| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- El Albani, Abderrazak, et al.
(författare)
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Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7302, s. 100-104
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Tidskriftsartikel (refereegranskat)abstract
- The evidence for macroscopic life during the Palaeoproterozoic era (2.5-1.6 Gyr ago) is controversial(1-5). Except for the nearly 2-Gyr-old coil-shaped fossil Grypania spiralis(6,7), which may have been eukaryotic, evidence for morphological and taxonomic bio-diversification of macroorganisms only occurs towards the beginning of the Mesoproterozoic era (1.6-1.0 Gyr)(8). Here we report the discovery of centimetre-sized structures from the 2.1-Gyr-old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, which we interpret as highly organized and spatially discrete populations of colonial organisms. The structures are up to 12 cm in size and have characteristic shapes, with a simple but distinct ground pattern of flexible sheets and, usually, a permeating radial fabric. Geochemical analyses suggest that the sediments were deposited under an oxygenated water column. Carbon and sulphur isotopic data indicate that the structures were distinct biogenic objects, fossilized by pyritization early in the formation of the rock. The growth patterns deduced from the fossil morphologies suggest that the organisms showed cell-to-cell signalling and coordinated responses, as is commonly associated with multicellular organization(9). The Gabon fossils, occurring after the 2.45-2.32-Gyr increase in atmospheric oxygen concentration(10), may be seen as ancient representatives of multicellular life, which expanded so rapidly 1.5 Gyr later, in the Cambrian explosion.
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| 3. |
- El Albani, Abderrazak, et al.
(författare)
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The 2.1 Ga old Francevillian biota: biogenicity, taphonomy and biodiversity.
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:6:e99438, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth’s surface environments following the first appreciable rise of free atmospheric oxygen concentrations ~2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. While most sedimentary successions deposited during this time interval have experienced thermal overprinting from burial diagenesis and metamorphism, the ca. 2.1 Ga black shales of the Francevillian B Formation (FB2) cropping out in southeastern Gabon have not. The Francevillian Formation contains centimeter-sized structures interpreted as organized and spatially discrete populations of colonial organisms living in an oxygenated marine ecosystem. Here, new material from the FB2 black shales is presented and analyzed to further explore its biogenicity and taphonomy. Our extended record comprises variably sized, shaped, and structured pyritized macrofossils of lobate, elongated, and rodshaped morphologies as well as abundant non-pyritized disk-shaped macrofossils and organic-walled acritarchs. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed the evolution and ecological expansion of complex megascopic life.
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| 4. |
- Penzenstadler, Birgit, et al.
(författare)
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ICT4S 2029 : What will be the Systems Supporting Sustainability in 15 Years?
- 2014
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Ingår i: Proceedings of the 2014 conference ict for sustainability. - Paris, France : Atlantis Press. ; , s. 30-39
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Konferensbidrag (refereegranskat)abstract
- Research is often inspired by visions of the future. These visions can take on various narrative forms, and can fall anywhere along the spectrum from utopian to dystopian. Even though we recognize the importance of such visions to help us shape research questions and inspire rich design spaces to be explored, the opportunity to discuss them is rarely given in a research context. Imagine how civilization will have changed in 15 years. What is your vision for systems that will be supporting sustainability in that time? Which transformational changes will have occurred in the mean time that allow for these systems? Is ICT even the right tool or does it contradict sustainability by making our world ever more complex? How can we make systems and our societies more sustainable and resilient by ICT4S? This paper presents a compilation of fictional abstracts for inspiration and discussion, and provides means to stimulate discussion on future research and contributes to ICT4S community building.
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| 5. |
- Ryder, Elizabeth, et al.
(författare)
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Temperature quenching of CDOM fluorescence sensors : temporal and spatial variability in the temperature response and a recommended temperature correction equation
- 2012
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Ingår i: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 10, s. 1004-1010
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Tidskriftsartikel (refereegranskat)abstract
- Field-based instruments measuring chromophoric dissolved organic matter (CDOM) fluorescence are often used as a proxy for dissolved organic carbon concentrations in lakes and streams. CDOM fluorescence yield is, however, affected by water temperature at the time of measurement, a factor which varies on both diel and seasonal timescales. A temperature correction must therefore be applied to these data. We present data on temporal and site-specific variability in temperature quenching of CDOM fluorescence for water from a humic lake and one of its main inflows in the west of Ireland. In addition, we present a temperature compensation equation and show that this equation is an improvement on methods previously proposed.
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