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  • 1
    Online Resource
    Online Resource
    De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 5 ( 2020-02-04), p. 2560-2569
    Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1902766117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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  • 2
    Online Resource
    Online Resource
    Searching Night and Day : A Dissociation of Effects of Circadian Phase and Time Awake on Visual Selective Attention and Vigilance
    SAGE Publications ; 2003
    In:  Psychological Science Vol. 14, No. 6 ( 2003-11), p. 549-557
    Details
    In: Psychological Science, SAGE Publications, Vol. 14, No. 6 ( 2003-11), p. 549-557
    Abstract: How does sleepiness affect selective attention? We studied the effect of circadian phase and time awake on visual search. The generalized-cognitive-slowing hypothesis predicts that search rate will be slower, feature guidance less effective, and response time (RT) lengthened when observers are sleepy. Observers performed spatial-configuration (finding a 5 among 2s) and conjunction (finding red vertical among red horizontal and green vertical) search tasks during 38 hr of wakefulness under constant conditions. Adverse circadian phases and elapsed time awake did lead to increased RT (corrected for errors). However, contrary to the hypothesis, search rates (indexed by RT × Set Size slopes) were constant across the protocol. This was true for conjunction as well as for spatial-configuration search, indicating that feature guidance was also insensitive to sleepiness. The locus of sleepiness effects on search is probably downstream from the bottleneck of attentional selection. Observers did trade accuracy for speed when sleepy. This implicates decision-stage impairments.
    Type of Medium: Online Resource
    ISSN: 0956-7976 , 1467-9280
    URL: Article
    DOI: 10.1046/j.0956-7976.2003.psci_1464.x
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2003
    detail.hit.zdb_id: 2022256-7
    SSG: 5,2
    Location Call Number Limitation Availability
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  • 3
    Online Resource
    Online Resource
    Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 15 ( 2016-04-12), p. 4086-4091
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 15 ( 2016-04-12), p. 4086-4091
    Abstract: Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N⋅ha −1 ⋅y −1 , we found a unimodal relationship; richness increased at low deposition levels and decreased above 8.7 and 13.4 kg N⋅ha −1 ⋅y −1 in open and closed-canopy vegetation, respectively. N deposition exceeded critical loads for loss of plant species richness in 24% of 15,136 sites examined nationwide. There were negative relationships between species richness and N deposition in 36% of 44 community gradients. Vulnerability to N deposition was consistently higher in more acidic soils whereas the moderating roles of temperature and precipitation varied across scales. We demonstrate here that negative relationships between N deposition and species richness are common, albeit not universal, and that fine-scale processes can moderate vegetation responses to N deposition. Our results highlight the importance of contingent factors when estimating ecosystem vulnerability to N deposition and suggest that N deposition is affecting species richness in forested and nonforested systems across much of the continental United States.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1515241113
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
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