| 1. |
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| 2. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 3. |
- Aumayr, Friedrich, et al.
(författare)
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Roadmap on photonic, electronic and atomic collision physics : III. Heavy particles
- 2019
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 52:17
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Tidskriftsartikel (refereegranskat)abstract
- We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. Roadmap III focusses on heavy particles: with zero to relativistic speeds. Modern theoretical and experimental approaches provide detailed insight into the wide range of many-body interactions involving projectiles and targets of varying complexity ranging from simple atoms, through molecules and clusters, complex biomolecules and nanoparticles to surfaces and crystals. These developments have been driven by technological progress and future developments will expand the horizon of the systems that can be studied. This Roadmap aims at looking back along the road, explaining the evolution of the field, and looking forward, collecting nineteen contributions from leading scientists in the field.
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| 4. |
- Mohammed Taha, Hiba, et al.
(författare)
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The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry
- 2022
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Ingår i: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 34:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).
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| 5. |
- Wassermann, Stella, et al.
(författare)
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p16INK4a is a beta-catenin target gene and indicates low survival in human colorectal tumors
- 2009
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Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 136:1, s. 196-205.e2
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND & AIMS: Human colorectal carcinomas display an infiltrative front of invasion where tumor cells undergo an epithelomesenchymal transition associated with low survival. Epithelomesenchymal transition is regulated by a nuclear beta-catenin accumulation, and subsequently, activation of beta-catenin/TCF4 target genes similar to CYCLIN D(1). Unexpectedly, these tumor cells are characterized by low proliferation, which correlates with the expression of the cell cycle inhibitor p16(INK4A). Therefore, we investigated the molecular mechanism of the transcriptional regulation of p16(INK4A) in colorectal cancer and its correlation with survival. METHODS: Molecular biological techniques were used for investigating the transcriptional mechanisms of the p16(INK4A) gene regulation. Moreover, p16(INK4A) expression was correlated with the 10-year survival of patients with colorectal carcinomas. RESULTS: In colorectal carcinomas, expression of the p16(INK4A) gene is regulated by beta-catenin/TCF4 and correlates with low survival rates of patients with tumors displaying an infiltrative front of invasion. CONCLUSIONS: beta-catenin/TCF4 regulates cell cycle promoting (c-MYC, CYCLIN D(1)) and inhibiting genes (p16(INK4A)) at the same time in the mesenchymally differentiated tumor cells at the front of invasion. The function of p16(INK4A) seems to supersede in this context thus leading to low proliferation. Moreover, these tumor cells seem to govern the outcome of colorectal cancer independently of their proliferation.
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| 6. |
- Ahlkrona, Josefin, et al.
(författare)
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Dynamically coupling the non-linear Stokes equations with the shallow ice approximation in glaciology : Description and first applications of the ISCAL method
- 2016
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 308, s. 1-19
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Tidskriftsartikel (refereegranskat)abstract
- We propose and implement a new method, called the Ice Sheet Coupled Approximation Levels (ISCAL) method, for simulation of ice sheet flow in large domains during long time-intervals. The method couples the full Stokes (FS) equations with the Shallow Ice Approximation (SIA). The part of the domain where SIA is applied is determined automatically and dynamically based on estimates of the modeling error. For a three dimensional model problem, ISCAL computes the solution substantially faster with a low reduction in accuracy compared to a monolithic FS. Furthermore, ISCAL is shown to be able to detect rapid dynamic changes in the flow. Three different error estimations are applied and compared. Finally, ISCAL is applied to the Greenland Ice Sheet on a quasi-uniform grid, proving ISCAL to be a potential valuable tool for the ice sheet modeling community.
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| 7. |
- Blösch, Günter, et al.
(författare)
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Twenty-three unsolved problems in hydrology (UPH) - a community perspective
- 2019
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Ingår i: Hydrological Sciences Journal. - : Informa UK Limited. - 0262-6667 .- 2150-3435. ; 64:10, s. 1141-1158
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Tidskriftsartikel (refereegranskat)abstract
- This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.
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| 8. |
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| 9. |
- Jakobsson, Martin, et al.
(författare)
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Ryder Glacier in northwest Greenland is shielded from warm Atlantic water by a bathymetric sill
- 2020
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Ingår i: Communications Earth & Environment. - : Springer Science and Business Media LLC. - 2662-4435. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- The processes controlling advance and retreat of outlet glaciers in fjords draining the Greenland Ice Sheet remain poorly known, undermining assessments of their dynamics and associated sea-level rise in a warming climate. Mass loss of the Greenland Ice Sheet has increased six-fold over the last four decades, with discharge and melt from outlet glaciers comprising key components of this loss. Here we acquired oceanographic data and multibeam bathymetry in the previously uncharted Sherard Osborn Fjord in northwest Greenland where Ryder Glacier drains into the Arctic Ocean. Our data show that warmer subsurface water of Atlantic origin enters the fjord, but Ryder Glacier’s floating tongue at its present location is partly protected from the inflow by a bathymetric sill located in the innermost fjord. This reduces under-ice melting of the glacier, providing insight into Ryder Glacier’s dynamics and its vulnerability to inflow of Atlantic warmer water.
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| 10. |
- O'Regan, Matt, et al.
(författare)
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The De Long Trough: A newly discovered glacial trough on the East Siberian continental margin
- 2017
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 13:9, s. 1269-1284
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Tidskriftsartikel (refereegranskat)abstract
- Ice sheets extending over parts of the East Siberian continental shelf have been proposed for the last glacial period and during the larger Pleistocene glaciations. The sparse data available over this sector of the Arctic Ocean have left the timing, extent and even existence of these ice sheets largely unresolved. Here we present new geophysical mapping and sediment coring data from the East Siberian shelf and slope collected during the 2014 SWERUS-C3 expedition (SWERUS-C3: Swedish - Russian - US Arctic Ocean Investigation of Climate-Cryosphere-Carbon Interactions). The multibeam bathymetry and chirp sub-bottom profiles reveal a set of glacial landforms that include grounding zone formations along the outer continental shelf, seaward of which lies a > 65m thick sequence of glacio-genic debris flows. The glacial landforms are interpreted to lie at the seaward end of a glacial trough - the first to be reported on the East Siberian margin, here referred to as the De Long Trough because of its location due north of the De Long Islands. Stratigraphy and dating of sediment cores show that a drape of acoustically laminated sediments covering the glacial deposits is older than similar to 50 cal kyr BP. This provides direct evidence for extensive glacial activity on the Siberian shelf that predates the Last Glacial Maximum and most likely occurred during the Saalian (Marine Isotope Stage (MIS) 6).
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