| 1. |
- Bergström, Anders, et al.
(författare)
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Grey wolf genomic history reveals a dual ancestry of dogs
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 607:7918, s. 313-320
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Tidskriftsartikel (refereegranskat)abstract
- The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
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| 2. |
- Locke, Adam E, et al.
(författare)
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Genetic studies of body mass index yield new insights for obesity biology.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 197-401
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
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| 3. |
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| 4. |
- Shungin, Dmitry, et al.
(författare)
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New genetic loci link adipose and insulin biology to body fat distribution.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 187-378
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Tidskriftsartikel (refereegranskat)abstract
- Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.
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| 5. |
- Allesøe, Rosa Lundbye, et al.
(författare)
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Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models
- 2023
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 41:3, s. 399-408
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Tidskriftsartikel (refereegranskat)abstract
- The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug–omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug–drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
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| 6. |
- Amat-Foraster, Maria, et al.
(författare)
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Modulation of thalamo-cortical activity by the NMDA receptor antagonists ketamine and phencyclidine in the awake freely-moving rat
- 2019
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Ingår i: Neuropharmacology. - : Elsevier BV. - 0028-3908. ; 158
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Tidskriftsartikel (refereegranskat)abstract
- Non-competitive N-methyl-D-aspartate receptor antagonists mimic schizophrenia symptoms and produce immediate and persistent antidepressant effects. We investigated the effects of ketamine and phencyclidine (PCP) on thalamo-cortical network activity in awake, freely-moving male Wistar rats to gain new insight into the neuronal populations and brain circuits involved in the effects of NMDA-R antagonists. Single unit and local field potential (LFP) recordings were conducted in mediodorsal/centromedial thalamus and in medial prefrontal cortex (mPFC) using microelectrode arrays. Ketamine and PCP moderately increased the discharge rates of principal neurons in both areas while not attenuating the discharge of mPFC GABAergic interneurons. They also strongly affected LFP activity, reducing beta power and increasing that of gamma and high-frequency oscillation bands. These effects were short-lasting following the rapid pharmacokinetic profile of the drugs, and consequently were not present at 24 h after ketamine administration. The temporal profile of both drugs was remarkably different, with ketamine effects peaking earlier than PCP effects. Although this study is compatible with the glutamate hypothesis for fast-acting antidepressant action, it does not support a local disinhibition mechanism as the source for the increased pyramidal neuron activity in mPFC. The short-lasting increase in thalamo-cortical activity is likely associated with the rapid psychotomimetic action of both agents but could also be part of a cascade of events ultimately leading to the persistent antidepressant effects of ketamine. Changes in spectral contents of high-frequency bands by the drugs show potential as translational biomarkers for target engagement of NMDA-R modulators.
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| 7. |
- Arat, Arzu, et al.
(författare)
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Organisation of preventive child health services : Key to socio-economic equity in vaccine uptake?
- 2020
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Ingår i: Scandinavian Journal of Public Health. - : SAGE Publications. - 1403-4948 .- 1651-1905. ; 48:5, s. 491-494
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Measles has made a comeback in Western Europe, with more cases being reported each year. One factor behind this development is low vaccination coverage in socially disadvantaged segments of the population in many countries. This study investigates whether socioeconomic patterns of uptake of the measles, mumps and rubella (MMR) vaccine in the Nordic countries differ by national organisation of preventive health services for children. METHODS: MMR vaccine uptake before the age of two years was analysed in register data from Denmark, Finland, Iceland and Sweden, linked to family indicators of socio-economic status (SES) from national registers. RESULTS: Denmark, a country where child vaccinations are administered by general practitioners, presented the lowest overall coverage of MMR at 83%. It also had the greatest difference between subpopulations of low and high SES at 14 percentage points. Finland, Iceland and Sweden, countries where preschool children are vaccinated in 'well-baby' clinics, had a higher overall coverage at 91-94%, with a more equal distribution between SES groups at 1-4 percentage points. CONCLUSIONS: This study suggests that the organisation of preventive health care in special units, 'well-baby' clinics, facilitates vaccine uptake among children with low SES in a Nordic welfare context.
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| 8. |
- Arnalds, Unnar B., et al.
(författare)
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A new look on the two-dimensional Ising model : thermal artificial spins
- 2016
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- We present a direct experimental investigation of the thermal ordering in an artificial analogue of an asymmetric two-dimensional Ising system composed of a rectangular array of nano-fabricated magnetostatically interacting islands. During fabrication and below a critical thickness of the magnetic material the islands are thermally fluctuating and thus the system is able to explore its phase space. Above the critical thickness the islands freeze-in resulting in an arrested thermalized state for the array. Determining the magnetic state we demonstrate a genuine artificial two-dimensional Ising system which can be analyzed in the context of nearest neighbor interactions.
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| 9. |
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| 10. |
- Beuch, Ulrike, et al.
(författare)
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Detection, distribution and control of Potato mop-top virus, a soil-borne virus, in northern Europe
- 2010
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Ingår i: Annals of Applied Biology. - : Wiley. - 0003-4746. ; 157, s. 163-178
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Forskningsöversikt (refereegranskat)abstract
- Potato mop-top virus (PMTV; genus Pomovirus; family Virgaviridae) is transmitted by the soil-borne Spongospora subterranea f.sp. subterranea, a protoctist that causes powdery scab on potato. PMTV is distributed widely in the potato growing areas in South and North America, Japan and northwestern Europe. This article reviews the current knowledge on detection, distribution and control of PMTV with focus on the Baltic Sea region. Since the 1980s, PMTV has caused great economic losses to potato production in the Nordic countries (Norway, Sweden, Denmark and Finland), but its occurrence in other countries of the Baltic Sea region remained unknown. To fill this knowledge gap, harmonised sampling and virus detection procedures including bioassays and serological and molecular methods were employed by 21 research institutions to detect PMTV in potato tubers and soil samples in 2005-2008. Potato growing areas were widely contaminated with PMTV in the Nordic countries. Only the main seed potato production area in northern Sweden and the High Grade seed potato production zone in Finland were negative for PMTV. Intensive and systematic surveys in Poland in 2004-2008 found no evidence of PMTV, except a single PMTV-infected tuber detected in 2008. Surveys in the Baltic countries (Lithuania, Latvia and Estonia) and northwestern Russia (Leningrad province) were negative for PMTV, except infection of minitubers in a screenhouse in Latvia in 2005. Varying percentages of tubers expressing spraing symptoms in Sweden, Norway, Denmark and Poland were infected with Tobacco rattle virus, and bioassays indicated similar results for Russia. Incidence of symptomless infections with PMTV was high in tubers of many potato cultivars. Here, we discuss the contrasting patterns of distribution of PMTV in the Baltic Sea region, factors playing a role in dispersal and establishment of PMTV in new fields and means for controlling PMTV and its spread to new areas. We emphasise the use of the current virus-specific methods for the detection of PMTV in symptomless potato tubers and the high risks of disseminating PMTV to new fields and areas in viruliferous resting spores of S. subterranea in the soil adhering to seed tubers. PMTV-resistant potato cultivars will provide the only sustainable means for preventing yield losses in the infested fields and the prospects of resistance breeding are summarised.
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