| 1. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 2. |
- Haw, David J., et al.
(author)
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Optimizing social and economic activity while containing SARS-CoV-2 transmission using DAEDALUS
- 2022
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In: Nature Computational Science. - : Springer Science and Business Media LLC. - 2662-8457. ; 2:4, s. 223-233
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Journal article (peer-reviewed)abstract
- To study the trade-off between economic, social and health outcomes in the management of a pandemic, DAEDALUS integrates a dynamic epidemiological model of SARS-CoV-2 transmission with a multi-sector economic model, reflecting sectoral heterogeneity in transmission and complex supply chains. The model identifies mitigation strategies that optimize economic production while constraining infections so that hospital capacity is not exceeded but allowing essential services, including much of the education sector, to remain active. The model differentiates closures by economic sector, keeping those sectors open that contribute little to transmission but much to economic output and those that produce essential services as intermediate or final consumption products. In an illustrative application to 63 sectors in the United Kingdom, the model achieves an economic gain of between £161 billion (24%) and £193 billion (29%) compared to a blanket lockdown of non-essential activities over six months. Although it has been designed for SARS-CoV-2, DAEDALUS is sufficiently flexible to be applicable to pandemics with different epidemiological characteristics.
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| 3. |
- Enright, Michael J., et al.
(author)
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Role of Atomic Structure on Exciton Dynamics and Photoluminescence in NIR Emissive InAs/InP/ZnSe Quantum Dots
- 2022
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 126:17, s. 7576-7587
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Journal article (peer-reviewed)abstract
- The development of bright, near-infrared-emissive quantum dots (QDs) is a necessary requirement for the realization of important new classes of technology. Specifically, there exist significant needs for brighter, heavy metal-free, near-infrared (NIR) QDs for applications with high radiative efficiency that span diverse applications, including down-conversion emitters for high-performance luminescent solar concentrators. We use a combination of theoretical and experimental approaches to synthesize bright, NIR luminescent InAs/InP/ZnSe QDs and elucidate fundamental material attributes that remain obstacles for development of near-unity NIR QD luminophores. First, using Monte Carlo ray tracing, we identify the atomic and electronic structural attributes of InAs core/shell, NIR emitters, whose luminescence properties can be tailored by synthetic design to match most beneficially those of high-performance, single-band-gap photovoltaic devices based on important semiconductor materials, such Si or GaAs. Second, we synthesize InAs/InP/ZnSe QDs based on the optical attributes found to maximize LSC performance and develop methods to improve the emissive qualities of NIR emitters with large, tunable Stokes ratios, narrow emission linewidths, and high luminescence quantum yields (here reaching 60 +/- 2%). Third, we employ atomistic electronic structure calculations to explore charge carrier behavior at the nanoscale affected by interfacial atomic structures and find that significant exciton occupation of the InP shell occurs in most cases despite the InAs/InP type I bulk band alignment. Furthermore, the density of the valence band maximum state extends anisotropically through the (111) crystal planes to the terminal InP surfaces/interfaces, indicating that surface defects, such as unpassivated phosphorus dangling bonds, located on the (111) facets play an outsized role in disrupting the valence band maximum and quenching photoluminescence.
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| 4. |
- Haw, David J., et al.
(author)
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Data needs for integrated economic-epidemiological models of pandemic mitigation policies
- 2022
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In: Epidemics. - : Elsevier. - 1755-4365 .- 1878-0067. ; 41
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Journal article (peer-reviewed)abstract
- The COVID-19 pandemic and the mitigation policies implemented in response to it have resulted in economic losses worldwide. Attempts to understand the relationship between economics and epidemiology has led to a new generation of integrated mathematical models. The data needs for these models transcend those of the individual fields, especially where human interaction patterns are closely linked with economic activity. In this article, we reflect upon modelling efforts to date, discussing the data needs that they have identified, both for understanding the consequences of the pandemic and policy responses to it through analysis of historic data and for the further development of this new and exciting interdisciplinary field.
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| 5. |
- Haw, David, et al.
(author)
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Report 35 : How can we keep schools and universities open? Differentiating closures by economic sector to optimize social and economic activity while containing SARS-CoV-2 transmission
- 2020
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Reports (other academic/artistic)abstract
- There is a trade-off between the education sector and other economic sectors in the control of SARS-CoV-2 transmission. Here we integrate a dynamic model of SARS-CoV-2 transmission with a 63-sector economic model reflecting sectoral heterogeneity in transmission and economic interdependence between sectors. We identify control strategies which optimize economic production while keeping schools and universities operational and constraining infections such that emergency hospital capacity is not exceeded. The model estimates an economic gain of between £163bn and £205bn for the United Kingdom compared to a blanket lockdown of non-essential activity over six months, depending on hospital capacity. Sectors identified as potential priorities for closure are contact-intensive and/or less economically productive.
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| 6. |
- Sodhi, Navjot S., et al.
(author)
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Barcoding Indo-Malayan birds
- 2007
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In: The Raffles bulletin of zoology. - 0217-2445. ; 55:2, s. 397-398
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Journal article (other academic/artistic)
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