| 1. |
- Ju, Young Seok, et al.
(författare)
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Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.
- 2015
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 25:6, s. 814-824
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.
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| 2. |
- Atsawawaranunt, Kamolphat, et al.
(författare)
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The SISAL database : a global resource to document oxygen and carbon isotope records from speleothems
- 2018
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 10:3, s. 1687-1713
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Tidskriftsartikel (refereegranskat)abstract
- Stable isotope records from speleothems provide information on past climate changes, most particularly information that can be used to reconstruct past changes in precipitation and atmospheric circulation. These records are increasingly being used to provide "out-of-sample" evaluations of isotope-enabled climate models. SISAL (Speleothem Isotope Synthesis and Analysis) is an international working group of the Past Global Changes (PAGES) project. The working group aims to provide a comprehensive compilation of speleothem isotope records for climate reconstruction and model evaluation. The SISAL database contains data for individual speleothems, grouped by cave system. Stable isotopes of oxygen and carbon (delta O-18, delta C-13) measurements are referenced by distance from the top or bottom of the speleothem. Additional tables provide information on dating, including information on the dates used to construct the original age model and sufficient information to assess the quality of each data set and to erect a standardized chronology across different speleothems. The metadata table provides location information, information on the full range of measurements carried out on each speleothem and information on the cave system that is relevant to the interpretation of the records, as well as citations for both publications and archived data.
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| 3. |
- Bliem, Roland, et al.
(författare)
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Adsorption and incorporation of transition metals at the magnetite Fe3O4(001) surface
- 2015
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 92:7
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Tidskriftsartikel (refereegranskat)abstract
- The adsorption of Ni, Co, Mn, Ti, and Zr at the (root 2 x root 2)R45 degrees-reconstructed Fe3O4(001) surface was studied by scanning tunneling microscopy, x-ray and ultraviolet photoelectron spectroscopy, low-energy electron diffraction (LEED), and density functional theory (DFT). Following deposition at room temperature, metals are either adsorbed as isolated adatoms or fill the subsurface cation vacancy sites responsible for the (root 2 x root 2)R45 degrees reconstruction. Both configurations coexist, but the ratio of adatoms to incorporated atoms depends on the metal; Ni prefers the adatom configuration, Co and Mn form adatoms and incorporated atoms in similar numbers, and Ti and Zr are almost fully incorporated. With mild annealing, all adatoms transition to the incorporated cation configuration. At high coverage, the (root 2 x root 2)R45 degrees reconstruction is lifted because all subsurface cation vacancies become occupied with metal atoms, and a (1 x 1) LEED pattern is observed. DFT+U calculations for the extreme cases, Ni and Ti, confirm the energetic preference for incorporation, with calculated oxidation states in good agreement with photoemission experiments. Because the site preference is analogous to bulk ferrite (XFe2O4) compounds, similar behavior is likely to be typical for elements forming a solid solution with Fe3O4.
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| 4. |
- Clear, Tony, et al.
(författare)
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Challenges and recommendations for the design and conduct of global software engineering courses : A systematic review
- 2016
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Ingår i: Proceedings of The 2015 Iticse Conference on Working Group Reports (Iticse-Wgp'15). - New York : ACM Press. - 9781450341462 ; , s. 1-39
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Konferensbidrag (refereegranskat)abstract
- Context: Global Software Engineering (GSE) has become the predominant form of software development for global companies and has given rise to a demand for students trained in GSE. In response, universities are developing courses and curricula around GSE and researchers have begun to disseminate studies of these new approaches.Problem: GSE differs from most other computer science fields, however, in that practice is inseparable from theory. As a result, educators looking to create GSE courses face a daunting task: integrating global practice into the local classroom.Aim: This study aims to ameliorate the very difficult task of teaching GSE by delineating the challenges and providing some recommendations for overcoming them.Method: To meet our aims we pose two research questions ("When teaching GSE to students in Higher Education, what are the (a) challenges, and (b) recommendations for addressing them") and then conduct a systematic literature review (SLR) to determine the answers to these questions. Our SLR follows a carefully designed and validated protocol.Results: We found 82 papers that addressed our research questions. Our findings indicate that in addition to the challenges posed by GSE in general, particular problems arise in educational situations. The majority of these challenges fall into the "global distance" category, though teamwork challenges and people issues (such as trust) also commonly arise. Organizational differences between institutions, differing skill sets between students in different locations, and varying cultural work norms, for example, all operate within educational settings in quite different ways than in professional development teams. Integrating cultural training, conducting teamwork exercises to build trust, and instructor monitoring of team communication are all examples of techniques that have been used successfully by educators according to our review.Conclusion: Despite the severity of the challenges in GSE education, many institutions have successfully developed courses and curricula targeting GSE. Indeed, for each of the challenges we have identified in the literature there are numerous recommendations for overcoming them. Instructors can use the recommendations given in this study as a starting point to running successful GSE courses.
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| 5. |
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| 6. |
- Meyer, H.F., et al.
(författare)
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Overview of physics studies on ASDEX Upgrade
- 2019
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:11
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Forskningsöversikt (refereegranskat)abstract
- The ASDEX Upgrade (AUG) programme, jointly run with the EUROfusion MST1 task force, continues to significantly enhance the physics base of ITER and DEMO. Here, the full tungsten wall is a key asset for extrapolating to future devices. The high overall heating power, flexible heating mix and comprehensive diagnostic set allows studies ranging from mimicking the scrape-off-layer and divertor conditions of ITER and DEMO at high density to fully non-inductive operation (q 95 = 5.5, ) at low density. Higher installed electron cyclotron resonance heating power 6 MW, new diagnostics and improved analysis techniques have further enhanced the capabilities of AUG. Stable high-density H-modes with MW m-1 with fully detached strike-points have been demonstrated. The ballooning instability close to the separatrix has been identified as a potential cause leading to the H-mode density limit and is also found to play an important role for the access to small edge-localized modes (ELMs). Density limit disruptions have been successfully avoided using a path-oriented approach to disruption handling and progress has been made in understanding the dissipation and avoidance of runaway electron beams. ELM suppression with resonant magnetic perturbations is now routinely achieved reaching transiently . This gives new insight into the field penetration physics, in particular with respect to plasma flows. Modelling agrees well with plasma response measurements and a helically localised ballooning structure observed prior to the ELM is evidence for the changed edge stability due to the magnetic perturbations. The impact of 3D perturbations on heat load patterns and fast-ion losses have been further elaborated. Progress has also been made in understanding the ELM cycle itself. Here, new fast measurements of and E r allow for inter ELM transport analysis confirming that E r is dominated by the diamagnetic term even for fast timescales. New analysis techniques allow detailed comparison of the ELM crash and are in good agreement with nonlinear MHD modelling. The observation of accelerated ions during the ELM crash can be seen as evidence for the reconnection during the ELM. As type-I ELMs (even mitigated) are likely not a viable operational regime in DEMO studies of 'natural' no ELM regimes have been extended. Stable I-modes up to have been characterised using -feedback. Core physics has been advanced by more detailed characterisation of the turbulence with new measurements such as the eddy tilt angle - measured for the first time - or the cross-phase angle of and fluctuations. These new data put strong constraints on gyro-kinetic turbulence modelling. In addition, carefully executed studies in different main species (H, D and He) and with different heating mixes highlight the importance of the collisional energy exchange for interpreting energy confinement. A new regime with a hollow profile now gives access to regimes mimicking aspects of burning plasma conditions and lead to nonlinear interactions of energetic particle modes despite the sub-Alfvénic beam energy. This will help to validate the fast-ion codes for predicting ITER and DEMO.
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| 7. |
- Meyer, H., et al.
(författare)
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Overview of progress in European medium sized tokamaks towards an integrated plasma-edge/wall solution
- 2017
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Ingår i: Nuclear Fusion. - : Institute of Physics Publishing (IOPP). - 0029-5515 .- 1741-4326. ; 57:10
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Tidskriftsartikel (refereegranskat)abstract
- Integrating the plasma core performance with an edge and scrape-off layer (SOL) that leads to tolerable heat and particle loads on the wall is a major challenge. The new European medium size tokamak task force (EU-MST) coordinates research on ASDEX Upgrade (AUG), MAST and TCV. This multi-machine approach within EU-MST, covering a wide parameter range, is instrumental to progress in the field, as ITER and DEMO core/pedestal and SOL parameters are not achievable simultaneously in present day devices. A two prong approach is adopted. On the one hand, scenarios with tolerable transient heat and particle loads, including active edge localised mode (ELM) control are developed. On the other hand, divertor solutions including advanced magnetic configurations are studied. Considerable progress has been made on both approaches, in particular in the fields of: ELM control with resonant magnetic perturbations (RMP), small ELM regimes, detachment onset and control, as well as filamentary scrape-off-layer transport. For example full ELM suppression has now been achieved on AUG at low collisionality with n = 2 RMP maintaining good confinement H-H(98,H-y2) approximate to 0.95. Advances have been made with respect to detachment onset and control. Studies in advanced divertor configurations (Snowflake, Super-X and X-point target divertor) shed new light on SOL physics. Cross field filamentary transport has been characterised in a wide parameter regime on AUG, MAST and TCV progressing the theoretical and experimental understanding crucial for predicting first wall loads in ITER and DEMO. Conditions in the SOL also play a crucial role for ELM stability and access to small ELM regimes.
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| 8. |
- Morel, Alexandra C., et al.
(författare)
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Carbon dynamics, net primary productivity and human-appropriated net primary productivity across a forest–cocoa farm landscape in West Africa
- 2019
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 25:8, s. 2661-2677
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Tidskriftsartikel (refereegranskat)abstract
- Terrestrial net primary productivity (NPP) is an important metric of ecosystem functioning; however, there are little empirical data on the NPP of human-modified ecosystems, particularly smallholder, perennial crops like cocoa (Theobroma cacao), which are extensive across the tropics. Human-appropriated NPP (HANPP) is a measure of the proportion of a natural system's NPP that has either been reduced through land-use change or harvested directly and, previously, has been calculated to estimate the scale of the human impact on the biosphere. Additionally, human modification can create shifts in NPP allocation and decomposition, with concomitant impacts on the carbon cycle. This study presents the results of 3 years of intensive monitoring of forest and smallholder cocoa farms across disturbance, management intensity, distance from forest and farm age gradients. We measured among the highest reported NPP values in tropical forest, 17.57 ± 2.1 and 17.7 ± 1.6 Mg C ha−1 year−1 for intact and logged forest, respectively; however, the average NPP of cocoa farms was still higher, 18.8 ± 2.5 Mg C ha−1 year−1, which we found was driven by cocoa pod production. We found a dramatic shift in litterfall residence times, where cocoa leaves decomposed more slowly than forest leaves and shade tree litterfall decomposed considerably faster, indicating significant changes in rates of nutrient cycling. The average HANPP value for all cocoa farms was 2.1 ± 1.1 Mg C ha−1 year−1; however, depending on the density of shade trees, it ranged from −4.6 to 5.2 Mg C ha−1 year−1. Therefore, rather than being related to cocoa yield, HANPP was reduced by maintaining higher shade levels. Across our monitored farms, 18.9% of farm NPP was harvested (i.e., whole cocoa pods) and only 1.1% (i.e., cocoa beans) was removed from the system, suggesting that the scale of HANPP in smallholder cocoa agroforestry systems is relatively small.
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| 9. |
- Morel, Alexandra C., et al.
(författare)
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The Ecological Limits of Poverty Alleviation in an African Forest-Agriculture Landscape
- 2019
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Ingår i: Frontiers in Sustainable Food Systems. - : Frontiers Media SA. - 2571-581X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Cocoa yields in Ghana remain low. This has variously been attributed to low rates of fertilizer application, pollinator limitation, and particularly dry growing conditions. In this paper we use an African forest-agriculture landscape dominated by cocoa (Theobroma cacao) to develop an ecological production function, allowing us to identify key ecological and management limits acting on cocoa yields simultaneously. These included more consistent application of fertilizers inter-annually, distributing rotting biomass throughout the farm and reducing the incidence of capsid attacks. By relaxing these limits, we estimate plausible increases in yields and, by extension, farm incomes. Our analysis reveals that resulting increases in cocoa yields requiring both ecological and intensive management interventions could be significant (113 ± 60%); however, benefits are disproportionately realized by the wealthiest households. We found that wealthier households benefited proportionally more from ecological intensification methods (e.g., leaving more rotting biomass in their farms) and the poorest households benefited proportionally more from capital-intensive intensification methods (e.g., pesticide and fertilizer applications). We treated poverty as multi-dimensional, and show that only certain dimensions of poverty (school attendance, assets, and food security) are significantly related to cocoa incomes, while several other dimensions (access to clean water, sanitation and electricity, and infant mortality) are not. We explore how increased household cocoa incomes could impact different dimensions of poverty. Our findings suggest, that if all households adopted the optimal level of each of these management options, and in so doing had similar poverty profiles to those households already managing optimally, we would see the community-averaged probability: a child of a household misses school decrease from 47 to 31%, a household would be able to acquire assets increase from 40 to 59% and a household would have access to an adequate amount of food increase from 62 to 79%.
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| 10. |
- Patil, Vrushali, et al.
(författare)
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APETALA2 control of barley internode elongation
- 2019
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Ingår i: Development (Cambridge). - : The Company of Biologists. - 1477-9129 .- 0950-1991. ; 146:11
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Tidskriftsartikel (refereegranskat)abstract
- Many plants dramatically elongate their stems during flowering, yet how this response is coordinated with the reproductive phase is unclear. We demonstrate that microRNA (miRNA) control of APETALA2 (AP2) is required for rapid, complete elongation of stem internodes in barley, especially of the final 'peduncle' internode directly underneath the inflorescence. Disrupted miR172 targeting of AP2 in the Zeo1.b barley mutant caused lower mitotic activity, delayed growth dynamics and premature lignification in the peduncle leading to fewer and shorter cells. Stage- and tissue-specific comparative transcriptomics between Zeo1.b and its parent cultivar showed reduced expression of proliferation-associated genes, ectopic expression of maturation-related genes and persistent, elevated expression of genes associated with jasmonate and stress responses. We further show that applying methyl jasmonate (MeJA) phenocopied the stem elongation of Zeo1.b, and that Zeo1.b itself was hypersensitive to inhibition by MeJA but less responsive to promotion by gibberellin. Taken together, we propose that miR172-mediated restriction of AP2 may modulate the jasmonate pathway to facilitate gibberellin-promoted stem growth during flowering.
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