| 1. |
- Abbasi, R., et al.
(author)
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The IceCube data acquisition system : Signal capture, digitization, and timestamping
- 2009
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In: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 601:3, s. 294-316
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Journal article (peer-reviewed)abstract
- IceCube is a km-scale neutrino observatory under construction at the South Pole with sensors both in the deep ice (InIce) and on the surface (IceTop). The sensors, called Digital Optical Modules (DOMs). detect, digitize and timestamp the signals from optical Cherenkov-radiation photons. The DOM Main Board (MB) data acquisition subsystem is connected to the central DAQ in the IceCube Laboratory (ICL) by a single twisted copper wire-pair and transmits packetized data on demand. Time calibration is maintained throughout the array by regular transmission to the DOMs of precisely timed analog signals, synchronized to a central GPS-disciplined clock. The design goals and consequent features, functional capabilities, and initial performance of the DOM MB, and the operation of a combined array of DOMs as a system, are described here. Experience with the first InIce strings and the IceTop stations indicates that the system design and performance goals have been achieved. (c) 2009 Elsevier B.V. All rights reserved.
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| 2. |
- Butterworth, J., et al.
(author)
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Les Houches 2013: Physics at TeV Colliders: Standard Model Working Group Report
- 2014
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Conference paper (peer-reviewed)abstract
- This Report summarizes the proceedings of the 2013 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt primarily with (1) the techniques for calculating standard model multi-leg NLO and NNLO QCD and NLO EW cross sections and (2) the comparison of those cross sections with LHC data from Run 1, and projections for future measurements in Run 2.
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| 3. |
- Bakker, D. C. E., et al.
(author)
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An update to the surface ocean CO2 atlas (SOCAT version 2)
- 2014
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 6:1, s. 69-90
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Journal article (peer-reviewed)abstract
- The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO 2 values) and extended data coverage (from 1968-2007 to 1968-2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models. © Author(s) 2014. CC Attribution 3.0 License.
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| 4. |
- Brownstein, Catherine A., et al.
(author)
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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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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Journal article (peer-reviewed)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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| 5. |
- Hock, R, et al.
(author)
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High Mountain Areas
- 2019
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In: IPCC Special Report on the Ocean and Cryosphere in a Changing Climate. - : IPCC - Intergovernmental Panel on Climate Change. ; , s. 131-202
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Book chapter (other academic/artistic)abstract
- The cryosphere (including, snow, glaciers, permafrost, lake and river ice) is an integral element of high- mountain regions, which are home to roughly 10% of the global population. Widespread cryosphere changes affect physical, biological and human systems in the mountains and surrounding lowlands, with impacts evident even in the ocean. Building on the IPCC’s Fifth Assessment Report (AR5), this chapter assesses new evidence on observed recent and projected changes in the mountain cryosphere as well as associated impacts, risks and adaptation measures related to natural and human systems. Impacts in response to climate changes independently of changes in the cryosphere are not assessed in this chapter. Polar mountains are included in Chapter 3, except those in Alaska and adjacent Yukon, Iceland, and Scandinavia, which are included in this chapter.
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| 8. |
- Ahlgrim, C., et al.
(author)
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Comparison of Molecular Multiplex and Singleplex Analysis of IgE to Grass Pollen Allergens in Untreated German Grass Pollen-Allergic Patients
- 2015
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In: Journal of investigational allergology & clinical immunology. - 1018-9068 .- 1698-0808. ; 25:3, s. 190-195
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Journal article (peer-reviewed)abstract
- Background: The ImmunoCAP ISAC 112 platform is the only commercially available molecular allergy IgE multiplex test. Data on the comparison of this rather novel test with the molecular singleplex ImmunoCAP IgE platform are lacking. Objective:To compare the multiplex ISAC 112 platform and the singleplex ImmunoCAP platform in regard to IgE to grass pollen allergens in untreated grass pollen allergic patients in Germany. Methods: Serum samples from 101 adults with grass pollen allergy were analyzed for specific IgE (sIgE) to 8 allergenic molecules from timothy grass pollen and to the 112 allergenic molecules included in the ISAC panel. The results for the multiplex and singleplex tests were subsequently analyzed statistically. Results: Comparison of sIgE to grass pollen allergens detected by ISAC 112 and the singleplex ImmunoCAP assay revealed the following correlation coefficients: 0.88 (rPhl p1), 0.96 (rPhl p2), 0.70 (nPhl p4), 0.94 (rPhl p5b), 0.92 (rPhl p6), 0.85 (rPhl p11), and 0.78 (rPhl p12). Conclusion: Molecular testing with ISAC 112 correlates well with the ImmunoCAP platform for respective molecular timothy grass pollen allergens.
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| 9. |
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| 10. |
- Darsow, U., et al.
(author)
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Heterogeneity of molecular sensitization profiles in grass pollen allergy - implications for immunotherapy?
- 2014
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In: Clinical and Experimental Allergy. - : Wiley. - 0954-7894 .- 1365-2222. ; 44:5, s. 778-786
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Journal article (peer-reviewed)abstract
- BackgroundData on molecular allergy diagnostics in adults with grass pollen allergy with regard to conjunctival and nasal provocation test outcome and specific immunotherapy are lacking to date. ObjectiveTo assess whether molecular allergy diagnostics for grass pollen allergens could help with predicting provocation test outcomes and serve as a basis for future component-resolved specific immunotherapy. MethodsSera of 101 adults with grass pollen allergy was analysed for IgE against timothy grass pollen (Phleum pratense), rPhl p 1, rPhl p 2, nPhl p 4, rPhl p 5b, rPhl p 6, rPhl p 7, rPhl p 11 and rPhl p12 and correlated with the individuals' outcome in the nasal and conjunctival provocation tests and investigated in regard to a potential component-resolved specific immunotherapy. ResultsAn increasing number of sensitizations to timothy grass allergens was correlated to a positive reaction in the conjunctival (4.9 vs. 3.6, P=0.003) and nasal provocation tests (4.5 vs. 2.2, P=0.0175). In molecular sensitization profiles, a substantial heterogeneity was detected, with none of the patients exactly matching the allergen composition of a previously published component-resolved specific immunotherapy containing Phl p 1, Phl p 2, Phl p 5a/b and Phl p 6. The results indicate that in 95% of the patients, a proportion of 50% of timothy-IgE would be targeted with such a specific immunotherapy, while in 50% and 10% of patients, 80% and 90% of timothy-IgE would be targeted, respectively. Conclusion and Clinical RelevanceMolecular allergy diagnostics is a prerequisite for future component-resolved specific immunotherapy due to the high heterogeneity of sensitization profiles. However, of current clinical relevance is the observed correlation between the number of sensitizations and provocation test outcome.
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| 11. |
- Glas, Gerie J., et al.
(author)
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Ventilation practices in burn patients-an international prospective observational cohort study
- 2021
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In: BURNS & TRAUMA. - : Oxford University Press. - 2321-3868 .- 2321-3876. ; 9
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Journal article (peer-reviewed)abstract
- Background: It is unknown whether lung-protective ventilation is applied in burn patients and whether they benefit from it. This study aimed to determine ventilation practices in burn intensive care units (ICUs) and investigate the association between lung-protective ventilation and the number of ventilator-free days and alive at day 28 (VFD-28). Methods: This is an international prospective observational cohort study including adult burn patients requiring mechanical ventilation. Low tidal volume (V-T) was defined as V-T <= 8 mL/kg predicted body weight (PBW). Levels of positive end-expiratory pressure (PEEP) and maximum airway pressures were collected. The association between V-T and VFD-28 was analyzed using a competing risk model. Ventilation settings were presented for all patients, focusing on the first day of ventilation. We also compared ventilation settings between patients with and without inhalation trauma. Results: A total of 160 patients from 28 ICUs in 16 countries were included. Low V-T was used in 74% of patients, median V-T size was 7.3 [interquartile range (IQR) 6.2-8.3] mL/kg PBW and did not differ between patients with and without inhalation trauma (p= 0.58). Median VFD-28 was 17 (IQR 0-26), without a difference between ventilation with low or high V-T (p= 0.98). All patients were ventilated with PEEP levels >= 5 cmH(2)O; 80% of patients had maximum airway pressures <30 cmH(2)O. Conclusion: In this international cohort study we found that lung-protective ventilation is used in the majority of burn patients, irrespective of the presence of inhalation trauma. Use of low V-T was not associated with a reduction in VFD-28.
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| 12. |
- Huang, D., et al.
(author)
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The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation
- 2017
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7:1
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Journal article (peer-reviewed)abstract
- The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells. In addition, we examined the dynamics of gene expression changes using inducible CDX2 embryonic stem (ES) cells, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we identify putative novel regulatory elements that repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.
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| 16. |
- Ampomah, Osei Y., et al.
(author)
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Nodulation and ecological significance of indigenous legumes in Scotland and Sweden
- 2012
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In: Symbiosis. - : Springer Nature. - 0334-5114 .- 1878-7665. ; 57:3, s. 133-148
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Journal article (peer-reviewed)abstract
- The ability of wild indigenous legumes to form root nodules capable of biological nitrogen (N 2) fixation has rarely been demonstrated for species in natural ecosystems in large parts of Europe. In order to understand and manage these ecosystems, it is important to demonstrate nodulation across a diverse range of environments, sites and climates. This study surveyed nodulation at a number of sites in Scotland and Sweden. Presence of nodules was noted and nodule structure and indicators of nitrogen fixation capacity were assessed using light and transmission electron microscopy. Soils from several sites were also sampled for carbon and nitrogen analysis. The collections comprised 24 species in Scotland, and 30 taxa in Sweden; 17 of these in common for both countries. Highest species numbers occurred in meadows, farmland margins, hedgerows, roadsides and wasteland. Coastal sites and sites in the mountainous region above the Arctic Circle hosted several rare species. All sampled species had features of N 2-fixing nodules such as pink colour (leghaemoglobin) when dissected and bacteroids. Nodule structure for a number of species is here reported for the first time and presence of the N 2-fixing enzyme nitrogenase is demonstrated in three previously not studied Swedish legume species. North European legumes may make significant contributions to the N-budgets of their ecosystems. Such species (and their symbionts) represent unique germplasm that may be adopted to empower advances in agriculture and conservation aimed at mitigation and adaptation to the effects of climate change.
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| 17. |
- Bustamante, Mercedes, et al.
(author)
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Ten new insights in climate science 2023
- 2023
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In: Global Sustainability. - : CAMBRIDGE UNIV PRESS. - 2059-4798. ; 7
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Research review (peer-reviewed)abstract
- Non-technical summary We identify a set of essential recent advances in climate change research with high policy relevance, across natural and social sciences: (1) looming inevitability and implications of overshooting the 1.5 degrees C warming limit, (2) urgent need for a rapid and managed fossil fuel phase-out, (3) challenges for scaling carbon dioxide removal, (4) uncertainties regarding the future contribution of natural carbon sinks, (5) intertwinedness of the crises of biodiversity loss and climate change, (6) compound events, (7) mountain glacier loss, (8) human immobility in the face of climate risks, (9) adaptation justice, and (10) just transitions in food systems.Technical summary The Intergovernmental Panel on Climate Change Assessment Reports provides the scientific foundation for international climate negotiations and constitutes an unmatched resource for researchers. However, the assessment cycles take multiple years. As a contribution to cross- and interdisciplinary understanding of climate change across diverse research communities, we have streamlined an annual process to identify and synthesize significant research advances. We collected input from experts on various fields using an online questionnaire and prioritized a set of 10 key research insights with high policy relevance. This year, we focus on: (1) the looming overshoot of the 1.5 degrees C warming limit, (2) the urgency of fossil fuel phase-out, (3) challenges to scale-up carbon dioxide removal, (4) uncertainties regarding future natural carbon sinks, (5) the need for joint governance of biodiversity loss and climate change, (6) advances in understanding compound events, (7) accelerated mountain glacier loss, (8) human immobility amidst climate risks, (9) adaptation justice, and (10) just transitions in food systems. We present a succinct account of these insights, reflect on their policy implications, and offer an integrated set of policy-relevant messages. This science synthesis and science communication effort is also the basis for a policy report contributing to elevate climate science every year in time for the United Nations Climate Change Conference.Social media summary We highlight recent and policy-relevant advances in climate change research - with input from more than 200 experts.
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| 21. |
- Huss-Marp, J, et al.
(author)
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Can Immunoglobulin E-measurement replace challenge tests in allergic rhinoconjunctivits to grass pollen?
- 2011
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In: CLINICAL AND EXPERIMENTAL ALLERGY. - 0954-7894. ; 41:8, s. 1116-1124
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Journal article (peer-reviewed)abstract
- BACKGROUND: There is minimal data available concerning the dose-response relationship between allergen exposure and clinical reactivity for outdoor aeroallergens, such as timothy grass pollen. Timothy pollen-specific IgE (sIgE) determinations might assist in predicting the clinical reactivity in patients with allergic rhinoconjunctivitis (ARC). METHODS: Allergen-sIgE antibody levels of timothy grass pollen were correlated with individual threshold doses eliciting allergic reactions in skin prick test (SPT), conjunctival (CPT) and nasal (NPT) provocation tests in patients suffering from pollen-induced rhinoconjunctivitis and healthy controls. RESULTS: One hundred and four patients with ARC (median age: 27 years; range: 18-64; females: 58%) and 36 controls (25 years (22-77); females: 70%) were included in the study. Ninety-six percent of the patients showed a positive reaction in the nasal and 57% showed a positive reaction in the conjunctival provocation. With regarding to titrated SPT, 98% of the patients showed a positive skin test reaction; correlating with the level of sIgE for timothy (P < 0.001). For both provocation protocols, there was no correlation between the provocation concentration at the reaction and the level of sIgE for timothy. The ratio of sIgE/total IgE correlated with the dilution level of SPT (P < 0.002) and CPT (P < 0.01), respectively. CONCLUSION AND CLINICAL RELEVANCE: A dose-response relationship between the levels of sIgE and clinical outcome of timothy allergen exposure could not be established. Although IgE-determination remains an important key element in allergy diagnosis, provocation tests are procedures of choice if the clinical relevance of an allergen has to be confirmed.
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| 25. |
- Sievers, E., et al.
(author)
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SRC inhibition represents a potential therapeutic strategy in liposarcoma
- 2015
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In: International Journal of Cancer. - : Wiley. - 0020-7136. ; 137:11, s. 2578-2588
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Journal article (peer-reviewed)abstract
- Liposarcomas (LS) are the most common malignant mesenchymal tumors, with an overall long-term mortality rate of 60%. LS comprise three major subtypes, i.e., well-differentiated/dedifferentiated liposarcoma (WDLS/DDLS), myxoid/round cell liposarcoma (MLS) and pleomorphic liposarcoma (PLS). Aiming at the preclinical identification of novel therapeutic options, we here investigate the functional significance of SRC in primary human LS and in LS-derived cell lines. Immunohistochemical and Western blot analyses reveal relevant levels of activated p-(Tyr416)-SRC in LS of the different subtypes with particular activation in MLS and PLS. Dysregulation of the SRC modifiers CSK and PTP1B was excluded as major reason for the activation of the kinase. Consistent siRNA-mediated knockdown of SRC or inhibition by the SRC inhibitor Dasatinib led to decreased proliferation of LS cell lines of the different subtypes, with MLS cells reacting particularly sensitive in MTT assays. Flow cytometric analyses revealed that this effect was due to a significant decrease in mitotic activity and an induction of apoptosis. SRC inhibition by Dasatinib resulted in dephosphorylation of SRC itself, its interacting partners FAK and IGF-IR as well as its downstream target AKT. Consistent with a particular role of SRC in cell motility, Dasatinib reduced the migratory and invasive potential of MLS cells in Boyden chamber and Matrigel chamber assays. In summary, we provide evidence that SRC activation plays an important role in LS biology and therefore represents a potential therapeutic target, particularly in MLS and PLS.
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