| 1. |
- Thomas, HS, et al.
(author)
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- 2019
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
- de Jong, R. S., et al.
(author)
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4MOST : Project overview and information for the First Call for Proposals
- 2019
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In: The Messenger. - : European Southern Observatory. - 0722-6691. ; 175, s. 3-11
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Journal article (other academic/artistic)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.
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| 5. |
- Gutierrez, C. P., et al.
(author)
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DES16C3cje : A low-luminosity, long-lived supernova
- 2020
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In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 496:1, s. 95-110
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Journal article (peer-reviewed)abstract
- We present DES16C3cje, a low-luminosity, long-lived type II supernova (SN II) at redshift 0.0618, detected by the Dark Energy Survey (DES). DES16C3cje is a unique SN. The spectra are characterized by extremely narrow photospheric lines corresponding to very low expansion velocities of less than or similar to 1500 km s(-1), and the light curve shows an initial peak that fades after 50 d before slowly rebrightening over a further 100 d to reach an absolute brightness of M-r similar to 15.5 mag. The decline rate of the late-time light curve is then slower than that expected from the powering by radioactive decay of Co-56, but is comparable to that expected from accretion power. Comparing the bolometric light curve with hydrodynamical models, we find that DES16C3cje can be explained by either (i) a low explosion energy (0.11 foe) and relatively large Ni-56 production of 0.075 M-circle dot from an similar to 15 M-circle dot red supergiant progenitor typical of other SNe II, or (ii) a relatively compact similar to 40 M-circle dot star, explosion energy of 1 foe, and 0.08 M-circle dot of Ni-56. Both scenarios require additional energy input to explain the late-time light curve, which is consistent with fallback accretion at a rate of similar to 0.5 x 10(-)(8) M-circle dot s(-1).
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| 6. |
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| 7. |
- Mavaddat, Nasim, et al.
(author)
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Prediction of Breast Cancer Risk Based on Profiling With Common Genetic Variants
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 107:5, s. 036-036
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Journal article (peer-reviewed)abstract
- Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. Methods: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. Results: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. Conclusions: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.
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| 8. |
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| 9. |
- Dunham, I, et al.
(author)
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The DNA sequence of human chromosome 22
- 1999
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 402:6761, s. 489-495
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Journal article (peer-reviewed)
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| 10. |
- Hampton, Stephanie E., et al.
(author)
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Ecology under lake ice
- 2017
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In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 20:1, s. 98-111
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Research review (peer-reviewed)abstract
- Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer ‘growing seasons’. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.
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| 11. |
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| 12. |
- 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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| 13. |
- Ademuyiwa, Adesoji O., et al.
(author)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Journal article (peer-reviewed)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 14. |
- Tempel, E., et al.
(author)
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An optimized tiling pattern for multiobject spectroscopic surveys : Application to the 4MOST survey
- 2020
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In: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 497:4, s. 4626-4643
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Journal article (peer-reviewed)abstract
- Large multiobject spectroscopic surveys require automated algorithms to optimize their observing strategy. One of the most ambitious upcoming spectroscopic surveys is the 4MOST survey. The 4MOST survey facility is a fibre-fed spectroscopic instrument on the VISTA telescope with a large enough field of view to survey a large fraction of the southern sky within a few years. Several Galactic and extragalactic surveys will be carried out simultaneously, so the combined target density will strongly vary. In this paper, we describe a new tiling algorithm that can naturally deal with the large target density variations on the sky and which automatically handles the different exposure times of targets. The tiling pattern is modelled as a marked point process, which is characterized by a probability density that integrates the requirements imposed by the 4MOST survey. The optimal tilling pattern with respect to the defined model is estimated by the tiles configuration that maximizes the proposed probability density. In order to achieve this maximization a simulated annealing algorithm is implemented. The algorithm automatically finds an optimal tiling pattern and assigns a tentative sky brightness condition and exposure time for each tile, while minimizing the total execution time that is needed to observe the list of targets in the combined input catalogue of all surveys. Hence, the algorithm maximizes the long-term observing efficiency and provides an optimal tiling solution for the survey. While designed for the 4MOST survey, the algorithm is flexible and can with simple modifications be applied to any other multiobject spectroscopic survey.
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| 15. |
- Tempel, E., et al.
(author)
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Probabilistic fibre-to-target assignment algorithm for multi-object spectroscopic surveys
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 635
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Journal article (peer-reviewed)abstract
- Context. Several new multi-object spectrographs are currently planned or under construction that are capable of observing thousands of Galactic and extragalactic objects simultaneously. Aims. In this paper we present a probabilistic fibre-to-target assignment algorithm that takes spectrograph targeting constraints into account and is capable of dealing with multiple concurrent surveys. We present this algorithm using the 4-m Multi-Object Spectroscopic Telescope (4MOST) as an example. Methods. The key idea of the proposed algorithm is to assign probabilities to fibre-target pairs. The assignment of probabilities takes the fibre positioner's capabilities and constraints into account. Additionally, these probabilities include requirements from surveys and take the required exposure time, number density variation, and angular clustering of targets across each survey into account. The main advantage of a probabilistic approach is that it allows for accurate and easy computation of the target selection function for the different surveys, which involves determining the probability of observing a target, given an input catalogue. Results. The probabilistic fibre-to-target assignment allows us to achieve maximally uniform completeness within a single field of view. The proposed algorithm maximises the fraction of successfully observed targets whilst minimising the selection bias as a function of exposure time. In the case of several concurrent surveys, the algorithm maximally satisfies the scientific requirements of each survey and no specific survey is penalised or prioritised. Conclusions. The algorithm presented is a proposed solution for the 4MOST project that allows for an unbiased targeting of many simultaneous surveys. With some modifications, the algorithm may also be applied to other multi-object spectroscopic surveys.
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| 16. |
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| 17. |
- Guiglion, G., et al.
(author)
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4MOST Survey Strategy Plan
- 2019
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In: Messenger. - 0722-6691. ; 175, s. 17-21
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Journal article (other academic/artistic)abstract
- The current status of and motivation for the 4MOST survey strategy, as developed by the Consortium science team, are presented here. Key elements of the strategy are described, such as sky coverage, number of visits and total exposure times in different parts of the sky, and how to deal with different observing conditions. The task of organising the strategy is not simple, with many different surveys that have vastly different target brightnesses and densities, sample completeness levels, and signal-to-noise requirements. We introduce here a number of concepts that we will use to ensure all surveys are optimised. Astronomers who are planning to submit a Participating Survey proposal are strongly encouraged to read this article and any relevant 4MOST Survey articles in this issue of The Messenger such that they can optimally complement and benefit from the planned surveys of the 4MOST Consortium.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
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| 22. |
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| 23. |
- Lauc, Gordan, et al.
(author)
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Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers
- 2013
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In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 9:1, s. e1003225-
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Journal article (peer-reviewed)abstract
- Glycosylation of immunoglobulin G (IgG) influences IgG effector function by modulating binding to Fc receptors. To identify genetic loci associated with IgG glycosylation, we quantitated N-linked IgG glycans using two approaches. After isolating IgG from human plasma, we performed 77 quantitative measurements of N-glycosylation using ultra-performance liquid chromatography (UPLC) in 2,247 individuals from four European discovery populations. In parallel, we measured IgG N-glycans using MALDI-TOF mass spectrometry (MS) in a replication cohort of 1,848 Europeans. Meta-analysis of genome-wide association study (GWAS) results identified 9 genome-wide significant loci (P<2.27x10(-9)) in the discovery analysis and two of the same loci (B4GALT1 and MGAT3) in the replication cohort. Four loci contained genes encoding glycosyltransferases (ST6GAL1, B4GALT1, FUT8, and MGAT3), while the remaining 5 contained genes that have not been previously implicated in protein glycosylation (IKZF1, IL6ST-ANKRD55, ABCF2-SMARCD3, SUV420H1, and SMARCB1-DERL3). However, most of them have been strongly associated with autoimmune and inflammatory conditions (e. g., systemic lupus erythematosus, rheumatoid arthritis, ulcerative colitis, Crohn's disease, diabetes type 1, multiple sclerosis, Graves' disease, celiac disease, nodular sclerosis) and/or haematological cancers (acute lymphoblastic leukaemia, Hodgkin lymphoma, and multiple myeloma). Follow-up functional experiments in haplodeficient Ikzf1 knock-out mice showed the same general pattern of changes in IgG glycosylation as identified in the meta-analysis. As IKZF1 was associated with multiple IgG N-glycan traits, we explored biomarker potential of affected N-glycans in 101 cases with SLE and 183 matched controls and demonstrated substantial discriminative power in a ROC-curve analysis (area under the curve=0.842). Our study shows that it is possible to identify new loci that control glycosylation of a single plasma protein using GWAS. The results may also provide an explanation for the reported pleiotropy and antagonistic effects of loci involved in autoimmune diseases and haematological cancer.
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Meister, Philip, et al.
(author)
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A global compilation of diatom silica oxygen isotope records from lake sediment - trends and implications for climate reconstruction
- 2024
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In: Climate of the Past. - 1814-9324. ; 20:2, s. 363-392
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Journal article (peer-reviewed)abstract
- Oxygen isotopes in biogenic silica (δ18OBSi) from lake sediments allow for quantitative reconstruction of past hydroclimate and proxy-model comparison in terrestrial environments. The signals of individual records have been attributed to different factors, such as air temperature (Tair), atmospheric circulation patterns, hydrological changes, and lake evaporation. While every lake has its own local set of drivers of δ18O variability, here we explore the extent to which regional or even global signals emerge from a series of paleoenvironmental records. This study provides a comprehensive compilation and combined statistical evaluation of the existing lake sediment δ18OBSi records, largely missing in other summary publications (i.e. PAGES network). For this purpose, we have identified and compiled 71 down-core records published to date and complemented these datasets with additional lake basin parameters (e.g. lake water residence time and catchment size) to best characterize the signal properties. Records feature widely different temporal coverage and resolution, ranging from decadal-scale records covering the past 150 years to records with multi-millennial-scale resolution spanning glacial-interglacial cycles. The best coverage in number of records (NCombining double low line37) and data points (NCombining double low line2112) is available for Northern Hemispheric (NH) extratropical regions throughout the Holocene (roughly corresponding to Marine Isotope Stage 1; MIS 1). To address the different variabilities and temporal offsets, records were brought to a common temporal resolution by binning and subsequently filtered for hydrologically open lakes with lake water residence times <100 years. For mid- to high-latitude (>45°N) lakes, we find common δ18OBSi patterns among the lake records during both the Holocene and Common Era (CE). These include maxima and minima corresponding to known climate episodes, such as the Holocene Thermal Maximum (HTM), Neoglacial Cooling, Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). These patterns are in line with long-term air temperature changes supported by previously published climate reconstructions from other archives, as well as Holocene summer insolation changes. In conclusion, oxygen isotope records from NH extratropical lake sediments feature a common climate signal at centennial (for CE) and millennial (for Holocene) timescales despite stemming from different lakes in different geographic locations and hence constitute a valuable proxy for past climate reconstructions.
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| 28. |
- Melo-Gonzalez, F, et al.
(author)
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Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria
- 2019
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In: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 216:4, s. 728-742
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Journal article (peer-reviewed)abstract
- Intestinal immune homeostasis is dependent upon tightly regulated and dynamic host interactions with the commensal microbiota. Immunoglobulin A (IgA) produced by mucosal B cells dictates the composition of commensal bacteria residing within the intestine. While emerging evidence suggests the majority of IgA is produced innately and may be polyreactive, mucosal-dwelling species can also elicit IgA via T cell–dependent mechanisms. However, the mechanisms that modulate the magnitude and quality of T cell–dependent IgA responses remain incompletely understood. Here we demonstrate that group 3 innate lymphoid cells (ILC3) regulate steady state interactions between T follicular helper cells (TfH) and B cells to limit mucosal IgA responses. ILC3 used conserved migratory cues to establish residence within the interfollicular regions of the intestinal draining lymph nodes, where they act to limit TfH responses and B cell class switching through antigen presentation. The absence of ILC3-intrinsic antigen presentation resulted in increased and selective IgA coating of bacteria residing within the colonic mucosa. Together these findings implicate lymph node resident, antigen-presenting ILC3 as a critical regulatory checkpoint in the generation of T cell–dependent colonic IgA and suggest ILC3 act to maintain tissue homeostasis and mutualism with the mucosal-dwelling commensal microbiota.
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| 29. |
- Sutton, Jill N., et al.
(author)
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A review of the stable isotope bio-geochemistry of the global silicon cycle and its associated trace elements
- 2018
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In: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 5
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Research review (peer-reviewed)abstract
- Silicon (Si) is the second most abundant element in the Earth’s crust and is an important nutrient in the ocean. The global Si cycle plays a critical role in regulating primary productivity and carbon cycling on the continents and in the oceans. Development of the analytical tools used to study the sources, sinks, and fluxes of the global Si cycle (e.g., elemental and stable isotope ratio data for Ge, Si, Zn, etc.) have recently led to major advances in our understanding of the mechanisms and processes that constrain the cycling of Si in the modern environment and in the past. Here, we provide background on the geochemical tools that are available for studying the Si cycle and highlight our current understanding of the marine, freshwater and terrestrial systems. We place emphasis on the geochemistry (e.g., Al/Si, Ge/Si, Zn/Si, δ13 C, δ15 N, δ18 O, δ30 Si) of dissolved and biogenic Si, present case studies, such as the Silicic Acid Leakage Hypothesis, and discuss challenges associated with the development of these environmental proxies for the global Si cycle. We also discuss how each system within the global Si cycle might change over time (i.e., sources, sinks, and processes) and the potential technical and conceptual limitations that need to be considered for future studies.
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| 30. |
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| 31. |
- Wayment-Steele, H. K., et al.
(author)
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Effects of Al3+ on Phosphocholine and Phosphoglycerol Containing Solid Supported Lipid Bilayers
- 2016
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In: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 32:7, s. 1771-1781
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Journal article (peer-reviewed)abstract
- Aluminum has attracted great attention recently as it has been suggested by several studies to be associated with increased risks for Alzheimer's and Parkinson's disease. The toxicity of the trivalent ion is assumed to derive from structural changes induced in lipid bilayers upon binding, though the mechanism of this process is still not well understood. In the present study we elucidate the effect of Al3+ on supported lipid bilayers (SLBs) using fluorescence microscopy, the quartz crystal microbalance with dissipation (QCM-D) technique, dual-polarization interferometry (DPI), and molecular dynamics (MD) simulations. Results from these techniques show that binding of Al3+ to SLBs containing negatively charged and neutral phospholipids induces irreversible changes such as domain formation. The measured variations in SLB thickness, birefringence, and density indicate a phase transition from a disordered to a densely packed ordered phase.
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| 32. |
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