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| 10. |
- Johnatty, S. E., et al.
(author)
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No evidence that GATA3 rs570613 SNP modifies breast cancer risk
- 2009
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In: Breast Cancer Research and Treatment. - : Springer. - 0167-6806 .- 1573-7217. ; 117:2, s. 371-379
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Journal article (peer-reviewed)abstract
- GATA-binding protein 3 (GATA3) is a transcription factor that is crucial to mammary gland morphogenesis and differentiation of progenitor cells, and has been suggested to have a tumor suppressor function. The rs570613 single nucleotide polymorphism (SNP) in intron 4 of GATA3 was previously found to be associated with a reduction in breast cancer risk in the Cancer Genetic Markers of Susceptibility project and in pooled analysis of two case-control studies from Norway and Poland (P trend = 0.004), with some evidence for a stronger association with estrogen receptor (ER) negative tumours [Garcia-Closas M et al. (2007) Cancer Epidemiol Biomarkers Prev 16:2269-2275]. We genotyped GATA3 rs570613 in 6,388 cases and 4,995 controls from the Breast Cancer Association Consortium (BCAC) and 5,617 BRCA1 and BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). We found no association between this SNP and breast cancer risk in BCAC cases overall (ORper-allele = 1.00, 95% CI 0.94-1.05), in ER negative BCAC cases (ORper-allele = 1.02, 95% CI 0.91-1.13), in BRCA1 mutation carriers RRper-allele = 0.99, 95% CI 0.90-1.09) or BRCA2 mutation carriers (RRper-allele = 0.93, 95% CI 0.80-1.07). We conclude that there is no evidence that either GATA3 rs570613, or any variant in strong linkage disequilibrium with it, is associated with breast cancer risk in women.
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| 11. |
- Thompson, B.A., et al.
(author)
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Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database
- 2014
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:2, s. 107-115
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Journal article (peer-reviewed)abstract
- The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases. © 2014 Nature America, Inc.
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| 12. |
- Cronin, M. F., et al.
(author)
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Developing an Observing Air-Sea Interactions Strategy (OASIS) for the global ocean
- 2022
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In: Ices Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 80:2, s. 367-73
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Journal article (peer-reviewed)abstract
- The Observing Air-Sea Interactions Strategy (OASIS) is a new United Nations Decade of Ocean Science for Sustainable Development programme working to develop a practical, integrated approach for observing air-sea interactions globally for improved Earth system (including ecosystem) forecasts, CO2 uptake assessments called for by the Paris Agreement, and invaluable surface ocean information for decision makers. Our "Theory of Change" relies upon leveraged multi-disciplinary activities, partnerships, and capacity strengthening. Recommendations from >40 OceanObs'19 community papers and a series of workshops have been consolidated into three interlinked Grand Ideas for creating #1: a globally distributed network of mobile air-sea observing platforms built around an expanded array of long-term time-series stations; #2: a satellite network, with high spatial and temporal resolution, optimized for measuring air-sea fluxes; and #3: improved representation of air-sea coupling in a hierarchy of Earth system models. OASIS activities are organized across five Theme Teams: (1) Observing Network Design & Model Improvement; (2) Partnership & Capacity Strengthening; (3) UN Decade OASIS Actions; (4) Best Practices & Interoperability Experiments; and (5) Findable-Accessible-Interoperable-Reusable (FAIR) models, data, and OASIS products. Stakeholders, including researchers, are actively recruited to participate in Theme Teams to help promote a predicted, safe, clean, healthy, resilient, and productive ocean.
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| 13. |
- Gille, T., et al.
(author)
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ERS International Congress 2021: highlights from the Respiratory Clinical Care and Physiology Assembly
- 2022
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In: European Respiratory Journal Open Research (ERJ Open Research). - : European Respiratory Society (ERS). - 2312-0541. ; 8:2
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Journal article (peer-reviewed)abstract
- It is a challenge to keep abreast of all the clinical and scientific advances in the field of respiratory medicine. This article contains an overview of laboratory-based science, randomised controlled trials and qualitative research that were presented during the 2021 European Respiratory Society International Congress within the sessions from the five groups of the Assembly 1 - Respiratory clinical care and physiology. Selected presentations are summarised from a wide range of topics: clinical problems, rehabilitation and chronic care, general practice and primary care, electronic/mobile health (e-health/m-health), clinical respiratory physiology, exercise and functional imaging.
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| 14. |
- Lossow, Stefan, 1977, et al.
(author)
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The SPARC water vapour assessment II: Profile-to-profile comparisons of stratospheric and lower mesospheric water vapour data sets obtained from satellites
- 2019
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 12:5, s. 2693-2732
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Journal article (peer-reviewed)abstract
- This work is distributed under the Creative Commons Attribution 4.0 License. Within the framework of the second SPARC (Stratosphere-troposphere Processes And their Role in Climate) water vapour assessment (WAVAS-II), profile-to-profile comparisons of stratospheric and lower mesospheric water vapour were performed by considering 33 data sets derived from satellite observations of 15 different instruments. These comparisons aimed to provide a picture of the typical biases and drifts in the observational database and to identify data-set-specific problems. The observational database typically exhibits the largest biases below 70 hPa, both in absolute and relative terms. The smallest biases are often found between 50 and 5 hPa. Typically, they range from 0.25 to 0.5 ppmv (5 % to 10 %) in this altitude region, based on the 50 % percentile over the different comparison results. Higher up, the biases increase with altitude overall but this general behaviour is accompanied by considerable variations. Characteristic values vary between 0.3 and 1 ppmv (4 % to 20 %). Obvious data-set-specific bias issues are found for a number of data sets. In our work we performed a drift analysis for data sets overlapping for a period of at least 36 months. This assessment shows a wide range of drifts among the different data sets that are statistically significant at the 2 σ uncertainty level. In general, the smallest drifts are found in the altitude range between about 30 and 10 hPa. Histograms considering results from all altitudes indicate the largest occurrence for drifts between 0.05 and 0.3 ppmv decade-1. Comparisons of our drift estimates to those derived from comparisons of zonal mean time series only exhibit statistically significant differences in slightly more than 3 % of the comparisons. Hence, drift estimates from profile-to-profile and zonal mean time series comparisons are largely interchangeable. As for the biases, a number of data sets exhibit prominent drift issues. In our analyses we found that the large number of MIPAS data sets included in the assessment affects our general results as well as the bias summaries we provide for the individual data sets. This is because these data sets exhibit a relative similarity with respect to the remaining data sets, despite the fact that they are based on different measurement modes and different processors implementing different retrieval choices. Because of that, we have by default considered an aggregation of the comparison results obtained from MIPAS data sets. Results without this aggregation are provided on multiple occasions to characterise the effects due to the numerous MIPAS data sets. Among other effects, they cause a reduction of the typical biases in the observational database.
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| 16. |
- Clerbaux, C., et al.
(author)
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CO measurements from the ACE-FTS satellite instrument: data analysis and validation using ground-based, airborne and spaceborne observations
- 2008
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 8, s. 2569-2594
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Journal article (peer-reviewed)abstract
- The Atmospheric Chemistry Experiment (ACE) mission was launched in August 2003 to sound the atmosphere by solar occultation. Carbon monoxide (CO), a good tracer of pollution plumes and atmospheric dynamics, is one of the key species provided by the primary instrument, the ACE-Fourier Transform Spectrometer (ACE-FTS). This instrument performs measurements in both the CO 1-0 and 2-0 ro-vibrational bands, from which vertically resolved CO concentration profiles are retrieved, from the mid-troposphere to the thermosphere. This paper presents an updated description of the ACE-FTS version 2.2 CO data product, along with a comprehensive validation of these profiles using available observations (February 2004 to December 2006). We have compared the CO partial columns with ground-based measurements using Fourier transform infrared spectroscopy and millimeter wave radiometry, and the volume mixing ratio profiles with airborne (both high-altitude balloon flight and airplane) observations. CO satellite observations provided by nadir-looking instruments (MOPITT and TES) as well as limb-viewing remote sensors (MIPAS, SMR and MLS) were also compared with the ACE-FTS CO products. We show that the ACE-FTS measurements provide CO profiles with small retrieval errors (better than 5% from the upper troposphere to 40 km, and better than 10% above). These observations agree well with the correlative measurements, considering the rather loose coincidence criteria in some cases. Based on the validation exercise we assess the following uncertainties to the ACE-FTS measurement data: better than 15% in the upper troposphere (8–12 km), than 30% in the lower stratosphere (12–30 km), and than 25% from 30 to 100 km.
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| 17. |
- Khosrawi, F., et al.
(author)
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The SPARC water vapour assessment II: Comparison of stratospheric and lower mesospheric water vapour time series observed from satellites
- 2018
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 11:7, s. 4435-4463
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Journal article (peer-reviewed)abstract
- Time series of stratospheric and lower mesospheric water vapour using 33 data sets from 15 different satellite instruments were compared in the framework of the second SPARC (Stratosphere-troposphere Processes And their Role in Climate) water vapour assessment (WAVAS-II). This comparison aimed to provide a comprehensive overview of the typical uncertainties in the observational database that can be considered in the future in observational and modelling studies, e.g addressing stratospheric water vapour trends. The time series comparisons are presented for the three latitude bands, the Antarctic (80°-70°S), the tropics (15°S-15°N) and the Northern Hemisphere mid-latitudes (50°-60°N) at four different altitudes (0.1, 3, 10 and 80hPa) covering the stratosphere and lower mesosphere. The combined temporal coverage of observations from the 15 satellite instruments allowed the consideration of the time period 1986-2014. In addition to the qualitative comparison of the time series, the agreement of the data sets is assessed quantitatively in the form of the spread (i.e. the difference between the maximum and minimum volume mixing ratios among the data sets), the (Pearson) correlation coefficient and the drift (i.e. linear changes of the difference between time series over time). Generally, good agreement between the time series was found in the middle stratosphere while larger differences were found in the lower mesosphere and near the tropopause. Concerning the latitude bands, the largest differences were found in the Antarctic while the best agreement was found for the tropics. From our assessment we find that most data sets can be considered in future observational and modelling studies, e.g. addressing stratospheric and lower mesospheric water vapour variability and trends, if data set specific characteristics (e.g. drift) and restrictions (e.g. temporal and spatial coverage) are taken into account.
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| 18. |
- Kiefer, M., et al.
(author)
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The SPARC water vapour assessment II: biases and drifts of water vapour satellite data records with respect to frost point hygrometer records
- 2023
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In: Atmospheric Measurement Techniques. - 1867-1381 .- 1867-8548. ; 16:19, s. 4589-4642
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Journal article (peer-reviewed)abstract
- Satellite data records of stratospheric water vapour have been compared to balloon-borne frost point hygrometer (FP) profiles that are coincident in space and time. The satellite data records of 15 different instruments cover water vapour data available from January 2000 through December 2016. The hygrometer data are from 27 stations all over the world in the same period. For the comparison, real or constructed averaging kernels have been applied to the hygrometer profiles to adjust them to the measurement characteristics of the satellite instruments. For bias evaluation, we have compared satellite profiles averaged over the available temporal coverage to the means of coincident FP profiles for individual stations. For drift determinations, we analysed time series of relative differences between spatiotemporally coincident satellite and hygrometer profiles at individual stations. In a synopsis we have also calculated the mean biases and drifts (and their respective uncertainties) for each satellite record over all applicable hygrometer stations in three altitude ranges (10-30 hPa, 30-100 hPa, and 100 hPa to tropopause). Most of the satellite data have biases <10 % and average drifts <1 % yr-1 in at least one of the respective altitude ranges. Virtually all biases are significant in the sense that their uncertainty range in terms of twice the standard error of the mean does not include zero. Statistically significant drifts (95 % confidence) are detected for 35 % of the ≈ 1200 time series of relative differences between satellites and hygrometers.
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| 19. |
- Kirchhoff, Tomas, et al.
(author)
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Breast cancer risk and 6q22.33 : combined results from Breast Cancer Association Consortium and Consortium of Investigators on Modifiers of BRCA1/2
- 2012
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In: PLOS ONE. - : Public library of science. - 1932-6203. ; 7:6
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Journal article (peer-reviewed)abstract
- Recently, a locus on chromosome 6q22.33 (rs2180341) was reported to be associated with increased breast cancer risk in the Ashkenazi Jewish (AJ) population, and this association was also observed in populations of non-AJ European ancestry. In the present study, we performed a large replication analysis of rs2180341 using data from 31,428 invasive breast cancer cases and 34,700 controls collected from 25 studies in the Breast Cancer Association Consortium (BCAC). In addition, we evaluated whether rs2180341 modifies breast cancer risk in 3,361 BRCA1 and 2,020 BRCA2 carriers from 11 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Based on the BCAC data from women of European ancestry, we found evidence for a weak association with breast cancer risk for rs2180341 (per-allele odds ratio (OR) = 1.03, 95% CI 1.00-1.06, p = 0.023). There was evidence for heterogeneity in the ORs among studies (I(2) = 49.3%; p = <0.004). In CIMBA, we observed an inverse association with the minor allele of rs2180341 and breast cancer risk in BRCA1 mutation carriers (per-allele OR = 0.89, 95%CI 0.80-1.00, p = 0.048), indicating a potential protective effect of this allele. These data suggest that that 6q22.33 confers a weak effect on breast cancer risk.
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| 20. |
- Korherr, C, et al.
(author)
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Identification of proangiogenic genes and pathways by high-throughput functional genomics: TBK1 and the IRF3 pathway
- 2006
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 103:11, s. 4240-4245
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Journal article (peer-reviewed)abstract
- A genome-wide phenotype screen was used to identify factors and pathways that induce proliferation of human umbilical vein endothelial cells (HUVEC). HUVEC proliferation is a recognized marker for factors that modulate vascularization. Screening “hits” included known proangiogenic factors, such as VEGF, FGF1, and FGF2 and additional factors for which a direct association with angiogenesis was not previously described. These include the kinase TBK1 as well as Toll-like receptor adaptor molecule and IFN regulatory factor 3. All three proteins belong to one signaling pathway that mediates induction of gene expression, including a mixture of secreted factors, which, in concert, mediate proliferative activity toward endothelial cells. TBK1 as the “trigger” of this pathway is induced under hypoxic conditions and expressed at significant levels in many solid tumors. This pattern of expression and the decreased expression of angiogenic factors in cultured cells upon RNA-interference-mediated ablation suggests that TBK1 is important for vascularization and subsequent tumor growth and a target for cancer therapy.
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| 21. |
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| 22. |
- Lossow, S., et al.
(author)
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The SPARC water vapour assessment II: comparison of annual, semi-annual and quasi-biennial variations in stratospheric and lower mesospheric water vapour observed from satellites
- 2017
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 10:3, s. 1111-1137
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Journal article (peer-reviewed)abstract
- In the framework of the second SPARC (Stratosphere-troposphere Processes And their Role in Climate) water vapour assessment (WAVAS-II), the amplitudes and phases of the annual, semi-annual and quasi-biennial variation in stratospheric and lower mesospheric water were compared using 30 data sets from 13 different satellite instruments. These comparisons aimed to provide a comprehensive overview of the typical uncertainties in the observational database which can be considered in subsequent observational and modelling studies. For the amplitudes, a good agreement of their latitude and altitude distribution was found. Quantitatively there were differences in particular at high latitudes, close to the tropopause and in the lower mesosphere. In these regions, the standard deviation over all data sets typically exceeded 0.2 ppmv for the annual variation and 0.1 ppmv for the semi-annual and quasi-biennial variation. For the phase, larger differences between the data sets were found in the lower mesosphere. Generally the smallest phase uncertainties can be observed in regions where the amplitude of the variability is large. The standard deviations of the phases for all data sets were typically smaller than a month for the annual and semi-annual variation and smaller than 5 months for the quasi-biennial variation. The amplitude and phase differences among the data sets are caused by a combination of factors. In general, differences in the temporal variation of systematic errors and in the observational sampling play a dominant role. In addition, differences in the vertical resolution of the data, the considered time periods and influences of clouds, aerosols as well as non-local thermodynamic equilibrium (NLTE) effects cause differences between the individual data sets. .1 Symposia of COSPAR Scientific Commission A, held during the Thirty-first COSPAR Scientific Assembly
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| 23. |
- Swart, Sebastiaan, 1983, et al.
(author)
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Constraining Southern ocean air-sea-ice fluxes through enhanced observations
- 2019
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In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
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Research review (peer-reviewed)abstract
- © 2019 Swart, Gille, Delille, Josey, Mazloff, Newman, Thompson, Thomson, Ward, Du Plessis, Kent, Girton, Gregor, H, Hyder, Pezzi, De Souza, Tamsitt, Weller and Zappa. Air-sea and air-sea-ice fluxes in the Southern Ocean play a critical role in global climate through their impact on the overturning circulation and oceanic heat and carbon uptake. The challenging conditions in the Southern Ocean have led to sparse spatial and temporal coverage of observations. This has led to a 'knowledge gap' that increases uncertainty in atmosphere and ocean dynamics and boundary-layer thermodynamic processes, impeding improvements in weather and climate models. Improvements will require both process-based research to understand the mechanisms governing air-sea exchange and a significant expansion of the observing system. This will improve flux parameterizations and reduce uncertainty associated with bulk formulae and satellite observations. Improved estimates spanning the full Southern Ocean will need to take advantage of ships, surface moorings, and the growing capabilities of autonomous platforms with robust and miniaturized sensors. A key challenge is to identify observing system sampling requirements. This requires models, Observing System Simulation Experiments (OSSEs), and assessments of the specific spatial-temporal accuracy and resolution required for priority science and assessment of observational uncertainties of the mean state and direct flux measurements. Year-round, high-quality, quasi-continuous in situ flux measurements and observations of extreme events are needed to validate, improve and characterize uncertainties in blended reanalysis products and satellite data as well as to improve parameterizations. Building a robust observing system will require community consensus on observational methodologies, observational priorities, and effective strategies for data management and discovery.
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| 24. |
- Tegtmeier, S., et al.
(author)
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SPARC Data Initiative: A comparison of ozone climatologies from international satellite limb sounders
- 2013
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In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 118:21, s. 12229-12247
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Journal article (peer-reviewed)abstract
- A comprehensive quality assessment of the ozone products from 18 limb-viewing satellite instruments is provided by means of a detailed intercomparison. The ozone climatologies in form of monthly zonal mean time series covering the upper troposphere to lower mesosphere are obtained from LIMS, SAGE I/II/III, UARS-MLS, HALOE, POAM II/III, SMR, OSIRIS, MIPAS, GOMOS, SCIAMACHY, ACE-FTS, ACE-MAESTRO, Aura-MLS, HIRDLS, and SMILES within 1978–2010. The intercomparisons focus on mean biases of annual zonal mean fields, interannual variability, and seasonal cycles. Additionally, the physical consistency of the data is tested through diagnostics of the quasi-biennial oscillation and Antarctic ozone hole. The comprehensive evaluations reveal that the uncertainty in our knowledge of the atmospheric ozone mean state is smallest in the tropical and midlatitude middle stratosphere with a 1σ multi-instrument spread of less than ±5%. While the overall agreement among the climatological data sets is very good for large parts of the stratosphere, individual discrepancies have been identified, including unrealistic month-to-month fluctuations, large biases in particular atmospheric regions, or inconsistencies in the seasonal cycle. Notable differences between the data sets exist in the tropical lower stratosphere (with a spread of ±30%) and at high latitudes (±15%). In particular, large relative differences are identified in the Antarctic during the time of the ozone hole, with a spread between the monthly zonal mean fields of ±50%. The evaluations provide guidance on what data sets are the most reliable for applications such as studies of ozone variability, model-measurement comparisons, detection of long-term trends, and data-merging activities.
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| 25. |
- Toohey, M., et al.
(author)
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Characterizing sampling biases in the trace gas climatologies of the SPARC Data Initiative
- 2013
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In: Journal of Geophysical Research. - : American Geophysical Union (AGU). - 0148-0227 .- 2156-2202 .- 2169-897X .- 2169-8996. ; 118:20, s. 11847-11862
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Journal article (peer-reviewed)abstract
- Monthly zonal mean climatologies of atmospheric measurements from satellite instruments can have biases due to the nonuniform sampling of the atmosphere by the instruments. We characterize potential sampling biases in stratospheric trace gas climatologies of the Stratospheric Processes and Their Role in Climate (SPARC) Data Initiative using chemical fields from a chemistry climate model simulation and sampling patterns from 16 satellite-borne instruments. The exercise is performed for the long-lived stratospheric trace gases O3 and H2O. Monthly sampling biases for O3 exceed 10% for many instruments in the high-latitude stratosphere and in the upper troposphere/lower stratosphere, while annual mean sampling biases reach values of up to 20% in the same regions for some instruments. Sampling biases for H2O are generally smaller than for O3, although still notable in the upper troposphere/lower stratosphere and Southern Hemisphere high latitudes. The most important mechanism leading to monthly sampling bias is nonuniform temporal sampling, i.e., the fact that for many instruments, monthly means are produced from measurements which span less than the full month in question. Similarly, annual mean sampling biases are well explained by nonuniformity in the month-to-month sampling by different instruments. Nonuniform sampling in latitude and longitude are shown to also lead to nonnegligible sampling biases, which are most relevant for climatologies which are otherwise free of biases due to nonuniform temporal sampling.
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