| 1. |
- Bertrand, Yann J., et al.
(författare)
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Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus : A Simulation Approach
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.
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| 2. |
- Bhatara, Anjali, et al.
(författare)
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Second Language Ability and Emotional Prosody Perception
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- The present study examines the effect of language experience on vocal emotion perception in a second language. Native speakers of French with varying levels of self-reported English ability were asked to identify emotions from vocal expressions produced by American actors in a forced-choice task, and to rate their pleasantness, power, alertness and intensity on continuous scales. Stimuli included emotionally expressive English speech (emotional prosody) and non-linguistic vocalizations (affect bursts), and a baseline condition with Swiss-French pseudo-speech. Results revealed effects of English ability on the recognition of emotions in English speech but not in non-linguistic vocalizations. Specifically, higher English ability was associated with less accurate identification of positive emotions, but not with the interpretation of negative emotions. Moreover, higher English ability was associated with lower ratings of pleasantness and power, again only for emotional prosody. This suggests that second language skills may sometimes interfere with emotion recognition from speech prosody, particularly for positive emotions.
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| 3. |
- Hench, Jürgen, et al.
(författare)
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The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.
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| 4. |
- Inoue, Yosuke, et al.
(författare)
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Neighborhood Characteristics and Cardiovascular Risk among Older People in Japan : Findings from the JAGES Project
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have found an association between neighborhood characteristics (i.e., aspects of the physical and social environment) and the incidence of cardiovascular disease (CVD) and elevated CVD risk. This study investigated the relationship between neighborhood characteristics and CVD risk among older people in Japan where research on this association is scarce. Data came from the Japan Gerontological Evaluation Study project; questionnaire data collected from 3,810 people aged 65 years or older living in 20 primary school districts in Aichi prefecture, Japan, was linked to a computed composite CVD risk score based on biomarker data (i.e., hemoglobin A1c, systolic blood pressure, diastolic blood pressure, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and estimated glomerular filtration rate). A sex-stratified multilevel linear regression analysis revealed that for male participants, living in neighborhoods with a higher perceived occurrence of traffic accidents and reduced personal safety was associated with an elevated CVD risk (coefficient = 1.08 per interquartile range increase, 95% confidence interval [CI] = 0.30 to 1.86) whereas males living in neighborhoods with a higher perceived proximity of exercise facilities had a lower risk (coefficient = −1.00, 95% CI = −1.78 to −0.21). For females, there was no statistically significant association between neighborhood characteristics and CVD risk. This study suggests that aspects of the neighborhood environment might be important for CVD morbidity and mortality in Japan, particularly among men.
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| 5. |
- Inoue, Y., et al.
(författare)
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The association between family members’ migration and cognitive function among people left behind in China
- 2019
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 14:9
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Tidskriftsartikel (refereegranskat)abstract
- While internal migration is widely occurring in countries across the world and older people are more likely to be left behind by family members who out-migrated to other locations, little attention has been paid to the cognitive health of those people who have been left behind (PLB). Understanding how these demographic patterns relate to older persons’ cognitive health may inform efforts to reduce the disease burden due to cognitive decline. Data came from the China Health and Nutrition Survey in 1997, 2000 and 2004. Participants aged 55 to 93 who participated in a cognitive function screening test (score range: 0–31) in two or more waves and provided information on family members’ migration (n = 1,267) were included in the analysis. A mixed linear model was used to investigate the association between being left behind by any members who had not resided in the household for at least 6 months at baseline and cognitive function. Approximately 10% of the participants had been left behind by family members who migrated out of their communities. A significant interaction was observed in relation to cognitive function between being left behind and the number of years from the first test. Specifically, there was a less steep decline in cognitive function of PLB compared to people not left behind. This longitudinal study showed that PLB tended to have a higher cognitive function compared to those not left behind due to their relatively stable transition in cognitive function during the study period.
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| 6. |
- Ivarsson, Magnus, et al.
(författare)
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Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin - A New Type of Cryptoendolithic Fungi
- 2015
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Ingår i: PLoS One. - : Public Library of Science (PLoS). ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basa- nites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II) oxidation to form Mn(III,VI) oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies.
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| 7. |
- Koyanagi, Ai, et al.
(författare)
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Psychotic-Like Experiences and Nonsuidical Self-Injury in England : Results from a National Survey
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Little is known about the association between psychotic-like experiences (PLEs) and nonsuicidal self-injury (NSSI) in the general adult population. Thus, the aim of this study was to examine the association using nationally-representative data from England.METHODS: Data from the 2007 Adult Psychiatric Morbidity Survey was analyzed. The sample consisted of 7403 adults aged ≥16 years. Five forms of PLEs (mania/hypomania, thought control, paranoia, strange experience, auditory hallucination) were assessed with the Psychosis Screening Questionnaire. The association between PLEs and NSSI was assessed by multivariable logistic regression. Hierarchical models were constructed to evaluate the influence of alcohol and drug dependence, common mental disorders, and borderline personality disorder symptoms on this association.RESULTS: The prevalence of NSSI was 4.7% (female 5.2% and male 4.2%), while the figures among those with and without any PLEs were 19.2% and 3.9% respectively. In a regression model adjusted for sociodemographic factors and stressful life events, most types of PLE were significantly associated with NSSI: paranoia (OR 3.57; 95%CI 1.96-6.52), thought control (OR 2.45; 95%CI 1.05-5.74), strange experience (OR 3.13; 95%CI 1.99-4.93), auditory hallucination (OR 4.03; 95%CI 1.56-10.42), and any PLE (OR 2.78; 95%CI 1.88-4.11). The inclusion of borderline personality disorder symptoms in the models had a strong influence on the association between PLEs and NSSI as evidenced by a large attenuation in the ORs for PLEs, with only paranoia continuing to be significantly associated with NSSI. Substance dependence and common mental disorders had little influence on the association between PLEs and NSSI.CONCLUSIONS: Borderline personality disorder symptoms may be an important factor in the link between PLEs and NSSI. Future studies on PLEs and NSSI should take these symptoms into account.
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| 8. |
- Kullenberg, Christopher, 1980, et al.
(författare)
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What are analog bulletin boards used for today? Analysing media uses, intermediality and technology affordances in Swedish bulletin board messages using a citizen science approach
- 2018
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:8
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Tidskriftsartikel (refereegranskat)abstract
- Analog bulletin boards are omnipresent in Swedish urban areas, yet little systematic knowledge about this communication medium exists. In the shadow of the rapid emergence of digital media the analog bulletin board has received less attention than its digital successors, many of them having incorporated similar functionality with novel technical solutions. In this study we used a citizen science method to collect 1167 messages from bulletin boards around Sweden aided by school children and teachers, with the purpose of shedding new light on what is communicated on the boards, by whom, using what types of technologies and in what way the messages refer to other media. Results show that the most common messages are invitations to events, such as concerts, lectures and sports events, followed by buy-and-sell ads for goods and services. The most frequent sender is an association, for example NGOs, sports associations or religious communities. Almost half of the sampled messages were professionally printed, about forty per cent were made by home printers. Only six per cent of the messages were handwritten, almost exclusively by private persons as senders. Moreover, we show how the analog bulletin board has adapted to recent changes in media technology—a media landscape which is saturated with electronic- and mobile media. Further, the bulletin board still holds a firm place in a media ecology where local communication is in demand, and exists in parallel with electronic media. Close to forty percent of the messages contained hyperlinks to web pages and we found (and removed for anonymization purposes) more than six hundred phone numbers from the dataset.
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| 9. |
- Kärblane, Kairi, et al.
(författare)
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ABCE1 is a highly conserved RNA silencing suppressor
- 2015
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosomerecycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.
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| 10. |
- Menichetti, Lorenzo, et al.
(författare)
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Interactions between a population of fallow deer (Dama dama), humans and crops in a managed composite temperate landscape in southern Sweden : Conflict or opportunity?
- 2019
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 14:4
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Tidskriftsartikel (refereegranskat)abstract
- Landscapes composed of agricultural land mixed with forest are desirable since they provide a wide range of diversified ecosystem services, unlike specialized agricultural landscapes, but that creates a trade-off between these land uses since wildlife usually feed on crops and reduce yields. In Nordic countries, where human population density is low and game hunting can be a viable economic alternative, mixed landscape systems are particularly interesting. To evaluate the economic sustainability of such systems we need to quantify wildlife damage to crops. One important species, being popular among Swedish hunters and therefore economically valuable, is fallow deer (Dama dama). Our objective was to evaluate the economic sustainability of mixed landscape systems including cultivated fields and commercial hunting of fallow deer. We studied the effects of excluding fallow deer by using 86 exclosures and adjacent plots in winter wheat and oat fields in south-west Sweden. We analyzed yield losses and interactions between spatial and temporal grazing patterns, anthropogenic landscape features, and topological characteristics of the landscape. We found that animals avoided exposed spots, irrespective of distance from human activity. We also found a seasonal grazing pattern related to the different growing periods of winter wheat (more grazed, emerging in autumn) and spring oat (less grazed, emerging in spring). We then compared the costs of crop damage against the commercial value of fallow deer hunting. The damage amounted to 375 ±196 € ha-1 for wheat and 152 ±138 € ha-1 for oat, corresponding to a total cost per animal of 82.7 ±81.0 €, while each animal had an estimated market value of approximately 100 €. Therefore the value of fallow deer presence compensated for the associated cost of crop damage. Profit could be further improved in this case by adopting additional management strategies. In general our study confirmed the economic feasibility of this particular mixed land management.
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