| 1. |
- Davies, Neil, et al.
(författare)
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The founding charter of the Genomic Observatories Network
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3:2
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Tidskriftsartikel (refereegranskat)abstract
- Abstract The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
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| 2. |
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| 3. |
- Hardisty, Alex R., et al.
(författare)
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BioVeL: A virtual laboratory for data analysis and modelling in biodiversity science and ecology
- 2016
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Ingår i: BMC Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- © 2016 The Author(s).Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
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| 4. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 5. |
- Stephens, Lucas, et al.
(författare)
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Archaeological assessment reveals Earth’s early transformation through land use
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 365:6456, s. 897-902
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Tidskriftsartikel (refereegranskat)abstract
- Humans began to leave lasting impacts on Earth’s surface starting 10,000 to 8000 years ago. Through a synthetic collaboration with archaeologists around the globe, Stephens et al. compiled a comprehensive picture of the trajectory of human land use worldwide during the Holocene (see the Perspective by Roberts). Hunter-gatherers, farmers, and pastoralists transformed the face of Earth earlier and to a greater extent than has been widely appreciated, a transformation that was essentially global by 3000 years before the present.Science, this issue p. 897; see also p. 865Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.
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| 6. |
- Ward, Helen, et al.
(författare)
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Using observations to improve modelled energy, water and carbon exchanges for urban areas
- 2015
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Ingår i: ICUC9 – 9 th International Conference on Urban Climate jointly with 12th Symposium on the Urban Environment. 20-24 July 2015, Toulouse, France.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Models are an essential tool for studying how our surroundings influence us and how we, intentionally or inadvertently, influence our surroundings. The Surface Urban Energy and Water balance Scheme (SUEWS) uses a basic meteorological forcing dataset and information about the surface cover to model components of the energy and water balance. The model was initially developed based on studies in North America and is now being run for multiple locations around the world. Here, we evaluate the model at two locations in the UK. A network of micrometeorological observations exists across London, enabling comparisons between the city centre and suburbs. The central London study site is one of the most highly urbanised and densely populated to date. 120 km to the west is the typical suburban town of Swindon. At both of these locations, extensive observational datasets spanning several years have been collected, and work has been undertaken to classify the surface characteristics. However, as detailed land cover and socio-economic information may not always be available, we consider the impact on model performance of using only easily accessible data to provide the required inputs. SUEWS is evaluated against observations of energy and water balance components (including turbulent heat fluxes from eddy covariance and scintillometry techniques). SUEWS estimates evaporation using an adapted Penman-Monteith formulation with a variable surface conductance. Analysis of observed surface conductances suggests adjustments to improve model performance. CO2 fluxes, closely linked to the surface conductance, are also examined. The central London and suburban Swindon sites behave differently, in terms of both the magnitude and temporal variability of CO2 exchanges. These differences are almost entirely a result of land use and land cover, and associated patterns of human behaviour. Simple models based on anthropogenic emissions inventories provide an indication of the magnitude of the CO2 release, however, at the suburban site vegetation plays an important role in CO2 uptake and must be incorporated too. With improved modelling capability, the exposure of the population to risks such as thermal stress or flooding can be better estimated. Having validated the model, the impact of policy decisions and future climate scenarios on the wellbeing of the citizens can be assessed.
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| 7. |
- Wright, Gillian, et al.
(författare)
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The Mid-infrared Instrument for JWST and Its In-flight Performance
- 2023
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Ingår i: Publications of the Astronomical Society of the Pacific. - 0004-6280 .- 1538-3873. ; 135:1046
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Tidskriftsartikel (refereegranskat)abstract
- The Mid-Infrared Instrument (MIRI) extends the reach of the James Webb Space Telescope (JWST) to 28.5 μm. It provides subarcsecond-resolution imaging, high sensitivity coronagraphy, and spectroscopy at resolutions of λ/Δλ ∼ 100-3500, with the high-resolution mode employing an integral field unit to provide spatial data cubes. The resulting broad suite of capabilities will enable huge advances in studies over this wavelength range. This overview describes the history of acquiring this capability for JWST. It discusses the basic attributes of the instrument optics, the detector arrays, and the cryocooler that keeps everything at approximately 7 K. It gives a short description of the data pipeline and of the instrument performance demonstrated during JWST commissioning. The bottom line is that the telescope and MIRI are both operating to the standards set by pre-launch predictions, and all of the MIRI capabilities are operating at, or even a bit better than, the level that had been expected. The paper is also designed to act as a roadmap to more detailed papers on different aspects of MIRI.
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| 8. |
- Zannoni, Nora, et al.
(författare)
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Effect of Ozone, Clothing, Temperature, and Humidity on the Total OH Reactivity Emitted from Humans
- 2021
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 55:20, s. 13614-13624
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Tidskriftsartikel (refereegranskat)abstract
- People influence indoor air chemistry through theirchemical emissions via breath and skin. Previous studies showed thatdirect measurement of total OH reactivity of human emissionsmatched that calculated from parallel measurements of volatile organiccompounds (VOCs) from breath, skin, and the whole body.In thisstudy, we determined, with direct measurements from twoindependent groups of four adult volunteers, the effect of indoortemperature and humidity, clothing coverage (amount of exposedskin), and indoor ozone concentration on the total OH reactivity ofgaseous human emissions.The results show that the measuredconcentrations of VOCs and ammonia adequately account for themeasured total OH reactivity. The total OH reactivity of humanemissions was primarily affected by ozone reactions with organic skinoilconstituents and increased with exposed skin surface, higher temperature, and higher humidity. Humans emitted a comparabletotal mixing ratio of VOCs and ammonia at elevated temperature-low humidity and elevated temperature-high humidity, withrelatively low diversity in chemical classes.In contrast, the total OH reactivity increased with higher temperature and higherhumidity, with a larger diversity in chemical classes compared to the total mixing ratio. Ozone present, carbonyl compounds were thedominant reactive compounds in all of the reported conditions.
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| 9. |
- Del Zotto, Michele, et al.
(författare)
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6D SCFTs and Phases of 5D Theories
- 2017
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Ingår i: Journal of High Energy Physics (JHEP). - 1126-6708 .- 1029-8479. ; :9
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Tidskriftsartikel (refereegranskat)abstract
- Starting from 6D superconformal field theories (SCFTs) realized via F-theory, we show how reduction on a circle leads to a uniform perspective on the phase structure of the resulting 5D theories, and their possible conformal fixed points. Using the correspon-dence between F-theory reduced on a circle and M-theory on the corresponding elliptically fibered Calabi-Yau threefold, we show that each 6D SCFT with minimal supersymmetry directly reduces to a collection of between one and four 5D SCFTs. Additionally, we find that in most cases, reduction of the tensor branch of a 6D SCFT yields a 5D generalization of a quiver gauge theory. These two reductions of the theory often correspond to different phases in the 5D theory which are in general connected by a sequence of flop transitions in the extended Kähler cone of the Calabi-Yau threefold. We also elaborate on the structure of the resulting conformal fixed points, and emergent flavor symmetries, as realized by M-theory on a canonical singularity.
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| 10. |
- Aparicio, S, et al.
(författare)
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Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.
- 1995
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 92:5, s. 1684-1688
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Tidskriftsartikel (refereegranskat)abstract
- Comparative vertebrate genome sequencing offers a powerful method for detecting conserved regulatory sequences. We propose that the compact genome of the teleost Fugu rubripes is well suited for this purpose. The evolutionary distance of teleosts from other vertebrates offers the maximum stringency for such evolutionary comparisons. To illustrate the comparative genome approach for F. rubripes, we use sequence comparisons between mouse and Fugu Hoxb-4 noncoding regions to identify conserved sequence blocks. We have used two approaches to test the function of these conserved blocks. In the first, homologous sequences were deleted from a mouse enhancer, resulting in a tissue-specific loss of activity when assayed in transgenic mice. In the second approach, Fugu DNA sequences showing homology to mouse sequences were tested for enhancer activity in transgenic mice. This strategy identified a neural element that mediates a subset of Hoxb-4 expression that is conserved between mammals and teleosts. The comparison of noncoding vertebrate sequences with those of Fugu, coupled to a transgenic bioassay, represents a general approach suitable for many genome projects.
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