| 1. |
- Ade, Peter, et al.
(författare)
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The Simons Observatory : science goals and forecasts
- 2019
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2
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Tidskriftsartikel (refereegranskat)abstract
- The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
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| 2. |
- Aken, Bronwen L., et al.
(författare)
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The Ensembl gene annotation system
- 2016
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Ingår i: Database. - : Oxford University Press (OUP). - 1758-0463.
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Tidskriftsartikel (refereegranskat)abstract
- The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.
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| 3. |
- Denver, Dee R, et al.
(författare)
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Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans.
- 2010
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:12
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Tidskriftsartikel (refereegranskat)abstract
- Deleterious mutation poses a serious threat to human health and the persistence of small populations. Although adaptive recovery from deleterious mutation has been well-characterized in prokaryotes, the evolutionary mechanisms by which multicellular eukaryotes recover from deleterious mutation remain unknown. We applied high-throughput DNA sequencing to characterize genomic divergence patterns associated with the adaptive recovery from deleterious mutation using a Caenorhabditis elegans recovery-line system. The C. elegans recovery lines were initiated from a low-fitness mutation-accumulation (MA) line progenitor and allowed to independently evolve in large populations (N ∼ 1000) for 60 generations. All lines rapidly regained levels of fitness similar to the wild-type (N2) MA line progenitor. Although there was a near-zero probability of a single mutation fixing due to genetic drift during the recovery experiment, we observed 28 fixed mutations. Cross-generational analysis showed that all mutations went from undetectable population-level frequencies to a fixed state in 10-20 generations. Many recovery-line mutations fixed at identical timepoints, suggesting that the mutations, if not beneficial, hitchhiked to fixation during selective sweep events observed in the recovery lines. No MA line mutation reversions were detected. Parallel mutation fixation was observed for two sites in two independent recovery lines. Analysis using a C. elegans interactome map revealed many predicted interactions between genes with recovery line-specific mutations and genes with previously accumulated MA line mutations. Our study suggests that recovery-line mutations identified in both coding and noncoding genomic regions might have beneficial effects associated with compensatory epistatic interactions.
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| 4. |
- Leblond, Claire S, et al.
(författare)
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Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments.
- 2014
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 10:9
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Tidskriftsartikel (refereegranskat)abstract
- SHANK genes code for scaffold proteins located at the post-synaptic density of glutamatergic synapses. In neurons, SHANK2 and SHANK3 have a positive effect on the induction and maturation of dendritic spines, whereas SHANK1 induces the enlargement of spine heads. Mutations in SHANK genes have been associated with autism spectrum disorders (ASD), but their prevalence and clinical relevance remain to be determined. Here, we performed a new screen and a meta-analysis of SHANK copy-number and coding-sequence variants in ASD. Copy-number variants were analyzed in 5,657 patients and 19,163 controls, coding-sequence variants were ascertained in 760 to 2,147 patients and 492 to 1,090 controls (depending on the gene), and, individuals carrying de novo or truncating SHANK mutations underwent an extensive clinical investigation. Copy-number variants and truncating mutations in SHANK genes were present in ∼1% of patients with ASD: mutations in SHANK1 were rare (0.04%) and present in males with normal IQ and autism; mutations in SHANK2 were present in 0.17% of patients with ASD and mild intellectual disability; mutations in SHANK3 were present in 0.69% of patients with ASD and up to 2.12% of the cases with moderate to profound intellectual disability. In summary, mutations of the SHANK genes were detected in the whole spectrum of autism with a gradient of severity in cognitive impairment. Given the rare frequency of SHANK1 and SHANK2 deleterious mutations, the clinical relevance of these genes remains to be ascertained. In contrast, the frequency and the penetrance of SHANK3 mutations in individuals with ASD and intellectual disability-more than 1 in 50-warrant its consideration for mutation screening in clinical practice.
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| 5. |
- Welch, Vivian, et al.
(författare)
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Health, social care and technological interventions to improve functional ability of older adults living at home : An evidence and gap map
- 2021
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Ingår i: Campbell Systematic Reviews. - : Wiley. - 1891-1803. ; 17:3
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Tidskriftsartikel (refereegranskat)abstract
- Background: By 2030, the global population of people older than 60 years is expected to be higher than the number of children under 10 years, resulting in major health and social care system implications worldwide. Without a supportive environment, whether social or built, diminished functional ability may arise in older people. Functional ability comprises an individual's intrinsic capacity and people's interaction with their environment enabling them to be and do what they value. Objectives: This evidence and gap map aims to identify primary studies and systematic reviews of health and social support services as well as assistive devices designed to support functional ability among older adults living at home or in other places of residence. Search Methods: We systematically searched from inception to August 2018 in: MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, CENTRAL, CINAHL, PsycINFO, AgeLine, Campbell Library, ASSIA, Social Science Citation Index and Social Policy & Practice. We conducted a focused search for grey literature and protocols of studies (e.g., ProQuest Theses and Dissertation Global, conference abstract databases, Help Age, PROSPERO, Cochrane and Campbell libraries and ClinicalTrials.gov). Selection Criteria: Screening and data extraction were performed independently in duplicate according to our intervention and outcome framework. We included completed and on-going systematic reviews and randomized controlled trials of effectiveness on health and social support services provided at home, assistive products and technology for personal indoor and outdoor mobility and transportation as well as design, construction and building products and technology of buildings for private use such as wheelchairs, and ramps. Data Collection and Analysis: We coded interventions and outcomes, and the number of studies that assessed health inequities across equity factors. We mapped outcomes based on the International Classification of Function, Disability and Health (ICF) adapted categories: intrinsic capacities (body function and structures) and functional abilities (activities). We assessed methodological quality of systematic reviews using the AMSTAR II checklist. Main Results: After de-duplication, 10,783 records were screened. The map includes 548 studies (120 systematic reviews and 428 randomized controlled trials). Interventions and outcomes were classified using domains from the International Classification of Function, Disability and Health (ICF) framework. Most systematic reviews (n = 71, 59%) were rated low or critically low for methodological quality. The most common interventions were home-based rehabilitation for older adults (n = 276) and home-based health services for disease prevention (n = 233), mostly delivered by visiting healthcare professionals (n = 474). There was a relative paucity of studies on personal mobility, building adaptations, family support, personal support and befriending or friendly visits. The most measured intrinsic capacity domains were mental function (n = 269) and neuromusculoskeletal function (n = 164). The most measured outcomes for functional ability were basic needs (n = 277) and mobility (n = 160). There were few studies which evaluated outcome domains of social participation, financial security, ability to maintain relationships and communication. There was a lack of studies in low- and middle-income countries (LMICs) and a gap in the assessment of health equity issues. Authors' Conclusions: There is substantial evidence for interventions to promote functional ability in older adults at home including mostly home-based rehabilitation for older adults and home-based health services for disease prevention. Remotely delivered home-based services are of greater importance to policy-makers and practitioners in the context of the COVID-19 pandemic. This map of studies published prior to the pandemic provides an initial resource to identify relevant home-based services which may be of interest for policy-makers and practitioners, such as home-based rehabilitation and social support, although these interventions would likely require further adaptation for online delivery during the COVID-19 pandemic. There is a need to strengthen assessment of social support and mobility interventions and outcomes related to making decisions, building relationships, financial security, and communication in future studies. More studies are needed to assess LMIC contexts and health equity issues.
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