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- Baranasic, D, et al.
(author)
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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
- 2022
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In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 54:7, s. 1037-
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Journal article (peer-reviewed)abstract
- Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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| 2. |
- Duncan, H F, et al.
(author)
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European Society of Endodontology position statement : Management of deep caries and the exposed pulp
- 2019
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In: International Endodontic Journal. - : John Wiley & Sons. - 0143-2885 .- 1365-2591. ; 52:7, s. 923-934
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Journal article (peer-reviewed)abstract
- This position statement on the management of deep caries and the exposed pulp represents the consensus of an expert committee, convened by the European Society of Endodontology (ESE). Preserving the pulp in a healthy state with sustained vitality, preventing apical periodontitis and developing minimally invasive biologically based therapies are key themes within contemporary clinical endodontics. The aim of this statement is to summarise current best evidence on the diagnosis and classification of deep caries and caries-induced pulpal disease, as well as indicating appropriate clinical management strategies for avoiding and treating pulp exposure in permanent teeth with deep or extremely deep caries. In presenting these findings, areas of controversy, low-quality evidence and uncertainties are highlighted, prior to recommendations for each area of interest. A recently published review article provides more detailed information, and was the basis for this position statement (Bjørndal et al. 2019, International Endodontic Journal). The intention of this position statement is to provide the practitioner with relevant clinical guidance in this rapidly developing area. An update will be provided within 5 years as further evidence emerges. This article is protected by copyright. All rights reserved.
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| 3. |
- Andersson, Jafet C. M., et al.
(author)
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Potential impacts of water harvesting and ecological sanitation on crop yield, evaporation and river flow regimes in the Thukela River basin, South Africa
- 2011
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In: Agricultural Water Management. - : Elsevier BV. - 0378-3774 .- 1873-2283. ; 98:7, s. 1113-1124
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Journal article (peer-reviewed)abstract
- In this study we explore the potential impacts of two strategies, namely in situ water harvesting (in situ WH) and fertilisation with stored human urine (Ecosan), to increase the water and nutrient availability in rain-fed smallholder agriculture in South Africa's Thukela River basin (29,000 km(2)). We use the soil and water assessment tool (SWAT) to simulate potential impacts on smallholder maize yields, river flow regimes, plant transpiration, and soil and canopy evaporation during 1997-2006. Based on the results, the impacts on maize yields are likely to be small with in situ WH (median change: 0%) but significant with Ecosan (median increase: 30%). The primary causes for these effects are high nitrogen stress on crop growth, and low or untimed soil moisture enhancement with in situ WH. However, the impacts vary significantly in time and space, occasionally resulting in yield increases of up to 40% with in situ WH. Soil fertility improvements primarily increase yield magnitudes, whereas soil moisture enhancements reduce spatial yield variability. Ecosan significantly improves the productivity of the evaporative fluxes by increasing transpiration (median: 2.8%, 4.7 mm season(-1)) and reducing soil and canopy evaporation (median: -1.7%, -4.5 mm season(-1)). In situ WH does not generally affect the river flow regimes. Occasionally, significant regime changes occur due to enhanced lateral and shallow aquifer return flows. This leads to higher risks of flooding in some areas, but also to enhanced low flows, which help sustain aquatic ecosystems in the basin.
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