| 1. |
- Donofrio, Claudio, et al.
(författare)
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Long-term Reproducibility for Jupyter Notebook
- 2023
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Konferensbidrag (refereegranskat)abstract
- Computational notebooks (e.g. Jupyter notebook) are a popular choice for interactive scientific computing to convey descriptive information together with executable source code. The user can annotate the scientific development of the work, the methods applied, describe ancillary data or the analysis of results, with text, illustrations, figures, and equations. Such ‘executable’ documents provide a paradigm shift in scientific writing, where not only the science is described, but the actual computation and source code are openly available and can be reproduced and validated.Therefore, it is of paramount importance to preserve these documents. A unique and persistent identification (PID) is essential together with providing enough information to execute the source code. Generating a PID for a Jupyter notebook is not technically challenging. We can automatically collect system and run-time information and, with a guided workflow for the user, assemble a rich set of metadata. The collected information allows us to recreate the computational environment and run the source code, which in return (theoretically) should produce the same results as published.The importance of providing a rich set of metadata for all digital objects in a human readable and machine actionable form is well understood and widely accepted as necessity for reproducibility, traceability, and provenance. This is reflected in the FAIR principles (Wilkinson, https://doi.org/10.1038/sdata.2016.18) which are regarded as gold standard by many scientific communities.Pimentel et al. (https://doi.org/10.1109/MSR.2019.00077) analysed over 800’000 Jupyter notebooks from GitHub. 24 % executed without errors and only 4 % produced the same results. The likelihood to successfully compile and run a decade old source code is slim. Long term support for well established operating systems varies between 5 to 10 years, user software support is usually shorter and looking at free and open-source repositories there is often no support (or best effort) offered.We present an approach to safely reproduce the computational environment in the future with a focus on long-term availability. Instead of trying to reinstall the computational environment based on the stored metadata, we propose to archive the docker image, the user space (user installed packages) and finally the source code. Recreating the system in this way is more like restoring a backup, where backup is the equivalent of an entire computer system. It does not solve all the problems but removes a great deal of complexity and uncertainty.Though there are shortcomings in our approach, we believe our solution will lower the threshold for scientists to provide rich meta data, code and results attached to a publication that can be reproduced in the far future.
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| 2. |
- Storm, Ida, et al.
(författare)
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A view of the European carbon flux landscape through the lens of the ICOS atmospheric observation network
- 2023
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Ingår i: Atmospheric Chemistry and Physics. - 1680-7316. ; 23:9, s. 4993-5008
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Tidskriftsartikel (refereegranskat)abstract
- The ICOS (Integrated Carbon Observation System) network of atmospheric measurement stations produces standardized data on greenhouse gas concentrations at 46 stations in 16 different European countries (March 2023). The placement of instruments on tall towers and mountains results in large influence regions (“concentration footprints”). The combined footprints for all the individual stations create a “lens” through which the network sees the European CO2 flux landscape. In this study, we summarize this view using quantitative metrics of the fluxes seen by individual stations and by the current and extended ICOS networks. Results are presented from both country level and pan-European perspectives, using open-source tools that we make available through the ICOS Carbon Portal. We target anthropogenic emissions from various sectors, as well as the land cover types found across Europe and their spatiotemporally varying fluxes. This recognizes different interests of different ICOS stakeholders. We specifically introduce “monitoring potential maps” to identify which regions have a relative underrepresentation of biospheric fluxes. This potential changes with the introduction of new stations, which we investigate for the planned ICOS expansion with 19 stations over the next few years.In our study focused on the summer of 2020, we find that the ICOS atmospheric station network has limited sensitivity to anthropogenic fluxes, as was intended in the current design. Its representation of biospheric fluxes follows the fractional representation of land cover and is generally well balanced considering the pan-European view. Exceptions include representation of grass and shrubland and broadleaf forest which are abundant in south-eastern European countries, particularly Croatia and Serbia. On the country scale, the representation shows larger imbalances, even within relatively densely monitored countries. The flexibility to consider individual ecosystems, countries, or their integrals across Europe demonstrates the usefulness of our analyses and can readily be reproduced for any network configuration within Europe.
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| 3. |
- Storm, Martin, et al.
(författare)
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Boendets miljöpåverkan : en litteraturstudie om miljöpåverkan i vardagen
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Syftet med denna rapport är att göra en sammanställning av den kunskap som finns när det gäller samband mellan boende och miljöpåverkan. De studier och den statistik som lyfts fram i litteraturstudien speglar kunskapsläget och synliggör kunskapsluckorna. Rapporten bidrar således till en ansats att sammanställa en kunskapsöversikt när det gäller boendets miljöpåverkan.Livsstilsperspektivet i studien innebär att boendets miljöpåverkan är detsamma som miljöpåverkan av hushållens vardagliga aktiviteter. Boendets miljöpåverkan avgränsas utifrån de miljöpåverkande områdena (som kan kopplas till hushållen) inom miljökvalitetsmålet God bebyggd miljö.En utgångspunkt i studien är att hustyp, upplåtelseform, hushållstyp, sociala faktorer samt bostadens geografiska läge är påverkansfaktorer som i varierande grad har betydelse för vardagsaktiviteternas miljöpåverkan. En annan utgångspunkt i studien är att individens vardagsbeteende påverkas av miljöpsykologiska faktorer som exempelvis hur tydlig en handlingsriktning är. Detta exemplifieras i rapporten för att visa på hur en förändrad livssituation oavsiktligt kan resultera i en ökad eller minskad iljöpåverkan.Studiens generella slutsatser är att:Miljöpåverkan skiljer sig åt främst beroende på om hushållet bor i småhus eller flerbostadshus. Det går dock inte att entydigt säga att boende i den ena eller andra hustypen är mer miljövänlig eftersom det skiljer sig åt beroende på vilken typ av vardagsaktivitet det handlar om. Miljöpåverkande vardagsbeteende är även mycket varierande mellan olika hushållstyper och sociala grupper.Användning av hushållsapparater är det område som det i dagsläget finns mest kunskap om. Inom de övriga användningsområdena finns det betydande kunskapsluckor om både hushållens miljöpåverkan och beteendemönster i vardagen. Särskilt med tanke på att uppvärmning av bostäder är en mycket större andel av hushållets energianvändning än hushållsel är det anmärkningsvärt att det inte finns mer kunskap om hushållens användning av uppvärmd bostadsyta.Hushållens möjligheter att minska sin miljöpåverkan i vardagen är generellt sett störst i småhus (äganderätt) och minst för hushåll i hyresrätt (flerbostadshus). Men möjligheterna skiljer sig åt beroende på vilken vardagsaktivitet det gäller.Olika faser i livet ger olika miljöpåverkan beroende på hustyp. En av studiens slutsatser är att miljöpåverkan skiljer sig åt främst beroende på om hushållet bor i småhus eller flerbostadshus. En utgångspunkt i studien är att hushållen påverkar miljön på olika sätt under olika faser i livet. Studien visar att beroende på faser i livet i fråga om ålder, inkomst och hushållstyp är sannolikheten stor att man bor i en viss hustyp, och därmed vilken typ av miljöpåverkan hushållet har.
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| 4. |
- Tuomi, Tiinamaija, et al.
(författare)
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Increased Melatonin Signaling Is a Risk Factor for Type 2 Diabetes
- 2016
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Ingår i: Cell Metabolism. - : Elsevier BV. - 1550-4131 .- 1932-7420. ; 23:6, s. 1067-1077
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Tidskriftsartikel (refereegranskat)abstract
- Type 2 diabetes (T2D) is a global pandemic. Genome-wide association studies (GWASs) have identified >100 genetic variants associated with the disease, including a common variant in the melatonin receptor 1 b gene (MTNR1B). Here, we demonstrate increased MTNR1B expression in human islets from risk G-allele carriers, which likely leads to a reduction in insulin release, increasing T2D risk. Accordingly, in insulin-secreting cells, melatonin reduced cAMP levels, and MTNR1B overexpression exaggerated the inhibition of insulin release exerted by melatonin. Conversely, mice with a disruption of the receptor secreted more insulin. Melatonin treatment in a human recall-by-genotype study reduced insulin secretion and raised glucose levels more extensively in risk G-allele carriers. Thus, our data support a model where enhanced melatonin signaling in islets reduces insulin secretion, leading to hyperglycemia and greater future risk of T2D. The findings also imply that melatonin physiologically serves to inhibit nocturnal insulin release.
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| 5. |
- Van Der Woude, Auke M., et al.
(författare)
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Near-real-time CO2 fluxes from CarbonTracker Europe for high-resolution atmospheric modeling
- 2023
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 15:2, s. 579-605
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Tidskriftsartikel (refereegranskat)abstract
- We present the CarbonTracker Europe High-Resolution (CTE-HR) system that estimates carbon dioxide (CO2) exchange over Europe at high resolution (0.1 × 0.2° ) and in near real time (about 2 months' latency). It includes a dynamic anthropogenic emission model, which uses easily available statistics on economic activity, energy use, and weather to generate anthropogenic emissions with dynamic time profiles at high spatial and temporal resolution (0.1×0.2° hourly). Hourly net ecosystem productivity (NEP) calculated by the Simple Biosphere model Version 4 (SiB4) is driven by meteorology from the European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis 5th Generation (ERA5) dataset. This NEP is downscaled to 0.1×0.2° using the high-resolution Coordination of Information on the Environment (CORINE) land-cover map and combined with the Global Fire Assimilation System (GFAS) fire emissions to create terrestrial carbon fluxes. Ocean CO2 fluxes are included in our product, based on Jena CarboScope ocean CO2 fluxes, which are downscaled using wind speed and temperature. Jointly, these flux estimates enable modeling of atmospheric CO2 mole fractions over Europe. We assess the skill of the CTE-HR CO2 fluxes (a) to reproduce observed anomalies in biospheric fluxes and atmospheric CO2 mole fractions during the 2018 European drought, (b) to capture the reduction of anthropogenic emissions due to COVID-19 lockdowns, (c) to match mole fraction observations at Integrated Carbon Observation System (ICOS) sites across Europe after atmospheric transport with the Transport Model, version 5 (TM5) and the Stochastic Time-Inverted Lagrangian Transport (STILT), driven by ECMWF-IFS, and (d) to capture the magnitude and variability of measured CO2 fluxes in the city center of Amsterdam (the Netherlands). We show that CTE-HR fluxes reproduce large-scale flux anomalies reported in previous studies for both biospheric fluxes (drought of 2018) and anthropogenic emissions (COVID-19 pandemic in 2020). After applying transport of emitted CO2, the CTE-HR fluxes have lower median root mean square errors (RMSEs) relative to mole fraction observations than fluxes from a non-informed flux estimate, in which biosphere fluxes are scaled to match the global growth rate of CO2 (poor person's inversion). RMSEs are close to those of the reanalysis with the CTE data assimilation system. This is encouraging given that CTE-HR fluxes did not profit from the weekly assimilation of CO2 observations as in CTE. We furthermore compare CO2 concentration observations at the Dutch Lutjewad coastal tower with high-resolution STILT transport to show that the high-resolution fluxes manifest variability due to different emission sectors in summer and winter. Interestingly, in periods where synoptic-scale transport variability dominates CO2 concentration variations, the CTE-HR fluxes perform similarly to low-resolution fluxes (5-10× coarsened). The remaining 10 % of the simulated CO2 mole fraction differs by >2 ppm between the low-resolution and high-resolution flux representation and is clearly associated with coherent structures ("plumes") originating from emission hotspots such as power plants. We therefore note that the added resolution of our product will matter most for very specific locations and times when used for atmospheric CO2 modeling. Finally, in a densely populated region like the Amsterdam city center, our modeled fluxes underestimate the magnitude of measured eddy covariance fluxes but capture their substantial diurnal variations in summertime and wintertime well. We conclude that our product is a promising tool for modeling the European carbon budget at a high resolution in near real time. The fluxes are freely available from the ICOS Carbon Portal (CC-BY-4.0) to be used for near-real-time monitoring and modeling, for example, as an a priori flux product in a CO2 data assimilation system. The data are available at 10.18160/20Z1-AYJ2 .
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