| 1. |
- Shimwell, T. W., et al.
(author)
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The LOFAR Two-metre Sky Survey: II. First data release
- 2019
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 622
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Research review (peer-reviewed)abstract
- The LOFAR Two-metre Sky Survey (LoTSS) is an ongoing sensitive, high-resolution 120-168 MHz survey of the entire northern sky for which observations are now 20% complete. We present our first full-quality public data release. For this data release 424 square degrees, or 2% of the eventual coverage, in the region of the HETDEX Spring Field (right ascension 10h45m00s to 15h30m00s and declination 45°00′00″ to 57°00′00″) were mapped using a fully automated direction-dependent calibration and imaging pipeline that we developed. A total of 325 694 sources are detected with a signal of at least five times the noise, and the source density is a factor of ∼10 higher than the most sensitive existing very wide-area radio-continuum surveys. The median sensitivity is S144 MHz = 71 μJy beam -1 and the point-source completeness is 90% at an integrated flux density of 0.45 mJy. The resolution of the images is 6″ and the positional accuracy is within 0.2″. This data release consists of a catalogue containing location, flux, and shape estimates together with 58 mosaic images that cover the catalogued area. In this paper we provide an overview of the data release with a focus on the processing of the LOFAR data and the characteristics of the resulting images. In two accompanying papers we provide the radio source associations and deblending and, where possible, the optical identifications of the radio sources together with the photometric redshifts and properties of the host galaxies. These data release papers are published together with a further ∼20 articles that highlight the scientific potential of LoTSS.
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| 3. |
- Nisbet, R. M., et al.
(author)
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Primary-productivity gradients and short-term population dynamics in open systems
- 1997
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In: Ecological Monographs. ; 67:4, s. 535-553
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Journal article (peer-reviewed)abstract
- We present three models representing the trophic and behavioral dynamics of a simple food chain (primary producers, grazers, and predators) at temporal scales shorter than the scale of consumer reproduction, and at the spatial scales typically employed in field experiments. These models incorporate flexible behavioral responses of organisms to their predators and resources in spatially heterogeneous environments that are open to immigration and emigration. The basic models include passive immigration at all trophic levels, producer growth rates and losses to grazer consumption, grazer emigration rate as a behavioral response to producer and predator densities, grazer losses to predator consumption, and predator emigration as a function of grazer density. We model this system as: (1) a set of ordinary differential equations (''well-mixed model''); (2) a set of partial differential equations describing a population of discrete grazers foraging on discrete patches of primary producers (''discrete-grazer model''); and (3) a set of simulation rules describing the movement and foraging of individual grazers and the growth of primary producers on discrete patches in explicit space (''individual-based model''). The ordinary differential-equation models produced similar results to individual-based models with well-mixed producers, and the discrete-grazer and individual-based models produced similar results when grazers possessed a long-term memory of patch reward rates. The well-mixed and discrete-grazer models thus represent specific, limiting cases of the general individual-based model. Multiple equilibria and sustained oscillations are possible but are less likely in the discrete-grazer and individual-based models than in the well-mixed model, because localized foraging of discrete grazers leads to the rapid development of spatial heterogeneity in producer biomass and, hence, to a decrease in overall primary production. All models predict that stable equilibrium densities of all trophic levels increase with enrichment, provided grazers increase their emigration rates as predator density increases. If increasing predator density leads to decreasing grazer-emigration rates, predator and grazer densities increase, but producer biomass may increase or decrease with enrichment. These results contrast with predictions from models that assume ideal free distributions of grazers and/or predators with respect to their resources. Our models also predict that densities at all trophic levels will increase with increasing producer immigration, and that producer density will decline with increasing grazer immigration and increase with increasing predator immigration. Our qualitative findings on enrichment are used to interpret an experiment dealing with the short-term dynamics of a stream community open to grazers and predators.
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| 5. |
- Logan, T. M., et al.
(author)
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Evaluating urban accessibility: leveraging open-source data and analytics to overcome existing limitations
- 2019
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In: Environment and Planning B: Urban Analytics and City Science. - : SAGE Publications. - 2399-8091 .- 2399-8083. ; 46:5, s. 897-913
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Journal article (peer-reviewed)abstract
- We revisit the standard methodology for evaluating proximity to urban services and recommend enhancements to address existing limitations. Existing approaches often simplify their measure of proximity by using large areal units and by imposing arbitrary distance thresholds. By doing so, these approaches risk overlooking vulnerable, access-poor populations - the very populations that such studies are often trying to identify. These limitations are primarily motivated by computational constraints. However, recent advances in computational power, open data, and open-source analytics permit high-resolution proximity analyses on large scales. Given the impetus for equitable accessibility in our communities, this is of fundamental importance for researchers and practitioners. In this paper, we present an approach that leverages these open source advances to (a) measure proximity using network distance at the building level, (b) estimate population at that level, and (c) present the resulting distributions so vulnerable populations can be identified. Using three cities and modes of transport, we demonstrate how the approach enhances existing measures and identifies service-poor populations where the previous methods fall short. The proximity results could be used alone, or as inputs to access metrics. Our collating of these components into an open source code provides opportunities for researchers and practitioners to explore fine-resolution, city-wide accessibility across multiple cities and the host of questions that follow.
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| 6. |
- Mills, James A., et al.
(author)
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Archiving Primary Data : Solutions for Long-Term Studies
- 2015
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In: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 30:10, s. 581-589
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Journal article (peer-reviewed)abstract
- The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (PIs) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.
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| 7. |
- Anderson, K. E., et al.
(author)
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Scaling population responses to spatial environmental variability in advection-dominated systems
- 2005
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In: Ecology Letters. ; 8:9, s. 933-943
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Journal article (peer-reviewed)abstract
- We model the spatial dynamics of an open population of organisms that disperse solely through advection in order to understand responses to multiscale environmental variability. We show that the distance over which a population responds to a localized perturbation, called the response length, can be characterized as an organisms average lifetime dispersal distance, unless there is strong density-dependence in demographic or dispersal rates. Continuous spatial fluctuations in demographic rates at scales smaller than the response length will be largely averaged in the population distribution, whereas those in per capita emigration rates will be strongly tracked. We illustrate these results using a parameterized example to show how responses to environmental variability may differ in streams with different average current velocities. Our model suggests an approach to linking local dynamics dominated by dispersal processes to larger-scale dynamics dominated by births and deaths.
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| 8. |
- Bell, Jordana T, et al.
(author)
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Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population.
- 2012
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In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:4
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Journal article (peer-reviewed)abstract
- Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype-phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.
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| 9. |
- Beutier, G., et al.
(author)
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Band Filling Control of the Dzyaloshinskii-Moriya Interaction in Weakly Ferromagnetic Insulators
- 2017
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In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 119:16
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Journal article (peer-reviewed)abstract
- We observe and explain theoretically a dramatic evolution of the Dzyaloshinskii-Moriya interaction (DMI) in the series of isostructural weak ferromagnets, MnCO3, FeBO3, CoCO3, and NiCO3. The sign of the interaction is encoded in the phase of the x-ray magnetic diffraction amplitude, observed through interference with resonant quadrupole scattering. We find very good quantitative agreement with first-principles electronic structure calculations, reproducing both sign and magnitude through the series, and propose a simplified "toy model" to explain the change in sign with 3d shell filling. The model gives insight into the evolution of the DMI in Mott and charge transfer insulators.
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| 10. |
- Brandon, Andrew M., et al.
(author)
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Log D7.4 and plasma protein binding of synthetic cannabinoid receptor agonists and a comparison of experimental and predicted lipophilicity
- 2023
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In: Drug Testing and Analysis. - : WILEY. - 1942-7603 .- 1942-7611.
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Journal article (peer-reviewed)abstract
- The emergence of new synthetic cannabinoid receptor agonists (SCRAs) onto the illicit drugs market continues to cause harm, and the overall availability of physicochemical and pharmacokinetic data for new psychoactive substances is lacking. The lipophilicity of 23 SCRAs and the plasma protein binding (PPB) of 11 SCRAs was determined. Lipophilicity was determined using a validated chromatographic hydrophobicity index (CHI) log D method; tested SCRAs showed moderate to high lipophilicity, with experimental log D-7.4 ranging from 2.48 (AB-FUBINACA) to 4.95 (4F-ABUTINACA). These results were also compared to in silico predictions generated using seven commercially available software packages and online tools (Canvas; ChemDraw; Gastroplus; MoKa; PreADMET; SwissADME; and XlogP). Licenced, dedicated software packages provided more accurate lipophilicity predictions than those which were free or had prediction as a secondary function; however, the latter still provided competitive estimates in most cases. PPB of tested SCRAs, as determined by equilibrium dialysis, was in the upper range of the lipophilicity scale, ranging from 90.8% (ADB-BUTINACA) to 99.9% (BZO-HEXOXIZID). The high PPB of these drugs may contribute to reduced rate of clearance and extended durations of pharmacological effects compared to lesser-bound SCRAs. The presented data improve understanding of the behaviour of these drugs in the body. Ultimately, similar data and predictions may be used in the prediction of the structure and properties of drugs yet to emerge on the illicit market.
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