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1.
  • Clark, Andrew G., et al. (författare)
  • Evolution of genes and genomes on the Drosophila phylogeny
  • 2007
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
  • Tidskriftsartikel (refereegranskat)abstract
    • Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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2.
  • Craddock, Nick, et al. (författare)
  • Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
  • 2010
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
  • Tidskriftsartikel (refereegranskat)abstract
    • Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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3.
  • Lindblad-Toh, Kerstin, et al. (författare)
  • Genome sequence, comparative analysis and haplotype structure of the domestic dog.
  • 2005
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
  • Tidskriftsartikel (refereegranskat)abstract
    • Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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4.
  • Stuchbery, Andrew, et al. (författare)
  • Calibration of Recoil-In-Vacuum attenuations from first principles : comparison with recent experimental data on Fe isotopes
  • 2015
  • Ingår i: Hyperfine Interactions. - : Springer. - 0304-3843 .- 1572-9540. ; 230:1, s. 169-174
  • Tidskriftsartikel (refereegranskat)abstract
    • Precession of aligned nuclear spin systems in ions recoiling from the target into vacuum (RIV) with consequent attenuation of angular distributions of emitted radiation is, in principle, a versatile method for measurement of g-factors of nuclear excited states of lifetimes in the pico-second range (Stone et al., Phys. Rev. Lett., 94, 192501, 2005 and Stuchbery and Stone, Phys. Rev. C, 76, 034307, 2007). Calibration of the observed attenuations has been achieved in favourable cases through comparison with measurements on states having previously known g-factors and lifetimes. The general lack of suitable states with known g-factors has limited application of the RIV method. This paper concerns the present status of efforts to describe the states of excited ions recoiling into vacuum in detail so that the average interaction can be estimated with useful precision from a-priori theory. The calculations use the GRASP2K package (Froese-Fischer et al. 1997 and Jonsson, Comp. Phys. Comm., 177, 597, 2007 & 184, 2197, 2013) to obtain, for each recoiling ion change state, the individual possible electronic states, their configurations, lifetimes and hyperfine interactions. It is assumed that all possible ionic states are produced, up to a chosen excitation energy. This energy is selected to approximate the energy at which all states have lifetimes far shorter than the nuclear state of interest. It is further assumed that the ionic state total electron angular momenta are randomly oriented in space. The first estimates of the average attenuation of emission distributions, as a function of the product g τ of the nuclear state g-factor and mean lifetime, used an averaged precession frequency obtained neglecting transitions between electronic states. Improved calculations, which include such transitions, are described.
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5.
  • Niemi, MEK, et al. (författare)
  • 2021
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6.
  • Kanai, M, et al. (författare)
  • 2023
  • swepub:Mat__t
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7.
  • Birney, Ewan, et al. (författare)
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  • 2007
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
  • 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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8.
  • Kun-Rodrigues, Celia, et al. (författare)
  • A comprehensive screening of copy number variability in dementia with Lewy bodies.
  • 2019
  • Ingår i: Neurobiology of aging. - : Elsevier BV. - 1558-1497 .- 0197-4580. ; 75
  • Tidskriftsartikel (refereegranskat)abstract
    • The role of genetic variability in dementia with Lewy bodies (DLB) is now indisputable; however, data regarding copy number variation (CNV) in this disease has been lacking. Here, we used whole-genome genotyping of 1454 DLB cases and 1525 controls to assess copy number variability. We used 2 algorithms to confidently detect CNVs, performed a case-control association analysis, screened for candidate CNVs previously associated with DLB-related diseases, and performed a candidate gene approach to fully explore the data. We identified 5 CNV regions with a significant genome-wide association to DLB; 2 of these were only present in cases and absent from publicly available databases: one of the regions overlapped LAPTM4B, a known lysosomal protein, whereas the other overlapped the NME1 locus and SPAG9. We also identified DLB cases presenting rare CNVs in genes previously associated with DLB or related neurodegenerative diseases, such as SNCA, APP, and MAPT. To our knowledge, this is the first study reporting genome-wide CNVs in a large DLB cohort. These results provide preliminary evidence for the contribution of CNVs in DLB risk.
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9.
  • Kun-Rodrigues, Celia, et al. (författare)
  • Analysis of C9orf72 repeat expansions in a large international cohort of dementia with Lewy bodies
  • 2017
  • Ingår i: Neurobiology of Aging. - : Elsevier BV. - 0197-4580 .- 1558-1497. ; 49
  • Tidskriftsartikel (refereegranskat)abstract
    • . C9orf72 repeat expansions are a common cause of amyotrophic lateral sclerosis and frontotemporal dementia. To date, no large-scale study of dementia with Lewy bodies (DLB) has been undertaken to assess the role of . C9orf72 repeat expansions in the disease. Here, we investigated the prevalence of . C9orf72 repeat expansions in a large cohort of DLB cases and identified no pathogenic repeat expansions in neuropathologically or clinically defined cases, showing that . C9orf72 repeat expansions are not causally associated with DLB.
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11.
  • Nicolas, Aude, et al. (författare)
  • Genome-wide Analyses Identify KIF5A as a Novel ALS Gene
  • 2018
  • Ingår i: Neuron. - : Cell Press. - 0896-6273 .- 1097-4199. ; 97:6, s. 1268-1283.e6
  • Tidskriftsartikel (refereegranskat)abstract
    • To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.
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15.
  • Bartling, Andrew W., et al. (författare)
  • Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionation
  • 2021
  • Ingår i: Energy & Environmental Science. - : Royal Society of Chemistry (RSC). - 1754-5692 .- 1754-5706. ; 14:8, s. 4147-4168
  • Tidskriftsartikel (refereegranskat)abstract
    • Reductive catalytic fractionation (RCF) is a promising approach to fractionate lignocellulose and convert lignin to a narrow product slate. To guide research towards commercialization, cost and sustainability must be considered. Here we report a techno-economic analysis (TEA), life cycle assessment (LCA), and air emission analysis of the RCF process, wherein biomass carbohydrates are converted to ethanol and the RCF oil is the lignin-derived product. The base-case process, using a feedstock supply of 2000 dry metric tons per day, methanol as a solvent, and H-2 gas as a hydrogen source, predicts a minimum selling price (MSP) of crude RCF oil of $1.13 per kg when ethanol is sold at $2.50 per gallon of gasoline-equivalent ($0.66 per liter of gasoline-equivalent). We estimate that the RCF process accounts for 57% of biorefinery installed capital costs, 77% of positive life cycle global warming potential (GWP) (excluding carbon uptake), and 43% of positive cumulative energy demand (CED). Of $563.7 MM total installed capital costs, the RCF area accounts for $323.5 MM, driven by high-pressure reactors. Solvent recycle and water removal via distillation incur a process heat demand equivalent to 73% of the biomass energy content, and accounts for 35% of total operating costs. In contrast, H-2 cost and catalyst recycle are relatively minor contributors to operating costs and environmental impacts. In the carbohydrate-rich pulps, polysaccharide retention is predicted not to substantially affect the RCF oil MSP. Analysis of cases using different solvents and hemicellulose as an in situ hydrogen donor reveals that reducing reactor pressure and the use of low vapor pressure solvents could reduce both capital costs and environmental impacts. Processes that reduce the energy demand for solvent separation also improve GWP, CED, and air emissions. Additionally, despite requiring natural gas imports, converting lignin as a biorefinery co-product could significantly reduce non-greenhouse gas air emissions compared to burning lignin. Overall, this study suggests that research should prioritize ways to lower RCF operating pressure to reduce capital expenses associated with high-pressure reactors, minimize solvent loading to reduce reactor size and energy required for solvent recovery, implement condensed-phase separations for solvent recovery, and utilize the entirety of RCF oil to maximize value-added product revenues.
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16.
  • Björklund, Patrik, et al. (författare)
  • Västerås slott : Slott och borgar
  • 2000
  • Rapport (populärvet., debatt m.m.)abstract
    • En majoritet av dagens byggnadsuppgifter gäller att hantera det redan byggda. När vi står inför situationen att restaurera en befintlig byggnad är det viktigt att förstå olika tidsperioders stilideal liksom byggnadsteknik och material. Först då kan vi göra en väl avvägd analys, som tar tillvara och utvecklar de kvaliteter som byggnaderna själva besitter. Därför är utbildningen upplagd som ett växelspel mellan föreläsningar, seminarier, exkursioner och en för året vald studieuppgift.Slott och borgar har varit läsårets tema. Vi har valt att arbeta med Västerås och Örebro slott - två ganska bortglömda Vasaslott som är väl värda att lyfta fram. Särskilt har vi studerat de senaste 300 årens förändringar, som inte tidigare ägnats lika stora forskarmöda som medelitden och Vasatiden. I dessa två exempel finns en provkarta på estetiska, praktiska och tekniska ingrepp från Carl Hårlemans tid och fram till idag.Studierna har således omfattat både gestaltning, funktion och byggnadsteknik. Avsikten är att visa på kvaliteter i de omvandlingar och restaureringar som skett, men också att peka på problem och analysera olika möjligheter inför framtiden. Arbetet har skett i samarbete med Statens fastighetsverk och är tänkt att utgöra ett underlag till vårdprogram och framtida restaureringsinsatser. 
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17.
  • Critchley, William R., et al. (författare)
  • Non-ischemic Heart Preservation via Hypothermic Cardioplegic Perfusion Induces Immunodepletion of Donor Hearts Resulting in Diminished Graft Infiltration Following Transplantation
  • 2020
  • Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Introduction: Many donor organs contain significant leukocyte reservoirs which upon transplantation activate recipient leukocytes to initiate acute rejection. We aimed to assess whether non-ischemic heart preservation via ex vivo perfusion promotes immunodepletion and alters the inflammatory status of the donor organ prior to transplantation. Methods: Isolated porcine hearts underwent ex vivo hypothermic, cardioplegic perfusion for 8 h. Leukocyte populations were quantified in left ventricle samples by flow cytometry. Cell-free DNA, cytokines, and chemokines were quantified in the perfusate. Tissue integrity was profiled by targeted proteomics and a histological assessment was performed. Heterotopic transplants comparing ex vivo hypothermic preservation and static cold storage were utilized to assess graft infiltration as a solid clinical endpoint. Results: Ex vivo perfusion significantly immunodepleted myocardial tissue. The perfusate displayed a selective, pro-inflammatory cytokine/chemokine pattern dominated by IFN-γ. The tissue molecular profile was improved following perfusion by diminished expression of nine pro-apoptotic and six ischemia-associated proteins. Histologically, no evidence of tissue damage was observed and cardiac troponin I was low throughout perfusion. Cell-free DNA was detected, the source of which may be necrotic/apoptotic leukocytes. Post-transplant graft infiltration was markedly reduced in terms of both leucocyte distribution and intensity of foci. Conclusions: These findings demonstrate that ex vivo perfusion significantly reduced donor heart immunogenicity via loss of resident leukocytes. Despite the pro-inflammatory cytokine pattern observed, a pro-survival and reduced ischemia-related profile was observed, indicating an improvement in graft viability by perfusion. Diminished graft infiltration was observed in perfused hearts compared with those preserved by static cold storage following 48 h of transplantation.
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18.
  • Davies, Neil, et al. (författare)
  • The founding charter of the Genomic Observatories Network
  • 2014
  • Ingår i: GigaScience. - 2047-217X. ; 3:2
  • 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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19.
  • Dixon-Suen, Suzanne C, et al. (författare)
  • Physical activity, sedentary time and breast cancer risk : a Mendelian randomisation study
  • 2022
  • Ingår i: British Journal of Sports Medicine. - : BMJ Publishing Group Ltd. - 0306-3674 .- 1473-0480. ; 56:20, s. 1157-1170
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVES: Physical inactivity and sedentary behaviour are associated with higher breast cancer risk in observational studies, but ascribing causality is difficult. Mendelian randomisation (MR) assesses causality by simulating randomised trial groups using genotype. We assessed whether lifelong physical activity or sedentary time, assessed using genotype, may be causally associated with breast cancer risk overall, pre/post-menopause, and by case-groups defined by tumour characteristics.METHODS: We performed two-sample inverse-variance-weighted MR using individual-level Breast Cancer Association Consortium case-control data from 130 957 European-ancestry women (69 838 invasive cases), and published UK Biobank data (n=91 105-377 234). Genetic instruments were single nucleotide polymorphisms (SNPs) associated in UK Biobank with wrist-worn accelerometer-measured overall physical activity (nsnps=5) or sedentary time (nsnps=6), or accelerometer-measured (nsnps=1) or self-reported (nsnps=5) vigorous physical activity.RESULTS: Greater genetically-predicted overall activity was associated with lower breast cancer overall risk (OR=0.59; 95% confidence interval (CI) 0.42 to 0.83 per-standard deviation (SD;~8 milligravities acceleration)) and for most case-groups. Genetically-predicted vigorous activity was associated with lower risk of pre/perimenopausal breast cancer (OR=0.62; 95% CI 0.45 to 0.87,≥3 vs. 0 self-reported days/week), with consistent estimates for most case-groups. Greater genetically-predicted sedentary time was associated with higher hormone-receptor-negative tumour risk (OR=1.77; 95% CI 1.07 to 2.92 per-SD (~7% time spent sedentary)), with elevated estimates for most case-groups. Results were robust to sensitivity analyses examining pleiotropy (including weighted-median-MR, MR-Egger).CONCLUSION: Our study provides strong evidence that greater overall physical activity, greater vigorous activity, and lower sedentary time are likely to reduce breast cancer risk. More widespread adoption of active lifestyles may reduce the burden from the most common cancer in women.
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20.
  • Elmelid, Andrea, et al. (författare)
  • Depressive symptoms, anxiety and academic motivation in youth : Do schools and families make a difference?
  • 2015
  • Ingår i: Journal of Adolescence. - : Wiley. - 0140-1971 .- 1095-9254. ; 45, s. 174-182
  • Tidskriftsartikel (refereegranskat)abstract
    • This longitudinal study aimed to examine the association between depressive and anxiety symptoms and academic motivation by gender, and whether positive school and family factors would be associated with academic motivation, in spite of the presence of such symptoms. Study participants were predominantly economically disadvantaged youths aged 13-15 years in a Northeastern US urban public school system. The Social and Health Assessment (SAHA) served as the basis for a survey undertaken in 2003 and 2004 with information being used from students who participated at both time points (N = 643). Multiple linear regression analyses showed that depressive symptoms were negatively associated with academic motivation, while anxiety was positively related to academic motivation in both genders. Teacher support, school attachment and parental control were positively related to academic motivation even in the presence of internalizing problems. The negative association of depressive symptoms with academic motivation may be potentially decreased by attachment to school.
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21.
  • Feng, Kent Y, et al. (författare)
  • Association Between Serum Albumin and Outcomes in Heart Failure and Secondary Mitral Regurgitation: The COAPT Trial.
  • 2023
  • Ingår i: European journal of heart failure. - : Wiley. - 1879-0844 .- 1388-9842.
  • Tidskriftsartikel (refereegranskat)abstract
    • Low serum albumin levels are associated with poor prognosis in numerous chronic disease states but the relationship between albumin and outcomes in patients with heart failure (HF) and secondary mitral regurgitation (SMR) has not been described.The randomized COAPT trial evaluated the safety and effectiveness of transcatheter edge-to-edge repair (TEER) with the MitraClip plus guideline-directed medical therapy (GDMT) versus GDMT alone in patients with symptomatic HF and moderate-to-severe or severe SMR. Baseline serum albumin levels were measured at enrollment. Among 614 patients enrolled in COAPT, 559 (91.0%) had available baseline serum albumin levels (median 4.0 g/dL, IQR 3.7-4.2 g/dL). Patients with albumin <4.0 g/dL compared with ≥4.0 g/dL were older and more likely to have ischemic cardiomyopathy and a hospitalization within the year prior to enrollment. After multivariable adjustment, patients with albumin <4.0 g/dL had higher 4-year rates of all-cause death (63.7% vs. 47.6%; adjusted HR 1.34, 95% CI 1.02-1.74; p=0.032), but there were no significant differences in heart failure hospitalizations (HFH) or all-cause hospitalizations according to baseline serum albumin level. The relative effectiveness of TEER plus GDMT versus GDMT alone was consistent in patients with low and high albumin levels (Pinteraction = 0.19 and 0.35 for death and HFH, respectively).Low baseline serum albumin levels were independently associated with reduced 4-year survival in patients with HF and severe SMR enrolled in the COAPT trial, but not with HFH. Patients treated with TEER derived similarly robust reductions in both death and HFH regardless of baseline albumin level. This article is protected by copyright. All rights reserved.
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22.
  • Ferrari, Raffaele, et al. (författare)
  • Frontotemporal dementia and its subtypes: a genome-wide association study.
  • 2014
  • Ingår i: Lancet Neurology. - 1474-4465. ; 13:7, s. 686-699
  • Tidskriftsartikel (refereegranskat)abstract
    • Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72-have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder.
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23.
  • Gallagher, Michael D., et al. (författare)
  • TMEM106B is a genetic modifier of frontotemporal lobar degeneration with C9orf72 hexanucleotide repeat expansions
  • 2014
  • Ingår i: Acta Neuropathologica. - : Springer Science and Business Media LLC. - 0001-6322 .- 1432-0533. ; 127:3, s. 407-418
  • Tidskriftsartikel (refereegranskat)abstract
    • Hexanucleotide repeat expansions in chromosome 9 open reading frame 72 (C9orf72) have recently been linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis, and may be the most common genetic cause of both neurodegenerative diseases. Genetic variants at TMEM106B influence risk for the most common neuropathological subtype of FTLD, characterized by inclusions of TAR DNA-binding protein of 43 kDa (FTLD-TDP). Previous reports have shown that TMEM106B is a genetic modifier of FTLD-TDP caused by progranulin (GRN) mutations, with the major (risk) allele of rs1990622 associating with earlier age at onset of disease. Here, we report that rs1990622 genotype affects age at death in a single-site discovery cohort of FTLD patients with C9orf72 expansions (n = 14), with the major allele correlated with later age at death (p = 0.024). We replicate this modifier effect in a 30-site international neuropathological cohort of FTLD-TDP patients with C9orf72 expansions (n = 75), again finding that the major allele associates with later age at death (p = 0.016), as well as later age at onset (p = 0.019). In contrast, TMEM106B genotype does not affect age at onset or death in 241 FTLD-TDP cases negative for GRN mutations or C9orf72 expansions. Thus, TMEM106B is a genetic modifier of FTLD with C9orf72 expansions. Intriguingly, the genotype that confers increased risk for developing FTLD-TDP (major, or T, allele of rs1990622) is associated with later age at onset and death in C9orf72 expansion carriers, providing an example of sign epistasis in human neurodegenerative disease.
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24.
  • Gardner, Emma, et al. (författare)
  • Field boundary features can stabilise bee populations and the pollination of mass-flowering crops in rotational systems
  • 2021
  • Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 58:10, s. 2287-2304
  • Tidskriftsartikel (refereegranskat)abstract
    • Pollinators experience large spatiotemporal fluctuations in resource availability when mass-flowering crops are rotated with resource-poor cereal crops. Yet, few studies have considered the effect this has on pollinator population stability, nor how this might be mitigated to maintain consistent crop pollination services. We assess the potential of boundary features (standard narrow 1 m grassy margins, hedgerows and wide 4 m agri-environment margins) to support and stabilise pollinator populations and pollination service in agricultural landscapes under crop rotation. Assuming a 6-year rotation, we use a process-based pollinator model to predict yearly pollinator population size and in-crop visitation rates to oilseed rape and field bean across 117 study landscapes in England with varying amounts of boundary features. We model both ground-nesting bumblebees and solitary bees and compare the predictions including and excluding boundary features from the landscapes. Ground-nesting bumblebee populations, whose longer-lifetime colonies benefit from continuity of resources, were larger and more stable (relative to the no-features scenario) in landscapes with more boundary features. Ground-nesting solitary bee populations were also larger but not significantly more stable, except with the introduction of wide permanent agri-environment margins, due to their shorter lifetimes and shorter foraging/dispersal ranges. Crop visitation by ground-nesting bumblebees was greater and more stable in landscapes with more boundary features, partly due to increased colony growth prior to crop flowering. Time averaged crop visitation by ground-nesting solitary bees was slightly lower, due to females dividing their foraging time between boundary features and the crop. However, despite this, the minimum pollination service delivered was higher, due to the more stable delivery. Synthesis and applications. Field boundary features have an important role in stabilising pollinator populations and pollination service in rotational systems, although maintenance of larger semi-natural habitat patches may be more effective for stabilising less mobile solitary bee populations. We recommend using combinations of boundary features, accounting for pollinator range when spacing features/rotating crops, and synchronising boundary feature management with crop rotation to maximise their stabilising benefits.
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25.
  • Gardner, Emma, et al. (författare)
  • Reliably predicting pollinator abundance : Challenges of calibrating process-based ecological models
  • 2020
  • Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 11:12, s. 1673-1689
  • Tidskriftsartikel (refereegranskat)abstract
    • Pollination is a key ecosystem service for global agriculture but evidence of pollinator population declines is growing. Reliable spatial modelling of pollinator abundance is essential if we are to identify areas at risk of pollination service deficit and effectively target resources to support pollinator populations. Many models exist which predict pollinator abundance but few have been calibrated against observational data from multiple habitats to ensure their predictions are accurate. We selected the most advanced process-based pollinator abundance model available and calibrated it for bumblebees and solitary bees using survey data collected at 239 sites across Great Britain. We compared three versions of the model: one parameterised using estimates based on expert opinion, one where the parameters are calibrated using a purely data-driven approach and one where we allow the expert opinion estimates to inform the calibration process. All three model versions showed significant agreement with the survey data, demonstrating this model's potential to reliably map pollinator abundance. However, there were significant differences between the nesting/floral attractiveness scores obtained by the two calibration methods and from the original expert opinion scores. Our results highlight a key universal challenge of calibrating spatially explicit, process-based ecological models. Notably, the desire to reliably represent complex ecological processes in finely mapped landscapes necessarily generates a large number of parameters, which are challenging to calibrate with ecological and geographical data that are often noisy, biased, asynchronous and sometimes inaccurate. Purely data-driven calibration can therefore result in unrealistic parameter values, despite appearing to improve model-data agreement over initial expert opinion estimates. We therefore advocate a combined approach where data-driven calibration and expert opinion are integrated into an iterative Delphi-like process, which simultaneously combines model calibration and credibility assessment. This may provide the best opportunity to obtain realistic parameter estimates and reliable model predictions for ecological systems with expert knowledge gaps and patchy ecological data.
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26.
  • Gupta Löfving, Sandra, et al. (författare)
  • Community violence exposure and severe posttraumatic stress in suburban American youth : risk and protective factors
  • 2015
  • Ingår i: Social Psychiatry and Psychiatric Epidemiology. - : Springer Science and Business Media LLC. - 0933-7954 .- 1433-9285. ; 50:4, s. 539-547
  • Tidskriftsartikel (refereegranskat)abstract
    • Purpose: The psychological effects of community violence exposure among inner-city youth are severe, yet little is known about its prevalence and moderators among suburban middle-class youth. This study aimed to assess the prevalence of community violence exposure among suburban American youth, to examine associated posttraumatic stress and to evaluate factors related to severe vs. less severe posttraumatic stress, such as co-existing internalizing and externalizing problems, as well as the effects of teacher support, parental warmth and support, perceived neighborhood safety and conventional involvement in this context. Method: Data were collected from 780 suburban, predominantly Caucasian middle-class high-school adolescents in the Northeastern US during the Social and Health Assessment (SAHA) study. Results: A substantial number of suburban youth were exposed to community violence and 24 % of those victimized by community violence developed severe posttraumatic stress. Depressive symptoms were strongly associated with higher levels and perceived teacher support with lower levels of posttraumatic stress. Conclusion: Similar to urban youth, youth living in suburban areas in North American settings may be affected by community violence. A substantial proportion of these youth reports severe posttraumatic stress and high levels of comorbid depressive symptoms. Teacher support may have a protective effect against severe posttraumatic stress and thus needs to be further assessed as a potential factor that can be used to mitigate the detrimental effects of violence exposure.
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27.
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28.
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29.
  • Harris, Valerie M., et al. (författare)
  • Klinefelters syndrome (47,XXY) is in excess among men with Sjogrens syndrome
  • 2016
  • Ingår i: Clinical Immunology. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 1521-6616 .- 1521-7035. ; 168, s. 25-29
  • Tidskriftsartikel (refereegranskat)abstract
    • Primary Sjogrens syndrome (pSS) has a strong female bias. We evaluated an X chromosome dose effect by analyzing 47,XXY (Klinefelters syndrome, 1 in 500 live male births) among subjects with pSS. 47,XXY was determined by examination of fluorescence intensity of single nucleotide polymorphisms from the X and Y chromosomes. Among 136 pSS men there were 4 with 47,XXY. This was significantly different from healthy controls (1 of 1254 had 47)0(Y, p = 0.0012 by Fishers exact test) as well men with rheumatoid arthritis (0 of 363 with 47,XXY), but not different compared to men with systemic lupus erythematosus (SLE) (4 of 136 versus 8 of 306, Fishers exact test p = NS). These results are consistent with the hypothesis that the number of X chromosomes is critical for the female bias of pSS, a property that may be shared with SLE but not RA. Published by Elsevier Inc.
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30.
  • Hinkley, Sasha, et al. (författare)
  • The JWST Early Release Science Program for the Direct Imaging and Spectroscopy of Exoplanetary Systems
  • 2022
  • Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1039
  • Tidskriftsartikel (refereegranskat)abstract
    • The direct characterization of exoplanetary systems with high-contrast imaging is among the highest priorities for the broader exoplanet community. As large space missions will be necessary for detecting and characterizing exo-Earth twins, developing the techniques and technology for direct imaging of exoplanets is a driving focus for the community. For the first time, JWST will directly observe extrasolar planets at mid-infrared wavelengths beyond 5 μm, deliver detailed spectroscopy revealing much more precise chemical abundances and atmospheric conditions, and provide sensitivity to analogs of our solar system ice-giant planets at wide orbital separations, an entirely new class of exoplanet. However, in order to maximize the scientific output over the lifetime of the mission, an exquisite understanding of the instrumental performance of JWST is needed as early in the mission as possible. In this paper, we describe our 55 hr Early Release Science Program that will utilize all four JWST instruments to extend the characterization of planetary-mass companions to ∼15 μm as well as image a circumstellar disk in the mid-infrared with unprecedented sensitivity. Our program will also assess the performance of the observatory in the key modes expected to be commonly used for exoplanet direct imaging and spectroscopy, optimize data calibration and processing, and generate representative data sets that will enable a broad user base to effectively plan for general observing programs in future Cycles.
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31.
  • Image, Mike, et al. (författare)
  • Does agri-environment scheme participation in England increase pollinator populations and crop pollination services?
  • 2022
  • Ingår i: Agriculture, Ecosystems and Environment. - : Elsevier BV. - 0167-8809. ; 325
  • Tidskriftsartikel (refereegranskat)abstract
    • Agri-environment schemes are programmes where landholders enter into voluntary agreements (typically with governments) to manage agricultural land for environmental protection and nature conservation objectives. Previous work at local scale has shown that these features can provide additional floral and nesting resources to support wild pollinators, which may indirectly increase floral visitation to nearby crops. However, the effect of entire schemes on this important ecosystem service has never previously been studied at national scale. Focusing on four wild pollinator guilds (ground-nesting bumblebees, tree-nesting bumblebees, ground-nesting solitary bees, and cavity-nesting solitary bees), we used a state-of-the-art, process-based spatial model to examine the relationship between participation in agri-environment schemes across England during 2016 and the predicted abundances of these guilds and their visitation rates to four pollinator dependent crops (oilseed rape, field beans, orchard fruit and strawberries). Our modelling predicts that significant increases in national populations of ground-nesting bumblebees and ground-nesting solitary bees have occurred in response to the schemes. Lack of significant population increases for other guilds likely reflects specialist nesting resource requirements not well-catered for in schemes. We do not predict statistically significant increases in visitation to pollinator-dependent crops at national level as a result of scheme interventions but do predict some localised areas of significant increase in bumblebee visitation to crops flowering in late spring. Lack of any significant change in visitation to crops which flower outside this season is likely due to a combination of low provision of nesting resource relative to floral resource by scheme interventions and low overall participation in more intensively farmed landscapes. We recommend future schemes place greater importance on nesting resource provision alongside floral resource provision, better cater for the needs of specialised species and promote more contiguous patches of semi-natural habitat to better support solitary bee visitation.
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32.
  • Isaksson, Johan, et al. (författare)
  • Community Violence Exposure and Eating Disorder Symptoms among Belgian, Russian and US Adolescents : Cross-Country and Gender Perspectives.
  • 2023
  • Ingår i: Child Psychiatry and Human Development. - : Springer. - 0009-398X .- 1573-3327.
  • Tidskriftsartikel (refereegranskat)abstract
    • Community violence exposure (CVE) is one of the most common adverse childhood experiences worldwide. Despite this, its potential effect on disordered eating in adolescents from different cultures is underexplored. In the present cross-sectional study, self-reported data were collected from 9751 students (Mean age = 14.27) from Belgium, Russia and the US on CVE (witnessing violence and violence victimization), eating disorder (ED) symptoms (ED thoughts with associated compensatory behaviors), and comorbid symptoms of posttraumatic stress, depression and anxiety. Increased CVE (from no exposure to witnessing to victimization) was associated with more ED symptoms, and the associations remained significant after adjusting for comorbid conditions. The associations were similar for adolescents across the three countries. No gender differences were observed in the association between CVE and ED symptoms, even though girls in general reported more ED symptoms than boys. We conclude that CVE appears to be associated with ED symptoms in three culturally different samples of adolescents.
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33.
  • Isaksson, Johan, et al. (författare)
  • Risk and Protective Factors for Problematic Drinking in Early Adolescence : A Systematic Approach
  • 2020
  • Ingår i: Child Psychiatry and Human Development. - : Springer. - 0009-398X .- 1573-3327. ; 51:2, s. 231-238
  • Tidskriftsartikel (refereegranskat)abstract
    • Alcohol use during early adolescence is associated with other risk behaviors as well as future health problems. Within the design of a larger prospective research program, a cohort of U.S. inner-city sixth-grade students (N = 1573, mean age = 12.10) were assessed and reassessed in the seventh-grade. Self-reported information was obtained on problems related to alcohol, fixed markers of risk (e.g. sex, age, SES), individual and interpersonal factors (e.g. internalizing and externalizing symptoms) and contextual factors (e.g. substance availability). Alcohol-related problems in seventh grade were foremost predicted by individual and interpersonal factors in the sixth grade including depressive symptoms, conduct problems, a decreased perception of wrongdoing, and affiliation with delinquent peers. In addition, alcohol use in the sixth grade and being of Hispanic or White ethnicity was also associated with subsequent alcohol-related problems. Interventions should be directed towards assessing and treating individual risk factors such as depression and externalizing symptoms.
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34.
  • Isaksson, Johan, et al. (författare)
  • Risk Factors Associated with Alcohol Use in Early Adolescence among American Inner-City Youth : A Longitudinal Study
  • 2020
  • Ingår i: Substance Use & Misuse. - : Taylor & Francis Group. - 1082-6084 .- 1532-2491. ; 55:3, s. 358-366
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Early alcohol use is associated with an increased risk for later alcohol dependence, as well as social and mental health problems. In this study, we investigate the risk factors (internalizing and externalizing behaviors) associated with early alcohol consumption over a period of 1 year, and examine whether the association is sex-specific. Methods: U.S. inner-city adolescents (N = 1785, Mean age = 12.11) were assessed and reassessed in the sixth and seventh grades (Mean age = 13.10). Self-reported information was obtained on the lifetime level of alcohol consumption, internalizing (depression, anxiety and posttraumatic stress [PTS]), and externalizing behaviors (sensation seeking, conduct problems and affiliation with delinquent peers). Associations between the variables were examined using structural equation modeling (SEM). Results: In an adjusted SEM analysis drinking by the sixth grade was primarily associated with externalizing behaviors, whereas PTS was linked to lower levels of alcohol consumption. In addition, alcohol consumption and greater externalizing behaviors by the sixth grade predicted higher alcohol consumption by the seventh grade, whereas anxiety and African American ethnicity were associated with less alcohol consumption. No sex differences were found in the association between internalizing and externalizing behaviors and drinking. However, in the adjusted SEM analysis female sex predicted higher lifetime consumption by the seventh grade. Conclusion: Sensation seeking behavior, conduct problems and affiliation with delinquent peers should be regarded as risk factors and taken into consideration when planning prevention efforts in order to decrease alcohol use in early adolescence.
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35.
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36.
  • Jiang, X., et al. (författare)
  • Shared heritability and functional enrichment across six solid cancers
  • 2019
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (r(g) = 0.57, p = 4.6 x 10(-8)), breast and ovarian cancer (r(g) = 0.24, p = 7 x 10(-5)), breast and lung cancer (r(g) = 0.18, p = 1.5 x 10(-6)) and breast and colorectal cancer (r(g) = 0.15, p = 1.1 x 10(-4)). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.
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37.
  • Jung, Audrey Y, et al. (författare)
  • Distinct reproductive risk profiles for intrinsic-like breast cancer subtypes : pooled analysis of population-based studies
  • 2022
  • Ingår i: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 114:12, s. 1706-1719
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Reproductive factors have been shown to be differentially associated with risk of estrogen receptor (ER) positive and ER-negative breast cancer. However, their associations with intrinsic-like subtypes are less clear.METHODS: Analyses included up to 23,353 cases, and 71,072 controls pooled from 31 population-based case-control or cohort studies in the Breast Cancer Association Consortium across 16 countries on 4 continents. Polytomous logistic regression was used to estimate the association between reproductive factors and risk of breast cancer by intrinsic-like subtypes (luminal A-like, luminal B-like, luminal B-HER2-like, HER2-enriched-like, and triple-negative) and by invasiveness. All statistical tests were 2-sided.RESULTS: Compared to nulliparous women, parous women had a lower risk of luminal A-like, luminal B-like, luminal B-HER2-like and HER2-enriched-like disease. This association was apparent only after approximately 10 years since last birth and became stronger with increasing time (odds ratio [OR] = 0.59, 95% confidence interval [CI] = 0.49 to 0.71; and OR = 0.36, 95% CI = 0.28 to 0.46; for multiparous women with luminal A-like tumors 20-<25 years after last birth and 45-<50 years after last birth, respectively). In contrast, parous women had a higher risk of triple-negative breast cancer right after their last birth (for multiparous women: OR = 3.12, 95%CI = 2.02 to 4.83) that was attenuated with time but persisted for decades (OR = 1.03, 95%CI = 0.79 to 1.34, for multiparous women 25 to < 30 years after last birth). Older age at first birth (P-heterogeneity<.001 for triple-negative compared to luminal-A like) and breastfeeding (P-heterogeneity<.001 for triple-negative compared to luminal-A like) were associated with lower risk of triple-negative but not with other disease subtypes. Younger age at menarche was associated with higher risk of all subtypes; older age at menopause was associated with higher risk of luminal A-like but not triple-negative breast cancer. Associations for in situ tumors were similar to luminal A-like.CONCLUSION: This large and comprehensive study demonstrates a distinct reproductive risk factor profile for triple-negative breast cancer compared to other subtypes, with implications for the understanding of disease etiology and risk prediction.
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38.
  • Kapoor, Pooja Middha, et al. (författare)
  • Combined associations of a polygenic risk score and classical risk factors with breast cancer risk
  • 2021
  • Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 113:3, s. 329-337
  • Tidskriftsartikel (refereegranskat)abstract
    • We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer. 
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39.
  • Karlsson, Elisabeth, et al. (författare)
  • Risk and protective factors for peer victimization : a 1-year follow-up study of urban American students
  • 2014
  • Ingår i: European Child and Adolescent Psychiatry. - : Springer Science and Business Media LLC. - 1018-8827 .- 1435-165X. ; 23:9, s. 773-781
  • Tidskriftsartikel (refereegranskat)abstract
    • This study examined whether internalizing problems, parental warmth and teacher support were associated with adolescents' experience of future peer victimization in school. Data were drawn from two rounds of the longitudinal Social and Health Assessment (SAHA). Study subjects comprised 593 US urban adolescents (aged 13.8 +/- A 0.8 years; 56 % female). Results showed that there was a substantial degree of continuity in peer victimization over a 1-year period. The presence of internalizing (anxiety, depressive and somatic) symptoms at baseline was associated with an increased risk of peer victimization over time. Both parental warmth and teacher support were uniquely associated with a lower risk for peer victimization. Implications of these findings for prevention efforts are discussed.
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40.
  • Kong, Jeremy, et al. (författare)
  • Incidence, Predictors, and Outcomes Associated With Worsening Renal Function in Patients With Heart Failure and Secondary Mitral Regurgitation: The COAPT Trial.
  • 2023
  • Ingår i: Journal of the American Heart Association. - 2047-9980. ; 12:14
  • Tidskriftsartikel (refereegranskat)abstract
    • Background The incidence and implications of worsening renal function (WRF) after mitral valve transcatheter edge-to-edge repair (TEER) in patients with heart failure (HF) are unknown. Therefore, the aim of this study was to determine the proportion of patients with HF and secondary mitral regurgitation who develop persistent WRF within 30 days following TEER, and whether this development portends a worse prognosis. Methods and Results In the COAPT (Cardiovascular Outcomes Assessment of the MitraClip Percutaneous Therapy for Heart Failure Patients With Functional Mitral Regurgitation) trial, 614 patients with HF and severe secondary mitral regurgitation were randomized to TEER with the MitraClip plus guideline-directed medical therapy (GDMT) versus GDMT alone. WRF was defined as serum creatinine increase ≥1.5× or ≥0.3 mg/dL from baseline persisting to day 30 or requiring renal replacement therapy. All-cause death and HF hospitalization rates between 30 days and 2 years were compared in patients with and without WRF. WRF at 30 days was present in 11.3% of patients (9.7% in the TEER plus GDMT group and 13.1% in the GDMT alone group; P=0.23). WRF was associated with all-cause death (hazard ratio [HR], 1.98 [95% CI, 1.3-3.03]; P=0.001) but not HF hospitalization (HR, 1.47 [ 95% CI, 0.97-2.24]; P=0.07) between 30 days and 2 years. Compared with GDMT alone, TEER reduced both death and HF hospitalization consistently in patients with and without WRF (Pinteraction=0.53 and 0.57, respectively). Conclusions Among patients with HF and severe secondary mitral regurgitation, the incidence of WRF at 30 days was not increased after TEER compared with GDMT alone. WRF was associated with greater 2-year mortality but did not attenuate the treatment benefits of TEER in reducing death and HF hospitalization compared with GDMT alone. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT01626079.
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41.
  • Koposov, Roman, et al. (författare)
  • Community Violence Exposure and School Functioning in Youth : Cross-Country and Gender Perspectives
  • 2021
  • Ingår i: Frontiers In Public Health. - : Frontiers Media S.A.. - 2296-2565. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Many children and adolescents experience violent events which can be associated with negative consequences for their development, mental health, school, and social functioning. However, findings between settings and on the role of gender have been inconsistent. This study aimed to investigate cross-country and gender differences in the relationship between community violence exposure (CVE) and school functioning in a sample of youths from three countries. Methods: A self-report survey was conducted among school students (12-17 years old) in Belgium (Antwerp, N = 4,743), Russia (Arkhangelsk, N = 2,823), and the US (New Haven, N = 4,101). Students were recruited from within classes that were randomly selected from within schools that had themselves been randomly selected (excepting New Haven, where all students were included). CVE was assessed with the Screening Survey of Exposure to Community Violence. School functioning was assessed with four measures: the Perceived Teacher Support scale, Negative Classroom Environment scale, and Academic Motivation and Perception of Safety at School scales. Multivariate Analyses of Covariance were performed to assess differences in the levels of school-related problem behaviors in boys and girls, who reported different degrees of CVE. Results: Participants in all three countries reported a relatively high prevalence of violence exposure (36.2% in Belgium, 39.3% in Russia and 45.2% in the US who witnessed violence), with a higher proportion of girls than boys witnessing violent events (varied from 37.4 to 51.6% between the countries), whereas boys reported more episodes of victimization by violence than girls (varied from 32.3 to 49.9% between the countries). Youths who experienced increased CVE (from no exposure to witnessing to victimization) reported an increase in all school functioning problems in all of the countries and this association was not gender-specific. Conclusions: Our findings suggest that regardless of differences in the level of CVE by country and gender, violence exposure is negatively associated with school functioning across countries. Nonetheless, even though reactions to community violence among adolescents may be expressed in a similar fashion, cross-country differences in social support systems should also be taken into account in order to provide culturally sensitive treatment modalities.
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42.
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43.
  • Lessard, Christopher J., et al. (författare)
  • Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjogren's syndrome
  • 2013
  • Ingår i: Nature Genetics. - : NATURE PUBLISHING GROUP, 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA. - 1061-4036 .- 1546-1718. ; 45:11, s. 1284-
  • Tidskriftsartikel (refereegranskat)abstract
    • Sjogrens syndrome is a common autoimmune disease (affecting similar to 0.7% of European Americans) that typically presents as keratoconjunctivitis sicca and xerostomia. Here we report results of a large-scale association study of Sjogrens syndrome. In addition to strong association within the human leukocyte antigen (HLA) region at 6p21 (P-meta = 7.65 x 10(-114)), we establish associations with IRF5-TNPO3 (P-meta = 2.73 x 10(-19)), STAT4 (Pmeta = 6.80 x 10-15), IL12A (P-meta = 1.17 x 10(-10)), FAM167ABLK (P-meta = 4.97 x 10(-10)), DDX6-CXCR5 (P-meta = 1.10 x 10(-8)) and TNIP1 (P-meta = 3.30 x 10(-8)). We also observed suggestive associations (P-meta andlt; 5 x 10(-5)) with variants in 29 other regions, including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2 and PHIP, among others. These results highlight the importance of genes that are involved in both innate and adaptive immunity in Sjogrens syndrome.
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44.
  • Li, He, et al. (författare)
  • Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons
  • 2017
  • Ingår i: PLOS Genetics. - : PUBLIC LIBRARY SCIENCE. - 1553-7390 .- 1553-7404. ; 13:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Sjogren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study. Multiple cis-eQTLs were associated with transcript levels of 2'-5'-oligoadenylate synthetase 1 (OAS1) peaking at rs10774671 (PeQTL = 6.05 x 10(-14)). Association of rs10774671 with SS susceptibility was identified and confirmed through meta-analysis of two independent cohorts (P-meta = 2.59 x 10(-9); odds ratio = 0.75; 95% confidence interval = 0.66-0.86). The risk allele of rs10774671 shifts splicing of OAS1 from production of the p46 isoform to multiple alternative transcripts, including p42, p48, and p44. We found that the isoforms were differentially expressed within each genotype in controls and patients with and without autoantibodies. Furthermore, our results showed that the three alternatively spliced isoforms lacked translational response to type I IFN stimulation. The p48 and p44 isoforms also had impaired protein expression governed by the 3' end of the transcripts. The SS risk allele of rs10774671 has been shown by others to be associated with reduced OAS1 enzymatic activity and ability to clear viral infections, as well as reduced responsiveness to IFN treatment. Our results establish OAS1 as a risk locus for SS and support a potential role for defective viral clearance due to altered IFN response as a genetic pathophysiological basis of this complex autoimmune disease.
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45.
  • Liu, Ke, et al. (författare)
  • X Chromosome Dose and Sex Bias in Autoimmune Diseases
  • 2016
  • Ingår i: Arthritis & Rheumatology. - : WILEY-BLACKWELL. - 2326-5191 .- 2326-5205. ; 68:5, s. 1290-1300
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective. More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47, XXX; occurring in similar to 1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjogrens syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls. Methods. All subjects in this study were female. We identified subjects with 47, XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47, XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction. Results. We found 47, XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67-86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18-123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47, XXX. There was an excess of 47, XXX among SLE and SS patients. Conclusion. The estimated prevalence of SLE and SS in women with 47, XXX was similar to 2.5 and similar to 2.9 times higher, respectively, than that in women with 46, XX and similar to 25 and similar to 41 times higher, respectively, than that in men with 46, XY. No statistically significant increase of 47, XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity.
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46.
  • Liu, Ke, et al. (författare)
  • X Chromosome Dose and Sex Bias in Autoimmune Diseases : Increased 47,XXX in Systemic Lupus Erythematosus and Sjögren's Syndrome
  • 2016
  • Ingår i: Arthritis & Rheumatology. - : Wiley. - 2326-5191 .- 2326-5205. ; 68:5, s. 1290-1300
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE:More than 80% of autoimmune disease is female dominant, but the mechanism for this female bias is poorly understood. We suspected an X chromosome dose effect and hypothesized that trisomy X (47,XXX, 1 in ∼1,000 live female births) would be increased in female predominant diseases (e.g. systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis [PBC] and rheumatoid arthritis [RA]) compared to diseases without female predominance (sarcoidosis) and controls.METHODS:We identified 47,XXX subjects using aggregate data from single nucleotide polymorphism (SNP) arrays and confirmed, when possible, by fluorescent in situ hybridization (FISH) or quantitative polymerase chain reaction (q-PCR).RESULTS:We found 47,XXX in seven of 2,826 SLE and three of 1,033 SS female patients, but only in two of the 7,074 female controls (p=0.003, OR=8.78, 95% CI: 1.67-86.79 and p=0.02, OR=10.29, 95% CI: 1.18-123.47; respectively). One 47,XXX subject was present for ∼404 SLE women and ∼344 SS women. 47,XXX was present in excess among SLE and SS subjects.CONCLUSION:The estimated prevalence of SLE and SS in women with 47,XXX was respectively ∼2.5 and ∼2.9 times higher than in 46,XX women and ∼25 and ∼41 times higher than in 46,XY men. No statistically significant increase of 47,XXX was observed in other female-biased diseases (PBC or RA), supporting the idea of multiple pathways to sex bias in autoimmunity. This article is protected by copyright. All rights reserved.
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47.
  • Major, Triin, et al. (författare)
  • Pro-IL-1β Is an Early Prognostic Indicator of Severe Donor Lung Injury During Ex Vivo Lung Perfusion
  • 2021
  • Ingår i: Transplantation. - 1534-6080. ; 105:4, s. 768-774
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Ex vivo lung perfusion (EVLP) is used to evaluate and recondition extended criteria donor lungs for transplantation. Interleukin-1β (IL-1β) has been identified as a prognostic indicator of nonrecovery during EVLP. This may be an effect of inflammasome activation or cellular necrosis following donation and graft preservation. Delineating the mechanism of IL-1β release is required. METHODS: The inactive intracellular precursor molecule, pro-IL-1β, was characterized along with the pro-IL-1β processing enzyme, caspase-1, in the perfusate of n = 20 human lungs that had undergone EVLP (n = 10 lungs that failed to recover and were discarded versus n = 10 lungs that reconditioned and were transplanted). In an experimental porcine model, n = 8 lungs underwent EVLP and were randomized to receive either a specific NLRP3 inflammasome inhibitor or control. RESULTS: Significant increases in pro-IL-1β and caspase-1 were observed in the perfusate from human lungs that did not recondition during EVLP compared with those that successfully reconditioned and were used for transplantation. Within the porcine EVLP, NLRP3 inflammasome inhibition reduced IL-1β within the perfusate compared with controls, but this had no impact on lung function, hemodynamics, or inflammation. CONCLUSIONS: Our data suggest that pro-IL-1β is passively released following cellular necrosis of the donor lung.
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48.
  • Manzoni, Claudia, et al. (författare)
  • Genome-wide analyses reveal a potential role for the MAPT, MOBP, and APOE loci in sporadic frontotemporal dementia
  • 2024
  • Ingår i: American Journal of Human Genetics. - 0002-9297. ; 111:7, s. 1316-1329
  • Tidskriftsartikel (refereegranskat)abstract
    • Frontotemporal dementia (FTD) is the second most common cause of early-onset dementia after Alzheimer disease (AD). Efforts in the field mainly focus on familial forms of disease (fFTDs), while studies of the genetic etiology of sporadic FTD (sFTD) have been less common. In the current work, we analyzed 4,685 sFTD cases and 15,308 controls looking for common genetic determinants for sFTD. We found a cluster of variants at the MAPT (rs199443; p = 2.5 × 10−12, OR = 1.27) and APOE (rs6857; p = 1.31 × 10−12, OR = 1.27) loci and a candidate locus on chromosome 3 (rs1009966; p = 2.41 × 10−8, OR = 1.16) in the intergenic region between RPSA and MOBP, contributing to increased risk for sFTD through effects on expression and/or splicing in brain cortex of functionally relevant in-cis genes at the MAPT and RPSA-MOBP loci. The association with the MAPT (H1c clade) and RPSA-MOBP loci may suggest common genetic pleiotropy across FTD and progressive supranuclear palsy (PSP) (MAPT and RPSA-MOBP loci) and across FTD, AD, Parkinson disease (PD), and cortico-basal degeneration (CBD) (MAPT locus). Our data also suggest population specificity of the risk signals, with MAPT and APOE loci associations mainly driven by Central/Nordic and Mediterranean Europeans, respectively. This study lays the foundations for future work aimed at further characterizing population-specific features of potential FTD-discriminant APOE haplotype(s) and the functional involvement and contribution of the MAPT H1c haplotype and RPSA-MOBP loci to pathogenesis of sporadic forms of FTD in brain cortex.
  •  
49.
  • Pinese, Mark, et al. (författare)
  • The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
  • 2020
  • Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing. Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.
  •  
50.
  • Porth, Oliver, et al. (författare)
  • The Event Horizon General Relativistic Magnetohydrodynamic Code Comparison Project
  • 2019
  • Ingår i: Astrophysical Journal, Supplement Series. - : American Astronomical Society. - 1538-4365 .- 0067-0049. ; 243:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent developments in compact object astrophysics, especially the discovery of merging neutron stars by LIGO, the imaging of the black hole in M87 by the Event Horizon Telescope, and high- precision astrometry of the Galactic Center at close to the event horizon scale by the GRAVITY experiment motivate the development of numerical source models that solve the equations of general relativistic magnetohydrodynamics (GRMHD). Here we compare GRMHD solutions for the evolution of a magnetized accretion flow where turbulence is promoted by the magnetorotational instability from a set of nine GRMHD codes: Athena++, BHAC, Cosmos++, ECHO, H-AMR, iharm3D, HARM-Noble, IllinoisGRMHD, and KORAL. Agreement among the codes improves as resolution increases, as measured by a consistently applied, specially developed set of code performance metrics. We conclude that the community of GRMHD codes is mature, capable, and consistent on these test problems.
  •  
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