| 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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| 8. |
- Karawita, Anjana C., et al.
(author)
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The swan genome and transcriptome, it is not all black and white
- 2023
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In: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Journal article (peer-reviewed)abstract
- BackgroundThe Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.ResultsHere, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.ConclusionTogether, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
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| 9. |
- Price, KM, et al.
(author)
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Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities
- 2022
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In: Translational psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 12:1, s. 495-
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Journal article (peer-reviewed)abstract
- Reading Disability (RD) is often characterized by difficulties in the phonology of the language. While the molecular mechanisms underlying it are largely undetermined, loci are being revealed by genome-wide association studies (GWAS). In a previous GWAS for word reading (Price, 2020), we observed that top single-nucleotide polymorphisms (SNPs) were located near to or in genes involved in neuronal migration/axon guidance (NM/AG) or loci implicated in autism spectrum disorder (ASD). A prominent theory of RD etiology posits that it involves disturbed neuronal migration, while potential links between RD-ASD have not been extensively investigated. To improve power to identify associated loci, we up-weighted variants involved in NM/AG or ASD, separately, and performed a new Hypothesis-Driven (HD)–GWAS. The approach was applied to a Toronto RD sample and a meta-analysis of the GenLang Consortium. For the Toronto sample (n = 624), no SNPs reached significance; however, by gene-set analysis, the joint contribution of ASD-related genes passed the threshold (p~1.45 × 10–2, threshold = 2.5 × 10–2). For the GenLang Cohort (n = 26,558), SNPs in DOCK7 and CDH4 showed significant association for the NM/AG hypothesis (sFDR q = 1.02 × 10–2). To make the GenLang dataset more similar to Toronto, we repeated the analysis restricting to samples selected for reading/language deficits (n = 4152). In this GenLang selected subset, we found significant association for a locus intergenic between BTG3-C21orf91 for both hypotheses (sFDR q < 9.00 × 10–4). This study contributes candidate loci to the genetics of word reading. Data also suggest that, although different variants may be involved, alleles implicated in ASD risk may be found in the same genes as those implicated in word reading. This finding is limited to the Toronto sample suggesting that ascertainment influences genetic associations.
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| 10. |
- Schweiger, Oliver, et al.
(author)
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Multiple stressors on biotic interactions: how climate change and alien species interact to affect pollination
- 2010
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In: Biological Reviews. - 1469-185X .- 1464-7931. ; 85:4, s. 777-795
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Research review (peer-reviewed)abstract
- Global change may substantially affect biodiversity and ecosystem functioning but little is known about its effects on essential biotic interactions. Since different environmental drivers rarely act in isolation it is important to consider interactive effects. Here, we focus on how two key drivers of anthropogenic environmental change, climate change and the introduction of alien species, affect plant-pollinator interactions. Based on a literature survey we identify climatically sensitive aspects of species interactions, assess potential effects of climate change on these mechanisms, and derive hypotheses that may form the basis of future research. We find that both climate change and alien species will ultimately lead to the creation of novel communities. In these communities certain interactions may no longer occur while there will also be potential for the emergence of new relationships. Alien species can both partly compensate for the often negative effects of climate change but also amplify them in some cases. Since potential positive effects are often restricted to generalist interactions among species, climate change and alien species in combination can result in significant threats to more specialist interactions involving native species.
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| 11. |
- Torkildsen, J. V., et al.
(author)
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App-Based Morphological Training Produces Lasting Effects on Word Knowledge in Primary School Children: A Randomized Controlled Trial
- 2022
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In: Journal of Educational Psychology. - : American Psychological Association (APA). - 0022-0663 .- 1939-2176. ; 114:4, s. 833-854
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Journal article (peer-reviewed)abstract
- Morphemes, the smallest meaning-bearing units of language, recur in many words. Therefore, morphological knowledge can facilitate the comprehension of novel words. This study tested the effectiveness of a morphological training program on children's learning and retention of exposed words and morphologically related unexposed words compared with an active control condition. Norwegian second graders (N = 717) unselected for ability were individually randomized to either a morphological (n = 366) or a mathematical training program (n = 351). Both programs lasted for 8 weeks and were delivered as self-contained apps in a classroom setting. The morphological training built on the principle that frequency of target elements together with variation of nontarget elements can support implicit learning. Treatment-blind examiners assessed participants' meaning-based knowledge (word comprehension and definitions) and code-based knowledge (word reading fluency and spelling) at pretraining, immediately post training, and at follow-up 6 months later. An intention-to-treat analysis showed lasting effects of the morphological training on meaning-based knowledge of exposed words (posttest: d = .37; follow-up: d = .31) and unexposed words containing trained morphemes (posttest: d = .27; follow-up: d = .27) and code-based knowledge of exposed words (posttest: d = .22; follow-up: d = .13). For code-based knowledge of unexposed words, there were significant training effects at the posttest (d = .12) but not follow-up (d = .05). There were no significant effects on a far-transfer measure of general vocabulary. These results demonstrate that a brief morphological training program can produce lasting and educationally meaningful gains in students' word knowledge. Educational Impact and Implications Statement Words can consist of several meaningful parts, or morphemes, such as -ist in guitarist and re- in reuse. Understanding common morphemes helps children infer the meanings of new words. In this study, we tested the effects of working with an educational application (app) focusing on morphemes. Children completed app exercises such as sorting words or pictures according to their meaning, combining morphemes to build words, or identifying the correct word or morpheme to fit a sentence or picture context. We found that the app was effective in improving Norwegian second graders' ability to explain, understand, read, and spell words, including words which were not shown in the app, but which contained trained morphemes. The brief low-cost training produced long-term effects with a minimal burden on teachers.
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| 12. |
- Ameen, Carly, et al.
(author)
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Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic
- 2019
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In: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 286:1916
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Journal article (peer-reviewed)abstract
- Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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| 13. |
- Hulme, Heather E., et al.
(author)
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Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection
- 2017
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
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Journal article (peer-reviewed)abstract
- Salmonella Typhimurium causes a self-limiting gastroenteritis that may lead to systemic disease. Bacteria invade the small intestine, crossing the intestinal epithelium from where they are transported to the mesenteric lymph nodes (MLNs) within migrating immune cells. MLNs are an important site at which the innate and adaptive immune responses converge but their architecture and function is severely disrupted during S. Typhimurium infection. To further understand host-pathogen interactions at this site, we used mass spectrometry imaging (MSI) to analyse MLN tissue from a murine model of S. Typhimurium infection. A molecule, identified as palmitoylcarnitine (PalC), was of particular interest due to its high abundance at loci of S. Typhimurium infection and MLN disruption. High levels of PalC localised to sites within the MLNs where B and T cells were absent and where the perimeter of CD169(+) sub capsular sinus macrophages was disrupted. MLN cells cultured ex vivo and treated with PalC had reduced CD4(+) CD25(+) T cells and an increased number of B220(+) CD19(+) B cells. The reduction in CD4(+) CD25(+) T cells was likely due to apoptosis driven by increased caspase-3/7 activity. These data indicate that PalC significantly alters the host response in the MLNs, acting as a decisive factor in infection outcome.
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| 14. |
- Hulme-Smith, Christopher, 1989-, et al.
(author)
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Enhanced thermal stability in nanostructured bainitic steel
- 2013
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In: Scripta Materialia. - : Acta Materialia Inc.. - 1359-6462 .- 1872-8456. ; 69:2, s. 191-194
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Journal article (peer-reviewed)abstract
- We report an attempt at increasing the thermal stability of nanocrystalline bainite to tempering heat treatments by enhancing the silicon concentration of the alloy. Validation experiments have been conducted using synchrotron X-irradiation during tempering heat treatment. It is found that the change in alloying successfully stabilizes the austenite at elevated temperatures by retarding cementite formation to temperatures as high as 500 ˚C. Other changes reflected in the lattice parameters of the major phases have revealed further information about the mechanisms involved.
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| 15. |
- Hulme-Smith, Christopher, 1989-, et al.
(author)
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Experimental evidence for non-cubic bainitic ferrite
- 2013
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In: Scripta Materialia. - : Acta Materialia Inc.. - 1359-6462 .- 1872-8456. ; 69:5, s. 409-412
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Journal article (peer-reviewed)abstract
- The first evidence is provided for the existence of a tetragonal or slightly orthorhombic unit cell of bainitic ferrite. It supports the hypothesis that the excess carbon that persists in the ferrite, which is in contact with austenite, is a consequence of an increased solubility due to the change in symmetry from the conventional cubic unit cell. The deviations from the cubic cell are maintained to elevated temperatures, as expected from an increased solubility of carbon in the ferrite.
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| 16. |
- Klem, M., et al.
(author)
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Screening for language delay: Growth trajectories of language ability in low- and high-performing children
- 2016
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In: Journal of Speech, Language and Hearing Research. - 1092-4388 .- 1558-9102. ; 59:5, s. 1035-1045
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Journal article (peer-reviewed)abstract
- Purpose: This study investigated the stability and growth of preschool language skills and explores latent class analysis as an approach for identifying children at risk of language impairment. Method: The authors present data from a large-scale 2-year longitudinal study, in which 600 children were assessed with a language-screening tool (LANGUAGE4) at age 4 years. Asubsample(n = 206) was assessed on measures of sentence repetition, vocabulary, and grammatical knowledge at ages 4, 5, and 6 years. Results: A global latent language factor showed a high degree of longitudinal stability in children between the ages of 4 to 6 years. A low-performing group showing a language deficit compared to their age peers at age 4 was identified on the basis of the LANGUAGE4. The growth-rates during this 2-year time period were parallel for the low-performing and 3 higher performing groups of children. Conclusions: There is strong stability in children’s language skills between the ages of 4 and 6 years. The results demonstrate that a simple language screening measure can successfully identify a low-performing group of children who show persistent language weaknesses between the ages of 4 and 6 years. © 2016 American Speech-Language-Hearing Association.
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| 17. |
- Thompson, EJ, et al.
(author)
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Long COVID burden and risk factors in 10 UK longitudinal studies and electronic health records
- 2022
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 3528-
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Journal article (peer-reviewed)abstract
- The frequency of, and risk factors for, long COVID are unclear among community-based individuals with a history of COVID-19. To elucidate the burden and possible causes of long COVID in the community, we coordinated analyses of survey data from 6907 individuals with self-reported COVID-19 from 10 UK longitudinal study (LS) samples and 1.1 million individuals with COVID-19 diagnostic codes in electronic healthcare records (EHR) collected by spring 2021. Proportions of presumed COVID-19 cases in LS reporting any symptoms for 12+ weeks ranged from 7.8% and 17% (with 1.2 to 4.8% reporting debilitating symptoms). Increasing age, female sex, white ethnicity, poor pre-pandemic general and mental health, overweight/obesity, and asthma were associated with prolonged symptoms in both LS and EHR data, but findings for other factors, such as cardio-metabolic parameters, were inconclusive.
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