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  • 1
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    Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-27
    Description: Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Atmosphere, Vol. 3, Pages 103-123: An Evaluation of Modeled Plume Injection Height with Satellite-Derived Observed Plume Height (2012)
    MDPI Publishing
    Details
    Publication Date: 2012-05-03
    Description: Plume injection height influences plume transport characteristics, such as range and potential for dilution. We evaluated plume injection height from a predictive wildland fire smoke transport model over the contiguous United States (U.S.) from 2006 to 2008 using satellite-derived information, including plume top heights from the Multi-angle Imaging SpectroRadiometer (MISR) Plume Height Climatology Project and aerosol vertical profiles from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP). While significant geographic variability was found in the comparison between modeled plumes and satellite-detected plumes, modeled plume heights were lower overall. In the eastern U.S., satellite-detected and modeled plume heights were similar (median height 671 and 660 m respectively). Both satellite-derived and modeled plume injection heights were higher in the western U.S. (2345 and 1172 m, respectively). Comparisons of modeled plume injection height to satellite-derived plume height at the fire location (R2 = 0.1) were generally worse than comparisons done downwind of the fire (R2 = 0.22). This suggests that the exact injection height is not as important as placement of the plume in the correct transport layer for transport modeling.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
    Published by MDPI Publishing
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  • 3
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    IJERPH, Vol. 16, Pages 2137: Machine Learning-Based Integration of High-Resolution Wildfire Smoke Simulations and Observations for Regional Health Impact Assessment (2019)
    MDPI
    Details
    Publication Date: 2019
    Description: Large wildfires are an increasing threat to the western U.S. In the 2017 fire season, extensive wildfires occurred across the Pacific Northwest (PNW). To evaluate public health impacts of wildfire smoke, we integrated numerical simulations and observations for regional fire events during August-September of 2017. A one-way coupled Weather Research and Forecasting and Community Multiscale Air Quality modeling system was used to simulate fire smoke transport and dispersion. To reduce modeling bias in fine particulate matter (PM2.5) and to optimize smoke exposure estimates, we integrated modeling results with the high-resolution Multi-Angle Implementation of Atmospheric Correction satellite aerosol optical depth and the U.S. Environmental Protection Agency AirNow ground-level monitoring PM2.5 concentrations. Three machine learning-based data fusion algorithms were applied: An ordinary multi-linear regression method, a generalized boosting method, and a random forest (RF) method. 10-Fold cross-validation found improved surface PM2.5 estimation after data integration and bias correction, especially with the RF method. Lastly, to assess transient health effects of fire smoke, we applied the optimized high-resolution PM2.5 exposure estimate in a short-term exposure-response function. Total estimated regional mortality attributable to PM2.5 exposure during the smoke episode was 183 (95% confidence interval: 0, 432), with 85% of the PM2.5 pollution and 95% of the consequent multiple-cause mortality contributed by fire emissions. This application demonstrates both the profound health impacts of fire smoke over the PNW and the need for a high-performance fire smoke forecasting and reanalysis system to reduce public health risks of smoke hazards in fire-prone regions.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI
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  • 4
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    Atmosphere, Vol. 3, Pages 103-123: An Evaluation of Modeled Plume Injection Height with Satellite-Derived Observed Plume Height (2012)
    MDPI Publishing
    Details
    Publication Date: 2012-01-19
    Description: Plume injection height influences plume transport characteristics, such as range and potential for dilution. We evaluated plume injection height from a predictive wildland fire smoke transport model over the contiguous United States (U.S.) from 2006 to 2008 using satellite-derived information, including plume top heights from the Multi-angle Imaging SpectroRadiometer (MISR) Plume Height Climatology Project and aerosol vertical profiles from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP). While significant geographic variability was found in the comparison between modeled plumes and satellite-detected plumes, modeled plume heights were lower overall. In the eastern U.S., satellite-detected and modeled plume heights were similar (median height 671 and 660 m respectively). Both satellite-derived and modeled plume injection heights were higher in the western U.S. (2345 and 1172 m, respectively). Comparisons of modeled plume injection height to satellite-derived plume height at the fire location (R2 = 0.1) were generally worse than comparisons done downwind of the fire (R2 = 0.22). This suggests that the exact injection height is not as important as placement of the plume in the correct transport layer for transport modeling.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
    Published by MDPI Publishing
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  • 5
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    Towards a transgenic model of Huntington's disease in a non-human primate (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-05-20
    Description: Non-human primates are valuable for modelling human disorders and for developing therapeutic strategies; however, little work has been reported in establishing transgenic non-human primate models of human diseases. Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder characterized by motor impairment, cognitive deterioration and psychiatric disturbances followed by death within 10-15 years of the onset of the symptoms. HD is caused by the expansion of cytosine-adenine-guanine (CAG, translated into glutamine) trinucleotide repeats in the first exon of the human huntingtin (HTT) gene. Mutant HTT with expanded polyglutamine (polyQ) is widely expressed in the brain and peripheral tissues, but causes selective neurodegeneration that is most prominent in the striatum and cortex of the brain. Although rodent models of HD have been developed, these models do not satisfactorily parallel the brain changes and behavioural features observed in HD patients. Because of the close physiological, neurological and genetic similarities between humans and higher primates, monkeys can serve as very useful models for understanding human physiology and diseases. Here we report our progress in developing a transgenic model of HD in a rhesus macaque that expresses polyglutamine-expanded HTT. Hallmark features of HD, including nuclear inclusions and neuropil aggregates, were observed in the brains of the HD transgenic monkeys. Additionally, the transgenic monkeys showed important clinical features of HD, including dystonia and chorea. A transgenic HD monkey model may open the way to understanding the underlying biology of HD better, and to the development of potential therapies. Moreover, our data suggest that it will be feasible to generate valuable non-human primate models of HD and possibly other human genetic diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652570/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652570/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Shang-Hsun -- Cheng, Pei-Hsun -- Banta, Heather -- Piotrowska-Nitsche, Karolina -- Yang, Jin-Jing -- Cheng, Eric C H -- Snyder, Brooke -- Larkin, Katherine -- Liu, Jun -- Orkin, Jack -- Fang, Zhi-Hui -- Smith, Yoland -- Bachevalier, Jocelyne -- Zola, Stuart M -- Li, Shi-Hua -- Li, Xiao-Jiang -- Chan, Anthony W S -- R01 AG019206/AG/NIA NIH HHS/ -- R01 AG019206-07/AG/NIA NIH HHS/ -- R01 NS036232/NS/NINDS NIH HHS/ -- R01 NS036232-09/NS/NINDS NIH HHS/ -- R01 NS041669/NS/NINDS NIH HHS/ -- R01 NS041669-07/NS/NINDS NIH HHS/ -- England -- Nature. 2008 Jun 12;453(7197):921-4. doi: 10.1038/nature06975. Epub 2008 May 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18488016" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Animals, Newborn ; Brain/metabolism/pathology ; Chorea/genetics/physiopathology ; *Disease Models, Animal ; Dystonia/genetics/physiopathology ; Exons/genetics ; Female ; Humans ; Huntington Disease/*genetics/metabolism/pathology/*physiopathology ; Macaca mulatta/*genetics ; Male ; Nerve Tissue Proteins/*genetics/metabolism ; Nuclear Proteins/*genetics/metabolism ; Peptides/genetics/metabolism ; Pregnancy ; Survival Analysis ; Trinucleotide Repeat Expansion/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Climate, Vol. 6, Pages 100: Multi-Model Forecasts of Very-Large Fire Occurences during the End of the 21st Century (2018)
    MDPI
    In: Climate
    Details
    Publication Date: 2018
    Description: Climate change is anticipated to influence future wildfire activity in complicated, and potentially unexpected ways. Specifically, the probability distribution of wildfire size may change so that incidents that were historically rare become more frequent. Given that fires in the upper tails of the size distribution are associated with serious economic, public health, and environmental impacts, it is important for decision-makers to plan for these anticipated changes. However, at least two kinds of structural uncertainties hinder reliable estimation of these quantities—those associated with the future climate and those associated with the impacts. In this paper, we incorporate these structural uncertainties into projections of very-large fire (VLF)—those in the upper 95th percentile of the regional size distribution—frequencies in the Continental United States during the last half of the 21st century by using Bayesian model averaging. Under both moderate and high carbon emission scenarios, large increases in VLF frequency are predicted, with larger increases typically observed under the highest carbon emission scenarios. We also report other changes to future wildfire characteristics such as large fire frequency, seasonality, and the conditional likelihood of very-large fire events.
    Electronic ISSN: 2225-1154
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Published by MDPI
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  • 7
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    Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene (2016)
    Springer Nature
    Details
    Publication Date: 2016-05-24
    Description: Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene Scientific Reports, Published online: 23 May 2016; doi:10.1038/srep26311
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 8
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    Identifying genetically driven clinical phenotypes using linear mixed models (2016)
    Springer Nature
    Details
    Publication Date: 2016-04-27
    Description: Article Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes. Nature Communications doi: 10.1038/ncomms11433 Authors: Jonathan D. Mosley, John S. Witte, Emma K. Larkin, Lisa Bastarache, Christian M. Shaffer, Jason H. Karnes, C. Michael Stein, Elizabeth Phillips, Scott J. Hebbring, Murray H. Brilliant, John Mayer, Zhan Ye, Dan M. Roden, Joshua C. Denny
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 9
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    Multi-scalar influence of weather and climate on very large-fires in the Eastern United States (2014)
    Wiley
    Details
    Publication Date: 2014-06-27
    Description: ABSTRACT A majority of area burned in the Eastern United States (EUS) results from a limited number of exceptionally large wildfires. Relationships between climatic conditions and the occurrence of very large-fires (VLF) in the EUS were examined using composite and climate-niche analyses that consider atmospheric factors across inter-annual, sub-seasonal and synoptic temporal scales. While most large-fires in the EUS coincided with below normal fuel moisture and elevated fire weather, VLF preferentially occurred during a long-term drought accompanied by more acute sub-seasonal drought realized through fuel moisture stress and elevated fire-weather conditions. These results were corroborated across the EUS, with varying influences of drought, fire danger and fire weather discriminating VLF from other large fires across different geographical regions. We also show that the probability of VLF conditioned by fire occurrence increases when long-term drought, depleted fuel moisture and elevated fire weather align. This framework illustrates the compounding role of different timescales in VLF occurrence and serves as a basis for improving VLF predictions with seasonal climate forecasts and climate change scenarios.
    Print ISSN: 0899-8418
    Electronic ISSN: 1097-0088
    Topics: Geosciences , Physics
    Published by Wiley
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  • 10
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    Modeling very large-fire occurrences over the continental United States from weather and climate forcing (2014)
    Institute of Physics
    Details
    Publication Date: 2014-12-01
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Institute of Physics
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