| 1. |
- Olson, Nathan D., et al.
(author)
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precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
- 2020
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Other publication (other academic/artistic)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 2. |
- Olson, Nathan D., et al.
(author)
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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
- 2022
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In: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
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Journal article (peer-reviewed)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 3. |
- Shang, Xiaobo, et al.
(author)
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Emerging materials for circularly polarized light detection
- 2022
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In: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 10:7, s. 2400-2410
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Research review (peer-reviewed)abstract
- Detecting circularly polarized light (CPL) signals is the key technique in many advanced sensing technologies. Over recent decades, many efforts have been devoted to both the material design and the device engineering of CPL photodetectors. CPL detectors with different sensing wavelengths have distinct applications in bio-imaging, drug discovery, and information encryption. In this review, we first introduce the working principle of state-of-the-art CPL photodetectors followed by a general material design strategy. We then systematically summarize the recent progress on the chiral materials developed for CPL detection, including inorganic metamaterials, organics, hybridized materials, etc. We compare and analyse the photocurrent dissymmetry factors of these systems and provide perspectives on strategies to improve the dissymmetry factors and extend the detection wavelength. We believe that the information we include in this review would attract broader interest from researchers working on different aspects of organic and hybridized semiconductor materials and devices.
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| 4. |
- Tian, Ye, et al.
(author)
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Holocene climate change in southern Oman deciphered by speleothem records and climate model simulations
- 2023
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In: Nature Communications. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Qunf Cave oxygen isotope (& delta;O-18(c)) record from southern Oman is one of the most significant of few Holocene Indian summer monsoon cave records. However, the interpretation of the Qunf & delta;O-18(c) remains in dispute. Here we provide a multi-proxy record from Qunf Cave and climate model simulations to reconstruct the Holocene local and regional hydroclimate changes. The results indicate that besides the Indian summer monsoon, the North African summer monsoon also contributes water vapor to southern Oman during the early to middle Holocene. In principle, Qunf & delta;O-18(c) values reflect integrated oxygen-isotope fractionations over a broad moisture transport swath from moisture sources to the cave site, rather than local precipitation amount alone, and thus the Qunf & delta;O-18(c) record characterizes primary changes in the Afro-Asian monsoon regime across the Holocene. In contrast, local climate proxies appear to suggest an overall slightly increased or unchanged wetness over the Holocene at the cave site. Southern Oman speleothem oxygen isotope and multi-proxy data reveal diverse changes in the Afro-Indian summer monsoon circulations and local hydroclimate conditions during the Holocene, confirming climate model simulations.
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| 5. |
- Cheng, Hai, et al.
(author)
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Milankovitch theory and monsoon
- 2022
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In: The Innovation. - : Elsevier BV. - 2666-6758. ; 3:6
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Research review (peer-reviewed)abstract
- The widely accepted “Milankovitch theory” explains insolation-induced waxing and waning of the ice sheets and their effect on the global climate on orbital timescales. In the past half century, however, the theory has often come under scrutiny, especially regarding its “100-ka problem.” Another drawback, but the one that has received less attention, is the “monsoon problem,” which pertains to the exclusion of monsoon dynamics in classic Milankovitch theory even though the monsoon prevails over the vast low-latitude (∼30° N to ∼30° S) region that covers half of the Earth's surface and receives the bulk of solar radiation. In this review, we discuss the major issues with the current form of Milankovitch theory and the progress made at the research forefront. We suggest shifting the emphasis from the ultimate outcomes of the ice volume to the causal relationship between changes in northern high-latitude insolation and ice age termination events (or ice sheet melting rate) to help reconcile the classic “100-ka problem.” We discuss the discrepancies associated with the characterization of monsoon dynamics, particularly the so-called “sea-land precession-phase paradox” and the “Chinese 100-ka problem.” We suggest that many of these discrepancies are superficial and can be resolved by applying a holistic “monsoon system science” approach. Finally, we propose blending the conventional Kutzbach orbital monsoon hypothesis, which calls for summer insolation forcing of monsoons, with Milankovitch theory to formulate a combined “Milankovitch-Kutzbach hypothesis” that can potentially explain the dual nature of orbital hydrodynamics of the ice sheet and monsoon systems, as well as their interplays and respective relationships with the northern high-latitude insolation and inter-tropical insolation differential.
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| 6. |
- Li, Hanying, et al.
(author)
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Understanding Interannual Variations of the Local Rainy Season over the Southwest Indian Ocean
- 2021
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In: Advances in Atmospheric Sciences. - : Springer Science and Business Media LLC. - 0256-1530 .- 1861-9533. ; 38:11, s. 1852-1862
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Journal article (peer-reviewed)abstract
- Located at the southern boundary of the tropical rainfall belt within the South Africa monsoon regime, Rodrigues Island, ∼2500 km east of East Africa, is ideally located to investigate climatic changes over the southwest Indian Ocean (SWIO). In this study, we investigate the climatic controls of its modern interannual rainfall variability in terms of teleconnection and local effects. We find that increased rainfall over the SWIO tends to occur in association with anomalously warm (cold) SSTs over the equatorial central Pacific (Maritime Continent), resembling the central Pacific El Niño, closely linked with the Victoria mode in the North Pacific. Our analyses show that the low-level convergence induced by warm SST over the equatorial central Pacific leads to anomalous low-level divergence over the Maritime Continent and convergence over a large area surrounding the Rodrigues Island, which leads to increased rainfall over the SWIO during the rainy season. Meanwhile, the excited Rossby wave along the tropical Indian Ocean transports more water vapor from the tropical convergence zone into the SWIO via intensified northwest wind. Furthermore, positive feedback induced by the Rossby wave response to the increased rainfall in the region contributes to the large interannual variations over the SWIO.
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