| 1. |
- Muhlemann, B., et al.
(författare)
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Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 115:29, s. 7557-7562
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Tidskriftsartikel (refereegranskat)abstract
- Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to similar to 70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from similar to 0.5 to similar to 6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed similar to 12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to similar to 5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.
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| 2. |
- Muhlemann, B., et al.
(författare)
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Ancient hepatitis B viruses from the Bronze Age to the Medieval period
- 2018
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 557:7705, s. 418-423
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Tidskriftsartikel (refereegranskat)abstract
- Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 x 10(-6-)1.51 x 10(-5) nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages(1,2). We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
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| 3. |
- Patterson, Nick, et al.
(författare)
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Large-scale migration into Britain during the Middle to Late Bronze Age
- 2022
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; , s. 588-594
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Tidskriftsartikel (refereegranskat)abstract
- Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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| 4. |
- Jones, Steven, et al.
(författare)
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Googling for opposites: a web-based study of antonym canonicity
- 2007
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Ingår i: Corpora. - 1755-1676. ; 2:2, s. 129-154
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Tidskriftsartikel (refereegranskat)abstract
- This paper seeks to explain why some semantically-opposed word pairs are more likely to be seen as canonical antonyms (for example, cold/hot) than others (icy/scorching, cold/fiery, freezing/hot, etc.). Specifically, it builds on research which has demonstrated that, in discourse, antonyms are inclined to favour certain frames, such as ‘X and Y alike’, ‘from X to Y’ and ‘either X or Y’ (Justeson and Katz, 1991; etc.), and to serve a limited range of discourse functions (Jones, 2002). Our premise is that the more canonical an antonym pair is, the greater the fidelity with which it will occupy such frames. Since an extremely large corpus is needed to identify meaningful patterns of co-occurrence, we turn to Internet data for this research. As well as enabling the notion of antonym canonicity to be revisited from a more empirical perspective, this approach also allows us to evaluate the appropriateness (and assess the risks) of using the World Wide Web as a corpus for studies into certain types of low-frequency textual phenomena.
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| 5. |
- Murphy, M. Lynne, et al.
(författare)
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Discourse functions of antonymy: a cross-linguistic investigation of Swedish and English
- 2009
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Ingår i: Journal of Pragmatics. - : Elsevier BV. - 0378-2166 .- 1879-1387. ; 41:11, s. 2159-2184
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Tidskriftsartikel (refereegranskat)abstract
- Jones (2002) identified several discourse functions of antonymy, each of which is loosely associated with a number of contrastive constructions in written English. Subsequent work (Jones, 2006; Jones and Murphy, 2005; Murphy and Jones, 2008) demonstrated that these functions are found in other modalities/registers of English, albeit with some differences in distribution. This article takes a first step in exploring discourse functions of antonymy in a language other than English. Because binary contrast has the potential to interact in different ways with the values and thought patterns of different cultures, we hypothesized that other languages differ from English in the ways in which antonyms are used in discourse. In this study of antonyms in Swedish, translational near-equivalents of pairs used by Jones were searched in the Swedish Parole corpus, and more than 4300 instances of co-occurring antonyms were found and analyzed in their sentential contexts. While the same range of antonym discourse functions is found in English and Swedish, the proportions of those functions differ significantly between the two languages. This paper both describes their functions (and the form of the functions) in Swedish and reflects on the similarities and differences with English.We ascribe some of the differences to the idiomaticity of certain componential expressions and discuss the possibility that certain cultural values affect some categories.
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| 6. |
- Jandrić, Petar, et al.
(författare)
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Teaching in the Age of Covid-19 : The New Normal
- 2022
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Ingår i: Postdigital Science and Education. - : Springer Science and Business Media LLC. - 2524-485X .- 2524-4868. ; 4:3, s. 877-1015
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Tidskriftsartikel (refereegranskat)abstract
- On 17 March 2020, Postdigital Science and Education launched a call for testimonies about teaching and learning during very frst Covid-19 lockdowns. The resulting article, ‘Teaching in the Age of Covid-19’ (attached), presents 81 written testimonies and 80 workspace photographs submitted by 84 authors from 19 countries. On 17 March 2021, Postdigital Science and Education launched a call for a sequel article of testimonies about teaching and learning during very first Covid-19 lockdowns. The resulting article, ‘Teaching in the Age of Covid-19—1 Year Later’(attached), consists of 74 textual testimonies and 76 workspace photographs submitted by 77 authors from 20 countries.These two articles have been downloaded almost 100,000 times and have been cited more than 100 times. This shows their value as historical documents. Recent analyses, such as ‘Teaching in the Age of Covid-19—A Longitudinal Study ’(attached), also indicate their strong potential for educational research. As the Covid-19 pandemic seems to wind down, pandemic experiences have entered the mainstream. They shape all educational research of today and arguably do not require special treatment. Yet, our unique series of pandemic testimonies provides a unique opportunity to longitudinally trace what happens to the same people over the years—and this opportunity should not be missed.Today, we launch a call for fnal sequel: Teaching in the Age of Covid-19—The New Normal. In this sequel, we would like to hear about ways in which you—contributors to the previous articles—have established your own new normal. We hope that this will be the last iteration in this series of testimony articles. Unless the world faces another strong pandemic outburst, we would like to end the series with this last article.
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| 7. |
- Jones, Samantha E., et al.
(författare)
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Lake and crannog : A 2500-year palaeoenvironmental record of continuity and change in NE Scotland
- 2022
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 285
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Tidskriftsartikel (refereegranskat)abstract
- Wetland environments have been important resources for human habitation since prehistoric times and in parts of northern Europe these have witnessed the construction of artificial islet settlements, known as ‘crannogs’ in Scotland and Ireland. This paper presents a high-resolution multi-proxy palaeoenvironmental study from the Loch of Leys, Aberdeenshire, Scotland, the site of a recently excavated crannog that provides a chronological context for its inhabitation. The combined datasets demonstrate that the first occupation from AD 20–210 coincided not only with a transitional phase from lake to wetland (mire) but also with the timing of the first major Roman campaigns in northeast Scotland. Techniques including microfossil analysis, geochemistry, IR-spectroscopy and physical properties integrated with archaeological and historical records have helped to better define both natural changes that took place in the wetland environment and human activity (agriculture, fires, metal working) spanning the Roman Iron Age through to the present. This has allowed a better understanding of the responses of existing Iron Age communities to Roman military activity (e.g. through continuity or change in land use) as well as the resources exploited in frontier zones during the Roman and post Roman eras. This has wider significance not just for Scotland but also for other parts of Europe that had similar frontiers and conflict zones during the Roman period.
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| 8. |
- Jones, G., et al.
(författare)
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An integrated dialect analysis tool using phonetics and acoustics
- 2019
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Ingår i: Lingua. - : Elsevier BV. - 0024-3841 .- 1872-6135. ; 221, s. 37-48
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to verify a computational phonetic and acoustic analysis tool created in the MATLAB environment. A dataset was obtained containing 3 broad American dialects (Northern, Western and New England) from the TIMIT database using words that also appeared in the Swadesh list. Each dialect consisted of 20 speakers uttering 10 sentences. Verification using phonetic comparisons between dialects was made by calculating the Levenshtein distance in Gabmap and the proposed software tool. Agreement between the linguistic distances using each analysis method was found. Each tool showed increasing linguistic distance as a function of increasing geographic distance, in a similar shape to Seguy’s curve. The proposed tool was then further developed to include acoustic characterisation capability of inter dialect dynamics. Significant variation between dialects was found for the pitch, trajectory length and spectral rate of change for 7 of the phonetic vowels investigated. Analysis of the vowel area using the 4 corner vowels indicated that for male speakers, geographically closer dialects have smaller variations in vowel space area than those further apart. The female utterances did not show a similar pattern of linguistic distance likely due to the lack of one corner vowel /u/, making the vowel space a triangle.
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| 9. |
- Mühlemann, Barbara, et al.
(författare)
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Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age
- 2020
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 369:6502
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Tidskriftsartikel (refereegranskat)abstract
- Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
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