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  • de Jong, R. S., et al. (författare)
  • 4MOST : Project overview and information for the First Call for Proposals
  • 2019
  • Ingår i: ; 175, s. 3-11
  • Tidskriftsartikel (övrigt vetenskapligt)abstract
    • We introduce the 4-metre Multi-Object Spectroscopic Telescope (4MOST), a new high-multiplex, wide-field spectroscopic survey facility under development for the four-metre-class Visible and Infrared Survey Telescope for Astronomy (VISTA) at Paranal. Its key specifications are: a large field of view (FoV) of 4.2 square degrees and a high multiplex capability, with 1624 fibres feeding two low-resolution spectrographs (R = λ/Δλ ~ 6500), and 812 fibres transferring light to the high-resolution spectrograph (R ~ 20 000). After a description of the instrument and its expected performance, a short overview is given of its operational scheme and planned 4MOST Consortium science; these aspects are covered in more detail in other articles in this edition of The Messenger. Finally, the processes, schedules, and policies concerning the selection of ESO Community Surveys are presented, commencing with a singular opportunity to submit Letters of Intent for Public Surveys during the first five years of 4MOST operations.
  • Buder, S., et al. (författare)
  • The GALAH survey : An abundance, age, and kinematic inventory of the solar neighbourhood made with TGAS
  • 2019
  • Ingår i: ; 624
  • Tidskriftsartikel (refereegranskat)abstract
    • The overlap between the spectroscopic Galactic Archaeology with HERMES (GALAH) survey and Gaia provides a high-dimensional chemodynamical space of unprecedented size. We present a first analysis of a subset of this overlap, of 7066 dwarf, turn-off, and subgiant stars. These stars have spectra from the GALAH survey and high parallax precision from the Gaia DR1 Tycho-Gaia Astrometric Solution. We investigate correlations between chemical compositions, ages, and kinematics for this sample. Stellar parameters and elemental abundances are derived from the GALAH spectra with the spectral synthesis code SPECTROSCOPY MADE EASY. We determine kinematics and dynamics, including action angles, from the Gaia astrometry and GALAH radial velocities. Stellar masses and ages are determined with Bayesian isochrone matching, using our derived stellar parameters and absolute magnitudes. We report measurements of Li, C, O, Na, Mg, Al, Si, K, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Cu, Zn, Y, as well as Ba and we note that we have employed non-LTE calculations for Li, O, Al, and Fe. We show that the use of astrometric and photometric data improves the accuracy of the derived spectroscopic parameters, especially log g. Focusing our investigation on the correlations between stellar age, iron abundance [Fe/H], and mean alpha-enhancement [alpha/Fe] of the magnitude-selected sample, we recover the result that stars of the high-a sequence are typically older than stars in the low-a sequence, the latter spanning iron abundances of -0.7 < [Fe/H] < +0.5. While these two sequences become indistinguishable in [alpha/Fe] vs. [Fe/H] at the metal-rich regime, we find that age can be used to separate stars from the extended high-a and the low-a sequence even in this regime. When dissecting the sample by stellar age, we find that the old stars (>8 Gyr) have lower angular momenta L-z than the Sun, which implies that they are on eccentric orbits and originate from the inner disc. Contrary to some previous smaller scale studies we find a continuous evolution in the high-alpha-sequence up to super-solar [Fe/H] rather than a gap, which has been interpreted as a separate "high-alpha metal-rich" population. Stars in our sample that are younger than 10 Gyr, are mainly found on the low alpha-sequence and show a gradient in L-z from low [Fe/H] > (L-z > L-z,L-circle dot) towards higher [Fe/H] (L-z < L-z,L-circle dot), which implies that the stars at the ends of this sequence are likely not originating from the close solar vicinity.
  • Fagerberg, Linn, et al. (författare)
  • Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
  • 2014
  • Ingår i: ; 13:2, s. 397-406
  • Tidskriftsartikel (refereegranskat)abstract
    • Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody- based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to 80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
  • Holgersson, G., et al. (författare)
  • Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy
  • 2010
  • Ingår i: Cancer Genomics & Proteomics. - 1109-6535 .- 1790-6245. ; 7:1, s. 1-7
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: To explore the usefulness of the expression of five potential cancer biomarkers in predicting outcome in patients with laryngeal cancer. Materials and Methods: In the present study, the Swedish National Cancer Registry databases were used to identify patients with laryngeal cancer diagnosed during the years 1978-2004 in the Uppsala-Örebro region and treated with radiotherapy. The expression of Ki-67, MutS homolog 2, (MSH2), p53, B-cell CLL/lymphoma 2 (Bcl-2) and cyclin D1 in the cancer cells was assessed immunohistochemically using tissue microarrays (TMAs) and its predictve value on survival and relapse was analyzed using Cox regression models. Results: A total of 39 patients were included in the present study. Nuclear MSH2 staining was statistically significantly correlated to Ki-67 expression (p=0.022). However, univariate and multivariate Cox analyses showed no statistically significant association between the expression of the investigated biomarkers and overall survival or relapse. Conclusion: The present exploratory study does not show any significant predictive value of the biomarkers examined with respect to survival or relapse. However, with larger patient cohorts, we believe that protein profiling using TMAs and immunohistochemistry is a feasible strategy for prognostic and predictive biomarker screening in laryngeal cancer.
  • Fagerberg, Linn, et al. (författare)
  • Contribution of Antibody-based Protein Profiling to the Human Chromosome-centric Proteome Project (C-HPP)
  • 2013
  • Ingår i: Journal of Proteome Research. - : The American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:6, s. 2439-2448
  • Tidskriftsartikel (refereegranskat)abstract
    • A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas (www.proteinatlas.org).
  • Nordanstig, Annika, et al. (författare)
  • Evaluation of the Swedish National Stroke Campaign : A population-based time-series study
  • Ingår i: International Journal of Stroke. - : Wiley-Blackwell. - 1747-4930 .- 1747-4949. ; 14:9, s. 862-870
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Time delay from stroke onset to hospital arrival is an important obstacle to recanalization therapy. To increase knowledge about stroke symptoms and potentially reduce delayed hospital arrival, a 27-month national public information campaign was conducted in Sweden. Aim: To assess the effects of a national stroke campaign in Sweden. Methods: This nationwide study included 97,840 patients with acute stroke, admitted to hospital and registered in the Swedish Stroke Register from 1 October 2010 to 31 December 2014 (one year before the campaign started to one year after the campaign ended). End points were (1) proportion of patients arriving at hospital within 3 h of stroke onset and (2) the proportion < 80 years of age receiving recanalization therapy. Results: During the campaign, both the proportion of patients arriving at hospital within 3 h (p < 0.05) and the proportion receiving recanalization therapy (p < 0.001) increased. These proportions remained stable the year after the campaign, and no significant improvements with respect to the two end points were observed during the year preceding the campaign. In a multivariable logistic regression model comparing the last year of the campaign with the year preceding the campaign, the odds ratio of arriving at hospital within 3 h was 1.05 (95% confidence interval (CI): 1.00–1.09) and that of receiving recanalization was 1.34 (95% CI: 1.24–1.46). Conclusion: The Swedish National Stroke Campaign was associated with a sustained increase in the proportion of patients receiving recanalization therapy and a small but significant improvement in the proportion arriving at hospital within 3 h.
  • Rauer, H., et al. (författare)
  • The PLATO 2.0 mission
  • 2014
  • Ingår i: Experimental Astronomy. - : Springer. - 0922-6435 .- 1572-9508. ; 38:1-2, s. 249-330
  • Tidskriftsartikel (refereegranskat)abstract
    • PLATO 2.0 has recently been selected for ESA's M3 launch opportunity (2022/24). Providing accurate key planet parameters (radius, mass, density and age) in statistical numbers, it addresses fundamental questions such as: How do planetary systems form and evolve? Are there other systems with planets like ours, including potentially habitable planets? The PLATO 2.0 instrument consists of 34 small aperture telescopes (32 with 25 s readout cadence and 2 with 2.5 s cadence) providing a wide field-of-view (2232 deg(2)) and a large photometric magnitude range (4-16 mag). It focuses on bright (4-11 mag) stars in wide fields to detect and characterize planets down to Earth-size by photometric transits, whose masses can then be determined by ground-based radial-velocity follow-up measurements. Asteroseismology will be performed for these bright stars to obtain highly accurate stellar parameters, including masses and ages. The combination of bright targets and asteroseismology results in high accuracy for the bulk planet parameters: 2 %, 4-10 % and 10 % for planet radii, masses and ages, respectively. The planned baseline observing strategy includes two long pointings (2-3 years) to detect and bulk characterize planets reaching into the habitable zone (HZ) of solar-like stars and an additional step-and-stare phase to cover in total about 50 % of the sky. PLATO 2.0 will observe up to 1,000,000 stars and detect and characterize hundreds of small planets, and thousands of planets in the Neptune to gas giant regime out to the HZ. It will therefore provide the first large-scale catalogue of bulk characterized planets with accurate radii, masses, mean densities and ages. This catalogue will include terrestrial planets at intermediate orbital distances, where surface temperatures are moderate. Coverage of this parameter range with statistical numbers of bulk characterized planets is unique to PLATO 2.0. The PLATO 2.0 catalogue allows us to e. g.: - complete our knowledge of planet diversity for low-mass objects, - correlate the planet mean density-orbital distance distribution with predictions from planet formation theories,- constrain the influence of planet migration and scattering on the architecture of multiple systems, and - specify how planet and system parameters change with host star characteristics, such as type, metallicity and age. The catalogue will allow us to study planets and planetary systems at different evolutionary phases. It will further provide a census for small, low-mass planets. This will serve to identify objects which retained their primordial hydrogen atmosphere and in general the typical characteristics of planets in such a low-mass, low-density range. Planets detected by PLATO 2.0 will orbit bright stars and many of them will be targets for future atmosphere spectroscopy exploring their atmospheres. Furthermore, the mission has the potential to detect exomoons, planetary rings, binary and Trojan planets. The planetary science possible with PLATO 2.0 is complemented by its impact on stellar and galactic science via asteroseismology as well as light curves of all kinds of variable stars, together with observations of stellar clusters of different ages. This will allow us to improve stellar models and study stellar activity. A large number of well-known ages from red giant stars will probe the structure and evolution of our Galaxy. Asteroseismic ages of bright stars for different phases of stellar evolution allow calibrating stellar age-rotation relationships. Together with the results of ESA's Gaia mission, the results of PLATO 2.0 will provide a huge legacy to planetary, stellar and galactic science.
  • Terent, A., et al. (författare)
  • Stroke unit care revisited: who benefits the most? A cohort study of 105 043 patients in Riks-Stroke, the Swedish Stroke Register
  • 2009
  • Ingår i: Journal of Neurology, Neurosurgery and Psychiatry. - : BMJ Publishing Group. - 1468-330X .- 0022-3050. ; 80:8, s. 881-887
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Treatment at stroke units is superior to treatment at other types of wards. The objective of the present study is to determine the effect size of stroke unit care in subgroups of patients with stroke. This information might be useful in a formal priority setting. Methods: All acute strokes reported to the Swedish Stroke Register from 2001 through 2005 were followed until January 2007. The subgroups were age (18-64, 65-74, 75-84, 85+ years and above), sex (male, female), stroke subtype (intracerebral haemorrhage, cerebral infarction and unspecified stroke) and level of consciousness (conscious, reduced, unconscious). Cox proportional hazards and logistic regression analyses were used to estimate the risk for death, institutional living or dependency. Results: 105 043 patients were registered at 86 hospitals. 79 689 patients (76%) were treated in stroke units and 25 354 patients (24%) in other types of wards. Stroke unit care was associated with better long-term survival in all subgroups. The best relative effect was seen among the following subgroups: age 18-64 years (hazard ratio (HR) for death 0.53; 0.49 to 0.58), intracerebral haemorrhage (HR 0.61; 0.58 to 0.65) and unconsciousness (HR 0.70; 0.66 to 0.75). Stroke unit care was also associated with reduced risk for death or institutional living after 3 months. Conclusions: Stroke unit care was associated with better long-term survival in all subgroups, but younger patients, patients with intracerebral haemorrhage and patients who were unconscious had the best relative effect and may be given the highest priority to this form of care.
  • Asplund, A., et al. (författare)
  • Expression profiling of microdissected cell populations selected from basal cells in normal epidermis and basal cell carcinoma
  • 2008
  • Ingår i: British Journal of Dermatology. - 0007-0963 .- 1365-2133. ; 158:3, s. 527-538
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Basal cell carcinomas (BCCs) are prevalent tumours with uniform histology that develop without any known precursor lesion. Alterations in the sonic hedgehog-patched1 signalling pathway are accepted as necessary events for tumorigenesis, and mutations in the patched1 gene are frequently present in tumours. Objectives To analyse transcript profiles in BCC. Methods We used laser-assisted microdissection to isolate and collect cell populations defined under the microscope. Peripheral cells from nests of BCC were selected to represent tumour cells, and normal keratinocytes from epidermis basal layer were used as control. Extracted RNA was amplified and hybridized on to a cDNA microarray. Results Our results show that BCC cells express a transcript signature that is significantly different from that of normal keratinocytes, and over 350 genes with various functions were identified as differentially expressed. The compiled data suggest an upregulation of the Wnt signalling pathway as a major event in BCC cells. Furthermore, tumour cells appear to have an increased sensitivity to oxygen radicals and dysregulated genes involved in antigen presentation. Results were validated at both the transcriptional level using real-time polymerase chain reaction and at the protein level using immunohistochemistry. Conclusions We show that microdissection in combination with robust strategies for RNA extraction, amplification and cDNA microarray analysis allow for reliable transcript profiling and that antibody-based proteomics provides an advantageous strategy for the analysis of corresponding differentially expressed proteins. We found that expression patterns were significantly altered in BCC cells compared with basal keratinocytes and that the Wnt signalling pathway was upregulated in tumour cells.
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