| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
- Le Clerc, S., et al.
(författare)
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HLA-DRB1 and HLA-DQB1 genetic diversity modulates response to lithium in bipolar affective disorders
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Bipolar affective disorder (BD) is a severe psychiatric illness, for which lithium (Li) is the gold standard for acute and maintenance therapies. The therapeutic response to Li in BD is heterogeneous and reliable biomarkers allowing patients stratification are still needed. A GWAS performed by the International Consortium on Lithium Genetics (ConLiGen) has recently identified genetic markers associated with treatment responses to Li in the human leukocyte antigens (HLA) region. To better understand the molecular mechanisms underlying this association, we have genetically imputed the classical alleles of the HLA region in the European patients of the ConLiGen cohort. We found our best signal for amino-acid variants belonging to the HLA-DRB1*11:01 classical allele, associated with a better response to Li (p < 1 x 10(-3); FDR < 0.09 in the recessive model). Alanine or Leucine at position 74 of the HLA-DRB1 heavy chain was associated with a good response while Arginine or Glutamic acid with a poor response. As these variants have been implicated in common inflammatory/autoimmune processes, our findings strongly suggest that HLA-mediated low inflammatory background may contribute to the efficient response to Li in BD patients, while an inflammatory status overriding Li anti-inflammatory properties would favor a weak response.
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| 4. |
- Cearns, M., et al.
(författare)
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Using polygenic scores and clinical data for bipolar disorder patient stratification and lithium response prediction: machine learning approach
- 2022
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Ingår i: British Journal of Psychiatry. - : Royal College of Psychiatrists. - 0007-1250 .- 1472-1465. ; 220:4, s. 219-228
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Tidskriftsartikel (refereegranskat)abstract
- Background Response to lithium in patients with bipolar disorder is associated with clinical and transdiagnostic genetic factors. The predictive combination of these variables might help clinicians better predict which patients will respond to lithium treatment. Aims To use a combination of transdiagnostic genetic and clinical factors to predict lithium response in patients with bipolar disorder. Method This study utilised genetic and clinical data (n = 1034) collected as part of the International Consortium on Lithium Genetics (ConLi(+)Gen) project. Polygenic risk scores (PRS) were computed for schizophrenia and major depressive disorder, and then combined with clinical variables using a cross-validated machine-learning regression approach. Unimodal, multimodal and genetically stratified models were trained and validated using ridge, elastic net and random forest regression on 692 patients with bipolar disorder from ten study sites using leave-site-out cross-validation. All models were then tested on an independent test set of 342 patients. The best performing models were then tested in a classification framework. Results The best performing linear model explained 5.1% (P = 0.0001) of variance in lithium response and was composed of clinical variables, PRS variables and interaction terms between them. The best performing non-linear model used only clinical variables and explained 8.1% (P = 0.0001) of variance in lithium response. A priori genomic stratification improved non-linear model performance to 13.7% (P = 0.0001) and improved the binary classification of lithium response. This model stratified patients based on their meta-polygenic loadings for major depressive disorder and schizophrenia and was then trained using clinical data. Conclusions Using PRS to first stratify patients genetically and then train machine-learning models with clinical predictors led to large improvements in lithium response prediction. When used with other PRS and biological markers in the future this approach may help inform which patients are most likely to respond to lithium treatment.
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| 5. |
- Amare, A. T., et al.
(författare)
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Association of polygenic score for major depression with response to lithium in patients with bipolar disorder
- 2021
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Ingår i: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 26, s. 2457-2470
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Tidskriftsartikel (refereegranskat)abstract
- Lithium is a first-line medication for bipolar disorder (BD), but only one in three patients respond optimally to the drug. Since evidence shows a strong clinical and genetic overlap between depression and bipolar disorder, we investigated whether a polygenic susceptibility to major depression is associated with response to lithium treatment in patients with BD. Weighted polygenic scores (PGSs) were computed for major depression (MD) at different GWAS p value thresholds using genetic data obtained from 2586 bipolar patients who received lithium treatment and took part in the Consortium on Lithium Genetics (ConLi(+)Gen) study. Summary statistics from genome-wide association studies in MD (135,458 cases and 344,901 controls) from the Psychiatric Genomics Consortium (PGC) were used for PGS weighting. Response to lithium treatment was defined by continuous scores and categorical outcome (responders versus non-responders) using measurements on the Alda scale. Associations between PGSs of MD and lithium treatment response were assessed using a linear and binary logistic regression modeling for the continuous and categorical outcomes, respectively. The analysis was performed for the entire cohort, and for European and Asian sub-samples. The PGSs for MD were significantly associated with lithium treatment response in multi-ethnic, European or Asian populations, at various p value thresholds. Bipolar patients with a low polygenic load for MD were more likely to respond well to lithium, compared to those patients with high polygenic load [lowest vs highest PGS quartiles, multi-ethnic sample: OR = 1.54 (95% CI: 1.18-2.01) and European sample: OR = 1.75 (95% CI: 1.30-2.36)]. While our analysis in the Asian sample found equivalent effect size in the same direction: OR = 1.71 (95% CI: 0.61-4.90), this was not statistically significant. Using PGS decile comparison, we found a similar trend of association between a high genetic loading for MD and lower response to lithium. Our findings underscore the genetic contribution to lithium response in BD and support the emerging concept of a lithium-responsive biotype in BD.
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| 6. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 7. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 8. |
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| 9. |
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| 10. |
- Zerbi, F. M., et al.
(författare)
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HIRES : The High Resolution Spectrograph for E-ELT
- 2014
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Ingår i: Ground-based and Airborne Instrumentation for Astronomy V. - : SPIE. - 9780819496157
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Konferensbidrag (refereegranskat)abstract
- The current instrumentation plan for the E-ELT foresees a High Resolution Spectrograph conventionally indicated as HIRES. Shaped on the study of extra-solar planet atmospheres, Pop-III stars and fundamental physical constants, HIRES is intended to embed observing modes at high-resolution (up to R=150000) and large spectral range (from the blue limit to the K band) useful for a large suite of science cases that can exclusively be tackled by the E-ELT. We present in this paper the solution for HIRES envisaged by the "HIRES initiative", the international collaboration established in 2013 to pursue a HIRES on E-ELT.
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| 11. |
- Gunduz, C., et al.
(författare)
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Hyperlipidaemia prevalence and cholesterol control in obstructive sleep apnoea: Data from the European sleep apnea database (ESADA)
- 2019
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Ingår i: Journal of Internal Medicine. - : Wiley. - 0954-6820 .- 1365-2796. ; 286:6, s. 676-688
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Tidskriftsartikel (refereegranskat)abstract
- Background and objective Obstructive sleep apnoea (OSA) and hyperlipidaemia are independent risk factors for cardiovascular disease. This study investigates the association between OSA and prevalence of hyperlipidaemia in patients of the European Sleep Apnea Database (ESADA) cohort. Methods The cross-sectional analysis included 11 892 patients (age 51.9 +/- 12.5 years, 70% male, body mass index (BMI) 31.3 +/- 6.6 kg/m(2), mean oxygen desaturation index (ODI) 23.7 +/- 25.5 events/h) investigated for OSA. The independent odds ratio (OR) for hyperlipidaemia in relation to measures of OSA (ODI, apnoea-hypopnoea index, mean and lowest oxygen saturation) was determined by means of general linear model analysis with adjustment for important confounders such as age, BMI, comorbidities and study site. Results Hyperlipidaemia prevalence increased from 15.1% in subjects without OSA to 26.1% in those with severe OSA, P < 0.001. Corresponding numbers in patients with diabetes were 8.5% and 41.5%, P < 0.001. Compared with ODI quartile I, patients in ODI quartiles II-IV had an adjusted OR (95% CI) of 1.33 (1.15-1.55), 1.37 (1.17-1.61) and 1.33 (1.12-1.58) (P < 0.001), respectively, for hyperlipidaemia. Obesity was defined as a significant risk factor for hyperlipidaemia. Subgroups of OSA patients with cardio-metabolic comorbidities demonstrated higher prevalence of HL. In addition, differences in hyperlipidaemia prevalence were reported in European geographical regions with the highest prevalence in Central Europe. Conclusion Obstructive sleep apnoea, in particular intermittent hypoxia, was independently associated with the prevalence of hyperlipidaemia diagnosis.
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| 12. |
- Gunduz, C., et al.
(författare)
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Long-term positive airway pressure therapy is associated with reduced total cholesterol levels in patients with obstructive sleep apnea: data from the European Sleep Apnea Database (ESADA)
- 2020
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Ingår i: Sleep Medicine. - : Elsevier BV. - 1389-9457. ; 75, s. 201-209
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Tidskriftsartikel (refereegranskat)abstract
- Background and aim: Obstructive sleep apnea (OSA) is an independent risk factor for dyslipidemia. The current study examined the effects of positive airway pressure (PAP) treatment on lipid status in the European Sleep Apnea Database (ESADA). Methods: The prospective cohort study enrolled 1564 OSA subjects (74% male, mean age 54 ± 11y, body mass index (BMI) 32.7 ± 6.6 kg/m2 and apnea-hypopnea index (AHI) 40.3 ± 24.4 n/h) undergoing PAP therapy for at least three months (mean 377.6 ± 419.5 days). Baseline and follow-up total cholesterol (TC) from nine centers were analyzed. Repeated measures and logistic regression tests (adjusted for age, sex, weight changes, lipid lowering medication, PAP compliance, and treatment duration) were used to compare changes in TC concentration. Incident risk for a coronary heart disease event (CHD) was used to compute a Framingham CHD risk score (estimated from age, BMI, blood pressure, and TC). Results: Adjusted means of TC decreased from 194.2 mg/dl to 189.3 mg/dl during follow-up (p = 0.019). A clinically significant (10%) reduction of TC at PAP follow-up was observed in 422 patients (27%). Duration of PAP therapy was identified as independent predictor for TC reduction, which implies an approximately 10% risk reduction for incident CHD events (from 26.7% to 24.1% in men and from 11.2% to 10.1% in women, p < 0.001 respectively). Conclusion: This observational study demonstrates a reduction of TC after long-term PAP treatment. The close association between TC concentration and cardiovascular (CV) mortality suggests that identification and treatment of OSA may have a beneficial effect on overall CV risk due to this mechanism. This possibility needs to be evaluated in prospective randomized studies. © 2020 Elsevier B.V.
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| 13. |
- Ostergaard, H. B., et al.
(författare)
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Estimating individual lifetime risk of incident cardiovascular events in adults with Type 2 diabetes: an update and geographical calibration of the DIAbetes Lifetime perspective model (DIAL2)
- 2023
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Ingår i: European Journal of Preventive Cardiology. - : Oxford University Press (OUP). - 2047-4873 .- 2047-4881. ; 30:1, s. 61-69
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Tidskriftsartikel (refereegranskat)abstract
- Aims The 2021 European Society of Cardiology cardiovascular disease (CVD) prevention guidelines recommend the use of (lifetime) risk prediction models to aid decisions regarding intensified preventive treatment options in adults with Type 2 diabetes, e.g. the DIAbetes Lifetime perspective model (DIAL model). The aim of this study was to update the DIAL model using contemporary and representative registry data (DIAL2) and to systematically calibrate the model for use in other European countries. Methods and results The DIAL2 model was derived in 467 856 people with Type 2 diabetes without a history of CVD from the Swedish National Diabetes Register, with a median follow-up of 7.3 years (interquartile range: 4.0-10.6 years) and comprising 63 824 CVD (including fatal CVD, non-fatal stroke and non-fatal myocardial infarction) events and 66 048 non-CVD mortality events. The model was systematically recalibrated to Europe's low- and moderate-risk regions using contemporary incidence data and mean risk factor distributions. The recalibrated DIAL2 model was externally validated in 218 267 individuals with Type 2 diabetes from the Scottish Care Information-Diabetes (SCID) and Clinical Practice Research Datalink (CPRD). In these individuals, 43 074 CVD events and 27 115 non-CVD fatal events were observed. The DIAL2 model discriminated well, with C-indices of 0.732 [95% confidence interval (CI) 0.726-0.739] in CPRD and 0.700 (95% CI 0.691-0.709) in SCID. Conclusion The recalibrated DIAL2 model provides a useful tool for the prediction of CVD-free life expectancy and lifetime CVD risk for people with Type 2 diabetes without previous CVD in the European low- and moderate-risk regions. These long-term individualized measures of CVD risk are well suited for shared decision-making in clinical practice as recommended by the 2021 CVD ESC prevention guidelines.
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| 14. |
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| 15. |
- De Cia, A., et al.
(författare)
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Dust-depletion sequences in damped Lyman-alpha absorbers A unified picture from low-metallicity systems to the Galaxy
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 596
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Tidskriftsartikel (refereegranskat)abstract
- We study metal depletion due to dust in the interstellar medium (ISM) to infer the properties of dust grains and characterize the metal and dust content of galaxies down to low metallicity and intermediate redshift z. We provide metal column densities and abundances of a sample of 70 damped Lyman-alpha absorbers (DLAs) towards quasars, observed at high spectral resolution with the Very Large Telescope (VLT) Ultraviolet and Visual Echelle Spectrograph (UVES). This is the largest sample of phosphorus abundances measured in DLAs so far. We use literature measurements for Galactic clouds to cover the high-metallicity end. We discover tight (scatter less than or similar to 0.2 dex) correlations between [Zn/Fe] and the observed relative abundances from dust depletion. This implies that grain growth in the ISM is an important process of dust production. These sequences are continuous in [Zn/Fe] from dust-free to dusty DLAs, and to Galactic clouds, suggesting that the availability of refractory metals in the ISM is crucial for dust production, regardless of the star formation history. We observe [S/Zn] up to similar to 0.25 dex in DLAs, which is broadly consistent with Galactic stellar abundances. Furthermore, we find a good agreement between the nucleosynthetic pattern of Galactic halo stars and our observations of the least dusty DLAs. This supports recent star formation in low-metallicity DLAs. The derived depletions of Zn, O, P, S, Si, Mg, Mn, Cr, and Fe correlate with [Zn/Fe], with steeper slopes for more refractory elements. P is mostly not affected by dust depletion. We present canonical depletion patterns to be used as reference in future studies of relative abundances and depletion. We derive the total (dust-corrected) metallicity, typically -2 8 [M/H](tot) less than or similar to 0 for DLAs, and scattered around solar metallicity for the Galactic ISM. The dust-to-metal ratio (DTM) increases with metallicity, again supporting the importance of grain growth for dust production. The dust extinction AV derived from the depletion is typically <0.2 mag in DLAs. Finally, we derive elemental abundances in dust, which is key to understanding the dust composition and its evolution. We observe similar abundances of Mg, Si, and Fe in dust; this suggests that grain species such as pyroxenes and iron oxides are more important than olivine, but this needs to be confirmed by more detailed analysis. Overall, we characterize dust depletion, nucleosynthesis, and dust-corrected metallicity in DLAs, providing a unified picture from low-metallicity systems to the Galactic ISM.
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| 16. |
- Kalman, Janos L, et al.
(författare)
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Investigating polygenic burden in age at disease onset in bipolar disorder: Findings from an international multicentric study.
- 2019
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Ingår i: Bipolar disorders. - : Wiley. - 1399-5618 .- 1398-5647. ; 21:1, s. 68-75
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Tidskriftsartikel (refereegranskat)abstract
- Bipolar disorder (BD) with early disease onset is associated with an unfavorable clinical outcome and constitutes a clinically and biologically homogenous subgroup within the heterogeneous BD spectrum. Previous studies have found an accumulation of early age at onset (AAO) in BD families and have therefore hypothesized that there is a larger genetic contribution to the early-onset cases than to late onset BD. To investigate the genetic background of this subphenotype, we evaluated whether an increased polygenic burden of BD- and schizophrenia (SCZ)-associated risk variants is associated with an earlier AAO in BD patients.A total of 1995 BD type 1 patients from the Consortium of Lithium Genetics (ConLiGen), PsyCourse and Bonn-Mannheim samples were genotyped and their BD and SCZ polygenic risk scores (PRSs) were calculated using the summary statistics of the Psychiatric Genomics Consortium as a training data set. AAO was either separated into onset groups of clinical interest (childhood and adolescence [≤18years] vs adulthood [>18years]) or considered as a continuous measure. The associations between BD- and SCZ-PRSs and AAO were evaluated with regression models.BD- and SCZ-PRSs were not significantly associated with age at disease onset. Results remained the same when analyses were stratified by site of recruitment.The current study is the largest conducted so far to investigate the association between the cumulative BD and SCZ polygenic risk and AAO in BD patients. The reported negative results suggest that such a polygenic influence, if there is any, is not large, and highlight the importance of conducting further, larger scale studies to obtain more information on the genetic architecture of this clinically relevant phenotype.
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| 17. |
- Mattsson, Lars, et al.
(författare)
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Dust-depletion sequences in damped Lyman-alpha absorbers II. The composition of cosmic dust, from low-metallicity systems to the Galaxy
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 624
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Tidskriftsartikel (refereegranskat)abstract
- Metals in the interstellar medium (ISM) of essentially all types of galaxies are observed to be depleted compared to the expected values. The depletion is most likely due to dust condensation in, for example, cold molecular clouds and various circumstellar and interstellar environments. The relative observed metal abundances should thereby reflect the composition of the ISM dust components. We aim at identifying the most dominant dust species or types, including silicate and iron oxide grains present in the ISM, using recent observations of dust depletion of galaxies at various evolutionary stages. We use the observed elemental abundances in dust of several metals (O, S, Si, Mg, and Fe) in different environments, considering systems with different metallicities and dust content, namely damped Lyman-alpha absorbers (DLAs) towards quasars and the Galaxy. We derive a possible dust composition by computationally finding the statistically expected elemental abundances in dust assuming a set of key dust species with the iron content as a free parameter. Carbonaceous dust is not considered in the present study. Metallic iron (likely in the form of inclusions in silicate grains) and iron oxides are important components of the mass composition of carbon-free dust. The latter make up a significant mass fraction (similar to 1/4 in some cases) of the oxygen-bearing dust and there are good reasons to believe that metallic iron constitutes a similar mass fraction of dust. Wustite (FeO) could be a simple explanation for the depletion of iron and oxygen because it is easily formed. There appears to be no silicate species clearly dominating the silicate mass, but rather a mix of iron-poor as well as iron-rich olivine and pyroxene. To what extent sulphur depletion is due to sulfides remains unclear. In general, there seems to be little evolution of the dust composition (not considering carbonaceous dust) from low-metallicity systems to the Galaxy.
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| 18. |
- Noterdaeme, P., et al.
(författare)
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Discovery of a compact gas-rich damped Lyman-alpha galaxy at z = 2.2 : evidence of a starburst driven outflow
- 2012
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 540, s. A63-
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Tidskriftsartikel (refereegranskat)abstract
- We present the detection of Ly alpha, [OIII], and H alpha emission associated with an extremely strong damped Lyman-alpha (DLA) system (N(HI) = 10(22.10) cm(-2)) at z = 2.207 towards the quasar SDSS J113520.39-001053.56. This is the largest Hi column density ever measured along a quasi-stellar object (QSO) line of sight, though typical of those often found in DLAs associated to gamma-ray bursts (GRBs). This absorption system can also be classified as an ultra-strong Mg II system with W-r(lambda 2796) similar or equal to 3.6 angstrom. The mean metallicity of the gas ([Zn/H] = -1.1) and dust depletion factors ([Zn/Fe] = 0.72, [Zn/Cr] = 0.49) are consistent with (and only marginally larger than) the mean values found in the general QSO-DLA population. The [OIII]-H alpha emitting region has a very small impact parameter with respect to the QSO line of sight, b approximate to 0.1 '' (0.9 kpc proper distance), and is unresolved. From the H alpha line, we measure a significant star formation rate (SFR) approximate to 25 M-circle dot yr(-1) (uncorrected for dust). The shape of the Ly alpha line is double-peaked, which is the signature of a resonant scattering of Ly alpha photons, and the Ly alpha emission is spatially extended. More strikingly, the blue and red Ly alpha peaks arise from distinct regions extended over a few kpc on either side of the star-forming region. We propose that this is the consequence of a Ly alpha transfer in outflowing gas. The presence of starburst-driven outflows is also in agreement with the high SFR together with the small size and low mass of the galaxy (M-vir similar to 10(10) M-circle dot). By placing constraints on the stellar UV continuum luminosity of the galaxy, we estimate an age of at most a few 10(7) yr, again consistent with a recent starburst scenario. We interpret these data as the observation of a young, gas-rich, compact starburst galaxy, from which material is expelled through collimated winds powered by the vigorous star formation activity. We substantiate this picture by modelling the radiative transfer of Ly alpha photons in the galactic counterpart. Though our model (a spherical galaxy with bipolar outflowing jets) is a simplistic representation of the true gas distribution and velocity field, the agreement between the observed and simulated properties is particularly good (spectral shape and width of the Lyman-alpha emission, spatial configuration, escape fraction as well as absorption kinematics, HI column density, and dust reddening). Finally, we propose that selecting DLAs with very high Hi column densities may be an efficient way of detecting star-forming galaxies at small impact parameters from the background QSO lines of sight.
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| 19. |
- Ranjan, A., et al.
(författare)
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Molecular gas and star formation in an absorption-selected galaxy : Hitting the bull's eye at z similar or equal to 2.46
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618
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Tidskriftsartikel (refereegranskat)abstract
- We present the detection and detailed analysis of a diffuse molecular cloud at z(abs) = 2.4636 towards the quasar SDSS J 1513+0352 (z(em) similar or equal to 2.68) observed with the X-shooter spectrograph at the Very Large Telescope. We measured very high column densities of atomic and molecular hydrogen with log N(H-I; H-2) similar or equal to 21.8; 21.3. This is the highest H-2 column density ever measured in an intervening damped Lyman-alpha system but we did not detect CO, implying log N(CO)/N(H-2) < -7.8, which could be due to a low metallicity of the cloud. From the metal absorption lines, we derived the metallicity to be Z similar or equal to 0.15 Z(circle dot) and determined the amount of dust by measuring the induced extinction of the background quasar light, A(V) similar or equal to 0.4. We simultaneously detected Lyman-alpha emission at the same redshift with a centroid located at a most probable impact parameter of only rho similar or equal to 1.4 kpc. We argue that the line of sight is therefore likely passing through the interstellar medium (ISM), as opposed to the circumgalactic medium (CGM), of a galaxy. The relation between the surface density of gas and that of star formation seems to follow the global empirical relation derived in the nearby Universe although our constraints on the star formation rate (SFR) and the galaxy extent remain too loose to be conclusive. We study the transition from atomic to molecular hydrogen using a theoretical description based on the microphysics of molecular hydrogen. We use the derived chemical properties of the cloud and physical conditions (T-k similar or equal to 90K and n similar or equal to 250 cm(3)) derived through the excitation of H-2 rotational levels and neutral carbon fine structure transitions to constrain the fundamental parameters that govern this transition. By comparing the theoretical and observed HI column densities, we are able to bring an independent constraint on the incident ultra-violet (UV) flux, which we find to be in agreement with that estimated from the observed SFR.
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| 20. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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