| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Gerkin, RC, et al.
(author)
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The best COVID-19 predictor is recent smell loss: a cross-sectional study
- 2020
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In: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- BackgroundCOVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19.MethodsThis preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery.ResultsBoth C19+ and C19-groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for ∼50% of participants and was best predicted by time since illness onset.ConclusionsAs smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4<OR<10), which can be deployed when viral lab tests are impractical or unavailable.
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| 6. |
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| 7. |
- Lopes-Lima, M., et al.
(author)
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Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications
- 2024
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In: Molecular Phylogenetics and Evolution. - : Academic Press Inc.. - 1055-7903 .- 1095-9513. ; 195
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Journal article (peer-reviewed)abstract
- The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectus stat. rev., Unio gontierii stat. rev., Unio mardinensis stat. rev., Unio nanus stat. rev., and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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| 8. |
- Bonde, J. P. E., et al.
(author)
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Occupational risk of COVID-19 across pandemic waves: a two-year national follow-up study of hospital admissions
- 2022
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In: Scandinavian Journal of Work Environment & Health. - : Scandinavian Journal of Work, Environment and Health. - 0355-3140 .- 1795-990X. ; 48:8, s. 672-677
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Journal article (peer-reviewed)abstract
- Objective Assuming that preventive measures to mitigate viral transmission of SARS-CoV-2 at the workplace may have been improved in the course of the COVID-19 pandemic, we examined the occupational risk of COVID-19 related hospital admission across the four pandemic waves in Denmark between week 8, 2020, and week 50, 2021. Methods The study included 4416 cases of COVID-19 related hospital admissions among 2.4 million Danish employees aged 20-69 with follow-up in 2020 through 2021. At-risk industrial sectors and a reference population were defined a priory by a job-exposure matrix on occupational risk for COVID-19. Incidence rate ratios (IRR) and potential effect modification by pandemic wave were computed with Poisson regression adjusted for demographic, social and health factors including completed COVID-19 vaccination. Results We observed an overall elevated relative risk in four of six at-risk industrial sectors, but the pandemic wave only modified the risk among healthcare employees, where the excess risk from a high initial level declined to background levels during the latest waves in models not adjusting for COVID-19 vaccination. In social care, education and transport, the elevated risk was not modified by pandemic wave. Conclusion Danish healthcare employees were to some extent protected against occupational transmission of SARS-CoV-2 during the two last pandemic waves even though the absolute risk conferred by occupation may not have been eliminated. Early vaccination of this group seems not to be the only explanation. The risk in other sectors remained elevated indicating a need to revisit preventive measures.
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| 9. |
- Tiselius, Peter, 1958, et al.
(author)
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Functional response of Oikopleura dioica to house clogging due to exposure to algae of different sizes
- 2003
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In: Marine Biology. - 0025-3162. ; 142:2, s. 253-261
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Journal article (peer-reviewed)abstract
- The functional response of the appendicularian Oikopleura dioica was investigated with a unialgal diet (Isochrysis galbana, 0-1,600 mug Cl-1) and with additions of specific concentrations of algae either smaller than the incurrent filter mesh size (Rhodomonas baltica, 90 mug Cl-1; Thalassiosira weissflogii, 60 mug Cl-1) or larger algae (Ceratium lineatum, 8 mug Cl-1; C. tripos, 52 mug C l(-1)). Clearance ranged from 0.13 to 3.3 ml mug C-1 h(-1) and followed a Michaelis-Menten curve corresponding to a maximum filtration rate (particles collected by both animal and house), FRmax = 164 ng C mug C-1 h(-1) and K-m = 64 mug C l(-1). Maximum pellet production was 9 pellets ind(-1) h(-1) and occurred at 100 mugC (-1). Pellet production was proportional to filtration rate below this level, but declined at higher concentrations. House production ranged from 0.5 to 5.5 houses ind(-1) day(-1) and the corresponding curve fit resulted in H-max = 4.6 houses ind(-1) day(-1) and K-m house = 32 mug Cl-1. Addition of edible small algae caused increased internal clogging of the houses, evidenced by significantly higher pigment concentrations in abandoned houses than in houses produced with I.. galbana as a single food. House production was not affected. In contrast, larger algae caused a significantly higher house production, but the algae were not collected on the houses. Increased levels of edible algae will not have negative effects on O. dioica at ecologically realistic concentrations. Ambient bloom concentrations of larger algae may, however, have a negative effect on the growth of O. dioica populations, owing to the compensatory increased house production.
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| 10. |
- Tönnesson, Kajsa, 1971, et al.
(author)
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Grazing impact of Oikopleura dioica and copepods on an autumn plankton community
- 2005
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In: Marine Biology Research. - : Informa UK Limited. - 1745-1000 .- 1745-1019. ; 1:5, s. 365-373
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Journal article (peer-reviewed)abstract
- Copepods and appendicularians are major grazers in the pelagic environment. They have different retention efficiencies for prey and may therefore exert a variable grazing pressure on the spectrum of pico- to micro-plankton. We determined clearance rates of both groups at one station during 24 h in the Gullmar fjord, west Sweden, in autumn 1999. Total potential prey biomass ranged from 75 mu g C l(-1) at the surface to 14 mu g C l(-1) at 30 m with a dominance of larger dinoflagellates (10-25 mu m athecate species and Gymnodinium /Gyrodinium sp.) and the pennate diatom Pseudo -nitzschia sp. Grazer biomass was dominated by copepods (Acartia clausi, Paracalanus parvus) and appendicularians (Oikopleura dioica). O. dioica showed non-selective clearance rates of 0.7-1.8 ml mu g C-1 h(-1) on most diatoms, flagellates and ciliates, whereas Pseudo -nitzschia sp. and dinoflagellates and ciliates > 25 mu m were not removed by O. dioica. Appendicularian grazing impact was 0.06% d(-1) on the phytoplankton and 0.4% d(-1) on bacterial biomass. Despite a seven-fold higher biomass, the grazing impact of copepods on phytoplankton biomass was only 0.28% d(-1) indicating that O. dioica had a proportionally greater impact and, in contrast to copepods, also utilised bacteria. The low observed grazing impact was due to a low grazer biomass and a prey community largely unavailable to the investigated grazers.
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