| 1. |
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| 2. |
- Achberger, Christine, 1968, et al.
(författare)
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State of the Climate in 2011
- 2012
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Ingår i: Bulletin of the American Meteorological Society. - 0003-0007. ; 93:7
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale climate patterns influenced temperature and weather patterns around the globe in 2011. In particular, a moderate-to-strong La Nina at the beginning of the year dissipated during boreal spring but reemerged during fall. The phenomenon contributed to historical droughts in East Africa, the southern United States, and northern Mexico, as well the wettest two-year period (2010-11) on record for Australia, particularly remarkable as this follows a decade-long dry period. Precipitation patterns in South America were also influenced by La Nina. Heavy rain in Rio de Janeiro in January triggered the country's worst floods and landslides in Brazil's history. The 2011 combined average temperature across global land and ocean surfaces was the coolest since 2008, but was also among the 15 warmest years on record and above the 1981-2010 average. The global sea surface temperature cooled by 0.1 degrees C from 2010 to 2011, associated with cooling influences of La Nina. Global integrals of upper ocean heat content for 2011 were higher than for all prior years, demonstrating the Earth's dominant role of the oceans in the Earth's energy budget. In the upper atmosphere, tropical stratospheric temperatures were anomalously warm, while polar temperatures were anomalously cold. This led to large springtime stratospheric ozone reductions in polar latitudes in both hemispheres. Ozone concentrations in the Arctic stratosphere during March were the lowest for that period since satellite records began in 1979. An extensive, deep, and persistent ozone hole over the Antarctic in September indicates that the recovery to pre-1980 conditions is proceeding very slowly. Atmospheric carbon dioxide concentrations increased by 2.10 ppm in 2011, and exceeded 390 ppm for the first time since instrumental records began. Other greenhouse gases also continued to rise in concentration and the combined effect now represents a 30% increase in radiative forcing over a 1990 baseline. Most ozone depleting substances continued to fall. The global net ocean carbon dioxide uptake for the 2010 transition period from El Nino to La Nina, the most recent period for which analyzed data are available, was estimated to be 1.30 Pg C yr(-1), almost 12% below the 29-year long-term average. Relative to the long-term trend, global sea level dropped noticeably in mid-2010 and reached a local minimum in 2011. The drop has been linked to the La Nina conditions that prevailed throughout much of 2010-11. Global sea level increased sharply during the second half of 2011. Global tropical cyclone activity during 2011 was well-below average, with a total of 74 storms compared with the 1981-2010 average of 89. Similar to 2010, the North Atlantic was the only basin that experienced above-normal activity. For the first year since the widespread introduction of the Dvorak intensity-estimation method in the 1980s, only three tropical cyclones reached Category 5 intensity level-all in the Northwest Pacific basin. The Arctic continued to warm at about twice the rate compared with lower latitudes. Below-normal summer snowfall, a decreasing trend in surface albedo, and above-average surface and upper air temperatures resulted in a continued pattern of extreme surface melting, and net snow and ice loss on the Greenland ice sheet. Warmer-than-normal temperatures over the Eurasian Arctic in spring resulted in a new record-low June snow cover extent and spring snow cover duration in this region. In the Canadian Arctic, the mass loss from glaciers and ice caps was the greatest since GRACE measurements began in 2002, continuing a negative trend that began in 1987. New record high temperatures occurred at 20 m below the land surface at all permafrost observatories on the North Slope of Alaska, where measurements began in the late 1970s. Arctic sea ice extent in September 2011 was the second-lowest on record, while the extent of old ice (four and five years) reached a new record minimum that was just 19% of normal. On the opposite pole, austral winter and spring temperatures were more than 3 degrees C above normal over much of the Antarctic continent. However, winter temperatures were below normal in the northern Antarctic Peninsula, which continued the downward trend there during the last 15 years. In summer, an all-time record high temperature of -12.3 degrees C was set at the South Pole station on 25 December, exceeding the previous record by more than a full degree. Antarctic sea ice extent anomalies increased steadily through much of the year, from briefly setting a record low in April, to well above average in December. The latter trend reflects the dispersive effects of low pressure on sea ice and the generally cool conditions around the Antarctic perimeter.
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| 3. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 4. |
- Birney, Ewan, et al.
(författare)
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Prepublication data sharing
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7261, s. 168-170
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Tidskriftsartikel (refereegranskat)abstract
- Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
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| 5. |
- Wendisch, M., et al.
(författare)
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Atmospheric and Surface Processes, and Feedback Mechanisms Determining Arctic Amplification: A Review of First Results and Prospects of the (AC)(3) Project
- 2023
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Ingår i: Bulletin of the American Meteorological Society. - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 104:1
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Tidskriftsartikel (refereegranskat)abstract
- Mechanisms behind the phenomenon of Arctic amplification are widely discussed. To contribute to this debate, the (AC)(3) project was established in 2016 (www.ac3-tr.de/). It comprises modeling and data analysis efforts as well as observational elements. The project has assembled a wealth of ground-based, airborne, shipborne, and satellite data of physical, chemical, and meteorological properties of the Arctic atmosphere, cryosphere, and upper ocean that are available for the Arctic climate research community. Short-term changes and indications of long-term trends in Arctic climate parameters have been detected using existing and new data. For example, a distinct atmospheric moistening, an increase of regional storm activities, an amplified winter warming in the Svalbard and North Pole regions, and a decrease of sea ice thickness in the Fram Strait and of snow depth on sea ice have been identified. A positive trend of tropospheric bromine monoxide (BrO) column densities during polar spring was verified. Local marine/biogenic sources for cloud condensation nuclei and ice nucleating particles were found. Atmospheric-ocean and radiative transfer models were advanced by applying new parameterizations of surface albedo, cloud droplet activation, convective plumes and related processes over leads, and turbulent transfer coefficients for stable surface layers. Four modes of the surface radiative energy budget were explored and reproduced by simulations. To advance the future synthesis of the results, cross-cutting activities are being developed aiming to answer key questions in four focus areas: lapse rate feedback, surface processes, Arctic mixed-phase clouds, and airmass transport and transformation.
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| 6. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 7. |
- Shupe, M. D., et al.
(författare)
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Overview of the MOSAiC expedition : Atmosphere
- 2022
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Ingår i: Elementa. - : University of California Press. - 2325-1026. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- With the Arctic rapidly changing, the needs to observe, understand, and model the changes are essential. To support these needs, an annual cycle of observations of atmospheric properties, processes, and interactions were made while drifting with the sea ice across the central Arctic during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition from October 2019 to September 2020. An international team designed and implemented the comprehensive program to document and characterize all aspects of the Arctic atmospheric system in unprecedented detail, using a variety of approaches, and across multiple scales. These measurements were coordinated with other observational teams to explore crosscutting and coupled interactions with the Arctic Ocean, sea ice, and ecosystem through a variety of physical and biogeochemical processes. This overview outlines the breadth and complexity of the atmospheric research program, which was organized into 4 subgroups: atmospheric state, clouds and precipitation, gases and aerosols, and energy budgets. Atmospheric variability over the annual cycle revealed important influences from a persistent large-scale winter circulation pattern, leading to some storms with pressure and winds that were outside the interquartile range of past conditions suggested by long-term reanalysis. Similarly, the MOSAiC location was warmer and wetter in summer than the reanalysis climatology, in part due to its close proximity to the sea ice edge. The comprehensiveness of the observational program for characterizing and analyzing atmospheric phenomena is demonstrated via a winter case study examining air mass transitions and a summer case study examining vertical atmospheric evolution. Overall, the MOSAiC atmospheric program successfully met its objectives and was the most comprehensive atmospheric measurement program to date conducted over the Arctic sea ice. The obtained data will support a broad range of coupled-system scientific research and provide an important foundation for advancing multiscale modeling capabilities in the Arctic.
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| 8. |
- Toller, W, et al.
(författare)
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Preoperative and perioperative use of levosimendan in cardiac surgery: European expert opinion.
- 2015
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Ingår i: International Journal of Cardiology. - : Elsevier BV. - 0167-5273 .- 1874-1754. ; 184, s. 323-336
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Forskningsöversikt (refereegranskat)abstract
- In cardiac surgery, postoperative low cardiac output has been shown to correlate with increased rates of organ failure and mortality. Catecholamines have been the standard therapy for many years, although they carry substantial risk for adverse cardiac and systemic effects, and have been reported to be associated with increased mortality. On the other hand, the calcium sensitiser and potassium channel opener levosimendan has been shown to improve cardiac function with no imbalance in oxygen consumption, and to have protective effects in other organs. Numerous clinical trials have indicated favourable cardiac and non-cardiac effects of preoperative and perioperative administration of levosimendan. A panel of 27 experts from 18 countries has now reviewed the literature on the use of levosimendan in on-pump and off-pump coronary artery bypass grafting and in heart valve surgery. This panel discussed the published evidence in these various settings, and agreed to vote on a set of questions related to the cardioprotective effects of levosimendan when administered preoperatively, with the purpose of reaching a consensus on which patients could benefit from the preoperative use of levosimendan and in which kind of procedures, and at which doses and timing should levosimendan be administered. Here, we present a systematic review of the literature to report on the completed and ongoing studies on levosimendan, including the newly commenced LEVO-CTS phase III study (NCT02025621), and on the consensus reached on the recommendations proposed for the use of preoperative levosimendan.
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| 9. |
- Garcia, Sarahi L, et al.
(författare)
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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
- 2018
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12:3, s. 742-755
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Tidskriftsartikel (refereegranskat)abstract
- To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.
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| 10. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 11. |
- O’Reilly, Catherine M., et al.
(författare)
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Rapid and highly variable warming of lake surface waters around the globe
- 2015
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 42:24
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Tidskriftsartikel (refereegranskat)abstract
- In this first worldwide synthesis of in situ and satellite-derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade−1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors—from seasonally ice-covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade−1) to ice-free lakes experiencing increases in air temperature and solar radiation (0.53°C decade−1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.
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| 12. |
- Styrud, J, et al.
(författare)
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Appendectomy versus antibiotic treatment in acute appendicitis. A prospective multicenter randomized controlled trial
- 2006
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Ingår i: World Journal of Surgery. - : Springer Science and Business Media LLC. - 0364-2313 .- 1432-2323. ; 30:6, s. 1033-1037
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Tidskriftsartikel (refereegranskat)abstract
- Background Appendectomy has been the treatment for acute appendicitis for over 120 years. Antibiotic treatment has occasionally been used in small uncontrolled studies, instead of operation, but this alternative has never before been tried in a multicenter randomized trial. Patients and Methods Male patients, 18–50 years of age, admitted to six different hospitals in Sweden between 1996 and 1999 were enrolled in the study. No women were enrolled by decision of the local ethics committee. If appendectomy was planned, patients were asked to participate, and those who agreed were randomized either to surgery or to antibiotic therapy. Patients randomized to surgery were operated on with open surgery or laparoscopically. Those randomized to antibiotic therapy were treated intravenously for 2 days, followed by oral treatment for 10 days. If symptoms did not resolve within 24 hours, an appendectomy was performed. Participants were monitored at the end of 1 week, 6 weeks, and 1 year. Results During the study period 252 men participated, 124 in the surgery group and 128 in the antibiotic group. The frequency of appendicitis was 97% in the surgery group and 5% had a perforated appendix. The complication rate was 14% in the surgery group. In the antibiotic group 86% improved without surgery; 18 patients were operated on within 24 hours, and the diagnosis of acute appendicitis was confirmed in all but one patient, and he was suffering from terminal ileitis. There were seven patients (5%) with a perforated appendix in this group. The rate of recurrence of symptoms of appendicitis among the 111 patients treated with antibiotics was 14% during the 1-year follow-up. Conclusions Acute nonperforated appendicitis can be treated successfully with antibiotics. However, there is a risk of recurrence in cases of acute appendicitis, and this risk should be compared with the risk of complications after appendectomy.
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| 13. |
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| 14. |
- Bendall, Matthew L, et al.
(författare)
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
- 2016
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 10:7, s. 1589-1601
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Tidskriftsartikel (refereegranskat)abstract
- Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the /`ecotype model/' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.
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| 15. |
- Czamara, D, et al.
(författare)
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Genome-Wide Copy Number Variant and High-Throughput Transcriptomics Analyses of Placental Tissues Underscore Persisting Child Susceptibility in At-Risk Pregnancies Cleared in Standard Genetic Testing
- 2022
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Ingår i: International journal of molecular sciences. - : MDPI AG. - 1422-0067. ; 23:19
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Tidskriftsartikel (refereegranskat)abstract
- Several studies have shown that children from pregnancies with estimated first-trimester risk based on fetal nuchal translucency thickness and abnormal maternal serum pregnancy protein and hormone levels maintain a higher likelihood of adverse outcomes, even if initial testing for known genetic conditions is negative. We used the Finnish InTraUterine cohort (ITU), which is a comprehensively characterized perinatal cohort consisting of 943 mothers and their babies followed throughout pregnancy and 18 months postnatally, including mothers shortlisted for prenatal genetic testing but cleared for major aneuploidies (cases: n = 544, 57.7%) and control pregnancies (n = 399, 42.3%). Using genome-wide genotyping and RNA sequencing of first-trimester and term placental tissue, combined with medical information from registry data and maternal self-report data, we investigated potential negative medical outcomes and genetic susceptibility to disease and their correlates in placenta gene expression. Case mothers did not present with higher levels of depression, perceived stress, or anxiety during pregnancy. Case children were significantly diagnosed more often with congenital malformations of the circulatory system (4.12 (95% CI [1.22–13.93]) higher hazard) and presented with significantly more copy number duplications as compared to controls (burden analysis, based on all copy number variants (CNVs) with at most 10% frequency, 823 called duplications in 297 cases versus 626 called duplications in 277 controls, p = 0.01). Fifteen genes showed differential gene expression (FDR < 0.1) in association with congenital malformations in first-trimester but not term placenta. These were significantly enriched for genes associated with placental dysfunction. In spite of normal routine follow-up prenatal testing results in early pregnancy, case children presented with an increased likelihood of negative outcomes, which should prompt vigilance in follow-up during pregnancy and after birth.
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| 16. |
- Farmakis, D., et al.
(författare)
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Levosimendan beyond inotropy and acute heart failure: Evidence of pleiotropic effects on the heart and other organs: An expert panel position paper
- 2016
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Ingår i: International Journal of Cardiology. - : Elsevier BV. - 0167-5273. ; 222, s. 303-312
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Tidskriftsartikel (refereegranskat)abstract
- Levosimendan is a positive inotrope with vasodilating properties (inodilator) indicated for decompensated heart failure (HF) patients with low cardiac output. Accumulated evidence supports several pleiotropic effects of levosimendan beyond inotropy, the heart and decompensated HF. Those effects are not readily explained by cardiac function enhancement and seem to be related to additional properties of the drug such as anti-inflammatory, anti-oxidative and anti-apoptotic ones. Mechanistic and proof-of-concept studies are still required to clarify the underlying mechanisms involved, while properly designed clinical trials are warranted to translate preclinical or early-phase clinical data into more robust clinical evidence. The present position paper, derived by a panel of 35 experts in the field of cardiology, cardiac anesthesiology, intensive care medicine, cardiac physiology, and cardiovascular pharmacology from 22 European countries, compiles the existing evidence on the pleiotropic effects of levosimendan, identifies potential novel areas of clinical application and defines the corresponding gaps in evidence and the required research efforts to address those gaps. © 2016 The Authors
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| 17. |
- Filipsson, Helena L., 1973, et al.
(författare)
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A major change in the phytoplankton of a Swedish sill fjord - A consequence of engineering work?
- 2005
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Ingår i: Estuarine Coastal and Shelf Science. - : Elsevier BV. - 0272-7714. ; 63:4, s. 551-560
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Tidskriftsartikel (refereegranskat)abstract
- A major phytoplankton change occurred during the late 1930s and early 1940s in Koljo Fjord, a sill fjord on the Swedish west coast. Dinoflagellate cyst concentrations increased tenfold over a short period of time, front hundreds of cysts per gram sediment to thousands; and the species composition of both dinoflagellate cysts and diatoms changed markedly. These changes took place during a period of extensive engineering work at the entrance to the fjord from the Skagerrak. At this time, the entire passage was straightened, a new channel was built in a previously shallow area, and the old connection was closed. This study investigates whether this engineering work could have sufficiently altered the surface-water circulation to bring about the change in the phytoplankton composition. Several mechanisms are explored by which the construction could have influenced the phytoplankton in the fjord. The primary mechanism is probably increased efficiency of tidal-generated surface-water exchange in the fjord, resulting in a larger transport of surface water from the Skagerrak and consequently a changed surface-water environment. This Study highlights how engineering work can have a Substantial impact on the local and regional marine environment, a factor that must not be overlooked in environmental planning. (c) 2005 Elsevier Ltd. All rights reserved.
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| 18. |
- Ghylin, Trevor W, et al.
(författare)
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Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
- 2014
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 8:12, s. 2503-2516
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Tidskriftsartikel (refereegranskat)abstract
- Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
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| 19. |
- Hamilton, Joshua J., et al.
(författare)
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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
- 2017
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Ingår i: mSystems. - 2379-5077. ; 2:4
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Tidskriftsartikel (refereegranskat)abstract
- An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the “seed set framework,†which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482–14487, 2008, https://doi.org/10.1073/pnas.0806162105 ), enables computational analysis of metabolic reconstructions while providing new insights into a microbe’s metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs.
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| 20. |
- Harland, Rex, et al.
(författare)
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A high-resolution dinoflagellate cyst record from latest Holocene sediments in Koljo Fjord, Sweden
- 2004
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Ingår i: Review of Palaeobotany and Palynology. - 0034-6667. ; 128:1-2, s. 119-141
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Tidskriftsartikel (refereegranskat)abstract
- A high-resolution dinoflagellate cyst record is detailed for the very latest Holocene sediments preserved in a silled fjord from western Sweden. Koljo Fjord is characterised by brackish water conditions together with intermittent deep-water renewal and oxygen depletion. The data provide information derived from the phytoplankton populations living in the surface waters, including possible changes to the nutrient availability and salinity regimes using an actualistic ecological approach. The cyst record provides evidence that the dinoflagellate populations within the surface waters of the fjord over the last 155 years or so have fluctuated markedly. The dinoflagellate cyst record from Core KG1A demonstrates a 10-fold increase in both total cyst numbers and Lingulodinium polyedrum since c. 1938, and a shift from assemblages with high Pentapharsodinium dalei to those with high L. polyedrum and Protoceratium reticulatum from about 1980. These fluctuations are singly and/or collectively indicative of possible cultural changes within the fjord; the effects of the North Atlantic Oscillation on both deep-water renewal and seasonality; nutrient enhancement (eutrophication?); and increased water column stability. (C) 2003 Elsevier B.V. All rights reserved.
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| 21. |
- Harland, Rex, et al.
(författare)
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A major change in the dinoflagellate cyst flora of Gullmar Fjord, Sweden, at around 1969/1970 and its possible explanation
- 2010
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Ingår i: Geological Society, London, Special Publications. - 0305-8719. ; 344, s. 75-82
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Tidskriftsartikel (refereegranskat)abstract
- An ultra high-resolution study of the latest Holocene dinoflagellate cysts from Gullmar Fjord, on the west coast of Sweden, provides evidence for the recognition of at least two major dinoflagellate communities within the fjord over the last 85 years. These communities may result from changes within the North Atlantic Oscillation (NAO) and hydrography of the fjord between the approximate years 1915 and 1999 and/or from the local pollution history. The dinoflagellate cyst populations were compared in detail with hydrographical parameters available from this fjord with its long historical instrumental records. The dinoflagellate cysts fail to demonstrate a convincing ongoing eutrophication for the fjord, although the reduction of Lingulodinium polyedrum partly coincides with the curtailment of activity at a sulphite pulp mill at Munkedal and canning activity at Lysekil, together with a cessation in the influx of untreated sewage from water closets. The significant change in the assemblage composition at about the late 1960s/early 1970s coincides with a change in the NAO from a negative phase to its present-day positive phase. The unravelling of local environmental effects from those associated with regional fluctuations is complex and needs to be approached with caution.
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| 22. |
- Harland, Rex, et al.
(författare)
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The seasonal occurrence of dinoflagellate cysts in surface sediments from Koljo Fjord, west coast of Sweden - a note
- 2004
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Ingår i: Review of Palaeobotany and Palynology. - 0034-6667. ; 128:1-2, s. 107-117
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Tidskriftsartikel (refereegranskat)abstract
- The opportunistic collection of the flocculent layer, over the spring to late summer seasons, has provided information on the seasonal dinoflagellate cyst sedimentation in Koljo Fjord, on the west coast of Sweden. The dinoflagellate cyst assemblages within the flocculent layer can be both diverse and contain many cysts. The cyst assemblages do not remain constant over time but demonstrate seasonality. Our very limited dataset of six samples suggests that the spring bloom is characterised by round, brown Protoperidinium cysts together with subsidiary Pentapharsodinium dalei and Protoperidinium conicum. The early summer assemblage differs in containing higher proportions of P. dalei with fewer round, brown Protoperidinium cysts together with relatively minor amounts of Lingulodinium polyedrum and Polykrikos schwartzii. The late summer cyst flora is co-dominated by Lingulodinium polyedrum and round, brown Protoperidinium cysts, together with minor amounts of P. dalei and Spiniferites spp. including Spiniferites bentorii. Cyst production within the different species occurs at times of the year when the surface water conditions within the fjord are suitable. This probably reflects, all or in part, the stability of the upper water column, the relative availability of nutrients and the overall phytoplankton productivity. (C) 2004 Elsevier B.V. All rights reserved.
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| 23. |
- He, Shaomei, et al.
(författare)
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Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
- 2017
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Ingår i: mSphere. - 2379-5042. ; 2:5
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Tidskriftsartikel (refereegranskat)abstract
- Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly) saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly) saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called " Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
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| 24. |
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| 25. |
- Linz, Alexandra M., et al.
(författare)
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Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
- 2018
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
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| 26. |
- Ostaszewski, Marek, et al.
(författare)
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
- 2021
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Ingår i: Molecular Systems Biology. - : John Wiley & Sons. - 1744-4292 .- 1744-4292. ; 17:10
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Tidskriftsartikel (refereegranskat)abstract
- We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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| 27. |
- Pérez-González, P.G.P., et al.
(författare)
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Improving the identification of high-z Herschel sources with position priors and optical/NIR and FIR/mm photometric redshifts
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518:Article Number: L15
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Tidskriftsartikel (refereegranskat)abstract
- We present preliminary results about the detection of high redshift (U)LIRGs in the Bullet cluster field by the PACS and SPIRE instruments within the Herschel Lensing Survey (HLS) Program. We describe in detail a photometric procedure designed to recover robust fluxes and deblend faint Herschel sources near the confusion noise. The method is based on the use of the positions of Spitzer/MIPS 24 mu m sources as priors. Our catalogs are able to reliably (5 sigma) recover galaxies with fluxes above 6 and 10 mJy in the PACS 100 and 160 mu m channels, respectively, and 12 to 18 mJy in the SPIRE bands. We also obtain spectral energy distributions covering the optical through the far-infrared/millimeter spectral ranges of all the Herschel detected sources, and analyze them to obtain independent estimations of the photometric redshift based on either stellar population or dust emission models. We exemplify the potential of the combined use of Spitzer position priors plus independent optical and IR photometric redshifts to robustly assign optical/NIR counterparts to the sources detected by Herschel and other (sub-)mm instruments.
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| 28. |
- Polovodova, Irina, 1980, et al.
(författare)
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Detailing the Little Ice Age on the Swedish west coast: a multi-proxy study of a sediment record from Gullmar Fjord
- 2014
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Ingår i: Marchant, M . & Hromic, T. (eds . ) 201 4 . Internation al Symposium on Foraminifera Forams 2014, Chile, 19 – 24 January 2014 , Abstract Volume . Grzybowski Foundation Special Publication, 20 , 124 pp.. - 9788388927355 ; , s. 38-39
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Gullmar Fjord, on the west coast of Sweden, represents a high-resolution environmental archive due to high sedimentation rates, low bioturbation and negligible tidal activity. In this study we attempt to detail the climatic and environmental changes in NE Europe during the last millennium by using a ca. 8-m long well dated sediment record from the deep fjord basin. According to the 14C-datings, the record includes the period of the late Holocene characterised by anomalously cold summers and well known as the Little Ice Age (LIA). Using a high-resolution stratigraphy of benthic foraminifera and dinoflagellate cysts along with lithology, bulk sediment geochemistry and foraminiferal δ13C we identify the timing of the cold period, reconstruct its various phases, and discuss the land-sea interactions occurring in the study area during that time. The onset of the LIA is indicated at ~1350 A.D by an increase in abundances of cold-water foraminifer Adercotryma glomerata and the cryophilic dinoflagellate cyst Islandinium cf. cezare. The first phase of the LIA was characterised by a stormy climate and higher productivity, as suggested by a foraminiferal assemblage of Nonionella iridea and Cassidulina laevigata. The hypothesis of higher productivity is supported by the isotopic and the dinoflagellate cyst records, which show a shift towards more negative δ13C values, and a marked increase in the microreticulate cysts of Gymnodinium nolleri at the onset of the LIA. The dinoflagellate species G. nolleri becomes relict towards the LIA termination and could be also associated with lower surface water temperatures at that time. It is likely that due to land use changes in the second part of the LIA there was an increased input of terrestrial organic matter to the fjord, which is indicated by lighter δ13C values and an increase of detritivorous and omnivorous foraminiferal species such as Textularia earlandi and Eggerelloides scaber. The climate deterioration during the climax of the LIA (1675-1704 A.D.) may have driven a decline in primary productivity, as suggested by the increase of agglutinated foraminiferal species, the presence of Hyalinea balthica, and a decline of N. iridea during that time.
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| 29. |
- Rex, M., et al.
(författare)
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The far-infrared/submillimeter properties of galaxies located behind the Bullet cluster
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518:Article Number: L13
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Tidskriftsartikel (refereegranskat)abstract
- The Herschel Lensing Survey (HLS) takes advantage of gravitational lensing by massive galaxy clusters to sample a population of high-redshift galaxies which are too faint to be detected above the confusion limit of current far-infrared/submillimeter telescopes. Measurements from 100-500 mu m bracket the peaks of the far-infrared spectral energy distributions of these galaxies, characterizing their infrared luminosities and star formation rates. We introduce initial results from our science demonstration phase observations, directed toward the Bullet cluster (1E0657-56). By combining our observations with LABOCA 870 mu m and AzTEC 1.1 mm data we fully constrain the spectral energy distributions of 19 MIPS 24 mu m-selected galaxies which are located behind the cluster. We find that their colors are best fit using templates based on local galaxies with systematically lower infrared luminosities. This suggests that our sources are not like local ultra-luminous infrared galaxies in which vigorous star formation is contained in a compact highly dust-obscured region. Instead, they appear to be scaled up versions of lower luminosity local galaxies with star formation occurring on larger physical scales.
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