| 1. |
- Middeldorp, Christel M., et al.
(författare)
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The Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia : design, results and future prospects
- 2019
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Ingår i: European Journal of Epidemiology. - : Springer Science and Business Media LLC. - 0393-2990 .- 1573-7284. ; 34:3, s. 279-300
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Tidskriftsartikel (refereegranskat)abstract
- The impact of many unfavorable childhood traits or diseases, such as low birth weight and mental disorders, is not limited to childhood and adolescence, as they are also associated with poor outcomes in adulthood, such as cardiovascular disease. Insight into the genetic etiology of childhood and adolescent traits and disorders may therefore provide new perspectives, not only on how to improve wellbeing during childhood, but also how to prevent later adverse outcomes. To achieve the sample sizes required for genetic research, the Early Growth Genetics (EGG) and EArly Genetics and Lifecourse Epidemiology (EAGLE) consortia were established. The majority of the participating cohorts are longitudinal population-based samples, but other cohorts with data on early childhood phenotypes are also involved. Cohorts often have a broad focus and collect(ed) data on various somatic and psychiatric traits as well as environmental factors. Genetic variants have been successfully identified for multiple traits, for example, birth weight, atopic dermatitis, childhood BMI, allergic sensitization, and pubertal growth. Furthermore, the results have shown that genetic factors also partly underlie the association with adult traits. As sample sizes are still increasing, it is expected that future analyses will identify additional variants. This, in combination with the development of innovative statistical methods, will provide detailed insight on the mechanisms underlying the transition from childhood to adult disorders. Both consortia welcome new collaborations. Policies and contact details are available from the corresponding authors of this manuscript and/or the consortium websites.
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| 2. |
- Tobias, Deirdre K, et al.
(författare)
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Second international consensus report on gaps and opportunities for the clinical translation of precision diabetes medicine
- 2023
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Ingår i: Nature Medicine. - 1546-170X. ; 29:10, s. 2438-2457
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Forskningsöversikt (refereegranskat)abstract
- Precision medicine is part of the logical evolution of contemporary evidence-based medicine that seeks to reduce errors and optimize outcomes when making medical decisions and health recommendations. Diabetes affects hundreds of millions of people worldwide, many of whom will develop life-threatening complications and die prematurely. Precision medicine can potentially address this enormous problem by accounting for heterogeneity in the etiology, clinical presentation and pathogenesis of common forms of diabetes and risks of complications. This second international consensus report on precision diabetes medicine summarizes the findings from a systematic evidence review across the key pillars of precision medicine (prevention, diagnosis, treatment, prognosis) in four recognized forms of diabetes (monogenic, gestational, type 1, type 2). These reviews address key questions about the translation of precision medicine research into practice. Although not complete, owing to the vast literature on this topic, they revealed opportunities for the immediate or near-term clinical implementation of precision diabetes medicine; furthermore, we expose important gaps in knowledge, focusing on the need to obtain new clinically relevant evidence. Gaps include the need for common standards for clinical readiness, including consideration of cost-effectiveness, health equity, predictive accuracy, liability and accessibility. Key milestones are outlined for the broad clinical implementation of precision diabetes medicine.
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| 3. |
- van der Valk, Ralf J P, et al.
(författare)
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A novel common variant in DCST2 is associated with length in early life and height in adulthood.
- 2015
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 24:4, s. 1155-68
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Tidskriftsartikel (refereegranskat)abstract
- Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 × 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; β = 0.046, SE = 0.008, P = 2.46 × 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 × 10(-4)) and adult height (N = 127 513; P = 1.45 × 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.
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| 4. |
- Davies, Neil, et al.
(författare)
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The founding charter of the Genomic Observatories Network
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3:2
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Tidskriftsartikel (refereegranskat)abstract
- Abstract The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
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| 5. |
- Walker, Mike, et al.
(författare)
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Formal definition and dating of the GSSP (Global Stratotype Section and Point) for the base of the Holocene using the Greenland NGRIP ice core, and selected auxiliary records
- 2009
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Ingår i: Journal of Quaternary Science. - : Wiley. - 1099-1417 .- 0267-8179. ; 24:1, s. 3-17
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Forskningsöversikt (refereegranskat)abstract
- The Greenland ice core from NorthGRIP (NGRIP) contains a proxy climate record across the Pleistocene-Holocene boundary of unprecedented clarity and resolution. Analysis of an array of physical and chemical parameters within the ice enables the base of the Holocene, as reflected in the first signs of climatic warming at the end of the Younger Dryas/Greenland Stadial 1 cold phase, to be located with a high degree of precision. This climatic event is most clearly reflected in an abrupt shift in deuterium excess values, accompanied by more gradual changes in delta O-18, dust concentration, a range of chemical species, and annual layer thickness. A timescale based on multi-parameter annual layer counting provides an age of 11 700 calendar yr b2k (before AD 2000) for the base of the Holocene, with a maximum counting error of 99 yr. A proposal that an archived core from this unique sequence should constitute the Global Stratotype Section and Point (GSSP) for the base of the Holocene Series/Epoch (Quaternary System/Period) has been ratified by the International Union of Geological Sciences. Five auxiliary stratotypes for the Pleistocene-Holocene boundary have also been recognised. Copyright (C) 2008 John Wiley & Sons, Ltd.
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| 6. |
- Walker, Mike, et al.
(författare)
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The Global Stratotype Section and Point (GSSP) for the base of the Holocene Series/Epoch (Quaternary System/Period) in the NGRIP ice core
- 2008
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Ingår i: Episodes. - 0705-3797. ; 31:2, s. 264-267
-
Tidskriftsartikel (refereegranskat)abstract
- The Greenland ice core from NorthGRIP (NGRIP) contains a proxy climate record across the Pleistocene-Holocene boundary of unprecedented clarity and resolution. Analysis of an array of physical and chemical parameters within the ice enables the base of the Holocene, as reflected in the first signs of climatic warming at the end of the Younger Dryas/Greenland Stadial 1 cold phase, to be located with a high degree of precision. This climatic event is most clearly reflected in an. abrupt shaft in deuterium excess values, accompanied by more gradual changes in delta O-18, dust concentration, a range of chemical species, and annual layer thickness. A timescale based on multi-parameter annual layer counting provides an age of 11,700 yr b2k (before AD2000) for the base of the Holocene, with, an estimated 2 sigma uncertainty of 99 yr: It is proposed that an archived core from this unique sequence should constitute the Global Stratotype Section and Point (GSSP) for the base of the Holocene Series/Epoch (Quaternary System/Period).
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| 7. |
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| 8. |
- de Vries, Paul S., et al.
(författare)
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Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5x10(-8) is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5x10(-8)), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.
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| 9. |
- Kilpeläinen, Tuomas O, et al.
(författare)
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Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.
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| 10. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 11. |
- Machiela, Mitchell J., et al.
(författare)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 12. |
- Percival, Carl J., et al.
(författare)
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Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation
- 2013
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Ingår i: Faraday discussions. - : Royal Society of Chemistry (RSC). - 1359-6640 .- 1364-5498. ; 165, s. 45-73
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Tidskriftsartikel (refereegranskat)abstract
- Carbonyl oxides (Criegee intermediates), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al., Sci. Total Environ., 2006, 360, 5, Gab et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of SO2 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipila et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved experimentally obtained estimates of the rate coefficients of Criegee intermediate reactions. Using both regional and global scale modelling, we show that this enhancement is likely to be highly variable spatially with local hot-spots in e. g. urban outflows. This conclusion is however contingent on a number of remaining uncertainties in Criegee intermediate chemistry.
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| 13. |
- Pinto, Dalila, et al.
(författare)
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Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders.
- 2014
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Ingår i: American journal of human genetics. - : Elsevier BV. - 1537-6605 .- 0002-9297. ; 94:5, s. 677-694
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Tidskriftsartikel (refereegranskat)abstract
- Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0× 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7× 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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| 14. |
- Serge, M. A., et al.
(författare)
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Testing the Effect of Relative Pollen Productivity on the REVEALS Model : A Validated Reconstruction of Europe-Wide Holocene Vegetation
- 2023
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Ingår i: Land. - : MDPI. - 2073-445X. ; 12:5
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Tidskriftsartikel (refereegranskat)abstract
- Reliable quantitative vegetation reconstructions for Europe during the Holocene are crucial to improving our understanding of landscape dynamics, making it possible to assess the past effects of environmental variables and land-use change on ecosystems and biodiversity, and mitigating their effects in the future. We present here the most spatially extensive and temporally continuous pollen-based reconstructions of plant cover in Europe (at a spatial resolution of 1 degrees x 1 degrees) over the Holocene (last 11.7 ka BP) using the 'Regional Estimates of VEgetation Abundance from Large Sites' (REVEALS) model. This study has three main aims. First, to present the most accurate and reliable generation of REVEALS reconstructions across Europe so far. This has been achieved by including a larger number of pollen records compared to former analyses, in particular from the Mediterranean area. Second, to discuss methodological issues in the quantification of past land cover by using alternative datasets of relative pollen productivities (RPPs), one of the key input parameters of REVEALS, to test model sensitivity. Finally, to validate our reconstructions with the global forest change dataset. The results suggest that the RPPs.st1 (31 taxa) dataset is best suited to producing regional vegetation cover estimates for Europe. These reconstructions offer a long-term perspective providing unique possibilities to explore spatial-temporal changes in past land cover and biodiversity.
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| 15. |
- Alfoeldi, Jessica, et al.
(författare)
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The genome of the green anole lizard and a comparative analysis with birds and mammals
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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| 16. |
- Beaumont, Robin N, et al.
(författare)
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Genome-wide association study of offspring birth weight in 86,577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics.
- 2018
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 1460-2083 .- 0964-6906. ; 27:4, s. 742-756
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) of birth weight have focused on fetal genetics, while relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86,577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P<5x10-8. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.
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| 17. |
- Bedford, Lynn, et al.
(författare)
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Depletion of 26S proteasomes in mouse brain neurons causes neurodegeneration and Lewy-like inclusions resembling human pale bodies
- 2008
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Ingår i: Journal of Neuroscience. - 0270-6474 .- 1529-2401. ; 28:33, s. 8189-98
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Tidskriftsartikel (refereegranskat)abstract
- Ubiquitin-positive intraneuronal inclusions are a consistent feature of the major human neurodegenerative diseases, suggesting that dysfunction of the ubiquitin proteasome system is central to disease etiology. Research using inhibitors of the 20S proteasome to model Parkinson's disease is controversial. We report for the first time that specifically 26S proteasomal dysfunction is sufficient to trigger neurodegenerative disease. Here, we describe novel conditional genetic mouse models using the Cre/loxP system to spatially restrict inactivation of Psmc1 (Rpt2/S4) to neurons of either the substantia nigra or forebrain (e.g., cortex, hippocampus, and striatum). PSMC1 is an essential subunit of the 26S proteasome and Psmc1 conditional knock-out mice display 26S proteasome depletion in targeted neurons, in which the 20S proteasome is not affected. Impairment of specifically ubiquitin-mediated protein degradation caused intraneuronal Lewy-like inclusions and extensive neurodegeneration in the nigrostriatal pathway and forebrain regions. Ubiquitin and alpha-synuclein neuropathology was evident, similar to human Lewy bodies, but interestingly, inclusion bodies contained mitochondria. We support this observation by demonstrating mitochondria in an early form of Lewy body (pale body) from Parkinson's disease patients. The results directly confirm that 26S dysfunction in neurons is involved in the pathology of neurodegenerative disease. The model demonstrates that 26S proteasomes are necessary for normal neuronal homeostasis and that 20S proteasome activity is insufficient for neuronal survival. Finally, we are providing the first reproducible genetic platform for identifying new therapeutic targets to slow or prevent neurodegeneration.
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| 18. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 19. |
- Block, Keith I., et al.
(författare)
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Designing a broad-spectrum integrative approach for cancer prevention and treatment
- 2015
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Ingår i: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
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Forskningsöversikt (refereegranskat)abstract
- Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broadspectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. (C) 2015 The Authors. Published by Elsevier Ltd.
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| 20. |
- Cumming, Graeme S., et al.
(författare)
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Research priorities for the sustainability of coral-rich western Pacific seascapes
- 2023
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Ingår i: Regional Environmental Change. - 1436-3798 .- 1436-378X. ; 23:2
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Tidskriftsartikel (refereegranskat)abstract
- Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation; elucidating drivers and mechanisms of change; understanding how seascape functions and services are produced, and how people depend on them; costs, benefits, and trade-offs to people in changing seascapes; improving seascape technologies and practices; learning to govern and manage seascapes for all; sustainable use, justice, and human well-being; bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions; and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.
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| 21. |
- Danesh, John, et al.
(författare)
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Plasma fibrinogen level and the risk of major cardiovascular diseases and nonvascular mortality: an individual participant meta-analysis
- 2005
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Ingår i: JAMA: The Journal of the American Medical Association. - : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 294:14, s. 1799-1809
-
Forskningsöversikt (refereegranskat)abstract
- CONTEXT: Plasma fibrinogen levels may be associated with the risk of coronary heart disease (CHD) and stroke. OBJECTIVE: To assess the relationships of fibrinogen levels with risk of major vascular and with risk of nonvascular outcomes based on individual participant data. DATA SOURCES: Relevant studies were identified by computer-assisted searches, hand searches of reference lists, and personal communication with relevant investigators. STUDY SELECTION: All identified prospective studies were included with information available on baseline fibrinogen levels and details of subsequent major vascular morbidity and/or cause-specific mortality during at least 1 year of follow-up. Studies were excluded if they recruited participants on the basis of having had a previous history of cardiovascular disease; participants with known preexisting CHD or stroke were excluded. DATA EXTRACTION: Individual records were provided on each of 154,211 participants in 31 prospective studies. During 1.38 million person-years of follow-up, there were 6944 first nonfatal myocardial infarctions or stroke events and 13,210 deaths. Cause-specific mortality was generally available. Analyses involved proportional hazards modeling with adjustment for confounding by known cardiovascular risk factors and for regression dilution bias. DATA SYNTHESIS: Within each age group considered (40-59, 60-69, and > or =70 years), there was an approximately log-linear association with usual fibrinogen level for the risk of any CHD, any stroke, other vascular (eg, non-CHD, nonstroke) mortality, and nonvascular mortality. There was no evidence of a threshold within the range of usual fibrinogen level studied at any age. The age- and sex- adjusted hazard ratio per 1-g/L increase in usual fibrinogen level for CHD was 2.42 (95% confidence interval [CI], 2.24-2.60); stroke, 2.06 (95% CI, 1.83-2.33); other vascular mortality, 2.76 (95% CI, 2.28-3.35); and nonvascular mortality, 2.03 (95% CI, 1.90-2.18). The hazard ratios for CHD and stroke were reduced to about 1.8 after further adjustment for measured values of several established vascular risk factors. In a subset of 7011 participants with available C-reactive protein values, the findings for CHD were essentially unchanged following additional adjustment for C-reactive protein. The associations of fibrinogen level with CHD or stroke did not differ substantially according to sex, smoking, blood pressure, blood lipid levels, or several features of study design. CONCLUSIONS: In this large individual participant meta-analysis, moderately strong associations were found between usual plasma fibrinogen level and the risks of CHD, stroke, other vascular mortality, and nonvascular mortality in a wide range of circumstances in healthy middle-aged adults. Assessment of any causal relevance of elevated fibrinogen levels to disease requires additional research.
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| 22. |
- Dow, Andy, et al.
(författare)
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What Happens to Digital Feedback? : Studying the Use of a Feedback Capture Platform by Care Organisations
- 2017
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Ingår i: PROCEEDINGS OF THE 2017 ACM SIGCHI CONFERENCE ON HUMAN FACTORS IN COMPUTING SYSTEMS (CHI'17). - New York, NY, USA : ASSOC COMPUTING MACHINERY. ; , s. 5813-5825
-
Konferensbidrag (refereegranskat)abstract
- In this paper we report on a four-month long field trial of ThoughtCloud, a feedback collection platform that allows people to leave ratings and audio or video responses to simple prompts. ThoughtCloud was trialled with four organisations providing care services for people with disabilities. We conducted interviews with staff and volunteers that used ThoughtCloud before, during and after its deployment, and workshops with service users and staff. While the collection of feedback was high, only one organisation regularly reviewed and responded to collected opinions. Furthermore, tensions arose around data access and sharing, and the mismatch of values between 'giving voice' and the capacity for staff to engage in feedback practices. We contribute insights into the challenges faced in using novel technologies in resource constrained organisations, and discuss opportunities for designs that give greater agency to service users to engage those that care for them in reflecting and responding to their opinions.
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| 23. |
- Gaughran, Fiona, et al.
(författare)
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Randomised control trial of the effectiveness of an integrated psychosocial health promotion intervention aimed at improving health and reducing substance use in established psychosis (IMPaCT)
- 2017
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Ingår i: BMC Psychiatry. - : Springer Science and Business Media LLC. - 1471-244X. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: People with psychosis have a reduced life expectancy of 10-20years, largely due to cardiovascular disease. This trial aimed to determine the effectiveness of a modular health promotion intervention (IMPaCT Therapy) in improving health and reducing cardiovascular risk in psychosis. Methods: A multicentre, two arm, parallel cluster RCT was conducted across five UK mental health NHS trusts. Community care coordinators (CC) were randomly assigned to training and supervision in delivering IMPaCT Therapy or treatment as usual (TAU) to current patients with psychosis (cluster). The primary outcome was the physical and mental health subscales of the Short form-36 (SF-36) questionnaire. Results: Of 104 care coordinators recruited, 52 (with 213 patients) were randomised to deliver IMPaCT therapy and 52 (with 193 patients) randomised to TAU. Of 406 patients, 318 (78%) and 301 (74%) attended 12- and 15-month follow-up respectively. IMPaCT therapy showed no significant effect on the physical or mental health component SF-36 scores versus TAU at 12 or 15months. No effect was observed for cardiovascular risk indicators, except for HDL cholesterol, which improved more with IMPACT therapy than TAU (Treatment effect (95% CI); 0.085 (0.007 to 0.16); p= 0.034). The 22% of patients who received >180min of IMPACT Therapy in addition to usual care achieved a greater reduction in waist circumference than did controls, which was clinically significant. Conclusion: Training and supervising community care coordinators to use IMPaCT therapy in patients with psychosis is insufficient to significantly improve physical or mental health quality of life. The search for effective, pragmatic interventions deliverable in health care services continues. Trial registration: The trial was retrospectively registered with ISRCTN registry on 23/4/2010 at ISRCTN58667926 ; recruitment started on 01/03/2010 with first randomization on 09.08.2010 ISRCTN58667926.
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| 24. |
- Hemann, Michael T, et al.
(författare)
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Evasion of the p53 tumour surveillance network by tumour-derived MYC mutants.
- 2005
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Ingår i: Nature. - 1476-4687. ; 436:7052, s. 807-11
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Tidskriftsartikel (refereegranskat)abstract
- The c-Myc oncoprotein promotes proliferation and apoptosis, such that mutations that disable apoptotic programmes often cooperate with MYC during tumorigenesis. Here we report that two common mutant MYC alleles derived from human Burkitt's lymphoma uncouple proliferation from apoptosis and, as a result, are more effective than wild-type MYC at promoting B cell lymphomagenesis in mice. Mutant MYC proteins retain their ability to stimulate proliferation and activate p53, but are defective at promoting apoptosis due to a failure to induce the BH3-only protein Bim (a member of the B cell lymphoma 2 (Bcl2) family) and effectively inhibit Bcl2. Disruption of apoptosis through enforced expression of Bcl2, or loss of either Bim or p53 function, enables wild-type MYC to produce lymphomas as efficiently as mutant MYC. These data show how parallel apoptotic pathways act together to suppress MYC-induced transformation, and how mutant MYC proteins, by selectively disabling a p53-independent pathway, enable tumour cells to evade p53 action during lymphomagenesis.
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| 25. |
- John Lowe, J., et al.
(författare)
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Inter-regional correlation of palaeoclimatic records for the last Glacial-Interglacial Transition : A protocol for improved precision recommended by the INTIMATE project group
- 2001
-
Ingår i: Quaternary Science Reviews. - 0277-3791. ; 20:11, s. 1175-1187
-
Tidskriftsartikel (refereegranskat)abstract
- The remit of the INTIMATE project of the INQUA Palaeoclimate Commission is to synthesise marine, terrestrial and ice-core data for the North Atlantic region during the Last Glacial-Interglacial Transition (LGIT: ca 13-1014C kyr BP; ca 15-11.5 ice-core kyr BP). A major problem, however, is the difficulty of effecting correlations at a temporal resolution that are adequate for defining 'leads' and 'lags' between the polar ice, terrestrial, marine, and atmospheric realms. The limitations of the dating and correlation methods currently employed are summarised, and new quality assurance protocols are proposed. These include recommendations on the contextual information that should accompany radiocarbon dates, procedures for radiocarbon calibration, the use of an event-stratigraphic approach in inter-regional correlations, and the more widespread use of time-parallel marker horizons (based on tephra layers, oxygen isotope stratigraphy, palaeomagnetic stratigraphy, and radiocarbon 'wiggle-matching') to underpin the geochronology and correlation of events during the LGIT. These protocols will be adopted by the INTIMATE project in future international, collaborative research and are recommended to other groups working on this important time period.
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| 26. |
- Kamuyu, Gathoni, et al.
(författare)
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Exposure to Multiple Parasites Is Associated with the Prevalence of Active Convulsive Epilepsy in Sub-Saharan Africa
- 2014
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Ingår i: PLoS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2727 .- 1935-2735. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epilepsy is common in developing countries, and it is often associated with parasitic infections. We investigated the relationship between exposure to parasitic infections, particularly multiple infections and active convulsive epilepsy (ACE), in five sites across sub-Saharan Africa. Methods and Findings: A case-control design that matched on age and location was used. Blood samples were collected from 986 prevalent cases and 1,313 age-matched community controls and tested for presence of antibodies to Onchocerca volvulus, Toxocara canis, Toxoplasma gondii, Plasmodium falciparum, Taenia solium and HIV. Exposure (seropositivity) to Onchocerca volvulus (OR = 1.98; 95% CI: 1.52-2.58, p<0.001), Toxocara canis (OR = 1.52; 95% CI: 1.23-1.87, p<0.001), Toxoplasma gondii (OR = 1.28; 95% CI: 1.04-1.56, p=0.018) and higher antibody levels (top tertile) to Toxocara canis (OR = 1.70; 95% CI: 1.30-2.24, p<0.001) were associated with an increased prevalence of ACE. Exposure to multiple infections was common (73.8% of cases and 65.5% of controls had been exposed to two or more infections), and for T. gondii and O. volvulus co-infection, their combined effect on the prevalence of ACE, as determined by the relative excess risk due to interaction (RERI), was more than additive (T. gondii and O. volvulus, RERI = 1.19). The prevalence of T. solium antibodies was low (2.8% of cases and 2.2% of controls) and was not associated with ACE in the study areas. Conclusion: This study investigates how the degree of exposure to parasites and multiple parasitic infections are associated with ACE and may explain conflicting results obtained when only seropositivity is considered. The findings from this study should be further validated.
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| 27. |
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| 28. |
- Lowe, Robert, et al.
(författare)
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Grounding Motivation in Energy Autonomy : A Study of Artificial Metabolism Constrained Robot Dynamics
- 2010
-
Ingår i: Artificial Life XII. - Cambridge, Massachusetts, London, England : MIT Press. - 9780262290753 - 0262290758 ; , s. 725-732
-
Konferensbidrag (refereegranskat)abstract
- We present an evolutionary robotics investigation into the metabolism constrained homeostatic dynamics of a simulated robot. Unlike existing research that has focused on either energy or motivation autonomy the robot described here is considered in terms of energy-motivation autonomy. This stipulation is made according to a requirement of autonomous systems to spatiotemporally integrate environmental and physiological sensed information. In our experiment, the latter is generated by a simulated artificial metabolism (a microbial fuel cell batch) and its integration with the former is determined by an E-GasNet-active vision interface. The investigation centres on robot performance in a three-dimensional simulator on a stereotyped two-resource problem. Motivationlike states emerge according to periodic dynamics identifiable for two viable sensorimotor strategies. Robot adaptivity is found to be sensitive to experimenter-manipulated deviations from evolved metabolic constraints. Deviations detrimentally affect the viability of cognitive (anticipatory) capacities even where constraints are significantly lessened. These results support the hypothesis that grounding motivationally autonomous robots is critical to adaptivity and cognition.
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| 29. |
- Lowe, Robert, et al.
(författare)
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Minimalist Social-Affective Value for Use in Joint Action : A Neural-Computational Hypothesis
- 2016
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Ingår i: Frontiers in Computational Neuroscience. - : Frontiers Media S.A.. - 1662-5188. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Joint Action is typically described as social interaction that requires coordination among two or more co-actors in order to achieve a common goal. In this article, we put forward a hypothesis for the existence of a neural-computational mechanism of affective valuation that may be critically exploited in Joint Action. Such a mechanism would serve to facilitate coordination between co-actors permitting a reduction of required information. Our hypothesized affective mechanism provides a value function based implementation of Associative Two-Process (ATP) theory that entails the classification of external stimuli according to outcome expectancies. This approach has been used to describe animal and human action that concerns differential outcome expectancies. Until now it has not been applied to social interaction. We describe our Affective ATP model as applied to social learning consistent with an “extended common currency” perspective in the social neuroscience literature. We contrast this to an alternative mechanism that provides an example implementation of the so-called social-specific value perspective. In brief, our Social-Affective ATP mechanism builds upon established formalisms for reinforcement learning (temporal difference learning models) nuanced to accommodate expectations (consistent with ATP theory) and extended to integrate non-social and social cues for use in Joint Action.
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| 30. |
- Lowe, Robert, et al.
(författare)
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Studying the Effects of Affective Memory in Joint Activity
- 2017
-
Ingår i: 7th Joint Action Meeting, London, United Kingdom.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In a previous article, we put forward a hypothesis for the existence of a neural-computational mechanism of affective memory that can be used to facilitate Joint Action between co-actors. Our hypothesized affective mechanism provides a value function implementation of Associative Two-Process (ATP) theory. This theory entails the classification of external stimuli according to differentially valuated outcome expectancies. This process can predominate in decision making or choice tasks over an alternative stimulus-response (‘habitual’) memory process. The ATP perspective has been used to describe animal and human action that concerns differentially rewarded outcomes. Until now it has not been applied to social interaction. We present experimental work that attempts to validate our social-affective ATP hypothesis – that affective-ATP memory processes can be exploited both in individual and social contexts. We do this in a scenario that requires human subjects to make stimulus response choices using a mouse controller in a computer game both in individual scenarios, and in relation to feedback from the choices of a (video recorded) other. The results provide some initial support for our hypothesis – subjects learn from another’s stimulus-outcomes and apply this to their own stimulus-response activity. We contend that follow up experiments are necessary to identify the types of social interaction that exploit, or not, a generalized, versus social-specific, (affective) value function.
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| 31. |
- Montebelli, Alberto, et al.
(författare)
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An Oxygen-Diffusion Cathode MFC Model for Simulation of Energy-Autonomous Robots
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present a macroscopic mathematical model of energy generation dynamics in oxygen-diffusion cathode microbial fuel cells (ODC-MFCs). The model is phenomenologically derived on the basis of actual experimental data, obtained by a battery of ODC-MFCs connected in series that supplied energy to a physical robot prototype. Due to its limited computational overhead, the simple set of equations is particularly suitable for the study of robot adaptive behavior under naturalistic energyconstraints in computer simulations, and as a tool for the design and optimization of stack configurations of large sets of MFCs.
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| 32. |
- Montebelli, Alberto, et al.
(författare)
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Microbial fuel cell driven behavioural dynamics in robot simulations
- 2010
-
Ingår i: Artificial Life XII. - Cambridge, Massachusetts : MIT Press. - 9780262290753 - 0262290758 ; , s. 749-756
-
Konferensbidrag (refereegranskat)abstract
- With the present study we report the first application of a recently proposed model for realistic microbial fuel cells (MFCs) energy generation dynamics, suitable for robotic simulations with minimal and extremely limited computational overhead. A simulated agent was adapted in order to engage in a viable interaction with its environment. It achieved energy autonomy by maintaining viable levels of the critical variables of MFCs, namely cathodic hydration and anodic substrate biochemical energy. After unsupervised adaptation by genetic algorithm, these crucial variables modulate the behavioral dynamics expressed by viable robots in their interaction with the environment. The analysis of this physically rooted and self-organized dynamic action selection mechanism constitutes a novel practical contribution of this work. We also compare two different viable strategies, a self-organized continuous and a pulsed behavior, in order to foresee the possible cognitive implications of such biologicalmechatronics hybrid symbionts in a novel scenario of ecologically grounded energy and motivational autonomy.
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| 33. |
- Nash, Gerard, et al.
(författare)
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Haemorheological result in a large multicentre study of claudicants treated with ketanserin
- 1990
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Ingår i: Clinical Hemorheology. - New York, USA : Pergamon Press. - 0271-5198. ; 10, s. 321-327
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Tidskriftsartikel (refereegranskat)abstract
- Abstract An international, multi-centre trial was carried out to test the haemorheological effects of ketanserin, a serotonin antagonist, after treatment of intermittent claudicants for 1 year. Haematological indices, whole blood viscosity, plasma viscosity and red cell and white cell filterabi1ity were measured using standardised techniques. Even so, inter-laboratory variability, and intra-laboratory changes in control values in some centres over the 1 year period proved to be major obstacles. The pooled data showed no evidence of haemorheological changes, although data from the single largest centre indicated slightly lowered haematocrit and blood and plasma viscosity. Any rheological effects of serotonin antagonists in intermittent claudicants are probably small and unlikely to be the main source of any clinical efficacy. In general, it would appear that standardisation and monitoring of laboratory techniques must be strictly carried out if there is to be any hope of successfully carrying out multi-centre haemorheological trials. . Key words: Blood Rheology; Claudication; Serotonin Antagonists;
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| 34. |
- O'Reilly, Kathleen M., et al.
(författare)
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Projecting the end of the Zika virus epidemic in Latin America : a modelling analysis
- 2018
-
Ingår i: BMC Medicine. - : BioMed Central. - 1741-7015. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Zika virus (ZIKV) emerged in Latin America and the Caribbean (LAC) region in 2013, with serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and the lack of a comprehensive collation of data from affected countries.Methods: Our analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 90 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vectorial capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories.Results: There was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 would present within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (p < 0.05) with the reported peak in incidence. The reporting rate varied across countries, with lower reporting rates for those with only confirmed cases compared to those who reported both confirmed and suspected cases.Conclusions: The findings suggest that the ZIKV epidemic is by and large over within LAC, with incidence projected to be low in most cities in 2018. Local low levels of transmission are probable, but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.
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| 35. |
- Rocklöv, Joacim, Professor, 1979-, et al.
(författare)
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Decision-support tools to build climate resilience against emerging infectious diseases in Europe and beyond
- 2023
-
Ingår i: The Lancet Regional Health. - : Elsevier. - 2666-7762. ; 32
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Forskningsöversikt (refereegranskat)abstract
- Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of infectious diseases in Europe. We propose a framework for the co-production of policy-relevant indicators and decision-support tools that track past, present, and future climate-induced disease risks across hazard, exposure, and vulnerability domains at the animal, human, and environmental interface. This entails the co-development of early warning and response systems and tools to assess the costs and benefits of climate change adaptation and mitigation measures across sectors, to increase health system resilience at regional and local levels and reveal novel policy entry points and opportunities. Our approach involves multi-level engagement, innovative methodologies, and novel data streams. We take advantage of intelligence generated locally and empirically to quantify effects in areas experiencing rapid urban transformation and heterogeneous climate-induced disease threats. Our goal is to reduce the knowledge-to-action gap by developing an integrated One Health—Climate Risk framework.
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| 36. |
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| 37. |
- Solé Navais, Pol, et al.
(författare)
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Genetic effects on the timing of parturition and links to fetal birth weight.
- 2023
-
Ingår i: Nature genetics. - 1546-1718. ; 55:4, s. 559-567
-
Tidskriftsartikel (refereegranskat)abstract
- The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n=195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed six associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles (n=136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal-fetal relationship between gestational duration and birth weight.
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| 38. |
- Sumner-Rooney, Lauren, et al.
(författare)
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Extraocular Vision in a Brittle Star Is Mediated by Chromatophore Movement in Response to Ambient Light
- 2020
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822. ; 30:2, s. 4-327
-
Tidskriftsartikel (refereegranskat)abstract
- Almost all animals can sense light, but only those with spatial vision can “see.” Conventionally, this was restricted to animals possessing discrete visual organs (eyes), but extraocular vision could facilitate vision without eyes. Echinoderms form the focus of extraocular vision research [1–7], and the brittle star Ophiocoma wendtii, which exhibits light-responsive color change and shelter seeking, became a key species of interest [4, 8, 9]. Both O. wendtii and an apparently light-indifferent congeneric, O. pumila, possess an extensive network of r-opsin-reactive cells, but its function remains unclear [4]. We show that, although both species are strongly light averse, O. wendtii orients to stimuli necessitating spatial vision for detection, but O. pumila does not. However, O. wendtii's response disappears when chromatophores are contracted within the skeleton. Combining immunohistochemistry, histology, and synchrotron microtomography, we reconstructed models of photoreceptors in situ and extracted estimated angular apertures for O. wendtii and O. pumila. Angular sensitivity estimates, derived from these models, support the hypothesis that chromatophores constitute a screening mechanism in O. wendtii, providing sufficient resolving power to detect the stimuli. RNA sequencing (RNA-seq) identified opsin candidates in both species, including multiple r-opsins and transduction pathway constituents, congruent with immunohistochemistry and studies of other echinoderms [10, 11]. Finally, we note that differing body postures between the two species during experiments may reflect aspect of signal integration. This represents one of the most detailed mechanisms for extraocular vision yet proposed and draws interesting parallels with the only other confirmed extraocular visual system, that of some sea urchins, which also possess chromatophores [1]. Sumner-Rooney et al. report extraocular vision in a brittle star, Ophiocoma wendtii. Visual behavior is absent in O. pumila, despite its similar photoreceptor networks, as well as dark-adapted O. wendtii. The authors propose that chromatophores provide screening pigment in O. wendtii, conferring vision to a dispersed photoreceptor system.
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| 39. |
- Thomsson, Kristina A, 1969, et al.
(författare)
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Intestinal mucins from cystic fibrosis mice show increased fucosylation due to an induced Fucalpha1-2 glycosyltransferase.
- 2002
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Ingår i: The Biochemical journal. - 0264-6021. ; 367:Pt 3, s. 609-16
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Tidskriftsartikel (refereegranskat)abstract
- In gene-targeted mouse models for cystic fibrosis (CF), the disease is mainly manifested by mucus obstruction in the intestine. To explore the mucus composition, mucins insoluble and soluble in 6 M guanidinium chloride were purified by three rounds of isopycnic ultracentrifugation from the small and large intestines of CF mice (Cftr(m1UNC)/Cftr(m1UNC)) and compared with wild-type mice. The amino acid composition was typical of that for mucins and showed increased amounts of the insoluble (2.5-fold increase) and soluble (7-fold increase) mucins in the small intestine of the CF mice compared with wild-type mice. Mucins from the large intestine of both wild-type and CF mice showed a high but constant level of fucosylation. In contrast, the insoluble and soluble mucins of the small intestine in CF mice revealed a large increase in fucose, whereas those of wild-type mice contained only small amounts of fucose. This increased fucosylation was analysed by releasing the O-linked oligosaccharides followed by GC-MS. NMR spectroscopy revealed that the increased fucosylation was due to an increased expression of blood group H epitopes (Fucalpha1-2Gal-). Northern-blot analysis, using a probe for the murine Fucalpha1-2 fucosyltransferase (Fut2), showed an up-regulation of this mRNA in the small intestine of the CF mice, suggesting that this enzyme is responsible for the observed increase in blood group H-type glycosylation. The reason for this up-regulation could be a direct or indirect effect of a non-functional CF transmembrane conductance regulator (CFTR) caused by the absence of CFTR channel.
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| 40. |
- van Akkooi, Alexander C. J., et al.
(författare)
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Neoadjuvant Systemic Therapy (NAST) in Patients with Melanoma: Surgical Considerations by the International Neoadjuvant Melanoma Consortium (INMC)
- 2022
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Ingår i: ANNALS OF SURGICAL ONCOLOGY. - : Springer Science and Business Media LLC. - 1068-9265 .- 1534-4681. ; 29:6, s. 3694-3708
-
Tidskriftsartikel (refereegranskat)abstract
- Exciting advances in melanoma systemic therapies have presented the opportunity for surgical oncologists and their multidisciplinary colleagues to test the neoadjuvant systemic treatment approach in high-risk, resectable metastatic melanomas. Here we describe the state of the science of neoadjuvant systemic therapy (NAST) for melanoma, focusing on the surgical aspects and the key role of the surgical oncologist in this treatment paradigm. This paper summarizes the past decade of developments in melanoma treatment and the current evidence for NAST in stage III melanoma specifically. Issues of surgical relevance are discussed, including the risk of progression on NAST prior to surgery. Technical aspects, such as the definition of resectability for melanoma and the extent and scope of routine surgery are presented. Other important issues, such as the utility of radiographic response evaluation and method of pathologic response evaluation, are addressed. Surgical complications and perioperative management of NAST related adverse events are considered. The International Neoadjuvant Melanoma Consortium has the goal of harmonizing NAST trials in melanoma to facilitate rapid advances with new approaches, and facilitating the comparison of results across trials evaluating different treatment regimens. Our ultimate goals are to provide definitive proof of the safety and efficacy of NAST in melanoma, sufficient for NAST to become an acceptable standard of care, and to leverage this platform to allow more personalized, biomarker-driven, tailored approaches to subsequent treatment and surveillance.
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| 41. |
- van Es, Michael A, et al.
(författare)
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Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis
- 2011
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Ingår i: Annals of Neurology. - : Wiley-Blackwell. - 0364-5134 .- 1531-8249. ; 70:6, s. 964-973
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Several studies have suggested an increased frequency of variants in the gene encoding angiogenin (ANG) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS patients have an increased risk to develop PD, and the prevalence of concomitant motor neuron disease in PD is higher than expected based on chance occurrence. We therefore investigated whether ANG variants could predispose to both ALS and PD.METHODS: We reviewed all previous studies on ANG in ALS and performed sequence experiments on additional samples, which allowed us to analyze data from 6,471 ALS patients and 7,668 controls from 15 centers (13 from Europe and 2 from the USA). We sequenced DNA samples from 3,146 PD patients from 6 centers (5 from Europe and 1 from the USA). Statistical analysis was performed using the variable threshold test, and the Mantel-Haenszel procedure was used to estimate odds ratios.RESULTS: Analysis of sequence data from 17,258 individuals demonstrated a significantly higher frequency of ANG variants in both ALS and PD patients compared to control subjects (p = 9.3 × 10(-6) for ALS and p = 4.3 × 10(-5) for PD). The odds ratio for any ANG variant in patients versus controls was 9.2 for ALS and 6.7 for PD.INTERPRETATION: The data from this multicenter study demonstrate that there is a strong association between PD, ALS, and ANG variants. ANG is a genetic link between ALS and PD.
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| 42. |
- Veres, Daniel S., 1977-
(författare)
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Terrestrial response to Dansgaard-Oeschger cycles and Heinrich events : the lacustrine record of Les Echets, south-eastern France
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Marine Isotope Stage (MIS) 3 was an interval characterized by large and abrupt temperature changes on a millennial time scale, the so-called Dansgaard-Oeschger (DO) cycles and Heinrich events. Evidence for this high-frequency climate variability has been identified in many marine and ice core records. Reconstructions from continental Europe, however, are still too scarce to form a comprehensive environmental picture for this time interval. In this thesis, high-resolution multi-proxy sedimentological, geochemical and chronological analyses were conducted on two long sediment sequences from the site of Les Echets, France. The main objective of this study was to determine the extent and nature of the lacustrine response to the rapid climate variability of MIS 3 and 2. The results indicate that the lake underwent recurrent shifts in lake status that closely followed temperature variations associated with DO cycles and Heinrich events which occurred between ca 60-20,000 years BP. Organic matter elemental and isotopic results indicate that most of the organic matter is mainly autochthonous suggesting that increased lake organic primary productivity commenced during DO interstadials. DO stadials and Heinrich events on the other hand are clearly marked by a reduction in productivity, organic matter oxidation and an increase in catchment erosion indicators. The results discussed in this thesis provide new insights into the response of a terrestrial ecosystem to millennial-scale climate variability and highlight the potential of multi-proxy studies in lake sediment research. This research also demonstrates that the Les Echets site may represent a potential link between the more fragmented central and northern continental European sites and marine and terrestrial records from the Mediterranean region.
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| 43. |
- Virta, Sari
(författare)
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Managing tensions in creative content development work : Cases from the media industry
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This dissertation explores organisational tensions and their management in creative content development work in the context of creative industries, particularly media. The study focuses on the dynamic relationship and complexities between current business (exploitation) and future business (exploration), where tensions become managerial issues. It builds on dualities as the overarching analytical concept. The combination of theorisations on ambidexterity, value networks and hybrid organisations is used to examine organisational tensions as dynamic interrelationships between the elements of dualities.This compilation dissertation builds on three qualitative case studies, which are investigated in six individual, empirical papers. The case organisations include a company from both public and private media, as well as a collaborative arrangement in a creative industry cluster. The longitudinal empirical data comprises diary writings, interviews, documentation and participant observations.The study extends the understanding about how and why organisational tensions pose a demanding managerial challenge to established companies. It suggests that these tensions cannot be solved as such; instead, they need to be managed “with” rather than “against”. The study contributes to previous literature by combining theoretical perspectives to create links between existing approaches on ambidexterity. Regarding clusters, the study offers new knowledge by shifting the focus from mere spatial co-location to shared value creation through collaborative relationships.As implications for practice, the study suggests that managerial effort is required to anticipate, identify, evaluate, and navigate tensions in creative work. The results emphasise the key importance of embracing interrelated, coexisting, enduring, and complex tensions as a multifaceted package.
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| 44. |
- Walker, Mike, et al.
(författare)
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Formal Subdivision of the Holocene Series/Epoch : A Summary
- 2019
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Ingår i: Journal of the Geological Society of India. - : Springer Science and Business Media LLC. - 0016-7622 .- 0974-6889. ; 93:2, s. 135-141
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Tidskriftsartikel (refereegranskat)abstract
- The Holocene Series/Epoch is the most recent series/epoch in the geological timescale, spanning the interval from 11,700 yr to the present day. Together with the subadjacent Pleistocene, it comprises the Quaternary System/Period. The Holocene record contains diverse geomorphological, biological, climatological and archaeological evidence, within sequences that are often continuous and extremely well-preserved at decadal, annual and even seasonal resolution. As a consequence, the Holocene is perhaps the most intensively-studied series/epoch within the entire Geological Time Scale. Yet until recently little attention had been paid to a formal subdivision of the Holocene. Here we describe an initiative by the Subcommission on Quaternary Stratigraphy (SQS) of the International Commission on Stratigraphy (ICS) to develop a formal stratigraphical subdivision of the Holocene, with three new stages/ages, two underpinned by Global Boundary Stratotype Sections and Points (GSSPs in an ice core, and a third in a speleothem. These stages/ages are defined together with their equivalent subseries/subepochs. The new stages/ages are the Greenlandian with its GSSP in the Greenland NGRIP2 ice core and dated at 11,700 yr b2k (before 2000 CE); the Northgrippian with its GSSP in the Greenland NGRIP1 ice core and dated to 8236 yr b2k; and the Meghalayan, with its GSSP in a speleothem from Mawmluh Cave, northeastern India, with a date of 4250 yr b2k. This subdivision was formally ratified by the Executive Committee of the International Union of Geological Sciences (IUGS) on 14 th June 2018.
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| 45. |
- Walker, Mike, et al.
(författare)
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Subdividing the Holocene Series/Epoch : formalization of stages/ages and subseries/subepochs, and designation of GSSPs and auxiliary stratotypes
- 2019
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Ingår i: Journal of Quaternary Science. - : Wiley. - 0267-8179 .- 1099-1417. ; 34:3, s. 173-186
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Tidskriftsartikel (refereegranskat)abstract
- The Holocene, which currently spans ~11 700 years, is the shortest series/epoch within the geological time scale (GTS), yet it contains a rich archive of evidence in stratigraphical contexts that are frequently continuous and often preserved at high levels of resolution. On 14 June 2018, the Executive Committee of the International Union of Geological Sciences formally ratified a proposal to subdivide the Holocene into three stages/ages, along with their equivalent subseries/subepochs, each anchored by a Global boundary Stratotype Section and Point (GSSP). The new stages are the Greenlandian (Lower/Early Holocene Subseries/Subepoch) with its GSSP in the Greenland NGRIP2 ice core and dated at 11 700 a b2k (before 2000 CE); the Northgrippian (Middle Holocene Subseries/Subepoch) with its GSSP in the Greenland NGRIP1 ice core and dated at 8236 a b2k; and the Meghalayan (Upper/Late Holocene Subseries/Subepoch) with its GSSP in a speleothem from Mawmluh Cave, north-eastern India, with a date of 4250 a b2k. We explain the nomenclature of the new divisions, describe the procedures involved in the ratification process, designate auxiliary stratotypes to support the GSSPs and consider the implications of the subdivision for defining the Anthropocene as a new unit within the GTS.
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| 46. |
- Wang, Gang, et al.
(författare)
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Spirometric phenotypes from early childhood to young adulthood : a Chronic Airway Disease Early Stratification study
- 2021
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Ingår i: ERJ Open Research. - : ERS Publications. - 2312-0541. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: The prevalences of obstructive and restrictive spirometric phenotypes, and their relation to early-life risk factors from childhood to young adulthood remain poorly understood. The aim was to explore these phenotypes and associations with well-known respiratory risk factors across ages and populations in European cohorts.Methods: We studied 49334 participants from 14 population-based cohorts in different age groups (⩽10, >10–15, >15–20, >20–25 years, and overall, 5–25 years). The obstructive phenotype was defined as forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) z-score less than the lower limit of normal (LLN), whereas the restrictive phenotype was defined as FEV1/FVC z-score ⩾LLN, and FVC z-score Results: The prevalence of obstructive and restrictive phenotypes varied from 3.2–10.9% and 1.8–7.7%, respectively, without clear age trends. A diagnosis of asthma (adjusted odds ratio (aOR=2.55, 95% CI 2.14–3.04), preterm birth (aOR=1.84, 1.27–2.66), maternal smoking during pregnancy (aOR=1.16, 95% CI 1.01–1.35) and family history of asthma (aOR=1.44, 95% CI 1.25–1.66) were associated with a higher prevalence of obstructive, but not restrictive, phenotype across ages (5–25 years). A higher current body mass index (BMI was more often observed in those with the obstructive phenotype but less in those with the restrictive phenotype (aOR=1.05, 95% CI 1.03–1.06 and aOR=0.81, 95% CI 0.78–0.85, per kg·m−2 increase in BMI, respectively). Current smoking was associated with the obstructive phenotype in participants older than 10 years (aOR=1.24, 95% CI 1.05–1.46).Conclusion: Obstructive and restrictive phenotypes were found to be relatively prevalent during childhood, which supports the early origins concept. Several well-known respiratory risk factors were associated with the obstructive phenotype, whereas only low BMI was associated with the restrictive phenotype, suggesting different underlying pathobiology of these two phenotypes.
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| 47. |
- Waterhouse, Christopher C M, et al.
(författare)
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Secretory cell hyperplasia and defects in Notch activity in a mouse model of leukocyte adhesion deficiency type II
- 2010
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Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 138:3, s. 1079-1090.e5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND & AIMS:Leukocyte adhesion deficiency II (LAD II) is a rare condition caused by defective protein fucosylation, causing decreased leukocyte rolling, psychomotor retardation, and poor growth. The ligand-binding activity of Notch, a gastrointestinal signaling protein, depends on O-fucosylation. We investigated Notch signaling and intestinal epithelial architecture in a mouse model of LAD II.METHODS:Mice lacking 3,5-epimerase/4-reductase (FX) or FX(-/-) bone marrow chimeras (with either wild-type or FX(-/-) bone marrow) were maintained on a fucose-free diet. Intestinal secretory epithelial cells were quantified by histology and immunohistochemistry. Reverse transcription-polymerase chain reaction and immunoblot analyses were used to detect Notch-regulated genes in isolated crypt epithelium. Intestinal leukocyte-endothelial interaction was quantified by intravital microscopy. The intestinal epithelium of 2-week-old FX(-/-) mice was transfected with an adenoviral vector expressing a constitutively active form of Notch.RESULTS: FX(-/-) mice rapidly exhibited secretory epithelial cell hyperplasia, reduced cell proliferation, and altered epithelial gene expression patterns consistent with reduced Notch signaling. These effects were reversed when mice were given dietary fucose or by adenoviral transfection of the intestinal epithelium with the Notch intracellular domain.CONCLUSIONS: In a mouse model of LAD II, secretory cell hyperplasia occurs in the small intestine and colon; these effects depend on Notch signaling. Defects in Notch signaling might therefore be involved in the pathogenesis of this rare pediatric condition.
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| 48. |
- Wennberg, Patrik, 1972-, et al.
(författare)
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Haemostatic and inflammatory markers are independently associated with a first-ever myocardial infarction in men and women
- 2012
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Ingår i: Thrombosis Research. - : Elsevier BV. - 0049-3848 .- 1879-2472. ; 129:1, s. 68-73
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Previous studies have shown that plasma levels of haemostatic and inflammatory markers are associated with risk of coronary heart disease (CHD). As haemostatic markers are also acute-phase reactants, it is not clear if their association with CHD is independent of inflammatory markers and established cardiovascular risk factors.Materials and Methods: We used a prospective incident case-control study design nested in two cohorts from Sweden. Baseline measurements of a panel of cardiovascular risk factors and eight established markers of haemostasis or inflammation were assessed in 469 first-ever myocardial infarction (MI) cases and 895 matched controls.Results: After adjustment for baseline values of established risk factors, von Willebrand factor appeared to have the strongest association with MI among the haemostatic markers assayed, with an odds ratio of 2.52 (95% CI, 1.72-3.67) for a comparison of individuals in extreme thirds of baseline levels. For a similar comparison, after adjustment for established risk factors and haemostatic markers, odds ratios for IL-6 and CRP were 1.67 (95% CI, 1.08-2.60) and 1.58 (95% CI, 1.03-2.41), respectively. The relative predictive ability of the individual markers over and above established risk factors was modest according to comparisons of Area under the Receiver Operating Characteristic (AUROC) curves. However, when all eight markers were combined in a single model, the AUROC curve was significantly increased to 0.820 (95% CI, 0.795-0.846) compared to 0.762 (95% CI, 0.732-0.791) for established risk factors only.Conclusions: These findings suggest that haemostasis and inflammation have at least partially separate roles in risk of myocardial infarction.
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| 49. |
- Wennberg, Patrik, et al.
(författare)
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Haemostatic and inflammatory markers are independently associated with myocardial infarction in men and women
- 2012
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Ingår i: Thrombosis Research. - : Elsevier BV. - 0049-3848 .- 1879-2472. ; 129:1, s. 68-73
-
Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Previous studies have shown that plasma levels of haemostatic and inflammatory markers are associated with risk of coronary heart disease (CHD). As haemostatic markers are also acute-phase reactants, it is not clear if their association with CHD is independent of inflammatory markers and established cardiovascular risk factors.MATERIALS AND METHODS: We used a prospective incident case-control study design nested in two cohorts from Sweden. Baseline measurements of a panel of cardiovascular risk factors and eight established markers of haemostasis or inflammation were assessed in 469 first-ever myocardial infarction (MI) cases and 895 matched controls.RESULTS: After adjustment for baseline values of established risk factors, von Willebrand factor appeared to have the strongest association with MI among the haemostatic markers assayed, with an odds ratio of 2.52 (95% CI, 1.72-3.67) for a comparison of individuals in extreme thirds of baseline levels. For a similar comparison, after adjustment for established risk factors and haemostatic markers, odds ratios for IL-6 and CRP were 1.67 (95% CI, 1.08-2.60) and 1.58 (95% CI, 1.03-2.41), respectively. The relative predictive ability of the individual markers over and above established risk factors was modest according to comparisons of Area under the Receiver Operating Characteristic (AUROC) curves. However, when all eight markers were combined in a single model, the AUROC curve was significantly increased to 0.820 (95% CI, 0.795-0.846) compared to 0.762 (95% CI, 0.732-0.791) for established risk factors only.CONCLUSIONS: These findings suggest that haemostasis and inflammation have at least partially separate roles in risk of myocardial infarction.
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