbation) have major impacts on ecosystem functions such as remineralization of organic matter and sediment-water exchange. As a tribute to Prof. Gaston Desrosiers by the Nereis Park association, eighteen laboratories carried out a collaborative experiment to acquire a global snapshot of particle reworking by the polychaete Hediste diversicolor at 16 sites surrounding the Northern Atlantic. Organisms and soft sediments were collected during May - July at different geographical locations and, using a common laboratory protocol, particulate fluorescent tracers (`luminophores') were used to quantify particle transport over a 10-day period. Particle mixing was quantified using the maximum penetration depth of tracers (MPD), particle diffusive coefficients (D-b), and non-local transport coefficients (r). Non-local coefficients (reflecting centimeter scale transport steps) ranged from 0.4 to 15 yr(-1), and were not correlated across sites with any measured biological (biomass, biovolume) or environmental parameters (temperature, grain size, organic matter). Maximum penetration depths (MPD) averaged similar to 10.7 cm (6.5-14.5 cm), and were similar to the global average bioturbation depth inferred from short-lived radiochemical tracers. MPD was also not correlated with measures of size (individual biomass), but increased with grain size and decreased with temperature. Bio-diffusion (D-b) correlated inversely with individual biomass (size) and directly with temperature over the environmental range (Q(10) similar to 1.7; 5-21 degrees C). The transport data were comparable in magnitude to rates reported for localized H. diversicolor populations of similar size, and confirmed some but not all correlations between sediment reworking and biological and environmental variables found in previous studies. The results imply that measures of particle reworking activities of a species from a single location can be generally extrapolated to different populations at similar conditions.
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| 27. |
- Hsiao, E. Y., et al.
(författare)
-
Carnegie Supernova Project-II : The Near-infrared Spectroscopy Program
- 2019
-
Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 131:995
-
Tidskriftsartikel (refereegranskat)abstract
- Shifting the focus of Type Ia supernova (SN Ia) cosmology to the near infrared (NIR) is a promising way to significantly reduce the systematic errors, as the strategy minimizes our reliance on the empirical width-luminosity relation and uncertain dust laws. Observations in the NIR are also crucial for our understanding of the origins and evolution of these events, further improving their cosmological utility. Any future experiments in the rest-frame NIR will require knowledge of the SN Ia NIR spectroscopic diversity, which is currently based on a small sample of observed spectra. Along with the accompanying paper, Phillips et al., we introduce the Carnegie Supernova Project-II (CSP-II), to follow-up nearby SNe Ia in both the optical and the NIR. In particular, this paper focuses on the CSP-II NIR spectroscopy program, describing the survey strategy, instrumental setups, data reduction, sample characteristics, and future analyses on the data set. In collaboration with the Harvard-Smithsonian Center for Astrophysics (CfA) Supernova Group, we obtained 661 NIR spectra of 157 SNe Ia. Within this sample, 451 NIR spectra of 90 SNe Ia have corresponding CSP-II follow-up light curves. Such a sample will allow detailed studies of the NIR spectroscopic properties of SNe Ia, providing a different perspective on the properties of the unburned material; the radioactive and stable nickel produced; progenitor magnetic fields; and searches for possible signatures of companion stars.
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| 28. |
- Ramonet, M., et al.
(författare)
-
The fingerprint of the summer 2018 drought in Europe on ground-based atmospheric CO 2 measurements : Atmospheric CO 2 anomaly
- 2020
-
Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 375:1810
-
Tidskriftsartikel (refereegranskat)abstract
- During the summer of 2018, a widespread drought developed over Northern and Central Europe. The increase in temperature and the reduction of soil moisture have influenced carbon dioxide (CO 2) exchange between the atmosphere and terrestrial ecosystems in various ways, such as a reduction of photosynthesis, changes in ecosystem respiration, or allowing more frequent fires. In this study, we characterize the resulting perturbation of the atmospheric CO 2 seasonal cycles. 2018 has a good coverage of European regions affected by drought, allowing the investigation of how ecosystem flux anomalies impacted spatial CO 2 gradients between stations. This density of stations is unprecedented compared to previous drought events in 2003 and 2015, particularly thanks to the deployment of the Integrated Carbon Observation System (ICOS) network of atmospheric greenhouse gas monitoring stations in recent years. Seasonal CO 2 cycles from 48 European stations were available for 2017 and 2018. Earlier data were retrieved for comparison from international databases or national networks. Here, we show that the usual summer minimum in CO 2 due to the surface carbon uptake was reduced by 1.4 ppm in 2018 for the 10 stations located in the area most affected by the temperature anomaly, mostly in Northern Europe. Notwithstanding, the CO 2 transition phases before and after July were slower in 2018 compared to 2017, suggesting an extension of the growing season, with either continued CO 2 uptake by photosynthesis and/or a reduction in respiration driven by the depletion of substrate for respiration inherited from the previous months due to the drought. For stations with sufficiently long time series, the CO 2 anomaly observed in 2018 was compared to previous European droughts in 2003 and 2015. Considering the areas most affected by the temperature anomalies, we found a higher CO 2 anomaly in 2003 (+3 ppm averaged over 4 sites), and a smaller anomaly in 2015 (+1 ppm averaged over 11 sites) compared to 2018. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
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| 29. |
- Kumar, Nitin, et al.
(författare)
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Adaptation of host transmission cycle during Clostridium difficile speciation
- 2019
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:9, s. 1315-1320
-
Tidskriftsartikel (refereegranskat)abstract
- Bacterial speciation is a fundamental evolutionary process characterized by diverging genotypic and phenotypic properties. However, the selective forces that affect genetic adaptations and how they relate to the biological changes that underpin the formation of a new bacterial species remain poorly understood. Here, we show that the spore-forming, healthcare-associated enteropathogen Clostridium difficile is actively undergoing speciation. Through large-scale genomic analysis of 906 strains, we demonstrate that the ongoing speciation process is linked to positive selection on core genes in the newly forming species that are involved in sporulation and the metabolism of simple dietary sugars. Functional validation shows that the new C. difficile produces spores that are more resistant and have increased sporulation and host colonization capacity when glucose or fructose is available for metabolism. Thus, we report the formation of an emerging C. difficile species, selected for metabolizing simple dietary sugars and producing high levels of resistant spores, that is adapted for healthcare-mediated transmission.
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| 30. |
- Pessi, T., et al.
(författare)
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A characterization of ASAS-SN core-collapse supernova environments with VLT+MUSE I. Sample selection, analysis of local environments, and correlations with light curve properties
- 2023
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 677
-
Tidskriftsartikel (refereegranskat)abstract
- Context. The analysis of core-collapse supernova (CCSN) environments can provide important information on the life cycle of massive stars and constrain the progenitor properties of these powerful explosions. The MUSE instrument at the Very Large Telescope (VLT) enables detailed local environment constraints of the progenitors of large samples of CCSNe. Using a homogeneous SN sample from the All-Sky Automated Survey for Supernovae (ASAS-SN) survey, an untargeted and spectroscopically complete transient survey, has enabled us to perform a minimally biased statistical analysis of CCSN environments.Aims. We analyze 111 galaxies observed by MUSE that hosted 112 CCSNe – 78 II, nine IIn, seven IIb, four Ic, seven Ib, three Ibn, two Ic-BL, one ambiguous Ibc, and one superluminous SN – detected or discovered by the ASAS-SN survey between 2014 and 2018. The majority of the galaxies were observed by the All-weather MUse Supernova Integral field Nearby Galaxies (AMUSING) survey. Here we analyze the immediate environment around the SN locations and compare the properties between the different CCSN types and their light curves.Methods. We used stellar population synthesis and spectral fitting techniques to derive physical parameters for all H II regions detected within each galaxy, including the star formation rate (SFR), Hα equivalent width (EW), oxygen abundance, and extinction.Results. We found that stripped-envelope supernovae (SESNe) occur in environments with a higher median SFR, Hα EW, and oxygen abundances than SNe II and SNe IIn/Ibn. Most of the distributions have no statistically significant differences, except between oxygen abundance distributions of SESNe and SNe II, and between Hα EW distributions of SESNe and SNe II. The distributions of SNe II and IIn are very similar, indicating that these events explode in similar environments. For the SESNe, SNe Ic have higher median SFRs, Hα EWs, and oxygen abundances than SNe Ib. SNe IIb have environments with similar SFRs and Hα EWs to SNe Ib, and similar oxygen abundances to SNe Ic. We also show that the postmaximum decline rate, s, of SNe II correlates with the Hα EW, and that the luminosity and the Δm15 parameter of SESNe correlate with the oxygen abundance, Hα EW, and SFR at their environments. This suggests a connection between the explosion mechanisms of these events to their environment properties.
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| 31. |
- Benjamin, Daniel J., et al.
(författare)
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Redefine statistical significance
- 2018
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Ingår i: Nature Human Behaviour. - : Nature Research (part of Springer Nature). - 2397-3374. ; 2:1, s. 6-10
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 32. |
- Borodina, I., et al.
(författare)
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Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine
- 2015
-
Ingår i: Metabolic Engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 27, s. 57-64
-
Tidskriftsartikel (refereegranskat)abstract
- Microbial fermentation of renewable feedstocks into plastic monomers can decrease our fossil dependence and reduce global CO2 emissions. 3-Hydroxypropionic acid (3HP) is a potential chemical building block for sustainable production of superabsorbent polymers and acrylic plastics. With the objective of developing Saccharolnyces cerevisiae as an efficient cell factory for high-level production of 3HP, we identified the beta-alanine biosynthetic route as the most economically attractive according to the metabolic modeling. We engineered and optimized a synthetic pathway for de novo biosynthesis of beta-alanine and its subsequent conversion into 3HP using a novel beta-alanine-pyruvate aminotransferase discovered in Bacillus cereus. The final strain produced 3HP at a titer of 13.7 +/- 0.3 g L-1 with a 0.14 +/- 0.0 C-mol C-mol(-1) yield on glucose in 80 h in controlled fed-batch fermentation in mineral medium at pH 5, and this work therefore lays the basis for developing a process for biological 3HP production.
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| 33. |
- Breznau, Nate, et al.
(författare)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
-
Tidskriftsartikel (refereegranskat)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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| 34. |
- Chatterjee, S., et al.
(författare)
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Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers
- 2019
-
Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 19:21-22
-
Tidskriftsartikel (refereegranskat)abstract
- While aberrant protein glycosylation is a recognized characteristic of human cancers, advances in glycoanalytics continue to discover new associations between glycoproteins and tumorigenesis. This glycomics‐centric study investigates a possible link between protein paucimannosylation, an under‐studied class of human N‐glycosylation [Man1‐3GlcNAc2Fuc0‐1], and cancer. The paucimannosidic glycans (PMGs) of 34 cancer cell lines and 133 tissue samples spanning 11 cancer types and matching non‐cancerous specimens are profiled from 467 published and unpublished PGC‐LC‐MS/MS N‐glycome datasets collected over a decade. PMGs, particularly Man2‐3GlcNAc2Fuc1, are prominent features of 29 cancer cell lines, but the PMG level varies dramatically across and within the cancer types (1.0–50.2%). Analyses of paired (tumor/non‐tumor) and stage‐stratified tissues demonstrate that PMGs are significantly enriched in tumor tissues from several cancer types including liver cancer (p = 0.0033) and colorectal cancer (p = 0.0017) and is elevated as a result of prostate cancer and chronic lymphocytic leukaemia progression (p < 0.05). Surface expression of paucimannosidic epitopes is demonstrated on human glioblastoma cells using immunofluorescence while biosynthetic involvement of N‐acetyl‐β‐hexosaminidase is indicated by quantitative proteomics. This intriguing association between protein paucimannosylation and human cancers warrants further exploration to detail the biosynthesis, cellular location(s), protein carriers, and functions of paucimannosylation in tumorigenesis and metastasis.
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| 35. |
- Damm, S., et al.
(författare)
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Formation of ferroelectrically defined Ag nanoarray patterns
- 2014
-
Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE - International Society for Optical Engineering. - 9781628410747
-
Konferensbidrag (refereegranskat)abstract
- In order to produce the most effective Ag nanoarrays for plasmon enhanced fluorescence and Raman scattering made using ferroelectric substrates, the optimum conditions for the creation of arrays must be identified. We study here Ag nanopattern arrays formed using ferroelectric lithography based on periodically proton exchanged (PPE) template methods. We examine different conditions in regard to deposition of Ag nanoparticles and analyze the plasmon enhanced signal from the resulting nanoarray. We apply FLIM (fluorescence lifetime imaging) to assess different Ag nanoarray preparation conditions on fluorescence emission from selected fluorphores. In addition, we apply Raman and luminescence spectroscopy with AFM (atomic force microscopy) to study the plasmon enhancement of luminescence and Raman from the Ag nanoarrays.
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| 36. |
- Hjelm, J., et al.
(författare)
-
Conducting polymers containing in-chain metal centers : Electropolymerization of oligothienyl-substituted {M(tpy)(2)} complexes and in situ conductivity studies, M = Os(II), Ru(II)
- 2005
-
Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 44:4, s. 1073-1081
-
Tidskriftsartikel (refereegranskat)abstract
- The electropolymerization of a series of Ru and Os bis-terpyridine complexes that form rodlike polymers with bithienyl, quaterthienyl, or hexathienyl bridges has been studied. Absorption spectroscopy, scanning electron microscopy, and cyclic voltammetry have been used to characterize the monomers and resulting polymer films. The absolute dc conductivity of the quaterthienyl-bridged {Ru(tpy)(2)} and {Os(tpy)(2)} polymers is unusually large and independent of the identity of the metal center at 1.6 x 10(-3) S cm(-1). The maximum conductivity occurs at the formal potential of each redox process, which typically is observed for systems where redox conduction is the dominant charge transport mechanism. Significantly, the dc conductivity of the metal-based redox couple observed in these polymers is 2 orders of magnitude higher than that of a comparable nonconjugated system.
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| 37. |
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| 38. |
- Kildegaard, K. R., et al.
(författare)
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Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway
- 2016
-
Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 15:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: In the future, oil-and gas-derived polymers may be replaced with bio-based polymers, produced from renewable feedstocks using engineered cell factories. Acrylic acid and acrylic esters with an estimated world annual production of approximately 6 million tons by 2017 can be derived from 3-hydroxypropionic acid (3HP), which can be produced by microbial fermentation. For an economically viable process 3HP must be produced at high titer, rate and yield and preferably at low pH to minimize downstream processing costs. Results: Here we describe the metabolic engineering of baker's yeast Saccharomyces cerevisiae for biosynthesis of 3HP via a malonyl-CoA reductase (MCR)-dependent pathway. Integration of multiple copies of MCR from Chloroflexus aurantiacus and of phosphorylation-deficient acetyl-CoA carboxylase ACC1 genes into the genome of yeast increased 3HP titer fivefold in comparison with single integration. Furthermore we optimized the supply of acetyl-CoA by overexpressing native pyruvate decarboxylase PDC1, aldehyde dehydrogenase ALD6, and acetyl-CoA synthase from Salmonella enterica SEacsL641P. Finally we engineered the cofactor specificity of the glyceraldehyde-3-phosphate dehydrogenase to increase the intracellular production of NADPH at the expense of NADH and thus improve 3HP production and reduce formation of glycerol as by-product. The final strain produced 9.8 +/- 0.4 g L-1 3HP with a yield of 13 % C-mol C-mol(-1) glucose after 100 h in carbon-limited fed-batch cultivation at pH 5. The 3HP-producing strain was characterized by C-13 metabolic flux analysis and by transcriptome analysis, which revealed some unexpected consequences of the undertaken metabolic engineering strategy, and based on this data, future metabolic engineering directions are proposed. Conclusions: In this study, S. cerevisiae was engineered for high-level production of 3HP by increasing the copy numbers of biosynthetic genes and improving flux towards precursors and redox cofactors. This strain represents a good platform for further optimization of 3HP production and hence an important step towards potential commercial bio-based production of 3HP.
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| 39. |
- Maury, J., et al.
(författare)
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EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
- 2016
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 11:3
-
Tidskriftsartikel (refereegranskat)abstract
- Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the beta-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L-1 of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity.
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| 40. |
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| 41. |
- Angelbratt, Jon, 1981, et al.
(författare)
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Carbon monoxide (CO) and ethane (C2H6) trends from ground-based solar FTIR measurements at six European stations, comparison and sensitivity analysis with the EMEP model
- 2011
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 11:17, s. 9253-9269
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Tidskriftsartikel (refereegranskat)abstract
- Trends in the CO and C(2)H(6) partial columns (similar to 0-15 km) have been estimated from four European ground-based solar FTIR (Fourier Transform InfraRed) stations for the 1996-2006 time period. The CO trends from the four stations Jungfraujoch, Zugspitze, Harestua and Kiruna have been estimated to -0.45 +/- 0.16%yr(-1), -1.00 +/- 0.24%yr(-1), -0.62 +/- 0.19%yr(-1) and -0.61 +/- 0.16%yr(-1), respectively. The corresponding trends for C(2)H(6) are -1.51 +/- 0.23%yr(-1), -2.11 +/- 0.30%yr(-1), -1.09 +/- 0.25%yr(-1) and -1.14 +/- 0.18%yr(-1). All trends are presented with their 2-sigma confidence intervals. To find possible reasons for the CO trends, the global-scale EMEP MSC-W chemical transport model has been used in a series of sensitivity scenarios. It is shown that the trends are consistent with the combination of a 20% decrease in the anthropogenic CO emissions seen in Europe and North America during the 1996-2006 period and a 20% increase in the anthropogenic CO emissions in East Asia, during the same time period. The possible impacts of CH(4) and biogenic volatile organic compounds (BVOCs) are also considered. The European and global-scale EMEP models have been evaluated against the measured CO and C(2)H(6) partial columns from Jungfraujoch, Zugspitze, Bremen, Harestua, Kiruna and Ny-Alesund. The European model reproduces, on average the measurements at the different sites fairly well and within 10-22% deviation for CO and 14-31% deviation for C(2)H(6). Their seasonal amplitude is captured within 6-35% and 9-124% for CO and C(2)H(6), respectively. However, 61-98% of the CO and C(2)H(6) partial columns in the European model are shown to arise from the boundary conditions, making the global-scale model a more suitable alternative when modeling these two species. In the evaluation of the global model the average partial columns for 2006 are shown to be within 1-9% and 37-50% of the measurements for CO and C(2)H(6), respectively. The global model sensitivity for assumptions made in this paper is also analyzed.
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| 42. |
- Didion, JP, et al.
(författare)
-
R2d2 Drives Selfish Sweeps in the House Mouse
- 2016
-
Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 1537-1719 .- 0737-4038. ; 33:6, s. 1381-1395
-
Tidskriftsartikel (refereegranskat)
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| 43. |
- Huerta, E. A., et al.
(författare)
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Enabling real-time multi-messenger astrophysics discoveries with deep learning
- 2019
-
Ingår i: Nature reviews physics. - : Springer Science and Business Media LLC. - 2522-5820. ; 1:10, s. 600-608
-
Forskningsöversikt (refereegranskat)abstract
- Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos. In this Expert Recommendation, we review the key challenges of real-time observations of gravitational wave sources and their electromagnetic and astroparticle counterparts, and make a number of recommendations to maximize their potential for scientific discovery. These recommendations refer to the design of scalable and computationally efficient machine learning algorithms; the cyber-infrastructure to numerically simulate astrophysical sources, and to process and interpret multi-messenger astrophysics data; the management of gravitational wave detections to trigger real-time alerts for electromagnetic and astroparticle follow-ups; a vision to harness future developments of machine learning and cyber-infrastructure resources to cope with the big-data requirements; and the need to build a community of experts to realize the goals of multi-messenger astrophysics. A group of experts suggests ways in which deep learning can be used to enhance the potential for discovery in multi-messenger astrophysics.
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| 44. |
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| 45. |
- Jandrić, Petar, et al.
(författare)
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Teaching in the Age of Covid-19
- 2020
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Ingår i: Postdigital Science and Education. - : Springer Science and Business Media LLC. - 2524-4868 .- 2524-485X. ; 2:3, s. 1069-1230
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- A collection of 84 author's testimonies and workspace photographs between 18 March and 5 May 2020.
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| 46. |
- Jandrić, Petar, et al.
(författare)
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Teaching in the Age of Covid-19—1 Year Later
- 2021
-
Ingår i: Postdigital Science and Education. - : Springer. - 2524-485X .- 2524-4868. ; 3:3, s. 1073-1223
-
Tidskriftsartikel (refereegranskat)
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| 47. |
- Jensen, N. B., et al.
(författare)
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EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae
- 2014
-
Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 14:2, s. 238-248
-
Tidskriftsartikel (refereegranskat)abstract
- Development of strains for efficient production of chemicals and pharmaceuticals requires multiple rounds of genetic engineering. In this study, we describe construction and characterization of EasyClone vector set for baker's yeast Saccharomyces cerevisiae, which enables simultaneous expression of multiple genes with an option of recycling selection markers. The vectors combine the advantage of efficient uracil excision reaction-based cloning and Cre-LoxP-mediated marker recycling system. The episomal and integrative vector sets were tested by inserting genes encoding cyan, yellow, and red fluorescent proteins into separate vectors and analyzing for co-expression of proteins by flow cytometry. Cells expressing genes encoding for the three fluorescent proteins from three integrations exhibited a much higher level of simultaneous expression than cells producing fluorescent proteins encoded on episomal plasmids, where correspondingly 95% and 6% of the cells were within a fluorescence interval of Log(10) mean +/- 15% for all three colors. We demonstrate that selective markers can be simultaneously removed using Cre-mediated recombination and all the integrated heterologous genes remain in the chromosome and show unchanged expression levels. Hence, this system is suitable for metabolic engineering in yeast where multiple rounds of gene introduction and marker recycling can be carried out.
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| 48. |
- Kildegaard, Kanchana R., et al.
(författare)
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Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance
- 2014
-
Ingår i: Metabolic engineering. - : Elsevier BV. - 1096-7176 .- 1096-7184. ; 26, s. 57-66
-
Tidskriftsartikel (refereegranskat)abstract
- Biologically produced 3-hydroxypropionic acid (3HP) is a potential source for sustainable acrylates and can also find direct use as monomer in the production of biodegradable polymers. For industrial scale production there is a need for robust cell factories tolerant to high concentration of 3HP, preferably at low pH. Through adaptive laboratory evolution we selected S. cerevisiae strains with improved tolerance to 3HP at pH 3.5. Genome sequencing followed by functional analysis identified the causal mutation in SFA1 gene encoding S-(hyclroxymerhyl)glutathione dehydrogenase. Based on our findings, we propose that 3HP toxicity is mediated by 3-hydroxypropionic aldehyde (reuterin ) and that glutathione-dependent reactions are used for reuterin detoxification. The identified molecular response to 3HP and reuterin may well be a general mechanism for handling resistance to organic acid and aldehydes by living cells. (C) 2014 International Metabolic Engineering Society Published by Elsevier Inc. On behalf of International Metabolic Engineering Society. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/)
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| 49. |
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| 50. |
- Ritter, C. D., et al.
(författare)
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Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding
- 2021
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 82, s. 746-760
-
Tidskriftsartikel (refereegranskat)abstract
- Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (varzeas) or by unfertile black waters (igapos), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.
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