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1.
  • Marschall, Tobias, et al. (author)
  • Computational pan-genomics : status, promises and challenges
  • 2018
  • In: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 19:1, s. 118-135
  • Journal article (peer-reviewed)abstract
    • Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
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2.
  • Stanaway, Jeffrey D., et al. (author)
  • Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
  • 2018
  • In: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
  • Journal article (peer-reviewed)abstract
    • Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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3.
  • Su, Zhan, et al. (author)
  • Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
  • 2012
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:10
  • Journal article (peer-reviewed)abstract
    • Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (Pcombined=4.09×10(-9); odds ratio (OR)=1.21, 95% confidence interval (CI)=1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (Pcombined=2.74×10(-10); OR=1.14, 95% CI=1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.
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4.
  • Abel, I, et al. (author)
  • Overview of the JET results with the ITER-like wall
  • 2013
  • In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10, s. 104002-
  • Journal article (peer-reviewed)abstract
    • Following the completion in May 2011 of the shutdown for the installation of the beryllium wall and the tungsten divertor, the first set of JET campaigns have addressed the investigation of the retention properties and the development of operational scenarios with the new plasma-facing materials. The large reduction in the carbon content (more than a factor ten) led to a much lower Z(eff) (1.2-1.4) during L- and H-mode plasmas, and radiation during the burn-through phase of the plasma initiation with the consequence that breakdown failures are almost absent. Gas balance experiments have shown that the fuel retention rate with the new wall is substantially reduced with respect to the C wall. The re-establishment of the baseline H-mode and hybrid scenarios compatible with the new wall has required an optimization of the control of metallic impurity sources and heat loads. Stable type-I ELMy H-mode regimes with H-98,H-y2 close to 1 and beta(N) similar to 1.6 have been achieved using gas injection. ELM frequency is a key factor for the control of the metallic impurity accumulation. Pedestal temperatures tend to be lower with the new wall, leading to reduced confinement, but nitrogen seeding restores high pedestal temperatures and confinement. Compared with the carbon wall, major disruptions with the new wall show a lower radiated power and a slower current quench. The higher heat loads on Be wall plasma-facing components due to lower radiation made the routine use of massive gas injection for disruption mitigation essential.
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5.
  • Berndt, Sonja I., et al. (author)
  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
  • 2013
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
  • Journal article (peer-reviewed)abstract
    • Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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6.
  • Furberg, Helena, et al. (author)
  • Genome-wide meta-analyses identify multiple loci associated with smoking behavior
  • 2010
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:5, s. 134-441
  • Journal article (peer-reviewed)abstract
    • Consistent but indirect evidence has implicated genetic factors in smoking behavior1,2. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology (ENGAGE) and Oxford-GlaxoSmithKline (Ox-GSK) consortia to follow up the 15 most significant regions (n > 140,000). We identified three loci associated with number of cigarettes smoked per day. The strongest association was a synonymous 15q25 SNP in the nicotinic receptor gene CHRNA3 (rs1051730[A], b = 1.03, standard error (s.e.) = 0.053, beta = 2.8 x 10(-73)). Two 10q25 SNPs (rs1329650[G], b = 0.367, s. e. = 0.059, beta = 5.7 x 10(-10); and rs1028936[A], b = 0.446, s. e. = 0.074, beta = 1.3 x 10(-9)) and one 9q13 SNP in EGLN2 (rs3733829[G], b = 0.333, s. e. = 0.058, P = 1.0 x 10(-8)) also exceeded genome-wide significance for cigarettes per day. For smoking initiation, eight SNPs exceeded genome-wide significance, with the strongest association at a nonsynonymous SNP in BDNF on chromosome 11 (rs6265[C], odds ratio (OR) = 1.06, 95% confidence interval (Cl) 1.04-1.08, P = 1.8 x 10(-8)). One SNP located near DBH on chromosome 9 (rs3025343[G], OR = 1.12, 95% Cl 1.08-1.18, P = 3.6 x 10(-8)) was significantly associated with smoking cessation.
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7.
  • Lango Allen, Hana, et al. (author)
  • Hundreds of variants clustered in genomic loci and biological pathways affect human height.
  • 2010
  • In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
  • Journal article (peer-reviewed)abstract
    • Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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8.
  • Lyons, Paul A, et al. (author)
  • Genetically Distinct Subsets within ANCA-Associated Vasculitis
  • 2012
  • In: New England Journal of Medicine. - : Massachusetts Medical Society. - 0028-4793 .- 1533-4406. ; 367:3, s. 214-223
  • Journal article (peer-reviewed)abstract
    • BACKGROUND less thanbrgreater than less thanbrgreater thanAntineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegeners granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. less thanbrgreater than less thanbrgreater thanMETHODS less thanbrgreater than less thanbrgreater thanA genomewide association study was performed in a discovery cohort of 1233 U. K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. less thanbrgreater than less thanbrgreater thanRESULTS less thanbrgreater than less thanbrgreater thanWe found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti-proteinase 3 ANCA was associated with HLA-DP and the genes encoding alpha(1)-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2x10(-89), P = 5.6x10(-12), and P = 2.6x10(-7), respectively). Anti-myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1x10(-8)). less thanbrgreater than less thanbrgreater thanCONCLUSIONS less thanbrgreater than less thanbrgreater thanThis study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA-associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA-associated vasculitis and myeloperoxidase ANCA-associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.)
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9.
  • McCallum, Fiona J., et al. (author)
  • Differing rates of antibody acquisition to merozoite antigens in malaria : Implications for immunity and surveillance
  • 2017
  • In: Journal of Leukocyte Biology. - 0741-5400 .- 1938-3673. ; 101:4, s. 913-925
  • Journal article (peer-reviewed)abstract
    • Antibodies play a key role in acquired human immunity to Plasmodium falciparum (Pf) malaria and target merozoites to reduce or prevent blood-stage replication and the development of disease. Merozoites present a complex array of antigens to the immune system, and currently, there is only a partial understanding of the targets of protective antibodies and how responses to different antigens are acquired and boosted. We hypothesized that there would be differences in the rate of acquisition of antibodies to different antigens and how well they are boosted by infection, which impacts the acquisition of immunity. We examined responses to a range of merozoite antigens in 2 different cohorts of children and adults with different age structures and levels of malaria exposure. Overall, antibodies were associated with age, exposure, and active infection, and the repertoire of responses increased with age and active infection. However, rates of antibody acquisition varied between antigens and different regions within an antigen following exposure to malaria, supporting our hypothesis. Antigen-specific responses could be broadly classified into early response types in which antibodies were acquired early in childhood exposure and late response types that appear to require substantially more exposure for the development of substantial levels. We identified antigen-specific responses that were effectively boosted after recent infection, whereas other responses were not. These findings advance our understanding of the acquisition of human immunity to malaria and are relevant to the development of malaria vaccines targeting merozoite antigens and the selection of antigens for use in malaria surveillance.
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10.
  • Romanelli, F, et al. (author)
  • Overview of the JET results
  • 2011
  • In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 51:9
  • Journal article (peer-reviewed)abstract
    • Since the last IAEA Conference JET has been in operation for one year with a programmatic focus on the qualification of ITER operating scenarios, the consolidation of ITER design choices and preparation for plasma operation with the ITER-like wall presently being installed in JET. Good progress has been achieved, including stationary ELMy H-mode operation at 4.5 MA. The high confinement hybrid scenario has been extended to high triangularity, lower ρ*and to pulse lengths comparable to the resistive time. The steady-state scenario has also been extended to lower ρ*and ν*and optimized to simultaneously achieve, under stationary conditions, ITER-like values of all other relevant normalized parameters. A dedicated helium campaign has allowed key aspects of plasma control and H-mode operation for the ITER non-activated phase to be evaluated. Effective sawtooth control by fast ions has been demonstrated with3He minority ICRH, a scenario with negligible minority current drive. Edge localized mode (ELM) control studies using external n = 1 and n = 2 perturbation fields have found a resonance effect in ELM frequency for specific q95values. Complete ELM suppression has, however, not been observed, even with an edge Chirikov parameter larger than 1. Pellet ELM pacing has been demonstrated and the minimum pellet size needed to trigger an ELM has been estimated. For both natural and mitigated ELMs a broadening of the divertor ELM-wetted area with increasing ELM size has been found. In disruption studies with massive gas injection up to 50% of the thermal energy could be radiated before, and 20% during, the thermal quench. Halo currents could be reduced by 60% and, using argon/deuterium and neon/deuterium gas mixtures, runaway electron generation could be avoided. Most objectives of the ITER-like ICRH antenna have been demonstrated; matching with closely packed straps, ELM resilience, scattering matrix arc detection and operation at high power density (6.2 MW m-2) and antenna strap voltages (42 kV). Coupling measurements are in very good agreement with TOPICA modelling. © 2011 IAEA, Vienna.
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11.
  • Sanders, Luciana M., et al. (author)
  • Carbon accumulation in Amazonian floodplain lakes : A significant component of Amazon budgets?
  • 2017
  • In: Limnology and Oceanography Letters. - : Wiley. - 2378-2242. ; 2:1, s. 29-35
  • Journal article (peer-reviewed)abstract
    • The Amazon floodplains cover approximately 10% of the Amazon Basin and are composed of predominantly anoxic sediments that may store large amounts of carbon. Our study combines Pb-210 derived sedimentation rates from four recently analyzed sediment cores (n = 4) with previously published organic carbon (OC) burial estimates (n = 18) to provide a broad, first order estimate of carbon accumulation in Amazon floodplain lakes. The OC burial rates were 266 +/- 57 g C m(-2) yr(-1). This rate is several folds greater than those reported for lakes in arctic, boreal, temperate, and tropical regions. The large amount and spatial variation of OC burial rates in these floodplain lakes highlights the need for increased sampling efforts to better measure these potentially important components of the Amazon Basin carbon budget.
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12.
  • Speliotes, Elizabeth K., et al. (author)
  • Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
  • 2010
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 937-948
  • Journal article (peer-reviewed)abstract
    • Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ~2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10−8), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.
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14.
  • Astrup, Arne, et al. (author)
  • The role of reducing intakes of saturated fat in the prevention of cardiovascular disease : where does the evidence stand in 2010?
  • 2011
  • In: American Journal of Clinical Nutrition. - : Elsevier BV. - 0002-9165 .- 1938-3207. ; 93:4, s. 684-688
  • Journal article (peer-reviewed)abstract
    • Current dietary recommendations advise reducing the intake of saturated fatty acids (SFAs) to reduce coronary heart disease (CHD) risk, but recent findings question the role of SFAs. This expert panel reviewed the evidence and reached the following conclusions: the evidence from epidemiologic, clinical, and mechanistic studies is consistent in finding that the risk of CHD is reduced when SFAs are replaced with polyunsaturated fatty acids (PUFAs). In populations who consume a Western diet, the replacement of 1% of energy from SFAs with PUFAs lowers LDL cholesterol and is likely to produce a reduction in CHD incidence of >= 2-3%. No clear benefit of substituting carbohydrates for SFAs has been shown, although there might be a benefit if the carbohydrate is unrefined and has a low glycemic index. Insufficient evidence exists to judge the effect on CHD risk of replacing SFAs with MUFAs. No clear association between SFA intake relative to refined carbohydrates and the risk of insulin resistance and diabetes has been shown. The effect of diet on a single biomarker is insufficient evidence to assess CHD risk. The combination of multiple biomarkers and the use of clinical end-points could help substantiate the effects on CHD. Furthermore, the effect of particular foods on CHD cannot be predicted solely by their content of total SFAs because individual SFAs may have different cardiovascular effects and major SFA food sources contain other constituents that could influence CHD risk. Research is needed to clarify the role of SFAs compared with specific forms of carbohydrates in CHD risk and to compare specific foods with appropriate alternatives.
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15.
  • Block, Keith I., et al. (author)
  • Designing a broad-spectrum integrative approach for cancer prevention and treatment
  • 2015
  • In: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
  • Research review (peer-reviewed)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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16.
  • Bohn, Thomas, et al. (author)
  • GOALS-JWST: NIRCam and MIRI Imaging of the Circumnuclear Starburst Ring in NGC 7469
  • 2023
  • In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 942:2
  • Journal article (peer-reviewed)abstract
    • We present James Webb Space Telescope (JWST) imaging of NGC 7469 with the Near-Infrared Camera and the Mid-InfraRed Instrument. NGC 7469 is a nearby, z = 0.01627, luminous infrared galaxy that hosts both a Seyfert Type-1.5 nucleus and a circumnuclear starburst ring with a radius of ∼0.5 kpc. The new near-infrared (NIR) JWST imaging reveals 66 star-forming regions, 37 of which were not detected by Hubble Space Telescope (HST) observations. Twenty-eight of the 37 sources have very red NIR colors that indicate obscurations up to A v ∼ 7 and a contribution of at least 25% from hot dust emission to the 4.4 μm band. Their NIR colors are also consistent with young (<5 Myr) stellar populations and more than half of them are coincident with the mid-infrared (MIR) emission peaks. These younger, dusty star-forming regions account for ∼6% and ∼17% of the total 1.5 and 4.4 μm luminosity of the starburst ring, respectively. Thanks to JWST, we find a significant number of young dusty sources that were previously unseen due to dust extinction. The newly identified 28 young sources are a significant increase compared to the number of HST-detected young sources (4-5). This makes the total percentage of the young population rise from ∼15% to 48%. These results illustrate the effectiveness of JWST in identifying and characterizing previously hidden star formation in the densest star-forming environments around active galactic nuclei (AGN).
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17.
  • Choi, Seo Eun, et al. (author)
  • Development and validation of language and visuospatial composite scores in ADNI
  • 2020
  • In: Alzheimer's and Dementia: Translational Research and Clinical Interventions. - : Wiley. - 2352-8737. ; 6:1
  • Journal article (peer-reviewed)abstract
    • Introduction: Composite scores may be useful to summarize overall language or visuospatial functioning in studies of older adults. Methods:We used item response theory to derive composite measures for language (ADNI-Lan) and visuospatial functioning (ADNI-VS) from the cognitive battery administered in the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We evaluated the scores among groups of people with normal cognition, mild cognitive impairment (MCI), and Alzheimer’s disease (AD) in terms of responsiveness to change, association with imaging findings, and ability to differentiate between MCI participants who progressed to AD dementia and those who did not progress. Results: ADNI-Lan andADNI-VSwere able to detect change over time and predict conversion fromMCI toAD. Theywere associated with most of the pre-specified magnetic resonance imaging measures. ADNI-Lan had strong associations with a cerebrospinal fluid biomarker pattern. Discussion: ADNI-Lan and ADNI-VS may be useful composites for language and visuospatial functioning in ADNI.
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18.
  • Ciacci, Carolina, et al. (author)
  • The gluten-free diet and its current application in coeliac disease and dermatitis herpetiformis
  • 2015
  • In: United European Gastroenterology journal. - : Sage Publications. - 2050-6406 .- 2050-6414. ; 3:2, s. 121-135
  • Research review (peer-reviewed)abstract
    • Background: A gluten-free diet (GFD) is currently the only available therapy for coeliac disease (CD). Objectives: We aim to review the literature on the GFD, the gluten content in naturally gluten-free (GF) and commercially available GF food, standards and legislation concerning the gluten content of foods, and the vitamins and mineral content of a GFD. Methods: We carried out a PubMed search for the following terms: Gluten, GFD and food, education, vitamins, minerals, calcium, Codex wheat starch and oats. Relevant papers were reviewed and for each topic a consensus among the authors was obtained. Conclusion: Patients with CD should avoid gluten and maintain a balanced diet to ensure an adequate intake of nutrients, vitamins, fibre and calcium. A GFD improves symptoms in most patients with CD. The practicalities of this however, are difficult, as (i) many processed foods are contaminated with gluten, (ii) staple GF foods are not widely available, and (iii) the GF substitutes are often expensive. Furthermore, (iv) the restrictions of the diet may adversely affect social interactions and quality of life. The inclusion of oats and wheat starch in the diet remains controversial.
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19.
  • Crane, Paul K., et al. (author)
  • Cognitively defined Alzheimer's dementia subgroups have distinct atrophy patterns
  • 2024
  • In: Alzheimer's and Dementia. - 1552-5260. ; 20:3, s. 1739-1752
  • Journal article (peer-reviewed)abstract
    • INTRODUCTION: We sought to determine structural magnetic resonance imaging (MRI) characteristics across subgroups defined based on relative cognitive domain impairments using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to compare cognitively defined to imaging-defined subgroups. METHODS: We used data from 584 people with Alzheimer's disease (AD) (461 amyloid positive, 123 unknown amyloid status) and 118 amyloid-negative controls. We used voxel-based morphometry to compare gray matter volume (GMV) for each group compared to controls and to AD-Memory. RESULTS: There was pronounced bilateral lower medial temporal lobe atrophy with relative cortical sparing for AD-Memory, lower left hemisphere GMV for AD-Language, anterior lower GMV for AD-Executive, and posterior lower GMV for AD-Visuospatial. Formal asymmetry comparisons showed substantially more asymmetry in the AD-Language group than any other group (p = 1.15 × 10−10). For overlap between imaging-defined and cognitively defined subgroups, AD-Memory matched up with an imaging-defined limbic predominant group. DISCUSSION: MRI findings differ across cognitively defined AD subgroups.
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20.
  • Davies, Paul, et al. (author)
  • Learning in Cultivated Gardens and other outdoor Landscapes
  • 2015
  • In: Darwin-Inspired Learning. - Rotterdam : SENSE. - 9789462098312
  • Book chapter (other academic/artistic)abstract
    • Much has been written on childhood experiences of gardens as places in which physical and imaginary experiences converge (e.g. Pollan, 1991). Similarly, recent research has examined the capacity of gardens and school grounds to provide artefacts and spaces for children to assimilate into imagined worlds (e.g. Malone & Tranter, 2003; Dowdell et al., 2011). In addition, a growing body of evidence affirms the rich educational opportunities provided by cultivated gardens and other outdoor landscapes (e.g. Rickinson et al., 2004; Malone, 2008). The role that learning away from the traditional classroom plays in education has a long history; for example, Johann Comenius (1592-1670) argued that education should be a social process, much of which should occur outside of normal schooling (Braund & Reiss, 2004; Nundy, 2001). The educational theorists Pestalozzi (1746-1827), Froebal (1782-1852), Montessori (1870-1952) and Dewey (1859-1952) all highlight aspects of learning out-of-doors. In particular they see cultivated gardens as environments in which to engage in active learning. By the time of Darwin in the Victorian era, informal learning about science had become embedded in society, with the rapid advances in science and technology leading many people to visit science exhibitions and museums, as well as zoological and botanical collections; with these experiences being seen as important for ‘lifelong learning’ (Anderson, 1997; Braund & Reiss, 2004). In addition, creating personal collections of flowers and fossils and going on public excursions to observe and learn the names of plants and animals was part of the fabric of Victorian life, activities which extended across boundaries of class (Secord, 1994). Darwin himself was immersed in collecting beetles from an early age (see Chapter 7) and driven by a deep curiosity to explore the natural world (see Chapter 27). Modern science lessons inhabit a range of environments beyond the classroom: science centres and museums, field visits, trips to universities and research institutions, botanic gardens and zoological collections (for example, Braund & Reiss, 2004; Sanders, 2007) along with the more local environments of parks, school gardens and adjacent streets (for example, Ross-Russell, 2001; Johnson, 2012). Darwin focused much of his science on learning out-of-doors and was interested in a broad range of both cultivated and other outdoor landscapes, whether it was the work he carried out on insectivorous plants in his glasshouses at Down House or his systematic surveys of the meadows surrounding his home (see Chapters 19 ). This chapter highlights the role cultivated and other outdoor landscapes can play in developing children’s understanding of the living world.
  •  
21.
  • Essah, Emmanuel, et al. (author)
  • Condensation and moisture transport in cold roofs: effects of roof underlay
  • 2009
  • In: Building Research and Information. - 1466-4321 .- 0961-3218. ; 37:2, s. 117-128
  • Journal article (peer-reviewed)abstract
    • Their form of construction makes pitched roofs with insulation on a horizontal ceiling, cold pitched roofs, intrinsically vulnerable to condensation. This study reports the results derived from using the simulation package HAM-Tools to investigate the risk of condensation in cold pitched roofs fitted with a vapour permeable underlay (VPU) of known characteristics. In order to visualize the effect of the VPUs on moisture transfer, several scenarios were modelled, and compared with the results from a conventional bituminous felt with high resistance (200MNs/g, Sd = 40m). The results obtained from the VPU showed that ventilation is essential in the roof to reduce condensation. However, a sensitivity analysis proved that reducing the overall tightness of the ceiling and using lower resistance VPUs would help in controlling condensation formation in the roof. To a large extent, the proposed characteristic performance of the VPU as predicted by manufacturers and some researchers may only be realistic if gaps in the ceiling are sealed completely during construction, which may be practically difficult given current construction practice.
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22.
  • Essah, Emmanuel, et al. (author)
  • Simulating the Energy Benefits and Reduction in Condensation Formation that is obtained from Houses with Cold Pitched Roofs
  • 2008
  • In: Proceedings of the 8th Symposium on Bulding Physics. - 9788778772657 ; :3, s. 1365-1371
  • Conference paper (peer-reviewed)abstract
    • Ventilation often accounts for a significant portion of the heating or cooling load of a building and also affects the moisture levels of buildings. Arguably in the UK, houses with cold pitched roofs, with insulation on a horizontal ceiling, are the most vulnerable to the formation of condensation in the roof. This study is a numerical investigation that compares the occurrence and the risk of condensation formation in a cold pitched roof fitted with two underlay (a vapour permeable underlay (VPU) and a bituminous felt). The energy benefits that would be obtained from reducing the ventilation gaps in the eaves and improving the airtightness of the ceiling are investigated. In order to visualize these effects, several cases and scenarios have been modelled with a HAM software package. The results showed that, the VPU with a very low vapour resistance, Sd
  •  
23.
  • Ezekowitz, Michael D., et al. (author)
  • Apixaban compared with parenteral heparin and/or vitamin K antagonist in patients with nonvalvular atrial fibrillation undergoing cardioversion : Rationale and design of the EMANATE trial
  • 2016
  • In: American Heart Journal. - : Elsevier BV. - 0002-8703 .- 1097-6744. ; 179, s. 59-68
  • Journal article (peer-reviewed)abstract
    • Background: Stroke prevention in anticoagulation-nafve patients with atrial fibrillation undergoing cardioversion has not been systematically studied.Objective: To determine outcomes in anticoagulation-naive patients (defined as those receiving an anticoagulant for <48 hours during the index episode of atrial fibrillation) scheduled for cardioversion.Methods: This is a randomized, prospective, open-label, real-world study comparing apixaban to heparin plus warfarin. Early image-guided cardioversion is encouraged. For apixaban, the usual dose is 5 mg BID with a dose reduction to 2.5 mg BID if 2 of the following are present: age >80 years, weight <60 kg, or serum creatinine >1.5 mg/dL. If cardioversion is immediate, a single starting dose of 10 mg (or 5 mg if the dose is down-titrated) of apixaban is administered. Cardioversion may be attempted up to 90 days after randomization. Patients are followed up for 30 days after cardioversion or 90 days postrandomization if cardioversion is not performed within that timeframe. Outcomes are stroke, systemic embolization, major bleeds, clinically relevant nonmajor bleeding, and death, all adjudication-blinded.Statistics: The warfarin-naive cohort from the ARISTOTLE study was considered the closest data set to the patients being recruited into this study. The predicted incidence of stroke, systemic embolism, and major bleeding within 30 days after randomization was approximately 0.75%. To adequately power for a noninferiority trial, approximately 48,000 participants would be needed, a number in excess of feasibility. The figure of 1,500 patients was considered clinically meaningful and achievable.
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24.
  • Garcia-Martin, E. Elena, et al. (author)
  • Sources, Composition, and Export of Particulate Organic Matter Across British Estuaries
  • 2023
  • In: Journal of Geophysical Research - Biogeosciences. - : American Geophysical Union (AGU). - 2169-8953 .- 2169-8961. ; 128:4
  • Journal article (peer-reviewed)abstract
    • Estuaries receive and process a large amount of particulate organic carbon (POC) prior to its export into coastal waters. Studying the origin of this POC is key to understanding the fate of POC and the role of estuaries in the global carbon cycle. Here, we evaluated the concentrations of POC, as well as particulate organic nitrogen (PON), and used stable carbon and nitrogen isotopes to assess their sources across 13 contrasting British estuaries during five different sampling campaigns over 1 year. We found a high variability in POC and PON concentrations across the salinity gradient, reflecting inputs, and losses of organic material within the estuaries. Catchment land cover appeared to influence the contribution of POC to the total organic carbon flux from the estuary to coastal waters, with POC contributions >36% in estuaries draining catchments with a high percentage of urban/suburban land, and <11% in estuaries draining catchments with a high peatland cover. There was no seasonal pattern in the isotopic composition of POC and PON, suggesting similar sources for each estuary over time. Carbon isotopic ratios were depleted (-26.7 +/- 0.42 parts per thousand, average +/- sd) at the lowest salinity waters, indicating mainly terrigenous POC (TPOC). Applying a two-source mixing model, we observed high variability in the contribution of TPOC at the highest salinity waters between estuaries, with a median value of 57%. Our results indicate a large transport of terrigenous organic carbon into coastal waters, where it may be buried, remineralized, or transported offshore. Plain Language Summary Estuaries transport and process a large amount terrigenous particulate organic matter (i.e., carbon and nitrogen) prior to its export to coastal waters. In order to understand the fate of organic carbon and the role of estuaries in the global carbon cycle it is essential to improve our knowledge on its composition, origin, and amount of carbon transported. We quantified the elemental concentrations and stable isotopes composition of carbon and nitrogen to quantify the amount of terrigenous particulate organic matter transported by 13 British estuaries, which drain catchments of diverse land cover under different hydrological conditions. We found a great variability in particulate organic carbon (POC) and particulate organic nitrogen concentrations across the salinity gradient, implying inputs, and losses of material within the estuaries. Each estuary had similar sources of particulate material throughout the year. In most of the estuaries, the POC had a terrigenous origin at the lowest salinity waters. The terrigenous organic carbon contribution decreased toward coastal waters with an average contribution of 57% at the highest salinity waters, indicating a large transport of terrigenous organic carbon into coastal waters.
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25.
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26.
  • Kaufmann, Tobias, et al. (author)
  • Common brain disorders are associated with heritable patterns of apparent aging of the brain
  • 2019
  • In: Nature Neuroscience. - : Nature Publishing Group. - 1097-6256 .- 1546-1726. ; 22:10, s. 1617-
  • Journal article (peer-reviewed)abstract
    • Common risk factors for psychiatric and other brain disorders are likely to converge on biological pathways influencing the development and maintenance of brain structure and function across life. Using structural MRI data from 45,615 individuals aged 3-96 years, we demonstrate distinct patterns of apparent brain aging in several brain disorders and reveal genetic pleiotropy between apparent brain aging in healthy individuals and common brain disorders.
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27.
  • Lamarre, Jean François, et al. (author)
  • Timing of Breeding Site Availability Across the North-American Arctic Partly Determines Spring Migration Schedule in a Long-Distance Neotropical Migrant
  • 2021
  • In: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 9
  • Journal article (peer-reviewed)abstract
    • Long-distance migrants are under strong selection to arrive on their breeding grounds at a time that maximizes fitness. Many arctic birds start nesting shortly after snow recedes from their breeding sites and timing of snowmelt can vary substantially over the breeding range of widespread species. We tested the hypothesis that migration schedules of individuals co-occurring at the same non-breeding areas are adapted to average local environmental conditions encountered at their specific and distant Arctic breeding locations. We predicted that timing of breeding site availability (measured here as the average snow-free date) should explain individual variation in departure time from shared non-breeding areas. We tested our prediction by tracking American Golden-Plovers (Pluvialis dominica) nesting across the North-American Arctic. These plovers use a non-breeding (wintering) area in South America and share a spring stopover area in the nearctic temperate grasslands, located >1,800 km away from their nesting locations. As plovers co-occur at the same non-breeding areas but use breeding sites segregated by latitude and longitude, we could disentangle the potential confounding effects of migration distance and timing of breeding site availability on individual migration schedule. As predicted, departure date of individuals stopping-over in sympatry was positively related to the average snow-free date at their respective breeding location, which was also related to individual onset of incubation. Departure date from the shared stopover area was not explained by the distance between the stopover and the breeding location, nor by the stopover duration of individuals. This strongly suggests that plover migration schedule is adapted to and driven by the timing of breeding site availability per se. The proximate mechanism underlying the variable migration schedule of individuals is unknown and may result from genetic differences or individual learning. Temperatures are currently changing at different speeds across the Arctic and this likely generates substantial heterogeneity in the strength of selection pressure on migratory schedule of arctic birds migrating sympatrically.
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28.
  • Levin-Schwartz, Yuri, et al. (author)
  • Exosomal miRNAs in urine associated with children's cardiorenal parameters : A cross-sectional study
  • 2021
  • In: Epigenetics. - : Future Medicine Ltd. - 1559-2294 .- 1559-2308. ; 13:7, s. 499-512
  • Journal article (peer-reviewed)abstract
    • Aims: The authors sought to examine associations between urinary exosomal miRNAs (exo-miRs), emerging biomarkers of renal health, and cardiorenal outcomes in early childhood. Materials & Methods: The authors extracted exo-miRs in urine from 88 healthy Mexican children aged 4-6 years. The authors measured associations between 193 exo-miRs and cardiorenal outcomes: systolic/diastolic blood pressure, estimated glomerular filtration rate and urinary sodium and potassium levels. The authors adjusted for age, sex, BMI, socioeconomic status, indoor tobacco smoke exposure and urine specific gravity. Results: Multiple exo-miRs were identified meeting a false discovery rate threshold of q < 0.1. Specifically, three exo-miRs had increased expression with urinary sodium, 17 with urinary sodium-to-potassium ratio and one with decreased estimated glomerular filtration rate. Conclusions: These results highlight urinary exo-miRs as early-life biomarkers of children's cardiorenal health.
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29.
  • Linden, S. T., et al. (author)
  • GOALS-JWST: Revealing the Buried Star Clusters in the Luminous Infrared Galaxy VV 114
  • 2023
  • In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 944:2
  • Journal article (peer-reviewed)abstract
    • We present the results of a James Webb Space Telescope NIRCam investigation into the young massive star cluster (YMC) population in the luminous infrared galaxy VV 114. We identify 374 compact YMC candidates with signal-to-noise ratios ≥ 3, 5, and 5 at F150W, F200W, and F356W, respectively. A direct comparison with our HST cluster catalog reveals that ∼20% of these sources are undetected at optical wavelengths. Based on yggdrasil stellar population models, we identify 17 YMC candidates in our JWST imaging alone with F150W - F200W and F200W - F356W colors suggesting they are all very young, dusty (A V = 5-15), and massive (105.8 < M ⊙ < 106.1). The discovery of these “hidden” sources, many of which are found in the “overlap” region between the two nuclei, quadruples the number of t < 3 Myr clusters and nearly doubles the number of t < 6 Myr clusters detected in VV 114. Now extending the cluster age distribution ( dN / d τ ∝ τ γ ) to the youngest ages, we find a slope of γ = −1.30 ± 0.39 for 106 < τ(yr) < 107, which is consistent with the previously determined value from 107 < τ(yr) < 108.5, and confirms that VV 114 has a steep age distribution slope for all massive star clusters across the entire range of cluster ages observed. Finally, the consistency between our JWST- and HST-derived age distribution slopes indicates that the balance between cluster formation and destruction has not been significantly altered in VV 114 over the last 0.5 Gyr.
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30.
  • Ludvigsson, Jonas F., 1969-, et al. (author)
  • Diagnosis and management of adult coeliac disease : guidelines from the British Society of Gastroenterology
  • 2014
  • In: Gut. - : BMJ Publishing Group Ltd. - 0017-5749 .- 1468-3288. ; 63:8, s. 1210-1228
  • Journal article (peer-reviewed)abstract
    • A multidisciplinary panel of 18 physicians and 3 non-physicians from eight countries (Sweden, UK, Argentina, Australia, Italy, Finland, Norway and the USA) reviewed the literature on diagnosis and management of adult coeliac disease (CD). This paper presents the recommendations of the British Society of Gastroenterology. Areas of controversies were explored through phone meetings and web surveys. Nine working groups examined the following areas of CD diagnosis and management: classification of CD; genetics and immunology; diagnostics; serology and endoscopy; follow-up; gluten-free diet; refractory CD and malignancies; quality of life; novel treatments; patient support; and screening for CD.
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31.
  • Ludvigsson, Jonas F., et al. (author)
  • Support for patients with celiac disease : A literature review
  • 2015
  • In: United European Gastroenterology journal. - : Wiley. - 2050-6406 .- 2050-6414. ; 3:2, s. 146-159
  • Research review (peer-reviewed)abstract
    • Background: Celiac disease (CD) is a lifelong disorder. Patients are at increased risk of complications and comorbidity. Objectives: We conducted a review of the literature on patient support and information in CD and aim to issue recommendations about patient information with regards to CD. Methods: Data source: We searched PubMed for English-language articles published between 1900 and June 2014, containing terms related to costs, economics of CD, or education and CD. Study selection: Papers deemed relevant by any of the participating authors were included in the study. Data synthesis: No quantitative synthesis of data was performed. Instead we formulated a consensus view of the information that should be offered to all patients with CD. Results: There are few randomized clinical trials examining the effect of patient support in CD. Patients and their families receive information from many sources. It is important that health care personnel guide the patient through the plethora of facts and comments on the Internet. An understanding of CD is likely to improve dietary adherence. Patients should be educated about current knowledge about risk factors for CD, as well as the increased risk of complications. Patients should also be advised to avoid other health hazards, such as smoking. Many patients are eager to learn about future non-dietary treatments of CD. This review also comments on novel therapies but it is important to stress that no such treatment is available at present. Conclusion: Based on mostly observational data, we suggest that patient support and information should be an integral part of the management of CD, and is likely to affect the outcome of CD.
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32.
  • Martin, Francis, et al. (author)
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
  • 2008
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7183, s. 7-88
  • Journal article (peer-reviewed)abstract
    • Mycorrhizal symbioses -- the union of roots and soil fungi -- are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate, and montane forests all depend upon ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of 2 ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here, we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-million-base genome assembly contains ~ 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features most notably a battery of effector-type small secreted proteins (SSP) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific proteins likely play a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell walls, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus which enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
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33.
  • Maxwell, Tania L., et al. (author)
  • Global dataset of soil organic carbon in tidal marshes
  • 2023
  • In: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
  • Journal article (peer-reviewed)abstract
    • Tidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this data we estimated a median (± median absolute deviation) value of 79.2 ± 38.1 Mg SOC ha−1 in the top 30 cm and 231 ± 134 Mg SOC ha−1 in the top 1 m of tidal marsh soils globally. This data can serve as a basis for future work, and may contribute to incorporation of tidal marsh ecosystems into climate change mitigation and adaptation strategies and policies.
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34.
  • Milisavljevic, Dan, et al. (author)
  • MULTI-WAVELENGTH OBSERVATIONS OF SUPERNOVA 2011ei : TIME-DEPENDENT CLASSIFICATION OF TYPE IIb AND Ib SUPERNOVAE AND IMPLICATIONS FOR THEIR PROGENITORS
  • 2013
  • In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 767:1, s. 71-
  • Journal article (peer-reviewed)abstract
    • We present X-ray, UV/optical, and radio observations of the stripped-envelope, core-collapse supernova (SN) 2011ei, one of the least luminous SNe IIb or Ib observed to date. Our observations begin with a discovery within similar to 1 day of explosion and span several months afterward. Early optical spectra exhibit broad, Type II-like hydrogen Balmer profiles that subside rapidly and are replaced by Type Ib-like He-rich features on a timescale of one week. High-cadence monitoring of this transition suggests absorption attributable to a high-velocity (greater than or similar to 12,000 km s(-1)) H-rich shell, which is likely present in many Type Ib events. Radio observations imply a shock velocity of v approximate to 0.13 c and a progenitor star average mass-loss rate of (M) over dot approximate to 1.4 x 10(-5) M-circle dot yr(-1) (assuming wind velocity v(w) = 10(3) km s(-1)). This is consistent with independent constraints from deep X-ray observations with Swift-XRT and Chandra. Overall, the multi-wavelength properties of SN 2011ei are consistent with the explosion of a lower-mass (3-4 M-circle dot), compact (R-* less than or similar to 1 x 10(11) cm), He-core star. The star retained a thin hydrogen envelope at the time of explosion, and was embedded in an inhomogeneous circumstellar wind suggestive of modest episodic mass loss. We conclude that SN 2011ei's rapid spectral metamorphosis is indicative of time-dependent classifications that bias estimates of the relative explosion rates for Type IIb and Ib objects, and that important information about a progenitor star's evolutionary state and mass loss immediately prior to SN explosion can be inferred from timely multi-wavelength observations.
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35.
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36.
  • Nandedkar, Sanjeev D., et al. (author)
  • THE EXTRAPOLATED REFERENCE VALUES PROCEDURE : THEORY, ALGORITHM, AND RESULTS IN PATIENTS AND CONTROL SUBJECTS
  • 2018
  • In: Muscle and Nerve. - : Wiley. - 0148-639X .- 1097-4598. ; 57:1, s. 90-95
  • Journal article (peer-reviewed)abstract
    • Introduction: Reference values (RVs) are required to separate normal from abnormal values obtained in electrodiagnostic (EDx) testing. However, it is frequently impractical to perform studies on control subjects to obtain RVs. The Extrapolated Reference Values (E-Ref) procedure extracts RVs from data obtained during clinically indicated EDx testing. We compared the E-Ref results with established RVs in several sets of EDx data.Methods: The mathematical basis for E-Ref was explored to develop an algorithm for the E-Ref procedure. To test the validity of this algorithm, it was applied to simulated and real jitter measurements from control subjects and patients with myasthenia gravis, and to nerve conduction studies from patients with various conditions referred for EDx studies.Results: There was good concordance between E-Ref and RVs for all evaluated data sets.Discussion: E-Ref is a promising method to develop RVs.
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37.
  • Nduva, George M., et al. (author)
  • Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya
  • 2022
  • In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
  • Journal article (peer-reviewed)abstract
    • HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006–2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2–20 sequences) were found—half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017–2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
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38.
  • Ning, Jue, et al. (author)
  • Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates
  • 2013
  • In: Genes & Development. - : Cold Spring Harbor Laboratory Press (CSHL). - 0890-9369 .- 1549-5477. ; 27:10, s. 1198-1215
  • Journal article (peer-reviewed)abstract
    • Fertilization is a crucial yet poorly characterized event in eukaryotes. Our previous discovery that the broadly conserved protein HAP2 (GCS1) functioned in gamete membrane fusion in the unicellular green alga Chlamydomonas and the malaria pathogen Plasmodium led us to exploit the rare biological phenomenon of isogamy in Chlamydomonas in a comparative transcriptomics strategy to uncover additional conserved sexual reproduction genes. All previously identified Chlamydomonas fertilization-essential genes fell into related clusters based on their expression patterns. Out of several conserved genes in a minus gamete cluster, we focused on Cre06.g280600, an ortholog of the fertilization-related Arabidopsis GEX1. Gene disruption, cell biological, and immunolocalization studies show that CrGEX1 functions in nuclear fusion in Chlamydomonas. Moreover, CrGEX1 and its Plasmodium ortholog, PBANKA_113980, are essential for production of viable meiotic progeny in both organisms and thus for mosquito transmission of malaria. Remarkably, we discovered that the genes are members of a large, previously unrecognized family whose first-characterized member, KAR5, is essential for nuclear fusion during yeast sexual reproduction. Our comparative transcriptomics approach provides a new resource for studying sexual development and demonstrates that exploiting the data can lead to the discovery of novel biology that is conserved across distant taxa.
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39.
  • Ogneva, Olga, et al. (author)
  • Particulate organic matter in the Lena River and its delta : from thepermafrost catchment to the Arctic Ocean
  • 2023
  • In: Biogeosciences. - 1726-4170 .- 1726-4189. ; 20:7, s. 1423-1441
  • Journal article (peer-reviewed)abstract
    • Rapid Arctic warming accelerates permafrost thaw, causing an additional release of terrestrial organic matter (OM) into rivers and, ultimately, after transport via deltas and estuaries, to the Arctic Ocean nearshore. The majority of our understanding of nearshore OM dynamics and fate has been developed from freshwater rivers despite the likely impact of highly dynamic estuarine and deltaic environments on the transformation, storage, and age of OM delivered to coastal waters. Here, we studied particulate organic carbon (POC) dynamics in the Lena River delta and compared them with POC dynamics in the Lena River main stem along a similar to 1600 km long transect from Yakutsk, downstream to the delta. We measured POC, total suspended matter (TSM), and carbon isotopes (delta C-13 and Delta C-14) in POC to compare riverine and deltaic OM composition and changes in OM source and fate during transport offshore. We found that TSM and POC concentrations decreased by 70% during transit from the main stem to the delta and Arctic Ocean. We found deltaic POC to be strongly depleted in C-13 relative to fluvial POC. Dual-carbon (Delta C-14 and delta C-13) isotope mixing model analyses indicated a significant phytoplankton contribution to deltaic POC (similar to 68 +/- 6 %) and suggested an additional input of permafrost-derived OM into deltaic waters (similar to 18 +/- 4% of deltaic POC originates from Pleistocene deposits vs. similar to 5 +/- 4% in the river main stem). Despite the lower concentration of POC in the delta than in the main stem (0.41 +/- 0.10 vs. 0.79 +/- 0.30 mg L-1, respectively), the amount of POC derived from Yedoma deposits in deltaic waters was almost twice as large as the amount of POC of Yedoma origin in the main stem (0.07 +/- 0.02 and 0.04 +/- 0.02 mg L-1, respectively). We assert that estuarine and deltaic processes require consideration in order to correctly understand OM dynamics throughout Arctic nearshore coastal zones and how these processes may evolve under future climate-driven change.
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40.
  • Rich, Jeffrey A., et al. (author)
  • GOALS-JWST: Pulling Back the Curtain on the AGN and Star Formation in VV 114
  • 2023
  • In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 944:2
  • Journal article (peer-reviewed)abstract
    • We present results from the James Webb Space Telescope Director’s Discretionary Time Early Release Science program 1328 targeting the nearby, luminous infrared galaxy, VV 114. We use the MIRI and NIRSpec instruments to obtain integral-field spectroscopy of the heavily obscured eastern nucleus (V114E) and surrounding regions. The spatially resolved, high-resolution spectra reveal the physical conditions in the gas and dust over a projected area of 2-3 kpc that includes the two brightest IR sources, the NE and SW cores. Our observations show for the first time spectroscopic evidence that the SW core hosts an active galactic nucleus as evidenced by its very low 6.2 μm and 3.3 μm polycyclic aromatic hydrocarbon equivalent widths (0.12 and 0.017 μm, respectively) and mid- and near-IR colors. Our observations of the NE core show signs of deeply embedded star formation including absorption features due to aliphatic hydrocarbons, large quantities of amorphous silicates, as well as HCN due to cool gas along the line of sight. We detect elevated [Fe ii]/Pfα consistent with extended shocks coincident with enhanced emission from warm H2, far from the IR-bright cores and clumps. We also identify broadening and multiple kinematic components in both H2 and fine structure lines caused by outflows and previously identified tidal features.
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41.
  • Sanders, Dawn, 1958, et al. (author)
  • Bringing Barad into Outdoor Learning: A Reflective Case Study Concerning Quadrats and Agential Cuts in Ecology Education
  • 2023
  • In: Patricia G. Patrick (ed.), How People Learn in Informal Science Environments. - Cham : Springer. - 9783031132902 ; , s. 313-333
  • Book chapter (peer-reviewed)abstract
    • As teaching and learning moves from the classroom to outdoor settings teachers and students often make shifts between socio-material planes of action from the indoor to outdoor classroom, the ecological setting and the investigative tools that they use. One such tool, common to ecological science, is the quadrat: a square frame mostly used for measuring plant populations in diverse habitats. Karen Barad’s theories on new materialism have influenced our thinking about exploring these shifts. Her theories of material agency emerge from her background in physics and draw extensively on the work of Niels Bohr. For Barad, material objects enact changes so, rather than seeing matter as inert, she argues that matter intra-acts resulting in new phenomena emerging. Few attempts have been made to ground her theories in outdoor learning practices. Drawing on our educational experiences developed with teacher students in the cities of Gothenburg and London we make public an extended reflective conversation on what happens, and what might happen, if a Baradian perspective is used to consider an outdoor science activity focused on ecology. In these reflections the quadrat is examined as a critical tool for framing layers of understanding through the lens of “agential cuts”; both on the part of the teacher, and the students, during acts of noticing and identifying the biodiverse forms and interactions within the quadrat. Thus, the theoretical focus in this work concerns the use of Barad’s “agential cuts” as a didactical frame on moving between the classroom and outdoor settings. Within this, we consider the conceptual and material possibilities the quadrat tool offers teaching and learning.
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42.
  • Sanders, Tina, et al. (author)
  • Seasonal nitrogen fluxes of the Lena River Delta
  • 2022
  • In: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 51:2, s. 423-438
  • Journal article (peer-reviewed)abstract
    • The Arctic is nutrient limited, particularly by nitrogen, and is impacted by anthropogenic global warming which occurs approximately twice as fast compared to the global average. Arctic warming intensifies thawing of permafrost-affected soils releasing their large organic nitrogen reservoir. This organic nitrogen reaches hydrological systems, is remineralized to reactive inorganic nitrogen, and is transported to the Arctic Ocean via large rivers. We estimate the load of nitrogen supplied from terrestrial sources into the Arctic Ocean by sampling in the Lena River and its Delta. We took water samples along one of the major deltaic channels in winter and summer in 2019 and sampling station in the central delta over a one-year cycle. Additionally, we investigate the potential release of reactive nitrogen, including nitrous oxide from soils in the Delta. We found that the Lena transported nitrogen as dissolved organic nitrogen to the coastal Arctic Ocean and that eroded soils are sources of reactive inorganic nitrogen such as ammonium and nitrate. The Lena and the Deltaic region apparently are considerable sources of nitrogen to nearshore coastal zone. The potential higher availability of inorganic nitrogen might be a source to enhance nitrous oxide emissions from terrestrial and aquatic sources to the atmosphere.
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43.
  • Schael, S, et al. (author)
  • Precision electroweak measurements on the Z resonance
  • 2006
  • In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
  • Research review (peer-reviewed)abstract
    • We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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44.
  • Smith, Jennifer A, et al. (author)
  • Genome-wide association study identifies 74 loci associated with educational attainment
  • 2016
  • In: Nature (London). - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 533:7604, s. 539-542
  • Journal article (peer-reviewed)abstract
    • Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.
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45.
  • Sonderby, Ida E., et al. (author)
  • Dose response of the 16p11.2 distal copy number variant on intracranial volume and basal ganglia
  • 2020
  • In: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 25:3, s. 584-602
  • Journal article (peer-reviewed)abstract
    • Carriers of large recurrent copy number variants (CNVs) have a higher risk of developing neurodevelopmental disorders. The 16p11.2 distal CNV predisposes carriers to e.g., autism spectrum disorder and schizophrenia. We compared subcortical brain volumes of 12 16p11.2 distal deletion and 12 duplication carriers to 6882 non-carriers from the large-scale brain Magnetic Resonance Imaging collaboration, ENIGMA-CNV. After stringent CNV calling procedures, and standardized FreeSurfer image analysis, we found negative dose-response associations with copy number on intracranial volume and on regional caudate, pallidum and putamen volumes (β = −0.71 to −1.37; P < 0.0005). In an independent sample, consistent results were obtained, with significant effects in the pallidum (β = −0.95, P = 0.0042). The two data sets combined showed significant negative dose-response for the accumbens, caudate, pallidum, putamen and ICV (P = 0.0032, 8.9 × 10−6, 1.7 × 10−9, 3.5 × 10−12 and 1.0 × 10−4, respectively). Full scale IQ was lower in both deletion and duplication carriers compared to non-carriers. This is the first brain MRI study of the impact of the 16p11.2 distal CNV, and we demonstrate a specific effect on subcortical brain structures, suggesting a neuropathological pattern underlying the neurodevelopmental syndromes.
  •  
46.
  • Stojanovski, Todor, et al. (author)
  • A commentary on (V)ISUF COVID-19 crisis calls (V stands for virtual)
  • 2020
  • In: Urban morphology. - : International Seminar on Urban Form. - 1027-4278. ; 24:2, s. 238-240
  • Journal article (other academic/artistic)abstract
    • In 2015, three language teachers working with student engineers at different European universities founded the Global Engineers Language Skills (GELS) network. The teachers' aims were to investigate and categorize necessary and desirable language and communication skills for engineers and ensure that these findings actively support the teaching and learning of additional languages in technical universities and engineering departments. We presented preliminary results of our work at CDIO's international conference in 2016. In this paper, we summarize the network's development since then, interpret the results of our investigations, and describe our work to disseminate our results and promote effective language and communication skills for engineering students. We also summarize our more recent work on enhancing the GELS framework of skills, applying for Erasmus+ KA2 funding, developing the GELS network from three to thirty universities through training events, integrating intercultural communication skills in our work, and teaching and learning through the medium of English.
  •  
47.
  • Stojanovski, Todor, et al. (author)
  • Rethinking Computer-Aided Architectural Design (CAAD) - From Generative Algorithms and Architectural Intelligence to Environmental Design and Ambient Intelligence
  • 2022
  • In: Computer-Aided Architectural Design. - Singapore : Springer Nature. ; , s. 62-83
  • Conference paper (peer-reviewed)abstract
    • Computer-Aided Architectural Design (CAAD) finds its historical precedents in technological enthusiasm for generative algorithms and architectural intelligence. Current developments in Artificial Intelligence (AI) and paradigms in Machine Learning (ML) bring new opportunities for creating innovative digital architectural tools, but in practice this is not happening. CAAD enthusiasts revisit generative algorithms, while professional architects and urban designers remain reluctant to use software that automatically generates architecture and cities. This paper looks at the history of CAAD and digital tools for Computer Aided Design (CAD), Building Information Modeling (BIM) and Geographic Information Systems (GIS) in order to reflect on the role of AI in future digital tools and professional practices. Architects and urban designers have diagrammatic knowledge and work with design problems on symbolic level. The digital tools gradually evolved from CAD to BIM software with symbolical architectural elements. The BIM software works like CAAD (CAD systems for Architects) or digital board for drawing and delivers plans, sections and elevations, but without AI. AI has the capability to process data and interact with designers. The AI in future digital tools for CAAD and Computer-Aided Urban Design (CAUD) can link to big data and develop ambient intelligence. Architects and urban designers can harness the benefits of analytical ambient intelligent AIs in creating environmental designs, not only for shaping buildings in isolated virtual cubicles. However there is a need to prepare frameworks for communication between AIs and professional designers. If the cities of the future integrate spatially analytical AI, are to be made smart or even ambient intelligent, AI should be applied to improving the lives of inhabitants and help with their daily living and sustainability.
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48.
  •  
49.
  • Taler, Sandra J., et al. (author)
  • KDOQI US Commentary on the 2012 KDIGO Clinical Practice Guideline for Management of Blood Pressure in CKD
  • 2013
  • In: American Journal of Kidney Diseases. - : Elsevier BV. - 1523-6838 .- 0272-6386. ; 62:2, s. 201-213
  • Journal article (other academic/artistic)abstract
    • In response to the 2012 KDIGO (Kidney Disease: Improving Global Outcomes) guideline for blood pressure management in patients with chronic kidney disease not on dialysis, the National Kidney Foundation organized a group of US experts in hypertension and transplant nephrology to review the recommendations and comment on their relevancy in the context of current US clinical practice and concerns. The overriding message was the dearth of clinical trial evidence to provide strong evidence-based recommendations. For patients with CKD with normal to mildly increased albuminuria, goal blood pressure has been relaxed to <= 140/90 mm Hg for both diabetic and nondiabetic patients. In contrast, KDIGO continues to recommend goal blood pressure <= 130/80 mm Hg for patients with chronic kidney disease with moderately or severely increased albuminuria and for all renal transplant recipients regardless of the presence of proteinuria, without supporting data. The expert panel thought the KDIGO recommendations were generally reasonable but lacking in sufficient evidence support and that additional studies are greatly needed. (C) 2013 by the National Kidney Foundation, Inc.
  •  
50.
  • Viljur, Mari-Liis, et al. (author)
  • The effect of natural disturbances on forest biodiversity : an ecological synthesis
  • 2022
  • In: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 97:5, s. 1930-1947
  • Journal article (peer-reviewed)abstract
    • Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q = 0 but not for q = 1 and q = 2, indicating that diversity–disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes. 
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