| 1. |
- Marouli, Eirini, et al.
(författare)
-
Rare and low-frequency coding variants alter human adult height
- 2017
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
-
Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
|
|
| 2. |
- Turcot, Valerie, et al.
(författare)
-
Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
|
|
| 3. |
- Zhao, Zhiming, et al.
(författare)
-
Reference model guided system design and implementation for interoperable environmental research infrastructures
- 2015
-
Ingår i: Proceedings - 11th IEEE International Conference on eScience, eScience 2015. - 9781467393256 ; , s. 551-556
-
Konferensbidrag (refereegranskat)abstract
- Environmental research infrastructures (RIs) support their respective research communities by integrating large-scale sensor/observation networks with data curation services, analytical tools and common operational policies. These RIs are developed as pillars of intra-and interdisciplinary research, however comprehension of the complex, pathologically interconnected aspects of the Earth's ecosystem increasingly requires that researchers conduct their experiments across infrastructure boundaries. Consequently, almost all data-related activities within these infrastructures, from data capture to data usage, needs to be designed to be broadly interoperable in order to enable real interdisciplinary innovation. The Data for Science theme in the EU Horizon 2020 project ENVRIPLUS intends to address this interoperability challenge as it relates to the design, implementation and operation of environmental science RIs, the theme focuses on key issues of data identification and citation, curation, cataloguing, processing, optimization, and provenance, supported by a generic cross-infrastructure reference model.
|
|
| 4. |
|
|
| 5. |
- Adamaki, Angeliki, et al.
(författare)
-
A European Dashboard showcasing the State of the Environment
- 2023
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The European Open Science Cloud is a pan-European initiative that aims at developing a federated infrastructure that supports scientific research and Open Science. Having the FAIR principles at the core of Open Science practices, the Environmental Research Infrastructures (ENVRIs) that operate in Europe collaborate at cluster level (the ENVRI cluster) continuously improving the FAIRness of their services and working towards becoming more interoperable among them but also with other clusters. To showcase the benefits of an integration platform that supports scientific workflows, the ENVRIs develop the “Dashboard for the State of the Environment” as a cross-discipline service to address with scientific facts the environmental concerns. The project brings together three scientific domains (Atmosphere, Biodiversity, Ocean) that each have set up analytical workflows to provide environmental indicators in real-time, allowing the users to visualise the “State of the Environment” by interacting with the service interface. The Dashboard is designed to be completely user configurable so that the users can select from a list the indicators to be shown and their order. Providers can add, remove and edit indicators through a standard REST API, that allows transferring all parameters, including the configuration of the indicators and how to provision data values and thumbnail interaction. The Dashboard is implemented and operated using engineering best practices, including YAML for the indicators’ descriptions and a robust and flexible container-based deployment. It builds on EOSC services like AAI, cloud services, and data storage, and the workflows that provide the indicators will also build on the EOSC and Research Infrastructure (RI) computing integration. As a proof of concept, a limited list of indicators is available, and we foresee that the participating RIs will provide many more indicator options in the near future. In addition, through the extension API it will be possible for new RIs to start providing indicators. The Dashboard service is completely open source, and, as the whole concept, it is designed to be flexible and expansible. Therefore, we encourage other clusters that are part of EOSC to use the service as another basis for disseminating their relevant indicators to a wider audience.
|
|
| 6. |
- Adamaki, Angeliki, et al.
(författare)
-
ENVRI-FAIR D5.2: Implementation plan for common development goals
- 2020
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- During the firstyear of the project the cluster worked on the data service requirement tracking and a technology landscape and gap analysis on the RI FAIR data/services level, to provide an up-to-date investigation of the most common gaps the ENVRIs need to bridge with respect to the FAIR principles and the EOSC requirements. The FAIRness analysis (D5.1) established that the participating RIs display a wide range of states of readiness. The present document uses this analysis to explain the actions that have been taken bythe ENVRI-FAIR partners during the second year of the project, and to define the common development goals and prepare an implementation plan at cluster level. During the WP5 Review Workshop in M10 of the project, a decision was made to form (six) cross-cutting Task Forces, which involve representatives from all subdomains, bringing together technical, scientific and managerial staff in order to coordinate the work on a common platform. The development of the ENVRI catalogue of services and other relevant technical issues, e.g. the authentication and authorisation of the cluster end-users, the role of persistent identifiers, triple stores and the best practices, the benefits of certifying data repositories and the available options, the technical approach of machine-readable licenses and their use for citation and usage tracking, and the design of interoperable demonstrators and cross-domain service prototypes, are introduced and discussed in the text.
|
|
| 7. |
- Adamaki, Angeliki, et al.
(författare)
-
ENVRI-FAIR D5.7: ENVRI-Hub design study
- 2023
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The ENVRI-Hub design study contains the analysis of the technical preconditions for the successful implementation of the design ENVRI-Hub as a centralised access interface to environmental data and services building upon the increase of FAIRness achieved in the ENVRI-FAIR project; it will be based on the validation results from WP7 and Task T5.4, and the achievements in the subdomain implementation work packages WP8-11 of this project.The design of the ENVRI-Hub started as a multifaceted initiative that brought together engineers, scientists, and managers to create a collaborative platform for environmental research and innovation, aiming at advancing environmental research in Europe. As a web platform, the ENVRI-Hub can provide access to environmental data and services offered by the European environmental Research Infrastructures. The data and services provided by the ENVRIs cover four domains of the Earth system, Atmosphere, Ocean, Solid Earth, and Biodiversity-Ecosystems. The ENVRI-Hub intends to facilitate multi-and-inter-disciplinary environmental research by making the data and services interoperable across the domains and easy to use by anyone in the ENVRI community. From different perspectives, depending on the role and interest of the user, the ENVRI-Hub encompasses various aspects, including technical considerations, scientific content, usability, and strategic management. This document describes the process of designing the ENVRI-Hub during the ENVRI-FAIR project, highlighting the key challenges and achievements as well as the potential of an operational ENVRI-Hub in the future.
|
|
| 8. |
- Adamaki, Angeliki, et al.
(författare)
-
ENVRI-FAIR Project brief on implementation of Open Science and EOSC targets
- 2021
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In the ENVRI-FAIR project brief on implementation of Open Science and EOSC targets the current achievements and planned activities in ENVRI-FAIR are summarised with regard to a) Integration with the EOSC infrastructure b) FAIR principles implementation and repositories c) Technical, semantic, legal and organisational interoperability d) Stewardship of data and e) Cross-cluster collaboration activities and achievements.
|
|
| 9. |
- Agustí-Panareda, Anna, et al.
(författare)
-
Global nature run data with realistic high-resolution carbon weather for the year of the Paris Agreement
- 2022
-
Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- The CO2 Human Emissions project has generated realistic high-resolution 9 km global simulations for atmospheric carbon tracers referred to as nature runs to foster carbon-cycle research applications with current and planned satellite missions, as well as the surge of in situ observations. Realistic atmospheric CO2, CH4 and CO fields can provide a reference for assessing the impact of proposed designs of new satellites and in situ networks and to study atmospheric variability of the tracers modulated by the weather. The simulations spanning 2015 are based on the Copernicus Atmosphere Monitoring Service forecasts at the European Centre for Medium Range Weather Forecasts, with improvements in various model components and input data such as anthropogenic emissions, in preparation of a CO2 Monitoring and Verification Support system. The relative contribution of different emissions and natural fluxes towards observed atmospheric variability is diagnosed by additional tagged tracers in the simulations. The evaluation of such high-resolution model simulations can be used to identify model deficiencies and guide further model improvements.
|
|
| 10. |
- Agustí-Panareda, Anna, et al.
(författare)
-
Modelling CO2 weather-why horizontal resolution matters
- 2019
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:11, s. 7347-7376
-
Tidskriftsartikel (refereegranskat)abstract
- Climate change mitigation efforts require information on the current greenhouse gas atmospheric concentrations and their sources and sinks. Carbon dioxide (CO2) is the most abundant anthropogenic greenhouse gas. Its variability in the atmosphere is modulated by the synergy between weather and CO2 surface fluxes, often referred to as CO2 weather. It is interpreted with the help of global or regional numerical transport models, with horizontal resolutions ranging from a few hundreds of kilometres to a few kilometres. Changes in the model horizontal resolution affect not only atmospheric transport but also the representation of topography and surface CO2 fluxes. This paper assesses the impact of horizontal resolution on the simulated atmospheric CO2 variability with a numerical weather prediction model. The simulations are performed using the Copernicus Atmosphere Monitoring Service (CAMS) CO2 forecasting system at different resolutions from 9 to 80 km and are evaluated using in situ atmospheric surface measurements and atmospheric column-mean observations of CO2, as well as radiosonde and SYNOP observations of the winds. The results indicate that both diurnal and day-to-day variability of atmospheric CO2 are generally better represented at high resolution, as shown by a reduction in the errors in simulated wind and CO2. Mountain stations display the largest improvements at high resolution as they directly benefit from the more realistic orography. In addition, the CO2 spatial gradients are generally improved with increasing resolution for both stations near the surface and those observing the total column, as the overall inter-station error is also reduced in magnitude. However, close to emission hotspots, the high resolution can also lead to a deterioration of the simulation skill, highlighting uncertainties in the high-resolution fluxes that are more diffuse at lower resolutions. We conclude that increasing horizontal resolution matters for modelling CO2 weather because it has the potential to bring together improvements in the surface representation of both winds and CO2 fluxes, as well as an expected reduction in numerical errors of transport. Modelling applications like atmospheric inversion systems to estimate surface fluxes will only be able to benefit fully from upgrades in horizontal resolution if the topography, winds and prior flux distribution are also upgraded accordingly. It is clear from the results that an additional increase in resolution might reduce errors even further. However, the horizontal resolution sensitivity tests indicate that the change in the CO2 and wind modelling error with resolution is not linear, making it difficult to quantify the improvement beyond the tested resolutions. Finally, we show that the high-resolution simulations are useful for the assessment of the small-scale variability of CO2 which cannot be represented in coarser-resolution models. These representativeness errors need to be considered when assimilating in situ data and high-resolution satellite data such as Greenhouse gases Observing Satellite (GOSAT), Orbiting Carbon Observatory-2 (OCO-2), the Chinese Carbon Dioxide Observation Satellite Mission (TanSat) and future missions such as the Geostationary Carbon Observatory (GeoCarb) and the Sentinel satellite constellation for CO2. For these reasons, the high-resolution CO2 simulations provided by the CAMS in real time can be useful to estimate such small-scale variability in real time, as well as providing boundary conditions for regional modelling studies and supporting field experiments.
|
|
| 11. |
- Bergamaschi, Peter, et al.
(författare)
-
European Obspack compilation of atmospheric carbon dioxide data from ICOS and non-ICOS European stations for the period 1972-2023; : obspack_co2_466_GLOBALVIEWplus_v8.0_2023-04-26
- 2023
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- This data package contains high accuracy CO2 dry air mole fractions from 58 ICOS and non-ICOS European observatories at in total 132 observation levels, collected by the ICOS Atmosphere Thematic Centre (ATC) and provided by the station contributors. The package is part of the Globalviewplus v8.0 data product, released in 2022 and is intended for use in carbon cycle inverse modeling, model evaluation, and satellite validation studies. Please report errors and send comments regarding this product to the ObsPack originators. Please read carefully the ObsPack Fair Use statement and cite appropriately. This is the sixth release of the GLOBALVIEWplus (GV+) cooperative data product. Please review the release notes for this product at www.esrl.noaa.gov/gmd/ccgg/obspack/release_notes.html. Metadata for this product are available at https://commons.datacite.org/doi.org/10.18160/CEC4-CAGK. Please visit http://www.gml.noaa.gov/ccgg/obspack/ for more information.
|
|
| 12. |
- Bergamaschi, Peter, et al.
(författare)
-
Inverse modelling of European CH4 emissions during 2006–2012 using different inverse models and reassessed atmospheric observations
- 2018
-
Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7324. ; 18:2, s. 901-920
-
Tidskriftsartikel (refereegranskat)abstract
- We present inverse modelling (top down) estimates of European methane (CH4) emissions for 2006–2012 based on a new quality-controlled and harmonised in situ data set from 18 European atmospheric monitoring stations. We applied an ensemble of seven inverse models and performed four inversion experiments, investigating the impact of different sets of stations and the use of a priori information on emissions. The inverse models infer total CH4 emissions of 26.8 (20.2–29.7) Tg CH4 yr−1 (mean, 10th and 90th percentiles from all inversions) for the EU-28 for 2006–2012 from the four inversion experiments. For comparison, total anthropogenic CH4 emissions reported to UNFCCC (bottom up, based on statistical data and emissions factors) amount to only 21.3 Tg CH4 yr−1 (2006) to 18.8 Tg CH4 yr−1 (2012). A potential explanation for the higher range of top-down estimates compared to bottom-up inventories could be the contribution from natural sources, such as peatlands, wetlands, and wet soils. Based on seven different wetland inventories from the Wetland and Wetland CH4 Inter-comparison of Models Project (WETCHIMP), total wetland emissions of 4.3 (2.3–8.2) Tg CH4 yr−1 from the EU-28 are estimated. The hypothesis of significant natural emissions is supported by the finding that several inverse models yield significant seasonal cycles of derived CH4 emissions with maxima in summer, while anthropogenic CH4 emissions are assumed to have much lower seasonal variability. Taking into account the wetland emissions from the WETCHIMP ensemble, the top-down estimates are broadly consistent with the sum of anthropogenic and natural bottom-up inventories. However, the contribution of natural sources and their regional distribution remain rather uncertain. Furthermore, we investigate potential biases in the inverse models by comparison with regular aircraft profiles at four European sites and with vertical profiles obtained during the Infrastructure for Measurement of the European Carbon Cycle (IMECC) aircraft campaign. We present a novel approach to estimate the biases in the derived emissions, based on the comparison of simulated and measured enhancements of CH4 compared to the background, integrated over the entire boundary layer and over the lower troposphere. The estimated average regional biases range between −40 and 20 % at the aircraft profile sites in France, Hungary and Poland.
|
|
| 13. |
- Bernatsky, Sasha, et al.
(författare)
-
Lupus-related single nucleotide polymorphisms and risk of diffuse large B-cell lymphoma
- 2017
-
Ingår i: Lupus Science and Medicine. - : BMJ. - 2053-8790. ; 4:1
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: Determinants of the increased risk of diffuse large B-cell lymphoma (DLBCL) in SLE are unclear. Using data from a recent lymphoma genome-wide association study (GWAS), we assessed whether certain lupus-related single nucleotide polymorphisms (SNPs) were also associated with DLBCL. Methods: GWAS data on European Caucasians from the International Lymphoma Epidemiology Consortium (InterLymph) provided a total of 3857 DLBCL cases and 7666 general-population controls. Data were pooled in a random-effects meta-analysis. Results: Among the 28 SLE-related SNPs investigated, the two most convincingly associated with risk of DLBCL included the CD40 SLE risk allele rs4810485 on chromosome 20q13 (OR per risk allele=1.09, 95% CI 1.02 to 1.16, p=0.0134), and the HLA SLE risk allele rs1270942 on chromosome 6p21.33 (OR per risk allele=1.17, 95% CI 1.01 to 1.36, p=0.0362). Of additional possible interest were rs2205960 and rs12537284. The rs2205960 SNP, related to a cytokine of the tumour necrosis factor superfamily TNFSF4, was associated with an OR per risk allele of 1.07, 95% CI 1.00 to 1.16, p=0.0549. The OR for the rs12537284 (chromosome 7q32, IRF5 gene) risk allele was 1.08, 95% CI 0.99 to 1.18, p=0.0765. Conclusions: These data suggest several plausible genetic links between DLBCL and SLE.
|
|
| 14. |
|
|
| 15. |
- Cats, Oded, 1983-, et al.
(författare)
-
How fair is the fare? Estimating travel patterns and the impacts of fare schemes for different user groups in Stockholm based on smartcard data : Final report for Trafik och Region 2018 SLL-KTH research project
- 2019
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- There is a rapid increase in the deployment, acquisition and analysis of automated fare collection (AFC) systems, enabling a profound change in the ability to analyze high-volume data that relate to observed passenger travel behavior and recurrent patterns. The analysis of such passively collected data offers direct access to a continuous flow of observed passenger behavior at a large scale, saving expensive data collection efforts. For a review of the spectrum of applications – from strategic demand estimation to operational service performance measurements.The FairAccess project leverages on the availability of Access-kort data for the vast majority of trips performed in Stockholm County. The overarching goal of this project is to develop means to analyse empirically the impacts of policy/planning measures based on disaggregate passively collected smart card data. This involves a series of analysis and modelling challenges. We develop and apply a series algorithms to infer of tap-out locations, infer vehicles and travel times, and infer transfers to that journeys can be composed. Tap-in records have been matched with corresponding inferred tap-out locations and time stamps for about 80% of all records. Thereafter, we construct time-dependent origin-destination matrices for which segmentations can be performed with respect to geographical and user product features.We demonstrate the approach and algorithms developed by performing a before-after analysis of the fare scheme change from zone-based to flat fares. We analyse changes in travel patterns and derive price elasticities for distinctive market segments. The introduced fare policy delivered the desirable result of an increased ridership through improved convenience of the single-use products. Nevertheless, the significance of the service convenience component was underestimated, which resulted in the price adjustments being not in line with the mobility effects.The planning and development of the Stockholm public transport system must rely on the best empirical foundations available to support evidence-based decision-making and make the right priorities. To this end, the development and analysis performed in the FairAccess project lay a necessary foundation for further methodological developments and analyses such as on-board crowding evaluation, demand forecasting and identifying user groups.
|
|
| 16. |
- Cebecauer, Matej, et al.
(författare)
-
Generating Network-Wide Travel Diaries and OD Matrices Using Stockholm County Smartcard Data
- 2020
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Bakgrund: The public transport system in Stockholm extends across the greater Stockholm area, covering ca 6,500 km2 and 2.3 million inhabitants. The system includes 21 commuter train, metro, light rail and tram lines spanning ca 470 km, around 490 bus lines spanning ca 9,100 km, and a number of ferry lines (SLL 2016). The main ticketing system is the Access system, which uses electronic tickets that are loaded onto contactless cards. The system was introduced in limited scale in 2008 and the average number of ticket validations per day has since grown to 1.9 million in 2018. Trafikförvaltningen, Region Stockholm is collecting access smartcard data for several years. Just for year 2017 smartcard data consist of approximately 680 million tap-in records. The majority of tap-ins are recorded at metro gates (45%) and upon boarding buses (41%) while the remaining consists of commuter trains, trams, and ferries. Each card has a unique number, which allows it to be traced and construct the complete journeys and travel diaries. There is a big potential in using these data for different analysis, evaluation, and planning of public transport. We present the framework that enables processing of raw access data in fusion with AVL and network data to the network-wide travel diaries. Furthermore, the estimated OD matrices can be used for measuring the impacts of various interventions such as fare policy and service design changes. The inferred travel diaries also allow for extracting passenger loads for each vehicle trip segment across the network at the same resolution as the flow outputs of schedule-based transit assignment models.Metod: Tickets are validated upon access to stations or boarding of vehicles but not on egress or alighting. In other words, the Access system is “tap-in only”. We propose a method to estimate the alighting station in a multimodal public transport system, where tap-in transactions are observed in a complex network. Similar to previous literature it is assumed that the alighting occurs within a certain distance of the next transaction. Furthermore, vehicle and time inference using AVL data is performed. Trip elements are assessed individually resulting in individual travel diaries.Resultat och slutsats: The implemented inference algorithms and the derived travel diaries facilitate the construction of OD matrices that are essential input for services planning. The performance of the inferring algorithms is: for the alighting station: 87%; for travel time 70% using AVL data exclusively; considering all trips even without alighting station 86% of all journeys have inferred destination; from which 73% have travel time estimated.
|
|
| 17. |
- Cerhan, James R., et al.
(författare)
-
Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma
- 2014
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:11, s. 1233-1238
-
Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 x 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 x 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 x 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 x 10(-13) and 3.63 x 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.
|
|
| 18. |
- Donofrio, Claudio, et al.
(författare)
-
Long-term Reproducibility for Jupyter Notebook
- 2023
-
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.
|
|
| 19. |
- Fallows, Richard A., et al.
(författare)
-
A LOFAR observation of ionospheric scintillation from two simultaneous travelling ionospheric disturbances
- 2020
-
Ingår i: Journal of Space Weather and Space Climate. - : EDP Sciences. - 2115-7251. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- This paper presents the results from one of the first observations of ionospheric scintillation taken using the Low-Frequency Array (LOFAR). The observation was of the strong natural radio source Cassiopeia A, taken overnight on 18-19 August 2013, and exhibited moderately strong scattering effects in dynamic spectra of intensity received across an observing bandwidth of 10-80 MHz. Delay-Doppler spectra (the 2-D FFT of the dynamic spectrum) from the first hour of observation showed two discrete parabolic arcs, one with a steep curvature and the other shallow, which can be used to provide estimates of the distance to, and velocity of, the scattering plasma. A cross-correlation analysis of data received by the dense array of stations in the LOFAR "core" reveals two different velocities in the scintillation pattern: a primary velocity of similar to 20-40 ms(-1) with a north-west to south-east direction, associated with the steep parabolic arc and a scattering altitude in the F-region or higher, and a secondary velocity of similar to 110 ms(-1) with a north-east to south-west direction, associated with the shallow arc and a scattering altitude in the D-region. Geomagnetic activity was low in the mid-latitudes at the time, but a weak sub-storm at high latitudes reached its peak at the start of the observation. An analysis of Global Navigation Satellite Systems (GNSS) and ionosonde data from the time reveals a larger-scale travelling ionospheric disturbance (TID), possibly the result of the high-latitude activity, travelling in the north-west to south-east direction, and, simultaneously, a smaller-scale TID travelling in a north-east to south-west direction, which could be associated with atmospheric gravity wave activity. The LOFAR observation shows scattering from both TIDs, at different altitudes and propagating in different directions. To the best of our knowledge this is the first time that such a phenomenon has been reported.
|
|
| 20. |
- Heiskanen, Jouni, et al.
(författare)
-
The Integrated Carbon Observation System in Europe
- 2022
-
Ingår i: Bulletin of the American Meteorological Society. - 0003-0007. ; 103:3, s. 855-872
-
Tidskriftsartikel (refereegranskat)abstract
- Since 1750, land-use change and fossil fuel combustion has led to a 46% increase in the atmospheric carbon dioxide (CO2) concentrations, causing global warming with substantial societal consequences. The Paris Agreement aims to limit global temperature increases to well below 2C above preindustrial levels. Increasing levels of CO2 and other greenhouse gases (GHGs), such as methane (CH4) and nitrous oxide (N2O), in the atmosphere are the primary cause of climate change. Approximately half of the carbon emissions to the atmosphere are sequestered by ocean and land sinks, leading to ocean acidification but also slowing the rate of global warming. However, there are significant uncertainties in the future global warming scenarios due to uncertainties in the size, nature, and stability of these sinks. Quantifying and monitoring the size and timing of natural sinks and the impact of climate change on ecosystems are important information to guide policy-makers' decisions and strategies on reductions in emissions. Continuous, long-term observations are required to quantify GHG emissions, sinks, and their impacts on Earth systems. The Integrated Carbon Observation System (ICOS) was designed as the European in situ observation and information system to support science and society in their efforts to mitigate climate change. It provides standardized and open data currently from over 140 measurement stations across 12 European countries. The stations observe GHG concentrations in the atmosphere and carbon and GHG fluxes between the atmosphere, land surface, and the oceans. This article describes how ICOS fulfills its mission to harmonize these observations, ensure the related long-term financial commitments, provide easy access to well-documented and reproducible high-quality data and related protocols and tools for scientific studies, and deliver information and GHG-related products to stakeholders in society and policy.
|
|
| 21. |
- Hellström, Margareta, et al.
(författare)
-
Identification and citation of digital research resources
- 2020
-
Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783030528294 - 9783030528287 ; 12003, s. 162-175
-
Bokkapitel (refereegranskat)abstract
- Environmental research infrastructures are often built on a large number of distributed observational or experimental sites, run by hundreds of scientists and technicians, financially supported and administrated by a large number of institutions. It becomes very important to acknowledge the data sources and their providers. There is also a strong need for common data citation tracking systems that allow data providers to identify downstream usage of their data so as to demonstrate their importance and show the impact to stakeholders and the public. This chapter highlights identification and citation in environmental RIs, reviews available technologies and develops common services for these operations. This chapter presents a suggested common system design for Identification and Citation, as well as an outline for negotiations and discussions with publishers and other actors in the scholarly data management and curation world.
|
|
| 22. |
|
|
| 23. |
- Johansson, Peter, et al.
(författare)
-
Deep sequencing of uveal melanoma identifies a recurrent mutation in PLCB4.
- 2016
-
Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 7:4, s. 4624-4631
-
Tidskriftsartikel (refereegranskat)abstract
- Next generation sequencing of uveal melanoma (UM) samples has identified a number of recurrent oncogenic or loss-of-function mutations in key driver genes including: GNAQ, GNA11, EIF1AX, SF3B1 and BAP1. To search for additional driver mutations in this tumor type we carried out whole-genome or whole-exome sequencing of 28 tumors or primary cell lines. These samples have a low mutation burden, with a mean of 10.6 protein changing mutations per sample (range 0 to 53). As expected for these sun-shielded melanomas the mutation spectrum was not consistent with an ultraviolet radiation signature, instead, a BRCA mutation signature predominated. In addition to mutations in the known UM driver genes, we found a recurrent mutation in PLCB4 (c.G1888T, p.D630Y, NM_000933), which was validated using Sanger sequencing. The identical mutation was also found in published UM sequence data (1 of 56 tumors), supporting its role as a novel driver mutation in UM. PLCB4 p.D630Y mutations are mutually exclusive with mutations in GNA11 and GNAQ, consistent with PLCB4 being the canonical downstream target of the former gene products. Taken together these data suggest that the PLCB4 hotspot mutation is similarly a gain-of-function mutation leading to activation of the same signaling pathway, promoting UM tumorigenesis.
|
|
| 24. |
- Justice, Anne E., et al.
(författare)
-
Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution
- 2019
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:3, s. 452-469
-
Tidskriftsartikel (refereegranskat)abstract
- Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF >= 5%) and nine low-frequency or rare (MAF < 5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.
|
|
| 25. |
- Kholodov, Yaroslav, et al.
(författare)
-
Public transport fare elasticities from smartcard data: Evidence from a natural experiment
- 2021
-
Ingår i: Transport Policy. - : Elsevier BV. - 0967-070X .- 1879-310X. ; 105, s. 35-43
-
Tidskriftsartikel (refereegranskat)abstract
- This paper develops a method for analysing the elasticity of travel demand to public transport fares. The methodology utilizes public transport smartcard data for collecting disaggregate full population data about passengers’ travel behaviour. The study extends previous work by deriving specific fare elasticities for distinct socioeconomic (e.g., car ownership and income) groups and public transport modes (metro, trains and buses), and by considering the directionality of the fare change. The case study involves a public transport fare policy introduced by the regional administration of Stockholm County in January 2017, where the zonal fare system for single-trip tickets was replaced by a flat-fare policy. The overall fare elasticity of travel funds is found to be −0.46. User sensitivity grows along with the journey distance. Metro users demonstrate the lowest sensitivity, followed by bus and commuter train riders. Low socioeconomic groups, in particular with respect to car ownership, tend to be less sensitive than the high-factor groups. In addition to the direct effect of changed fares, simplification and unification of the fare scheme appears to have substantially contributed to its attractiveness. The flat fare may allow the geographic disparity of public transport travel to be reduced and new users to be attracted from remote areas who are more prone to own cars.
|
|
