| 1. |
- 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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| 2. |
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| 3. |
- Deschout, H., et al.
(author)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2014
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In: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. - 9781632666246
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Conference paper (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 4. |
- Deschout, Hendrik, et al.
(author)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2013
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In: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. ; 3, s. 2010-2012
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Conference paper (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 5. |
- Deschout, H., et al.
(author)
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On-chip light sheet illumination enables diagnostic size and concentration measurements of membrane vesicles in biofluids
- 2014
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In: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1741-1747
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Journal article (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in biofluids, like blood or saliva, are emerging as potential non-invasive biomarkers for diseases, such as cancer. Techniques capable of measuring the size and concentration of membrane vesicles directly in biofluids are urgently needed. Fluorescence single particle tracking microscopy has the potential of doing exactly that by labelling the membrane vesicles with a fluorescent label and analysing their Brownian motion in the biofluid. However, an unbound dye in the biofluid can cause high background intensity that strongly biases the fluorescence single particle tracking size and concentration measurements. While such background intensity can be avoided with light sheet illumination, current set-ups require specialty sample holders that are not compatible with high-throughput diagnostics. Here, a microfluidic chip with integrated light sheet illumination is reported, and accurate fluorescence single particle tracking size and concentration measurements of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours are demonstrated.
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| 6. |
- Jiguet, F., et al.
(author)
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Identifying the winter grounds of the recently described Barbary Reed Warbler (Acrocephalus baeticatus ambiguus)
- 2022
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In: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 165:1, s. 204-213
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Journal article (peer-reviewed)abstract
- The Iberian and North African populations of reed warblers have been described recently as a separate taxon, ambiguus, forming a sister clade to the Sahelian subspecies minor of African Reed Warbler Acrocephalus baeticatus. Although the breeding range of ambiguus has been identified, the migration strategy of its populations remained unknown. We deployed geolocators and sampled the innermost primary from breeding adults in Spain for stable hydrogen (delta H-2) analyses and also analysed stable carbon (delta C-13) and nitrogen (delta N-15) isotopes in feathers collected in two reed warbler taxa (Acrocephalus scirpaceus and Acrocephalus baeticatus ambiguus) in Morocco, to identify the moulting and wintering sites of these populations. Ring recoveries, geolocator tracks and probabilistic assignments to origin from delta H-2 values indicate that Spanish ambiguus are likely to moult south of the Sahara and winter in West Africa, probably from Mauretania to southern Mali and Ivory Coast. Moroccan ambiguus, however, undergo post-breeding moult north of the Sahara, and possibly then migrate to West Africa. With other populations of ambiguus breeding from Algeria to Libya and probably wintering further east in the Sahelian belt, the Barbary Reed Warbler can therefore be considered a trans-Saharan migrant, with a post-breeding moult strategy that varies between populations, and probably structured according to breeding latitude.
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| 7. |
- Morrison, C. A., et al.
(author)
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Bird population declines and species turnover are changing the acoustic properties of spring soundscapes
- 2021
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Natural sounds, and bird song in particular, play a key role in building and maintaining our connection with nature, but widespread declines in bird populations mean that the acoustic properties of natural soundscapes may be changing. Using data-driven reconstructions of soundscapes in lieu of historical recordings, here we quantify changes in soundscape characteristics at more than 200,000 sites across North America and Europe. We integrate citizen science bird monitoring data with recordings of individual species to reveal a pervasive loss of acoustic diversity and intensity of soundscapes across both continents over the past 25 years, driven by changes in species richness and abundance. These results suggest that one of the fundamental pathways through which humans engage with nature is in chronic decline, with potentially widespread implications for human health and well-being.
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| 8. |
- Olsson, Urban, 1954, et al.
(author)
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Mitochondrial phylogeny of the Eurasian/African reed warbler complex (Acrocephalus, Aves). Disagreement between morphological and molecular evidence and cryptic divergence: A case for resurrecting Calamoherpe ambigua Brehm 1857
- 2016
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 102, s. 30-44
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Journal article (peer-reviewed)abstract
- A tree based on the mitochondrial cyt b gene for 278 samples from throughout the range of the Eurasian Reed Warbler Acrocephalus scirpaceus - African Reed Warbler A. baeticatus complex shows well supported geographically structured divergence for eight distinct lineages. The phylogenetic structuring together with the clarification of priority, provided by sequence data from seven type specimens, suggests that both taxonomy and distribution boundaries are in need of revision. The Iberian and Moroccan populations form a well-supported Glade, and we propose that these are treated as taxonomically distinct, under the name ambiguus (Brehm, 1857). We propose that the names scirpaceus, fuscus, avicenniae, ambiguus, minor, cinnamomeus, hallae and baeticatus are used for the well supported clades in the complex, which we recommend to treat as one polytypic species, A. scirpaceus, pending studies of gene flow and assortative mating in the contact zones. (C) 2016 Elsevier Inc. All rights reserved.
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| 9. |
- Pellissier, V., et al.
(author)
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Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data
- 2020
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In: Conservation Biology. - : Wiley. - 0888-8892 .- 1523-1739. ; 34:3, s. 666-676
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Journal article (peer-reviewed)abstract
- The European Union's Natura 2000 (N2000) is among the largest international networks of protected areas. One of its aims is to secure the status of a predetermined set of (targeted) bird and butterfly species. However, nontarget species may also benefit from N2000. We evaluated how the terrestrial component of this network affects the abundance of nontargeted, more common bird and butterfly species based on data from long-term volunteer-based monitoring programs in 9602 sites for birds and 2001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased (slope estimates ranged from 0.101 [SD 0.042] to 3.51 [SD 1.30]) as the proportion of landscape covered by N2000 sites increased. This positive relationship existed for 27 of the 104 butterfly species (estimates ranged from 0.382 [SD 0.163] to 4.28 [SD 0.768]), although most butterflies were generalists. For most species, when land-cover covariates were accounted for these positive relationships were not evident, meaning land cover may be a determinant of positive effects of the N2000 network. The increase in abundance as N2000 coverage increased correlated with the specialization index for birds, but not for butterflies. Although the N2000 network supports high abundance of a large spectrum of species, the low number of specialist butterflies with a positive association with the N2000 network shows the need to improve the habitat quality of N2000 sites that could harbor open-land butterfly specialists. For a better understanding of the processes involved, we advocate for standardized collection of data at N2000 sites.
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