| 1. |
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| 2. |
- Arndt, D. S., et al.
(författare)
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State of the Climate in 2016
- 2017
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280
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Tidskriftsartikel (refereegranskat)abstract
- In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
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| 3. |
- Arndt, D. S., et al.
(författare)
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STATE OF THE CLIMATE IN 2017
- 2018
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
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Forskningsöversikt (refereegranskat)
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| 4. |
- Brawand, David, et al.
(författare)
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The genomic substrate for adaptive radiation in African cichlid fish
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 375-381
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Tidskriftsartikel (refereegranskat)abstract
- Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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| 5. |
- Crowther-Swanepoel, Dalemari, et al.
(författare)
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Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:2, s. 132-136
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Tidskriftsartikel (refereegranskat)abstract
- To identify new risk variants for chronic lymphocytic leukemia (CLL), we conducted a genome-wide association study of 299,983 tagging SNPs, with validation in four additional series totaling 2,503 cases and 5,789 controls. We identified four new risk loci for CLL at 2q37.3 (rs757978, FARP2; odds ratio (OR) = 1.39; P = 2.11 x 10(-9)), 8q24.21 (rs2456449; OR = 1.26; P = 7.84 x 10(-10)), 15q21.3 (rs7169431; OR = 1.36; P = 4.74 x 10(-7)) and 16q24.1 (rs305061; OR = 1.22; P = 3.60 x 10(-7)). We also found evidence for risk loci at 15q25.2 (rs783540, CPEB1; OR = 1.18; P = 3.67 x 10(-6)) and 18q21.1 (rs1036935; OR = 1.22; P = 2.28 x 10(-6)). These data provide further evidence for genetic susceptibility to this B-cell hematological malignancy.
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| 6. |
- Garcia-Martin, E. Elena, et al.
(författare)
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Sources, Composition, and Export of Particulate Organic Matter Across British Estuaries
- 2023
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Ingår i: Journal of Geophysical Research - Biogeosciences. - : American Geophysical Union (AGU). - 2169-8953 .- 2169-8961. ; 128:4
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Tidskriftsartikel (refereegranskat)abstract
- Estuaries receive and process a large amount of particulate organic carbon (POC) prior to its export into coastal waters. Studying the origin of this POC is key to understanding the fate of POC and the role of estuaries in the global carbon cycle. Here, we evaluated the concentrations of POC, as well as particulate organic nitrogen (PON), and used stable carbon and nitrogen isotopes to assess their sources across 13 contrasting British estuaries during five different sampling campaigns over 1 year. We found a high variability in POC and PON concentrations across the salinity gradient, reflecting inputs, and losses of organic material within the estuaries. Catchment land cover appeared to influence the contribution of POC to the total organic carbon flux from the estuary to coastal waters, with POC contributions >36% in estuaries draining catchments with a high percentage of urban/suburban land, and <11% in estuaries draining catchments with a high peatland cover. There was no seasonal pattern in the isotopic composition of POC and PON, suggesting similar sources for each estuary over time. Carbon isotopic ratios were depleted (-26.7 +/- 0.42 parts per thousand, average +/- sd) at the lowest salinity waters, indicating mainly terrigenous POC (TPOC). Applying a two-source mixing model, we observed high variability in the contribution of TPOC at the highest salinity waters between estuaries, with a median value of 57%. Our results indicate a large transport of terrigenous organic carbon into coastal waters, where it may be buried, remineralized, or transported offshore. Plain Language Summary Estuaries transport and process a large amount terrigenous particulate organic matter (i.e., carbon and nitrogen) prior to its export to coastal waters. In order to understand the fate of organic carbon and the role of estuaries in the global carbon cycle it is essential to improve our knowledge on its composition, origin, and amount of carbon transported. We quantified the elemental concentrations and stable isotopes composition of carbon and nitrogen to quantify the amount of terrigenous particulate organic matter transported by 13 British estuaries, which drain catchments of diverse land cover under different hydrological conditions. We found a great variability in particulate organic carbon (POC) and particulate organic nitrogen concentrations across the salinity gradient, implying inputs, and losses of material within the estuaries. Each estuary had similar sources of particulate material throughout the year. In most of the estuaries, the POC had a terrigenous origin at the lowest salinity waters. The terrigenous organic carbon contribution decreased toward coastal waters with an average contribution of 57% at the highest salinity waters, indicating a large transport of terrigenous organic carbon into coastal waters.
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| 7. |
- Joshi, Peter K, et al.
(författare)
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Directional dominance on stature and cognition in diverse human populations
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 523:7561, s. 459-462
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Tidskriftsartikel (refereegranskat)abstract
- Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.
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| 8. |
- Law, Philip J., et al.
(författare)
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Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- B-cell malignancies (BCM) originate from the same cell of origin, but at different maturation stages and have distinct clinical phenotypes. Although genetic risk variants for individual BCMs have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. We explored genome-wide association studies of chronic lymphocytic leukaemia (CLL, N = 1,842), Hodgkin lymphoma (HL, N = 1,465) and multiple myeloma (MM, N = 3,790). We identified a novel pleiotropic risk locus at 3q22.2 (NCK1, rs11715604, P = 1.60 × 10-9) with opposing effects between CLL (P = 1.97 × 10-8) and HL (P = 3.31 × 10-3). Eight established non-HLA risk loci showed pleiotropic associations. Within the HLA region, Ser37 + Phe37 in HLA-DRB1 (P = 1.84 × 10-12) was associated with increased CLL and HL risk (P = 4.68 × 10-12), and reduced MM risk (P = 1.12 × 10-2), and Gly70 in HLA-DQB1 (P = 3.15 × 10-10) showed opposing effects between CLL (P = 3.52 × 10-3) and HL (P = 3.41 × 10-9). By integrating eQTL, Hi-C and ChIP-seq data, we show that the pleiotropic risk loci are enriched for B-cell regulatory elements, as well as an over-representation of binding of key B-cell transcription factors. These data identify shared biological pathways influencing the development of CLL, HL and MM. The identification of these risk loci furthers our understanding of the aetiological basis of BCMs.
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| 9. |
- Marouli, Eirini, et al.
(författare)
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Rare and low-frequency coding variants alter human adult height
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
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Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
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| 10. |
- Patterson, Nick, et al.
(författare)
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Large-scale migration into Britain during the Middle to Late Bronze Age
- 2022
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; , s. 588-594
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Tidskriftsartikel (refereegranskat)abstract
- Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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| 11. |
- Speedy, Helen E., et al.
(författare)
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A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:1, s. 56-
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) of chronic lymphocytic leukemia (CLL) have shown that common genetic variation contributes to the heritable risk of CLL. To identify additional CLL susceptibility loci, we conducted a GWAS and performed a meta-analysis with a published GWAS totaling 1,739 individuals with CLL (cases) and 5,199 controls with validation in an additional 1,144 cases and 3,151 controls. A combined analysis identified new susceptibility loci mapping to 3q26.2 (rs10936599, P = 1.74 x 10(-9)), 4q26 (rs6858698, P = 3.07 x 10(-9)), 6q25.2 (IPCEF1, rs2236256, P = 1.50 x 10(-10)) and 7q31.33 (POT1, rs17246404, P = 3.40 x 10(-8)). Additionally, we identified a promising association at 5p15.33 (CLPTM1L, rs31490, P = 1.72 x 10(-7)) and validated recently reported putative associations at 5p15.33 (TERT, rs10069690, P = 1.12 x 10(-10)) and 8q22.3 (rs2511714, P = 2.90 x 10(-9)). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CLL.
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| 12. |
- Surendran, Praveen, et al.
(författare)
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Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals
- 2020
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 52:12, s. 1314-1332
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Tidskriftsartikel (refereegranskat)abstract
- Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to similar to 1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency <= 0.01) variant BP associations (P < 5 x 10(-8)), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were similar to 8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets.
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| 13. |
- Turcot, Valerie, et al.
(författare)
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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
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| 14. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 15. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 16. |
- Abercrombie, Daniel, et al.
(författare)
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Dark Matter benchmark models for early LHC Run-2 Searches : Report of the ATLAS/CMS Dark Matter Forum
- 2020
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Ingår i: Physics of the Dark Universe. - : Elsevier BV. - 2212-6864. ; 27
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Tidskriftsartikel (refereegranskat)abstract
- This document is the final report of the ATLAS-CMS Dark Matter Forum, a forum organized by the ATLAS and CMS collaborations with the participation of experts on theories of Dark Matter, to select a minimal basis set of dark matter simplified models that should support the design of the early LHC Run-2 searches. A prioritized, compact set of benchmark models is proposed, accompanied by studies of the parameter space of these models and a repository of generator implementations. This report also addresses how to apply the Effective Field Theory formalism for collider searches and present the results of such interpretations.
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| 17. |
- Ades, M., et al.
(författare)
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Global Climate : in State of the climate in 2019
- 2020
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
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Tidskriftsartikel (refereegranskat)
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| 18. |
- Ades, M., et al.
(författare)
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GLOBAL CLIMATE
- 2020
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Ingår i: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
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Tidskriftsartikel (refereegranskat)
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| 19. |
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| 20. |
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| 21. |
- Berg, Sylvia, 1986-, et al.
(författare)
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Exceptionally high whole-rock delta O-18 values in intra-caldera rhyolites from Northeast Iceland
- 2018
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Ingår i: Mineralogical magazine. - : MINERALOGICAL SOC. - 0026-461X .- 1471-8022. ; 82:5, s. 1147-1168
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Tidskriftsartikel (refereegranskat)abstract
- The Icelandic crust is characterized by low delta O-18 values that originate from pervasive high-temperature hydrothermal alteration by O-18-depleted meteoric waters. Igneous rocks in Iceland with delta O-18 values significantly higher than unaltered oceanic crust (similar to 5.7 parts per thousand) are therefore rare. Here we report on rhyolitic intra-caldera samples from a cluster of Neogene central volcanoes in Borgarfjorour Eystri, Northeast Iceland, that show whole-rock delta O-18 values between +2.9 and +17.6 parts per thousand (n = 6), placing them among the highest delta O-18 values thus far recorded for Iceland. Extra-caldera rhyolite samples from the region, in turn, show delta O-18 whole-rock values between +3.7 and +7.8 parts per thousand (n = 6), consistent with the range of previously reported Icelandic rhyolites. Feldspar in the intra-caldera samples (n = 4) show delta O-18 values between +4.9 and +18.7 parts per thousand, whereas pyroxene (n = 4) shows overall low delta O-18 values of +4.0 to +4.2 parts per thousand, consistent with regional rhyolite values. In combination with the evidence from mineralogy and rock H2O contents, the high whole-rock delta O-18 values of the intra-caldera rhyolites appear to be the result of pervasive isotopic exchange during subsolidus hydrothermal alteration with O-18-enriched water. This alteration conceivably occurred in a near-surface hot spring environment at the distal end of an intra-caldera hydrothermal system. and was probably fed by waters that had already undergone significant isotope exchange with the country rock. Alternatively, O-18-enriched alteration fluids may have been produced during evaporation and boiling of standing water in former caldera lakes, which then interacted with the intra-caldera rock suites. Irrespective of the exact exchange processes involved, a previously unrecognized and highly localized delta O-18-enriched rock composition exists on Iceland and thus probably within the Icelandic crust too.
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| 22. |
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| 23. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
-
Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 24. |
- Birney, Ewan, et al.
(författare)
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Prepublication data sharing
- 2009
-
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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| 25. |
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| 26. |
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| 27. |
- Chami, Nathalie, et al.
(författare)
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Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits
- 2016
-
Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 99:1, s. 8-21
-
Tidskriftsartikel (refereegranskat)abstract
- Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 x 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 x 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 x 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 x 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 x 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.
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| 28. |
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| 29. |
- Darmawan, Herlan, et al.
(författare)
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Hidden mechanical weaknesses within lava domes provided by buried high-porosity hydrothermal alteration zones
- 2022
-
Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Catastrophic lava dome collapse is considered an unpredictable volcanic hazard because the physical properties, stress conditions, and internal structure of lava domes are not well understood and can change rapidly through time. To explain the locations of dome instabilities at Merapi volcano, Indonesia, we combined geochemical and mineralogical analyses, rock physical property measurements, drone-based photogrammetry, and geoinformatics. We show that a horseshoe-shaped alteration zone that formed in 2014 was subsequently buried by renewed lava extrusion in 2018. Drone data, as well as geomechanical, mineralogical, and oxygen isotope data suggest that this zone is characterized by high-porosity hydrothermally altered materials that are mechanically weak. We additionally show that the new lava dome is currently collapsing along this now-hidden weak alteration zone, highlighting that a detailed understanding of dome architecture, made possible using the monitoring techniques employed here, is essential for assessing hazards associated with dome and edifice failure at volcanoes worldwide.
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| 30. |
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| 31. |
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| 32. |
- Deegan, Frances M, et al.
(författare)
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Sunda arc mantle source δ18O value revealed by intracrystal isotope analysis
- 2021
-
Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 12:1, s. 1-10
-
Tidskriftsartikel (refereegranskat)abstract
- Magma plumbing systems underlying subduction zone volcanoes extend from the mantle through the overlying crust and facilitate protracted fractional crystallisation, assimilation, and mixing, which frequently obscures a clear view of mantle source compositions. In order to see through this crustal noise, we present intracrystal Secondary Ion Mass Spectrometry (SIMS) δ18O values in clinopyroxene from Merapi, Kelut, Batur, and Agung volcanoes in the Sunda arc, Indonesia, under which the thickness of the crust decreases from ca. 30 km at Merapi to ≤20 km at Agung. Here we show that mean clinopyroxene δ18O values decrease concomitantly with crustal thickness and that lavas from Agung possess mantle-like He-Sr-Nd-Pb isotope ratios and clinopyroxene mean equilibrium melt δ18O values of 5.7 ‰ (±0.2 1 SD) indistinguishable from the δ18O range for Mid Ocean Ridge Basalt (MORB). The oxygen isotope composition of the mantle underlying the East Sunda Arc is therefore largely unaffected by subduction-driven metasomatism and may thus represent a sediment-poor arc end-member.
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| 33. |
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| 34. |
- Deegan, Frances, et al.
(författare)
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Sunda arc mantle source delta O-18 value revealed by intracrystal isotope analysis
- 2021
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Magma plumbing systems underlying subduction zone volcanoes extend from the mantle through the overlying crust and facilitate protracted fractional crystallisation, assimilation, and mixing, which frequently obscures a clear view of mantle source compositions. In order to see through this crustal noise, we present intracrystal Secondary Ion Mass Spectrometry (SIMS) delta O-18 values in clinopyroxene from Merapi, Kelut, Batur, and Agung volcanoes in the Sunda arc, Indonesia, under which the thickness of the crust decreases from ca. 30km at Merapi to <= 20km at Agung. Here we show that mean clinopyroxene delta O-18 values decrease concomitantly with crustal thickness and that lavas from Agung possess mantle-like He-Sr-Nd-Pb isotope ratios and clinopyroxene mean equilibrium melt delta O-18 values of 5.7 (+/- 0.2 1SD) indistinguishable from the delta O-18 range for Mid Ocean Ridge Basalt (MORB). The oxygen isotope composition of the mantle underlying the East Sunda Arc is therefore largely unaffected by subduction-driven metasomatism and may thus represent a sediment-poor arc end-member. Subduction zone volcanoes are underlain by extensive magma plumbing systems, which can obscure original mantle source signals. Here, the authors show that intra-crystal oxygen isotope analysis of clinopyroxenes from the Sunda arc (Indonesia) reveal the delta 18 O value of the sub-arc mantle.
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| 35. |
- Do, Ron, et al.
(författare)
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Common variants associated with plasma triglycerides and risk for coronary artery disease
- 2013
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1345-
-
Tidskriftsartikel (refereegranskat)abstract
- Triglycerides are transported in plasma by specific triglyceride-rich lipoproteins; in epidemiological studies, increased triglyceride levels correlate with higher risk for coronary artery disease (CAD). However, it is unclear whether this association reflects causal processes. We used 185 common variants recently mapped for plasma lipids (P < 5 x 10(-8) for each) to examine the role of triglycerides in risk for CAD. First, we highlight loci associated with both low-density lipoprotein cholesterol (LDL-C) and triglyceride levels, and we show that the direction and magnitude of the associations with both traits are factors in determining CAD risk. Second, we consider loci with only a strong association with triglycerides and show that these loci are also associated with CAD. Finally, in a model accounting for effects on LDL-C and/or high-density lipoprotein cholesterol (HDL-C) levels, the strength of a polymorphism's effect on triglyceride levels is correlated with the magnitude of its effect on CAD risk. These results suggest that triglyceride-rich lipoproteins causally influence risk for CAD.
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| 36. |
- Donoghue, Eleanor, et al.
(författare)
-
Fluid-Rock Interaction in the Miocene, Post-Caldera, Tejeda Intrusive Complex, Gran Canaria (Canary Islands) : Insights from Mineralogy, and O- and H-Isotope Geochemistry
- 2010
-
Ingår i: Journal of Petrology. - : Oxford University Press (OUP). - 0022-3530 .- 1460-2415. ; 51:10, s. 2149-2176
-
Tidskriftsartikel (refereegranskat)abstract
- The intra-caldera volcaniclastic deposits of the Miocene Tejeda caldera on Gran Canaria host an similar to 12 km diameter intrusive complex comprising a peralkaline, trachytic to phonolitic cone sheet swarm surrounding a central core of hypabyssal syenite stocks. Both intrusive rock types display textural and mineralogical features indicative of secondary fluid-rock interaction, including (1) deuteric mineral phases (e.g. aegirine, alkali-amphibole, analcime), (2) turbid alkali feldspars, and (3) hydrothermal mineral phases (phyllosilicates, Fe-Ti oxides, Mn-oxides, and quartz). Altered cone sheets have whole-rock delta O-18 values ranging from 0 center dot 1 to 10 center dot 0 parts per thousand (n = 22), and whole-rock delta D values between -62 and -149 parts per thousand (n = 28). Three altered syenite samples have whole-rock delta O-18 values of 2 center dot 5, 1 center dot 5, and 0 center dot 9 parts per thousand, and corresponding delta D values of -91, -99, and -121 parts per thousand. The H2O concentrations of the altered cone sheets range from 0 center dot 4 to 0 center dot 8 wt % (n = 28), and the altered syenites have H2O concentrations of 0 center dot 5, 0 center dot 5, and 0 center dot 6 wt %, respectively. The majority of altered samples are depleted in O-18 relative to the typical delta O-18 range for unaltered trachytes and syenites (delta O-18 = 6-8 parts per thousand), indicative of interaction with local meteoric water (delta O-18 c. -8 parts per thousand) at temperatures epsilon 150 degrees C. Only one cone sheet sample appears petrographically unaltered and has a typical 'igneous' isotopic composition (delta O-18 = 7 center dot 1 parts per thousand, delta D = -48 parts per thousand) and a relatively high H2O concentration (2 center dot 2 wt %). A weak correlation (r = 0 center dot 55) between delta D and H2O is observed in the cone sheets, reflecting the combined effects of magmatic H2O exsolution, and subsequent deuteric and hydrothermal alteration. No systematic variation in delta O-18 or delta D was detected across the cone sheet swarm, most likely reflecting overprinting of isotopic compositions during successive intrusive events. However, the highest delta O-18 values (8 center dot 2-10 center dot 0 parts per thousand) occur in clay-bearing cone sheets from the central part of the intrusive complex, suggesting enhanced infiltration of relatively cool meteoric water in this area. Overall, at least three phases of fluid-rock interaction can be distinguished: (1) deuteric alteration (c. 300-500 degrees C) by late magmatic fluids expelled from a solidifying crystal mush; (2) hydrothermal alteration (epsilon 150-300 degrees C) by meteoric water during the final stages of crystallization and/or immediately following solidification of the intrusive complex; (3) retrograde alteration related to the influx of relatively cool (150 degrees C) meteoric waters.
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| 37. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
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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| 38. |
- Erzurumluoglu, A. Mesut, et al.
(författare)
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Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci
- 2020
-
Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 25:10, s. 2392-2409
-
Tidskriftsartikel (refereegranskat)abstract
- Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
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| 39. |
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| 40. |
- Geiger, Harri, et al.
(författare)
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Magma plumbing for the 2014-2015 Holuhraun eruption, Iceland
- 2016
-
Ingår i: Geochemistry Geophysics Geosystems. - 1525-2027. ; 17:8, s. 2953-2968
-
Tidskriftsartikel (refereegranskat)abstract
- The 2014-2015 Holuhraun eruption on Iceland was located within the Askja fissure swarm but was accompanied by caldera subsidence in the Baroarbunga central volcano 45 km to the southwest. Geophysical monitoring of the eruption identified a seismic swarm that migrated from Baroarbunga to the Holuhraun eruption site over the course of two weeks. In order to better understand this lateral connection between Baroarbunga and Holuhraun, we present mineral textures and compositions, mineral-melt-equilibrium calculations, whole rock and trace element data, and oxygen isotope ratios for selected Holuhraun samples. The Holuhraun lavas are compositionally similar to recorded historical eruptions from the Baroarbunga volcanic system but are distinct from the historical eruption products of the nearby Askja system. Thermobarometry calculations indicate a polybaric magma plumbing system for the Holuhraun eruption, wherein clinopyroxene and plagioclase crystallized at average depths of approximate to 17 km and approximate to 5 km, respectively. Crystal resorption textures and oxygen isotope variations imply that this multilevel plumbing system facilitated magma mixing and assimilation of low-O-18 Icelandic crust prior to eruption. In conjunction with the existing geophysical evidence for lateral migration, our results support a model of initial vertical magma ascent within the Baroarbunga plumbing system followed by lateral transport of aggregated magma batches within the upper crust to the Holuhraun eruption site.
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| 41. |
- Geiger, Harri, et al.
(författare)
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Multi-level magma plumbing at Agung and Batur volcanoes increases risk of hazardous eruptions
- 2018
-
Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- The island of Bali in Indonesia is home to two active stratovolcanoes, Agung and Batur, but relatively little is known of their underlying magma plumbing systems. Here we define magma storage depths and isotopic evolution of the 1963 and 1974 eruptions using mineral-melt equilibrium thermobarometry and oxygen and helium isotopes in mineral separates. Olivine crystallised from a primitive magma and has average delta O-18 values of 4.8%. Clinopyroxene records magma storage at the crust-mantle boundary, and displays mantle-like isotope values for Helium (8.62 R-A) and delta O-18 (5.0-5.8%). Plagioclase reveals crystallisation in upper crustal storage reservoirs and shows delta O-18 values of 5.5-6.4%. Our new thermobarometry and isotope data thus corroborate earlier seismic and InSAR studies that inferred upper crustal magma storage in the region. This type of multi-level plumbing architecture could drive replenishing magma to rapid volatile saturation, thus increasing the likelihood of explosive eruptions and the consequent hazard potential for the population of Bali.
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| 42. |
- Gonzalez-Maurel, Osvaldo, et al.
(författare)
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Constraining the sub-arc, parental magma composition for the giant Altiplano-Puna Volcanic Complex, northern Chile
- 2020
-
Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- The Andean continental arc is built upon the thickest crust on Earth, whose eruption products reflect varying degrees of crustal assimilation. In order to robustly model magma evolution and assimilation at subduction zones such as the Andes, the compositions of parental magmas feeding crustal magma reservoirs need to be defined. Here we present new olivine and clinopyroxene oxygen isotope data from rare mafic volcanic rocks erupted at the margins of the giant Altiplano-Puna Magma Body (APMB) of the Altiplano-Puna Volcanic Complex, Central Andes. Existing olivine and pyroxene delta O-18 values for the Central Andes are highly variable and potentially not representative of sub-arc parental compositions. However, new olivine (n=6) and clinopyroxene (n=12) delta O-18 values of six Central Andean volcanoes presented here display a narrow range, with averages at 6.0 parts per thousand +/- 0.2 (2 sigma S.D.) and 6.7 parts per thousand +/- 0.3 (2 sigma S.D.), consistent with a common history for the investigated minerals. These data allow us to estimate the delta O-18 values of sub-arc, parental melts to ca. 7.0 parts per thousand +/- 0.2 (2 sigma S.D.). Parental melts feeding the APMB and associated volcanic centres are postulated to form in the felsic continental crust following assimilation of up to 28% high-delta O-18 basement rocks by mantle-derived magmas.
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| 43. |
- Hadfield, James, et al.
(författare)
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Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
- 2017
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory Press. - 1088-9051 .- 1549-5469. ; 27:7, s. 1220-1229
-
Tidskriftsartikel (refereegranskat)abstract
- Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.
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| 44. |
- Heap, Michael J., et al.
(författare)
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Whole-rock oxygen isotope ratios as a proxy for the strength and stiffness of hydrothermally altered volcanic rocks
- 2022
-
Ingår i: Bulletin of Volcanology. - : Springer Nature. - 0258-8900 .- 1432-0819. ; 84:8
-
Tidskriftsartikel (refereegranskat)abstract
- Hydrothermal alteration is considered to increase the likelihood of dome or flank collapse by compromising stability. Understanding how such alteration influences rock properties, and providing independent metrics for alteration that can be used to estimate these parameters, is therefore important to better assess volcanic hazards and mitigate risk. We explore the possibility of using whole-rock delta O-18 and delta D values and water contents, metrics that can potentially track alteration, to estimate the strength (compressive and tensile) and Young's modulus (i.e. "stiffness") of altered (acid-sulphate) volcanic rocks from La Soufriere de Guadeloupe (Eastern Caribbean). The delta O-18 values range from 5.8 to 13.2 parts per thousand, delta D values from - 151 to - 44 parts per thousand, and water content from 0.3 to 5.1 wt%. We find that there is a good correlation between delta O-18 values and laboratory-measured strength and Young's modulus, but that these parameters do not vary systematically with delta D or water content (likely due to their pre-treatment at 200 degrees C). Empirical linear relationships that allow strength and Young's modulus to be estimated using delta O-18 values are provided using our new data and published data for Merapi volcano (Indonesia). Our study highlights that delta O-18 values can be used to estimate the strength and Young's modulus of volcanic rocks, and could therefore be used to provide parameters for volcano stability modelling. One advantage of this technique is that delta O-18 only requires a small amount of material, and can therefore provide rock property estimates in scenarios where material is limited, such as borehole cuttings or when sampling large blocks is impracticable.
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| 45. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
-
Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
-
Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 46. |
- Huffman, Jennifer E., et al.
(författare)
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Modulation of Genetic Associations with Serum Urate Levels by Body-Mass-Index in Humans
- 2015
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:3
-
Tidskriftsartikel (refereegranskat)abstract
- We tested for interactions between body mass index (BMI) and common genetic variants affecting serum urate levels, genome-wide, in up to 42569 participants. Both stratified genome-wide association (GWAS) analyses, in lean, overweight and obese individuals, and regression-type analyses in a non BMI-stratified overall sample were performed. The former did not uncover any novel locus with a major main effect, but supported modulation of effects for some known and potentially new urate loci. The latter highlighted a SNP at RBFOX3 reaching genome-wide significant level (effect size 0.014, 95% CI 0.008-0.02, P-inter= 2.6 x 10(-8)). Two top loci in interaction term analyses, RBFOX3 and ERO1LB-EDAR-ADD, also displayed suggestive differences in main effect size between the lean and obese strata. All top ranking loci for urate effect differences between BMI categories were novel and most had small magnitude but opposite direction effects between strata. They include the locus RBMS1-TANK (men, Pdifflean-overweight= 4.7 x 10(-8)), a region that has been associated with several obesity related traits, and TSPYL5 (men, Pdifflean-overweight= 9.1 x 10(-8)), regulating adipocytes-produced estradiol. The top-ranking known urate loci was ABCG2, the strongest known gout risk locus, with an effect halved in obese compared to lean men (Pdifflean-obese= 2 x 10(-4)). Finally, pathway analysis suggested a role for N-glycan biosynthesis as a prominent urate-associated pathway in the lean stratum. These results illustrate a potentially powerful way to monitor changes occurring in obesogenic environment.
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| 47. |
- Ikram, M. Arfan, et al.
(författare)
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Common variants at 6q22 and 17q21 are associated with intracranial volume
- 2012
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:5, s. 539-544
-
Tidskriftsartikel (refereegranskat)abstract
- During aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our genome-wide association study (GWAS) in 8,175 community-dwelling elderly persons did not reveal any associations at genome-wide significance (P < 5 x 10(-8)) for brain volume. In contrast, intracranial volume was significantly associated with two loci: rs4273712 (P = 3.4 x 10(-11)), a known height-associated locus on chromosome 6q22, and rs9915547 (P = 1.5 x 10(-12)), localized to the inversion on chromosome 17q21. We replicated the associations of these loci with intracranial volume in a separate sample of 1,752 elderly persons (P = 1.1 x 10(-3) for 6q22 and 1.2 x 10(-3) for 17q21). Furthermore, we also found suggestive associations of the 17q21 locus with head circumference in 10,768 children (mean age of 14.5 months). Our data identify two loci associated with head size, with the inversion at 17q21 also likely to be involved in attaining maximal brain size.
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| 48. |
- Jeffery, Adam J., et al.
(författare)
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The pre-eruptive magma plumbing system of the 2007–2008 dome-forming eruption of Kelut volcano, East Java, Indonesia
- 2013
-
Ingår i: Contributions to Mineralogy and Petrology. - : Springer Science and Business Media LLC. - 0010-7999 .- 1432-0967. ; 166:1, s. 275-308
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Tidskriftsartikel (refereegranskat)abstract
- Kelut volcano, East Java, is an active volcanic complex hosting a summit crater lake that has been the source of some of Indonesia’s most destructive lahars. In November 2007, an effusive eruption lasting approximately 7 months led to the formation of a 260-m-high and 400-m-wide lava dome that displaced most of the crater lake. The 2007–2008 Kelut dome comprises crystal-rich basaltic andesite with a texturally complex crystal cargo of strongly zoned and in part resorbed plagioclase (An47–94), orthopyroxene (En64–72, Fs24–32, Wo2–4), clinopyroxene (En40–48, Fs14–19, Wo34–46), Ti-magnetite (Usp16–34) and trace amounts of apatite, as well as ubiquitous glomerocrysts of varying magmatic mineral assemblages. In addition, the notable occurrence of magmatic and crustal xenoliths (meta-basalts, amphibole-bearing cumulates, and skarn-type calc-silicates and meta-volcaniclastic rocks) is a distinct feature of the dome. New petrographical, whole rock major and trace element data, mineral chemistry as well as oxygen isotope data for both whole rocks and minerals indicate a complex regime of magma-mixing, decompression-driven resorption, degassing and crystallisation and crustal assimilation within the Kelut plumbing system prior to extrusion of the dome. Detailed investigation of plagioclase textures alongside crystal size distribution analyses provide evidence for magma mixing as a major pre-eruptive process that blends multiple crystal cargoes together. Distinct magma storage zones are postulated, with a deeper zone at lower crustal levels or near the crust-mantle boundary (>15 km depth), a second zone at mid-crustal levels (~10 km depth) and several magma storage zones distributed throughout the uppermost crust (<10 km depth). Plagioclase-melt and amphibole hygrometry indicate magmatic H2O contents ranging from ~8.1 to 8.6 wt.% in the lower crustal system to ~1.5 to 3.3 wt.% in the mid to upper crust. Pyroxene and plagioclase δ18O values range from 5.4 to 6.7 ‰, and 6.5 to 7.6 ‰, respectively. A single whole rock analysis of the 2007–2008 dome lava gave a δ18O value of 7.6 ‰, whereas meta-basaltic and calc-silicate xenoliths are characterised by δ18O values of 6.2 and 10.3 ‰, respectively. Magmatic δ18O values calculated from individual pyroxene and plagioclase analyses range from 5.7 to 7.0 ‰, and 6.2 to 7.4 ‰, respectively. This range in O-isotopic compositions is explained by crystallisation of pyroxenes in the lower to mid-crust, where crustal contamination is either absent or masked by assimilation of material having similar δ18O values to the ascending melts. This population is mixed with isotopically distinct plagioclase and pyroxenes that crystallised from a more contaminated magma in the upper crustal system. Binary bulk mixing models suggest that shallow-level, recycled volcaniclastic sedimentary rocks together with calc-silicates and/or limestones are the most likely contaminants of the 2007–2008 Kelut magma, with the volcaniclastic sediments being dominant.
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