| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
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| 4. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 5. |
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| 6. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 7. |
- Ching, Tao-Chung, et al.
(author)
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The JCMT BISTRO-2 Survey: Magnetic Fields of the Massive DR21 Filament
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:2
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Journal article (peer-reviewed)abstract
- We present 850 mu m dust polarization observations of the massive DR21 filament from the B-fields In STar-forming Region Observations (BISTRO) survey, using the POL-2 polarimeter and the SCUBA-2 camera on the James Clerk Maxwell Telescope. We detect ordered magnetic fields perpendicular to the parsec-scale ridge of the DR21 main filament. In the subfilaments, the magnetic fields are mainly parallel to the filamentary structures and smoothly connect to the magnetic fields of the main filament. We compare the POL-2 and Planck dust polarization observations to study the magnetic field structures of the DR21 filament on 0.1-10 pc scales. The magnetic fields revealed in the Planck data are well-aligned with those of the POL-2 data, indicating a smooth variation of magnetic fields from large to small scales. The plane-of-sky magnetic field strengths derived from angular dispersion functions of dust polarization are 0.6-1.0 mG in the DR21 filament and similar to 0.1 mG in the surrounding ambient gas. The mass-to-flux ratios are found to be magnetically supercritical in the filament and slightly subcritical to nearly critical in the ambient gas. The alignment between column density structures and magnetic fields changes from random alignment in the low-density ambient gas probed by Planck to mostly perpendicular in the high-density main filament probed by James Clerk Maxwell Telescope. The magnetic field structures of the DR21 filament are in agreement with MHD simulations of a strongly magnetized medium, suggesting that magnetic fields play an important role in shaping the DR21 main filament and subfilaments.
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| 8. |
- Karoly, Janik, et al.
(author)
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The JCMT BISTRO Survey: Studying the Complex Magnetic Field of L43
- 2023
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In: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 952:1
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Journal article (peer-reviewed)abstract
- We present observations of polarized dust emission at 850 mu m from the L43 molecular cloud, which sits in the Ophiuchus cloud complex. The data were taken using SCUBA-2/POL-2 on the James Clerk Maxwell Telescope as a part of the BISTRO large program. L43 is a dense (N-H2 similar to 10(22) - 10(23) cm(-2)) complex molecular cloud with a submillimeter-bright starless core and two protostellar sources. There appears to be an evolutionary gradient along the isolated filament that L43 is embedded within, with the most evolved source closest to the Sco OB2 association. One of the protostars drives a CO outflow that has created a cavity to the southeast. We see a magnetic field that appears to be aligned with the cavity walls of the outflow, suggesting interaction with the outflow. We also find a magnetic field strength of up to similar to 160 +/- 30 mu G in the main starless core and up to similar to 90 +/- 40 mu G in the more diffuse, extended region. These field strengths give magnetically super- and subcritical values, respectively, and both are found to be roughly trans-Alfvenic. We also present a new method of data reduction for these denser but fainter objects like starless cores.
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| 9. |
- Mahajan, Anubha, et al.
(author)
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
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In: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
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Journal article (peer-reviewed)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
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| 10. |
- Luo, Yang, et al.
(author)
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Three-dimensional and temperature-dependent electronic structure of the heavy-fermion compound CePt2In7 studied by angle-resolved photoemission spectroscopy
- 2020
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In: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 101:11
-
Journal article (peer-reviewed)abstract
- The three-dimensional and temperature-dependent electronic structures of the heavy-fermion superconductor CePt2In7 are investigated. Angle-resolved photoemission spectroscopy using variable photon energy establishes the existence of quasi-two- and three-dimensional Fermi surface topologies. Temperature-dependent 4d-4f on-resonance photoemission spectroscopies data reveal that heavy quasiparticle bands begin to form at a temperature well above the characteristic (coherence) temperature T+. The emergence of low-lying crystal electric field excitation may be responsible for the "relocalization" or the precursor to the establishment of heavy electrons coherence in heavy-fermion compounds. These findings provide critical insight into understanding the hybridization in heavy-fermion systems.
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| 11. |
- Meng, Yuan, et al.
(author)
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Fate and risk assessment of emerging contaminants in reclaimed water production processes
- 2021
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In: Frontiers of Environmental Science and Engineering. - : Springer. - 2095-2201 .- 2095-221X. ; 15:5
-
Journal article (peer-reviewed)abstract
- Reclaimed water has been widely applied in irrigation and industrial production. Revealing the behavior of emerging contaminants in the production process of reclaimed water is the first prerequisite for developing relevant water quality standards. This study investigated 43 emerging contaminants, including 22 pharmaceuticals and personal care products (PPCPs), 11 organophosphorus flame retardants (OPFRs), and 10 antibiotic resistance genes (ARGs) in 3 reclaimed wastewater treatment plants (RWTPs) in Beijing. The composition profiles and removal efficiencies of these contaminants in RWTPs were determined. The results indicated that the distribution characteristics of the different types of contaminants in the three RWTPs were similar. Caffeine, sul2 and tris(1-chloro-2-propyl) phosphate were the dominant substances in the wastewater, and their highest concentrations were 27104 ng/L, 1.4 x 10(7) copies/mL and 262 ng/L, respectively. Ofloxacin and sul2 were observed to be the dominant substances in the sludge, and their highest concentrations were 5419 ng/g and 3.7 x 10(8) copies/g, respectively. Anaerobic/anoxic/oxic system combined with the membrane bioreactor process achieved a relatively high aqueous removal of PPCPs (87%). ARGs and OPFRs were challenging to remove, with average removal rates of 6.5% and 31%, respectively. Quantitative meta-analysis indicated that tertiary treatment processes performed better in emerging contaminant removal than secondary processes. Diethyltoluamide exhibited the highest mass load discharge, with 33.5 mg/d per 1000 inhabitants. Octocrylene and tris(2-ethylhexyl) phosphate posed high risks (risk quotient>1.0) to aquatic organisms. This study provides essential evidence to screen high priority pollutants and develop corresponding standard in RWTPs.
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| 12. |
- Song, Jiao-Jiao, et al.
(author)
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The 4f-Hybridization Strength in CemMnIn3m+2n Heavy-Fermion Compounds Studied by Angle-Resolved Photoemission Spectroscopy
- 2021
-
In: Chinese Physics Letters. - : IOP Publishing. - 0256-307X .- 1741-3540. ; 38:10
-
Journal article (peer-reviewed)abstract
- We systemically investigate the nature of Ce 4f electrons in structurally layered heavy-fermion compounds CemMnIn3m+2n (with M = Co, Rh, Jr, and Pt, m = 1, 2, n = 0-2), at low temperature using on-resonance angle-resolved photoemission spectroscopy. Three heavy quasiparticle bands f(0), f(7/2)(1) and f(5/2)(1), are observed in all compounds, whereas their intensities and energy locations vary greatly with materials. The strong f(0) states imply that the localized electron behavior dominates the Ce 4f states. The Ce 4f electrons are partially hybridized with the conduction electrons, making them have the dual nature of localization and itinerancy. Our quantitative comparison reveals that the f(5/2)(1)-f (0) intensity ratio is more suitable to reflect the 4f-state hybridization strength.
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| 13. |
- Yuan, Jun, et al.
(author)
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Understanding energetic disorder in electron-deficient-core-based non-fullerene solar cells
- 2020
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In: Science in China Series B. - : SCIENCE PRESS. - 1674-7291 .- 1869-1870. ; 63:8, s. 1159-1168
-
Journal article (peer-reviewed)abstract
- Recent advances in material design for organic solar cells (OSCs) are primarily focused on developing near-infrared non-fullerene acceptors, typically A-DA D-A type acceptors (where A abbreviates an electron-withdrawing moiety and D, an electron-donor moiety), to achieve high external quantum efficiency while maintaining low voltage loss. However, the charge transport is still constrained by unfavorable molecular conformations, resulting in high energetic disorder and limiting the device performance. Here, a facile design strategy is reported by introducing the "wing" (alkyl chains) at the terminal of the DA D central core of the A-DA D-A type acceptor to achieve a favorable and ordered molecular orientation and therefore facilitate charge carrier transport. Benefitting from the reduced disorder, the electron mobilities could be significantly enhanced for the "wing"-containing molecules. By carefully changing the length of alkyl chains, the mobility of acceptor has been tuned to match with that of donor, leading to a minimized charge imbalance factor and a high fill factor (FF). We further provide useful design strategies for highly efficient OSCs with high FF.
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| 14. |
- Yuan, Ya Hua, et al.
(author)
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Angle-resolved photoemission spectroscopy view on the nature of Ce 4f electrons in the antiferromagnetic Kondo lattice CePd5Al2
- 2021
-
In: Physical Review B. - : American Physical Society (APS). - 2469-9969 .- 2469-9950. ; 103:12
-
Journal article (peer-reviewed)abstract
- We report an angle-resolved photoemission spectroscopy study of the antiferromagnetic Kondo lattice CePd5Al2, focusing on the quasi-two-dimensional k-space nature of its Fermi surface and, tuning photon energy to the Ce 4d-4f on-resonance transition, the hybridization of the Ce 4f state. A strong shoulder feature on the f0 peak was detected, suggesting hybridization between conduction and f bands. On-resonance spectra revealed narrow, yet hybridized quasiparticle bands with sharp peaks and ∼ 9 meV energy dispersion near the Fermi energy EF. The observed dispersive hybridized f band can be well described by a hybridization-band picture based on the periodic Anderson model (PAM). Hence, the 4f electrons in CePd5Al2 display a dual nature, with both localized and itinerant features, but with dominantly localized character.
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| 15. |
- Byun, Jinyoung, et al.
(author)
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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer
- 2022
-
In: Nature Genetics. - : Nature Research. - 1061-4036 .- 1546-1718. ; 54:8, s. 1167-1177
-
Journal article (peer-reviewed)abstract
- To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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| 16. |
- Liu, Wei, et al.
(author)
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Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride
- 2022
-
In: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
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| 17. |
- Yang, Hao, et al.
(author)
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Intramolecular hydroxyl nucleophilic attack pathway by a polymeric water oxidation catalyst with single cobalt sites
- 2022
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In: Nature Catalysis. - : Springer Nature. - 2520-1158. ; 5:5, s. 414-429
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Journal article (peer-reviewed)abstract
- Exploration of efficient water oxidation catalysts (WOCs) is the primary challenge in conversion of renewable energy into fuels. Here we report a molecularly well-defined heterogeneous WOC with Aza-fused, pi-conjugated, microporous polymer (Aza-CMP) coordinated single cobalt sites (Aza-CMP-Co). The single cobalt sites in Aza-CMP-Co exhibited superior activity under alkaline and near-neutral conditions. Moreover, the molecular nature of the isolated catalytic sites makes Aza-CMP-Co a reliable model for studying the heterogeneous water oxidation mechanism. By a combination of experimental and theoretical results, a pH-dependent nucleophilic attack pathway for O-O bond formation was proposed. Under alkaline conditions, the intramolecular hydroxyl nucleophilic attack (IHNA) process with which the adjacent -OH group nucleophilically attacks Co4+=O was identified as the rate-determining step. This process leads to lower activation energy and accelerated kinetics than those of the intermolecular water nucleophilic attack (WNA) pathway. This study provides significant insights into the crucial function of electrolyte pH in water oxidation catalysis and enhancement of water oxidation activity by regulation of the IHNA pathway.
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| 18. |
- Cheng, Chao, et al.
(author)
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Mosaic chromosomal alterations are associated with increased lung cancer risk : insight from the INTEGRAL-ILCCO cohort analysis
- 2023
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In: Journal of Thoracic Oncology. - : Elsevier. - 1556-0864 .- 1556-1380.
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Journal article (peer-reviewed)abstract
- Introduction: Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. Methods: In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. Results: We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. Conclusions: Our study established a link between mCAs in white blood cells and increased risk of lung cancer.
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| 19. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
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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| 20. |
- Guo, Ruiqi, et al.
(author)
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Exploiting Flexible Memristors Based on Solution-Processed Colloidal CuInSe2 Nanocrystals
- 2020
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In: Advanced Electronic Materials. - : Wiley. - 2199-160X. ; 6:5
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Journal article (peer-reviewed)abstract
- Compared to analogous bulk materials, colloidal nanocrystals have presented a powerful platform for building up electronic devices on the nano/micrometer scale and flexible portable electronic apparatus with the benefits of solution-based processing approach at room temperature. Herein, memristors based on CuInSe2 (CISe) colloidal nanocrystals prepared using a solution-based process at room temperature are constructed. The memristors exhibit obvious bipolar resistive switching performance with a high–low resistance ratio larger than 5.7 and a steady retention time over 104 s. This is attributed to the copper ion redox reaction and the migration of these ions under an applied electric field. When the SET voltage is reached, the ions are separated from one of the electrodes, and the memristor changes from a low-resistance state (LRS) to a high-resistance state (HRS). Conversely, when the voltage reaches the RESET voltage, the memristor switches from a HRS to a LRS. In addition, the flexible memristor can be fabricated by spincoating nanocrystal solution onto polyethylene terephthalate (PET) at room temperature, showing excellent reproducibility of the performance including 100 times of continuous operation, 104 s of reproducible reading, 600 times of antifatigue testing, and thermal stability up to 95 °C. The flexible devices demonstrate promising applications for portable electronic devices.
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| 21. |
- Hao, Zifan, et al.
(author)
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High-performance eight-channel system with fractal superconducting nanowire single-photon detectors
- 2024
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In: Chip. - : Elsevier B.V.. - 2709-4723 .- 2772-2724. ; 3:2
-
Journal article (peer-reviewed)abstract
- Superconducting nanowire single-photon detectors (SNSPDs) have become a mainstream photon-counting technology that has been widely applied in various scenarios. So far, most multi-channel SNSPD systems, either reported in literature or commercially available, are polarization sensitive, that is, the system detection efficiency (SDE) of each channel is dependent on the state of polarization of the to-be-detected photons. Here, we reported an eight-channel system with fractal SNSPDs working in the wavelength range of 930 to 940 nm, which are all featured with low polarization sensitivity. In a close-cycled Gifford-McMahon cryocooler system with the base temperature of 2.2 K, we installed and compared the performance of two types of devices: (1) SNSPD, composed of a single, continuous nanowire and (2) superconducting nanowire avalanche photodetector (SNAP), composed of 16 cascaded units of two nanowires electrically connected in parallel. The highest SDE among the eight channels reaches 96−5+4%, with the polarization sensitivity of 1.02 and a dark-count rate of 13 counts per second. The average SDE for eight channels for all states of polarization is estimated to be 90 ± 5%. It is concluded that both the SNSPDs and the SNAPs can reach saturated, high SDE at the wavelength of interest, and the SNSPDs show lower dark-count (false-count) rates, whereas the SNAPs show better properties in the time domain. With the adoption of this system, we showcased the measurements of the second-order photon-correlation functions of light emission from a single-photon source based on a semiconductor quantum dot and from a pulsed laser. It is believed that this work will provide new choices of systems with single-photon detectors combining the merits of high SDE, low polarization sensitivity, and low noise that can be tailored for different applications.
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| 22. |
- Jha, Debesh, et al.
(author)
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A comprehensive analysis of classification methods in gastrointestinal endoscopy imaging
- 2021
-
In: Medical Image Analysis. - 1361-8415 .- 1361-8423. ; 70
-
Journal article (peer-reviewed)abstract
- Gastrointestinal (GI) endoscopy has been an active field of research motivated by the large number of highly lethal GI cancers. Early GI cancer precursors are often missed during the endoscopic surveillance. The high missed rate of such abnormalities during endoscopy is thus a critical bottleneck. Lack of attentiveness due to tiring procedures, and requirement of training are few contributing factors. An automatic GI disease classification system can help reduce such risks by flagging suspicious frames and lesions. GI endoscopy consists of several multi-organ surveillance, therefore, there is need to develop methods that can generalize to various endoscopic findings. In this realm, we present a comprehensive analysis of the Medico GI challenges: Medical Multimedia Task at MediaEval 2017, Medico Multimedia Task at MediaEval 2018, and BioMedia ACM MM Grand Challenge 2019. These challenges are initiative to set-up a benchmark for different computer vision methods applied to the multi-class endoscopic images and promote to build new approaches that could reliably be used in clinics. We report the performance of 21 participating teams over a period of three consecutive years and provide a detailed analysis of the methods used by the participants, highlighting the challenges and shortcomings of the current approaches and dissect their credibility for the use in clinical settings. Our analysis revealed that the participants achieved an improvement on maximum Mathew correlation coefficient (MCC) from 82.68% in 2017 to 93.98% in 2018 and 95.20% in 2019 challenges, and a significant increase in computational speed over consecutive years.
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| 23. |
- Li, Huidong, et al.
(author)
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Attributing the impacts of ecological engineering and climate change on carbon uptake in Northeastern China
- 2023
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In: Landscape Ecology. - 0921-2973 .- 1572-9761. ; 38:12, s. 3945-3960
-
Journal article (peer-reviewed)abstract
- Context: In the past decades, several ecological engineering (eco-engineering) programs have been conducted in China, leading to a significant increase in regional carbon sink. However, the contribution of different eco-engineering programs to carbon uptake is still not clear, as the location of different programs is difficult to identify, and their impacts are concurrent with climate change. Objectives: We aim to detect the location of eco-engineering programs and attribute the impacts of eco-engineering and climate change on vegetation dynamics and carbon uptake in Northeastern China during 2000–2020. Methods: We developed a new framework to detect the location of eco-engineering programs by combining a temporal pattern analysis method and Markov model, and to attribute the impacts of eco-engineering and climate change on vegetation greenness and carbon uptake by combining a neighbor contrast method within a sliding window and trend analysis on the normalized difference vegetation index (NDVI) and gross primary production (GPP). Results: We identified four main forestry eco-engineering programs: croplands to forest (CtoF), grasslands to forest (GtoF), savannas to forest (StoF), and natural forest conservation (NFC) programs, whose areas accounted for 2.11%, 1.89%, 3.41%, and 1.72% of the total study area, respectively. Both eco-engineering and climate change contributed to the increase in greenness and carbon uptake. Compared to climate change effect, eco-engineering increased NDVI and GPP by 121% and 21.43% on average, respectively. Specifically, the eco-engineering-induced increases in GPP were 54.1%, 9.46%, 8.13%, and 24.20% for CtoF, GtoF, StoF, and NFC, respectively. Conclusions: These findings highlight the important and direct contribution of eco-engineering on vegetation greening with positive effects on carbon sequestration at a fine scale, providing an important implication for eco-engineering planning and management towards a carbon-neutral future.
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| 24. |
- Li, Shuijie, et al.
(author)
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Impaired oxygen-sensitive regulation of mitochondrial biogenesis within the von Hippel–Lindau syndrome
- 2022
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In: Nature Metabolism. - : Nature Publishing Group. - 2522-5812. ; 4:6, s. 739-758
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Journal article (peer-reviewed)abstract
- Mitochondria are the main consumers of oxygen within the cell. How mitochondria sense oxygen levels remains unknown. Here we show an oxygen-sensitive regulation of TFAM, an activator of mitochondrial transcription and replication, whose alteration is linked to tumours arising in the von Hippel–Lindau syndrome. TFAM is hydroxylated by EGLN3 and subsequently bound by the von Hippel–Lindau tumour-suppressor protein, which stabilizes TFAM by preventing mitochondrial proteolysis. Cells lacking wild-type VHL or in which EGLN3 is inactivated have reduced mitochondrial mass. Tumorigenic VHL variants leading to different clinical manifestations fail to bind hydroxylated TFAM. In contrast, cells harbouring the Chuvash polycythaemia VHLR200W mutation, involved in hypoxia-sensing disorders without tumour development, are capable of binding hydroxylated TFAM. Accordingly, VHL-related tumours, such as pheochromocytoma and renal cell carcinoma cells, display low mitochondrial content, suggesting that impaired mitochondrial biogenesis is linked to VHL tumorigenesis. Finally, inhibiting proteolysis by targeting LONP1 increases mitochondrial content in VHL-deficient cells and sensitizes therapy-resistant tumours to sorafenib treatment. Our results offer pharmacological avenues to sensitize therapy-resistant VHL tumours by focusing on the mitochondria.
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| 25. |
- Liu, Wei, et al.
(author)
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A-pi-A structured non-fullerene acceptors for stable organic solar cells with efficiency over 17%
- 2022
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In: Science in China Series B. - : SCIENCE PRESS. - 1674-7291 .- 1869-1870. ; 65:7, s. 1374-1382
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Journal article (peer-reviewed)abstract
- With the development of photovoltaic materials, especially the small molecule acceptors (SMAs), organic solar cells (OSCs) have made breakthroughs in power conversion efficiencies (PCEs). However, the stability of high-performance OSCs remains a critical challenge for future technological applications. To tackle the inherent instability of SMA materials under the ambient conditions, much effort has been made to improve OSCs stability, including device modification and new materials design. Here we proposed a new electron acceptor design strategy and developed a "quasi-macromolecule" (QM) with an A-pi-A structure, where the functionalized pi-bridge is used as a linker between two SMAs (A), to improve the long-term stability without deteriorating device efficiencies. Such type of QMs enables excellent synthetic flexibility to modulate their optical/electro-chemical properties, crystallization and aggregation behaviors by changing the A and pi units. Moreover, QMs possess a unique long conjugated backbone combining high molecular weight over 3.5 kDa with high purity. Compared with the corresponding SMA BTP-4F-OD (Y6-OD), the devices based on newly synthesized A-pi-A type acceptors QM1 and QM2 could exhibit better device stability and more promising PCEs of 17.05% and 16.36%, respectively. This kind of "molecular-framework" (A-pi-A) structure provides a new design strategy for developing high-efficiency and -stability photovoltaic materials.
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