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| 3. |
- Appeltans, W., et al.
(author)
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The Magnitude of Global Marine Species Diversity
- 2012
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 22:23, s. 2189-2202
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Journal article (peer-reviewed)abstract
- Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are similar to 226,000 eukaryotic marine species described. More species were described in the past decade (similar to 20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are similar to 170,000 synonyms, that 58,000-72,000 species are collected but not yet described, and that 482,000-741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7-1.0 million marine species. Past rates of description of new species indicate there may be 0.5 +/- 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
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| 16. |
- Aidas, Kestutis, et al.
(author)
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The Dalton quantum chemistry program system
- 2014
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In: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Journal article (peer-reviewed)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 20. |
- Basaiawmoit, R V, et al.
(author)
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SAXS Models of TGFBIp Reveal a Trimeric Structure and Show That the Overall Shape Is Not Affected by the Arg124His Mutation
- 2011
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In: JOURNAL OF MOLECULAR BIOLOGY. - : Elsevier Science B.V., Amsterdam. - 0022-2836. ; 408:3, s. 503-513
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Journal article (peer-reviewed)abstract
- Human transforming growth factor beta induced protein (TGFBIp) is composed of 683 residues, including an N-terminal cysteine-rich (EMI) domain, four homologous fasciclin domains, and an Arg-Gly-Asp (RGD) motif near the C-terminus. The protein is of interest because mutations in the TGFBI gene encoding TGFBIp lead to corneal dystrophy (CD), a condition where protein aggregates within the cornea compromise transparency. The complete three-dimensional structure of TGFBIp is not yet available, with the exception of a partial X-ray structure of the archetype FAS1 domain derived from Drosophila fasciclin-1. In this study, small-angle X-ray scattering (SAXS) models of intact wild-type (WT) human TGFBIp and a mutant (R124H) are presented. The mutation R124H leads to a variant of granular CD. The deduced structure of the TGFBIp monomer consists of four FAS1 domains in a simple "beads-on-a-string" arrangement, constructed by the superimposition of four consecutive Drosophila fasciclin domains. The SAXS-based model of the TGFBIp R124H mutant displayed no structural differences from WT. Both WT TGFBIp and the R124H mutant formed trimers at higher protein concentrations. The similar association properties and three-dimensional shape of the two proteins suggest that the mutation does not induce any major structural rearrangements, but points towards the role of other corneal-specific factors in the formation of corneal R124H deposits.
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| 21. |
- Benz, A. O., et al.
(author)
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Hydrides in young stellar objects : Radiation tracers in a protostar-disk-outflow system
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 521, s. L35-
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Journal article (peer-reviewed)abstract
- Context. Hydrides of the most abundant heavier elements are fundamental molecules in cosmic chemistry. Some of them trace gas irradiated by UV or X-rays. Aims: We explore the abundances of major hydrides in W3 IRS5, a prototypical region of high-mass star formation. Methods: W3 IRS5 was observed by HIFI on the Herschel Space Observatory with deep integration (≃2500 s) in 8 spectral regions. Results: The target lines including CH, NH, H3O+, and the new molecules SH+, H2O+, and OH+ are detected. The H2O+ and OH+ J = 1-0 lines are found mostly in absorption, but also appear to exhibit weak emission (P-Cyg-like). Emission requires high density, thus originates most likely near the protostar. This is corroborated by the absence of line shifts relative to the young stellar object (YSO). In addition, H2O+ and OH+ also contain strong absorption components at a velocity shifted relative to W3 IRS5, which are attributed to foreground clouds. Conclusions: The molecular column densities derived from observations correlate well with the predictions of a model that assumes the main emission region is in outflow walls, heated and irradiated by protostellar UV radiation. Herschel is an ESA space observatory with science instruments provided by a European-led Principal Investigator consortia and with important participation from NASA.Appendix (page 5) is only available in electronic form at http://www.aanda.org
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| 22. |
- Campos, Paula F., et al.
(author)
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Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene
- 2010
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In: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:22, s. 4863-4875
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Journal article (peer-reviewed)abstract
- Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 C-14 ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 C-14 ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.
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| 25. |
- Edvardsen, Hege, et al.
(author)
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SNP in TXNRD2 Associated With Radiation-Induced Fibrosis : A Study of Genetic Variation in Reactive Oxygen Species Metabolism and Signaling.
- 2013
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In: International journal of radiation oncology, biology, physics. - : Elsevier BV. - 1879-355X .- 0360-3016. ; 86:4, s. 791-9
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Journal article (peer-reviewed)abstract
- PURPOSE: The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs).METHODS AND MATERIALS: 92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients.RESULTS: Subcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P≤.005).CONCLUSION: Development of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.
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| 26. |
- Edvardsen, H., et al.
(author)
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SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance
- 2010
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In: The Pharmacogenomics Journal. - : Springer Science and Business Media LLC. - 1470-269X .- 1473-1150. ; 10:6, s. 513-523
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Journal article (peer-reviewed)abstract
- The dose of docetaxel is currently calculated based on body surface area and does not reflect the pharmacokinetic, metabolic potential or genetic background of the patients. The influence of genetic variation on the clearance of docetaxel was analysed in a two-stage analysis. In step one, 583 single-nucleotide polymorphisms (SNPs) in 203 genes were genotyped on samples from 24 patients with locally advanced non-small cell lung cancer. We found that many of the genes harbour several SNPs associated with clearance of docetaxel. Most notably these were four SNPs in EGF, three SNPs in PRDX4 and XPC, and two SNPs in GSTA4, TGFBR2, TNFAIP2, BCL2, DPYD and EGFR. The multiple SNPs per gene suggested the existence of common haplotypes associated with clearance. These were confirmed with detailed haplotype analysis. On the basis of analysis of variance (ANOVA), quantitative mutual information score (QMIS) and Kruskal-Wallis (KW) analysis SNPs significantly associated with clearance of docetaxel were confirmed for GSTA4, PRDX4, TGFBR2 and XPC and additional putative markers were found in CYP2C8, EPHX1, IGF2, IL1R2, MAPK7, NDUFB4, TGFBR3, TPMT (2 SNPs), (P<0.05 or borderline significant for all three methods, 14 SNPs in total). In step two, these 14 SNPs were genotyped in additional 9 samples and the results combined with the genotyping results from the first step. For 7 of the 14 SNPs, the results are still significant/borderline significant by all three methods: ANOVA, QMIS and KW analysis strengthening our hypothesis that they are associated with the clearance of docetaxel..
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| 27. |
- Fich, M., et al.
(author)
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Herschel-PACS spectroscopy of the intermediate mass protostar NGC 7129 FIRS 2
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518:Article Number: L86
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Journal article (peer-reviewed)abstract
- Aims. We present preliminary results of the first Herschel spectroscopic observations of NGC 7129 FIRS2, an intermediate mass star-forming region. We attempt to interpret the observations in the framework of an in-falling spherical envelope. Methods. The PACS instrument was used in line spectroscopy mode ( R = 1000-5000) with 15 spectral bands between 63 and 185 mu m. This provided good detections of 26 spectral lines seen in emission, including lines of H2O, CO, OH, O I, and C II. Results. Most of the detected lines, particularly those of H2O and CO, are substantially stronger than predicted by the spherical envelope models, typically by several orders of magnitude. In this paper we focus on what can be learned from the detected CO emission lines. Conclusions. It is unlikely that the much stronger than expected line emission arises in the (spherical) envelope of the YSO. The region hot enough to produce such high excitation lines within such an envelope is too small to produce the amount of emission observed. Virtually all of this high excitation emission must arise in structures such as as along the walls of the outflow cavity with the emission produced by a combination of UV photon heating and/or non-dissociative shocks.
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| 28. |
- Kristensen, L. E., et al.
(author)
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Water in low-mass star-forming regions with Herschel . HIFI spectroscopy of NGC 1333
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 521, s. L30-
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Journal article (peer-reviewed)abstract
- “Water In Star-forming regions with Herschel” (WISH) is a key programme dedicated to studying the role of water and related species during the star-formation process and constraining the physical and chemical properties of young stellar objects. The Heterodyne Instrument for the Far-Infrared (HIFI) on the Herschel Space Observatory observed three deeply embedded protostars in the low-mass star-forming region NGC 1333 in several H_216O, H_218O, and CO transitions. Line profiles are resolved for five H_216O transitions in each source, revealing them to be surprisingly complex. The line profiles are decomposed into broad (>20 km s-1), medium-broad (~5-10 km s-1), and narrow (<5 km s-1) components. The H_218O emission is only detected in broad 110-101 lines (>20 km s-1), indicating that its physical origin is the same as for the broad H_216O component. In one of the sources, IRAS4A, an inverse P Cygni profile is observed, a clear sign of infall in the envelope. From the line profiles alone, it is clear that the bulk of emission arises from shocks, both on small (⪉1000 AU) and large scales along the outflow cavity walls (~10 000 AU). The H2O line profiles are compared to CO line profiles to constrain the H2O abundance as a function of velocity within these shocked regions. The H2O/CO abundance ratios are measured to be in the range of ~0.1-1, corresponding to H2O abundances of ~10-5-10-4 with respect to H2. Approximately 5-10% of the gas is hot enough for all oxygen to be driven into water in warm post-shock gas, mostly at high velocities. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.Tables 2 and 3 (page 6) are only available in electronic form at http://www.aanda.org
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| 31. |
- Lindström, Ulf, et al.
(author)
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Validity of ankylosing spondylitis and spondyloarthritis diagnoses in the Swedish National Patient Register
- 2014
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In: Annals of the Rheumatic Diseases. - : BMJ Publishing Group. - 0003-4967 .- 1468-2060. ; 32:5, s. 802-802
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Journal article (other academic/artistic)abstract
- Background: Epidemiological studies of spondyloarthritis (SpA) are scarce. Using ICD-codes from the Swedish National Patient Register (NPR) offers unique possibilities for such studies. For this purpose, the validity of these ICD-codes needs to be determined.Objectives: To validate the ICD-codes for ankylosing spondylitis (AS) and SpA in the NPR against established classification criteria (modified New York (mNY), ASAS, Amor and ESSG criteria).Methods: All patients with an ICD-code of AS or SpA in the NPR 1966-2009 at a visit to a specialist in rheumatology or internal medicine, or corresponding hospitalization, were identified (n=20074). Following a structured procedure to achieve geographical representativeness, 500 random patients with a registered diagnosis of AS or SpA in 2007-2009 were selected. A structured review of clinical records, with extraction of necessary information for the established classification criteria was performed and positive predictive values (PPV) were calculated.Results: In this cohort 11472 (34% women) patients had received an AS diagnosis and 11004 (56% women) a SpA diagnosis. The overlap group having received both types of diagnoses had similar frequencies for fulfillment of mNY criteria, symptoms and signs of back disease as the group having been coded as AS only.Of those being coded as AS only, the PPV for fulfilling the mNY, any criteria set and any of the included criteria elements were 70%, 89% and 96% respectively.Of those with SpA (without AS ever) the corresponding PPV values were 20%, 79% and 99% respectively.Conclusions: A diagnosis of AS or SpA (without AS) had a high validity, suggesting that case identification based on ICD-codes in the Swedish NPR can be used for epidemiological studies of these diseases.
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| 32. |
- Meijerink, R., et al.
(author)
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Evidence for CO Shock Excitation in NGC 6240 from Herschel SPIRE Spectroscopy
- 2013
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In: Astrophysical Journal Letters. - 2041-8213 .- 2041-8205. ; 762:2, s. L16-L20
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Journal article (peer-reviewed)abstract
- We present Herschel SPIRE FTS spectroscopy of the nearby luminous infrared galaxy NGC 6240. In total 20 linesare detected, including CO J = 4−3 through J = 13−12, 6 H2O rotational lines, and [C i] and [N ii] fine-structurelines. The CO to continuum luminosity ratio is 10 times higher in NGC 6240 than Mrk 231. Although the COladdersof NGC 6240 and Mrk 231 are very similar, UV and/or X-ray irradiation are unlikely to be responsible for theexcitation of the gas in NGC 6240.We applied both C and J shock models to the H2 v = 1–0 S(1) and v = 2–1 S(1)lines and the CO rotational ladder. The CO ladder is best reproduced by amodel with shock velocity vs = 10 km s−1and a pre-shock density nH = 5 × 104 cm−3. We find that the solution best fitting the H2 lines is degenerate. The shock velocities and number densities range between vs = 17–47 km s−1 and nH = 107–5×104 cm−3, respectively.The H2 lines thus need a much more powerful shock than the CO lines.We deduce that most of the gas is currently moderately stirred up by slow (10 km s−1) shocks while only a small fraction (1%) of the interstellar mediumis exposed to the high-velocity shocks. This implies that the gas is rapidly losing its highly turbulent motions. We argue that a high CO line-to-continuum ratio is a key diagnostic for the presence of shocks.
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| 33. |
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| 34. |
- Møller, J B, et al.
(author)
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Longitudinal Modeling of the Relationship Between Mean Plasma Glucose and HbA1c Following Antidiabetic Treatments
- 2013
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In: CPT. - : Wiley. - 2163-8306. ; 2, s. e82-
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Journal article (peer-reviewed)abstract
- Late-phase clinical trials within diabetes generally have a duration of 12-24 weeks, where 12 weeks may be too short to reach steady-state glycated hemoglobin (HbA1c). The main determinant for HbA1c is blood glucose, which reaches steady state much sooner. In spite of this, few publications have used individual data to assess the time course of both glucose and HbA1c, for predicting HbA1c. In this paper, we present an approach for predicting HbA1c at end-of-trial (24-28 weeks) using glucose and HbA1c measurements up to 12 weeks. The approach was evaluated using data from 4 trials covering 12 treatment arms (oral antidiabetic drug, glucagon-like peptide-1, and insulin treatment) with measurements at 24-28 weeks to evaluate predictions vs. observations. HbA1c percentage was predicted for each arm at end-of-trial with a mean prediction error of 0.14% [0.01;0.24]. Furthermore, end points in terms of HbA1c reductions relative to comparator were accurately predicted. The proposed model provides a good basis to optimize late-stage clinical development within diabetes.
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| 35. |
- Skou, N., et al.
(author)
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Future spaceborne ocean missions using high sensitivity multiple-beam radiometers
- 2014
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In: Joint 2014 IEEE International Geoscience and Remote Sensing Symposium, IGARSS 2014 and the 35th Canadian Symposium on Remote Sensing, CSRS 2014; Quebec Convention CentreQuebec City; Canada; 13 July 2014 through 18 July 2014. - 9781479957750 ; , s. 2546-2549
-
Conference paper (peer-reviewed)abstract
- Design considerations concerning a scanning as well as a push-broom microwave radiometer system are presented. Strict requirements to spatial and radiometric resolution leads to a multiple-beam scanner achieving good sensitivity through integration over many beams, or to a push-broom system where sensitivity is not a problem. Strict requirements to land contamination leads to a dense feed array system. Resource demands, especially power, are important issues, and first estimates are presented.
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| 36. |
- Stevens, Kristen N, et al.
(author)
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19p13.1 is a triple negative-specific breast cancer susceptibility locus
- 2012
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In: Cancer Research. - 0008-5472 .- 1538-7445. ; 72, s. 1795-
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Journal article (peer-reviewed)abstract
- The 19p13.1 breast cancer susceptibility locus is a modifier of breast cancer risk in BRCA1 mutation carriers and is also associated with risk of ovarian cancer. Here we investigated 19p13.1 variation and risk of breast cancer subtypes, defined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status, using 48,869 breast cancer cases and 49,787 controls from the Breast Cancer Association Consortium (BCAC). Variants from 19p13.1 were not associated with breast cancer overall or with ER-positive breast cancer but were significantly associated with ER-negative breast cancer risk [rs8170 Odds Ratio (OR)=1.10, 95% Confidence Interval (CI) 1.05 - 1.15, p=3.49 x 10-5] and triple negative (TN) (ER, PR and HER2 negative) breast cancer [rs8170 OR=1.22, 95% CI 1.13 - 1.31, p=2.22 x 10-7]. However, rs8170 was no longer associated with ER-negative breast cancer risk when TN cases were excluded [OR=0.98, 95% CI 0.89 - 1.07, p=0.62]. In addition, a combined analysis of TN cases from BCAC and the Triple Negative Breast Cancer Consortium (TNBCC) (n=3,566) identified a genome-wide significant association between rs8170 and TN breast cancer risk [OR=1.25, 95% CI 1.18 - 1.33, p=3.31 x 10-13]. Thus, 19p13.1 is the first triple negative-specific breast cancer risk locus and the first locus specific to a histological subtype defined by ER, PR, and HER2 to be identified. These findings provide convincing evidence that genetic susceptibility to breast cancer varies by tumor subtype and that triple negative tumors and other subtypes likely arise through distinct etiologic pathways.
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| 37. |
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| 38. |
- Wyrowski, F., et al.
(author)
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Variations in H2O+/H2O ratios toward massive star-forming regions
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 521, s. L34-
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Journal article (peer-reviewed)abstract
- Early results from the Herschel Space Observatory revealed the water cation H2O+ to be an abundant ingredient of the interstellar medium. Here we present new observations of the H2O and H2O+ lines at 1113.3 and 1115.2 GHz using the Herschel Space Observatory toward a sample of high-mass star-forming regions to observationally study the relation between H2O and H2O+. Nine out of ten sources show absorption from H2O+ in a range of environments: the molecular clumps surrounding the forming and newly formed massive stars, bright high-velocity outflows associated with the massive protostars, and unrelated low-density clouds along the line of sight. Column densities per velocity component of H2O+ are found in the range of 10(12) to a few 10(13) cm(-2). The highest N(H2O+) column densities are found in the outflows of the sources. The ratios of H2O+/H2O are determined in a range from 0.01 to a few and are found to differ strongly between the observed environments with much lower ratios in the massive (proto) cluster envelopes (0.01-0.1) than in outflows and diffuse clouds. Remarkably, even for source components detected in H2O in emission, H2O+ is still seen in absorption.
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| 39. |
- Yildiz, U. A., et al.
(author)
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Herschel/HIFI observations of high-J CO lines in the NGC 1333 low-mass star-forming region
- 2010
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 521, s. L40-
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Journal article (peer-reviewed)abstract
- Herschel/HIFI observations of high-J lines (up to J(u) = 10) of (CO)-C-12, (CO)-C-13 and (CO)-O-18 are presented toward three deeply embedded low-mass protostars, NGC 1333 IRAS 2A, IRAS 4A, and IRAS 4B, obtained as part of the Water In Star-forming regions with Herschel (WISH) key program. The spectrally-resolved HIFI data are complemented by ground-based observations of lower-J CO and isotopologue lines. The (CO)-C-12 10-9 profiles are dominated by broad (FWHM 25-30 km s(-1)) emission. Radiative transfer models are used to constrain the temperature of this shocked gas to 100-200 K. Several CO and (CO)-C-13 line profiles also reveal a medium-broad component (FWHM5-10 km s(-1)), seen prominently in H2O lines. Column densities for both components are presented, providing a reference for determining abundances of other molecules in the same gas. The narrow (CO)-O-18 9-8 lines probe the warmer part of the quiescent envelope. Their intensities require a jump in the CO abundance at an evaporation temperature around 25 K, thus providing new direct evidence for a CO ice evaporation zone around low-mass protostars.
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