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1.
  • Beal, Jacob, et al. (author)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • 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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  • 2019
  • Journal article (peer-reviewed)
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3.
  • Kristan, Matej, et al. (author)
  • The Sixth Visual Object Tracking VOT2018 Challenge Results
  • 2019
  • In: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
  • Conference paper (peer-reviewed)abstract
    • The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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5.
  • Leebens-Mack, James H., et al. (author)
  • One thousand plant transcriptomes and the phylogenomics of green plants
  • 2019
  • In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
  • Journal article (peer-reviewed)abstract
    • Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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9.
  • An, Junghwa, et al. (author)
  • Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
  • 2010
  • In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
  • Journal article (peer-reviewed)abstract
    • This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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10.
  • Arzoumanian, Doris, et al. (author)
  • Dust polarized emission observations of NGC 6334: BISTRO reveals the details of the complex but organized magnetic field structure of the high-mass star-forming hub-filament network
  • 2021
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 647
  • Journal article (peer-reviewed)abstract
    • Context. Molecular filaments and hubs have received special attention recently thanks to new studies showing their key role in star formation. While the (column) density and velocity structures of both filaments and hubs have been carefully studied, their magnetic field (B-field) properties have yet to be characterized. Consequently, the role of B-fields in the formation and evolution of hub-filament systems is not well constrained. Aims. We aim to understand the role of the B-field and its interplay with turbulence and gravity in the dynamical evolution of the NGC 6334 filament network that harbours cluster-forming hubs and high-mass star formation. Methods. We present new observations of the dust polarized emission at 850 μm toward the 2 pc × 10 pc map of NGC 6334 at a spatial resolution of 0.09 pc obtained with the James Clerk Maxwell Telescope (JCMT) as part of the B-field In STar-forming Region Observations (BISTRO) survey. We study the distribution and dispersion of the polarized intensity (PI), the polarization fraction (PF), and the plane-of-The-sky B-field angle (χB_POS) toward the whole region, along the 10 pc-long ridge and along the sub-filaments connected to the ridge and the hubs. We derived the power spectra of the intensity and χBPOS along the ridge crest and compared them with the results obtained from simulated filaments. Results. The observations span 3 orders of magnitude in Stokes I and PI and 2 orders of magnitude in PF (from 0.2 to 20%). A large scatter in PI and PF is observed for a given value of I. Our analyses show a complex B-field structure when observed over the whole region ( 10 pc); however, at smaller scales (1 pc), χBPOS varies coherently along the crests of the filament network. The observed power spectrum of χBPOS can be well represented with a power law function with a slope of-1.33 ± 0.23, which is 20% shallower than that of I. We find that this result is compatible with the properties of simulated filaments and may indicate the physical processes at play in the formation and evolution of star-forming filaments. Along the sub-filaments, χBPOS rotates frombeing mostly perpendicular or randomly oriented with respect to the crests to mostly parallel as the sub-filaments merge with the ridge and hubs. This variation of the B-field structure along the sub-filaments may be tracing local velocity flows of infalling matter in the ridge and hubs. Our analysis also suggests a variation in the energy balance along the crests of these sub-filaments, from magnetically critical or supercritical at their far ends to magnetically subcritical near the ridge and hubs. We also detect an increase in PF toward the high-column density (NH2 â 1023 cm-2) star cluster-forming hubs. These latter large PF values may be explained by the increase in grain alignment efficiency due to stellar radiation from the newborn stars, combined with an ordered B-field structure. Conclusions. These observational results reveal for the first time the characteristics of the small-scale (down to 0.1 pc) B-field structure of a 10 pc-long hub-filament system. Our analyses show variations in the polarization properties along the sub-filaments that may be tracing the evolution of their physical properties during their interaction with the ridge and hubs. We also detect an impact of feedback from young high-mass stars on the local B-field structure and the polarization properties, which could put constraints on possible models for dust grain alignment and provide important hints as to the interplay between the star formation activity and interstellar B-fields.
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11.
  • Cao, Lina, et al. (author)
  • Atomically dispersed iron hydroxide anchored on Pt for preferential oxidation of CO in H-2
  • 2019
  • In: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 565:7741, s. 631-635
  • Journal article (peer-reviewed)abstract
    • Proton-exchange-membrane fuel cells (PEMFCs) are attractive next-generation power sources for use in vehicles and other applications(1), with development efforts focusing on improving the catalyst system of the fuel cell. One problem is catalyst poisoning by impurity gases such as carbon monoxide (CO), which typically comprises about one per cent of hydrogen fuel(2-4). A possible solution is on-board hydrogen purification, which involves preferential oxidation of CO in hydrogen (PROX)(3-7). However, this approach is challenging(8-15) because the catalyst needs to be active and selective towards CO oxidation over a broad range of low temperatures so that CO is efficiently removed (to below 50 parts per million) during continuous PEMFC operation (at about 353 kelvin) and, in the case of automotive fuel cells, during frequent cold-start periods. Here we show that atomically dispersed iron hydroxide, selectively deposited on silica-supported platinum (Pt) nanoparticles, enables complete and 100 per cent selective CO removal through the PROX reaction over the broad temperature range of 198 to 380 kelvin. We find that the mass-specific activity of this system is about 30 times higher than that of more conventional catalysts consisting of Pt on iron oxide supports. In situ X-ray absorption fine-structure measurements reveal that most of the iron hydroxide exists as Fe-1(OH)(x) clusters anchored on the Pt nanoparticles, with density functional theory calculations indicating that Fe-1(OH)(x)-Pt single interfacial sites can readily react with CO and facilitate oxygen activation. These findings suggest that in addition to strategies that target oxide-supported precious-metal nanoparticles or isolated metal atoms, the deposition of isolated transition-metal complexes offers new ways of designing highly active metal catalysts.
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12.
  • Chen, Zhishan, et al. (author)
  • Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
  • 2024
  • In: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
  • Journal article (peer-reviewed)abstract
    • Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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13.
  • Ching, Tao-Chung, et al. (author)
  • The JCMT BISTRO-2 Survey: Magnetic Fields of the Massive DR21 Filament
  • 2022
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:2
  • 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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14.
  • Doi, Yasuo, et al. (author)
  • The JCMT BISTRO Survey: Magnetic Fields Associated with a Network of Filaments in NGC 1333
  • 2020
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 899:1
  • Journal article (peer-reviewed)abstract
    • We present new observations of the active star formation region NGC 1333 in the Perseus molecular cloud complex from the James Clerk Maxwell Telescope B-Fields In Star-forming Region Observations (BISTRO) survey with the POL-2 instrument. The BISTRO data cover the entire NGC 1333 complex (∼1.5 pc ? 2 pc) at 0.02 pc resolution and spatially resolve the polarized emission from individual filamentary structures for the first time. The inferred magnetic field structure is complex as a whole, with each individual filament aligned at different position angles relative to the local field orientation. We combine the BISTRO data with low- and high- resolution data derived from Planck and interferometers to study the multiscale magnetic field structure in this region. The magnetic field morphology drastically changes below a scale of ∼1 pc and remains continuous from the scales of filaments (∼0.1 pc) to that of protostellar envelopes (∼0.005 pc or ∼1000 au). Finally, we construct simple models in which we assume that the magnetic field is always perpendicular to the long axis of the filaments. We demonstrate that the observed variation of the relative orientation between the filament axes and the magnetic field angles are well reproduced by this model, taking into account the projection effects of the magnetic field and filaments relative to the plane of the sky. These projection effects may explain the apparent complexity of the magnetic field structure observed at the resolution of BISTRO data toward the filament network.
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15.
  • Dong, Yi-Min, et al. (author)
  • Development and Validation of a Nomogram for Assessing Survival in Patients With COVID-19 Pneumonia
  • 2021
  • In: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 72:4, s. 652-660
  • Journal article (peer-reviewed)abstract
    • Background. The outbreak of coronavirus disease 2019 (COVID-19) has spread worldwide and continues to threaten peoples' health as well as put pressure on the accessibility of medical systems. Early prediction of survival of hospitalized patients will help in the clinical management of COVID-19, but a prediction model that is reliable and valid is still lacking. Methods. We retrospectively enrolled 628 confirmed cases of COVID-19 using positive RT-PCR tests for SARS-CoV-2 in Tongji Hospital, Wuhan, China. These patients were randomly grouped into a training (60%) and a validation (40%) cohort. In the training cohort, LASSO regression analysis and multivariate Cox regression analysis were utilized to identify prognostic factors for in-hospital survival of patients with COVID-19. A nomogram based on the 3 variables was built for clinical use. AUCs, concordance indexes (C-index), and calibration curves were used to evaluate the efficiency of the nomogram in both training and validation cohorts. Results. Hypertension, higher neutrophil-to-lymphocyte ratio, and increased NT-proBNP values were found to be significantly associated with poorer prognosis in hospitalized patients with COVID-19. The 3 predictors were further used to build a prediction nomogram. The C-indexes of the nomogram in the training and validation cohorts were 0.901 and 0.892, respectively. The AUC in the training cohort was 0.922 for 14-day and 0.919 for 21-day probability of in-hospital survival, while in the validation cohort this was 0.922 and 0.881, respectively. Moreover, the calibration curve for 14- and 21-day survival also showed high coherence between the predicted and actual probability of survival. Conclusions. We built a predictive model and constructed a nomogram for predicting in-hospital survival of patients with COVID-19. This model has good performance and might be utilized clinically in management of COVID-19.
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16.
  • Dong, Yi-Min, et al. (author)
  • Reply to Collins et al
  • 2021
  • In: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 73:3, s. 558-559
  • Journal article (other academic/artistic)
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17.
  • Eswaraiah, Chakali, et al. (author)
  • The JCMT BISTRO Survey: Revealing the Diverse Magnetic Field Morphologies in Taurus Dense Cores with Sensitive Submillimeter Polarimetry
  • 2021
  • In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 912:2
  • Journal article (peer-reviewed)abstract
    • We have obtained sensitive dust continuum polarization observations at 850 μm in the B213 region of Taurus using POL-2 on SCUBA-2 at the James Clerk Maxwell Telescope as part of the B-fields in STar-forming Region Observations (BISTRO) survey. These observations allow us to probe magnetic field (B-field) at high spatial resolution (∼2000 au or ∼0.01 pc at 140 pc) in two protostellar cores (K04166 and K04169) and one prestellar core (Miz-8b) that lie within the B213 filament. Using the Davis-Chandrasekhar-Fermi method, we estimate the B-field strengths in K04166, K04169, and Miz-8b to be 38 ± 14, 44 ± 16, and 12 ± 5 μG, respectively. These cores show distinct mean B-field orientations. The B-field in K04166 is well ordered and aligned parallel to the orientations of the core minor axis, outflows, core rotation axis, and large-scale uniform B-field, in accordance with magnetically regulated star formation via ambipolar diffusion taking place in K04166. The B-field in K04169 is found to be ordered but oriented nearly perpendicular to the core minor axis and large-scale B-field and not well correlated with other axes. In contrast, Miz-8b exhibits a disordered B-field that shows no preferred alignment with the core minor axis or large-scale field. We found that only one core, K04166, retains a memory of the large-scale uniform B-field. The other two cores, K04169 and Miz-8b, are decoupled from the large-scale field. Such a complex B-field configuration could be caused by gas inflow onto the filament, even in the presence of a substantial magnetic flux.
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18.
  • Fenstermacher, M.E., et al. (author)
  • DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
  • 2022
  • In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
  • Journal article (peer-reviewed)abstract
    • DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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19.
  • Gu, Peng, et al. (author)
  • A metabolite from commensal Candida albicans enhances the bactericidal activity of macrophages and protects against sepsis
  • 2023
  • In: Cellular & Molecular Immunology. - London : Nature Publishing Group. - 1672-7681 .- 2042-0226. ; 20:10, s. 1156-1170
  • Journal article (peer-reviewed)abstract
    • The gut microbiome is recognized as a key modulator of sepsis development. However, the contribution of the gut mycobiome to sepsis development is still not fully understood. Here, we demonstrated that the level of Candida albicans was markedly decreased in patients with bacterial sepsis, and the supernatant of Candida albicans culture significantly decreased the bacterial load and improved sepsis symptoms in both cecum ligation and puncture (CLP)-challenged mice and Escherichia coli-challenged pigs. Integrative metabolomics and the genetic engineering of fungi revealed that Candida albicans-derived phenylpyruvate (PPA) enhanced the bactericidal activity of macrophages and reduced organ damage during sepsis. Mechanistically, PPA directly binds to sirtuin 2 (SIRT2) and increases reactive oxygen species (ROS) production for eventual bacterial clearance. Importantly, PPA enhanced the bacterial clearance capacity of macrophages in sepsis patients and was inversely correlated with the severity of sepsis in patients. Our findings highlight the crucial contribution of commensal fungi to bacterial disease modulation and expand our understanding of the host-mycobiome interaction during sepsis development. © 2023, The Author(s), under exclusive licence to CSI and USTC.
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20.
  • Jhun, Mina-A, et al. (author)
  • A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids
  • 2021
  • In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
  • Journal article (peer-reviewed)abstract
    • Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups. Abnormal blood lipid levels are important risk factors for cardiovascular and other various diseases. Here the authors conduct a large-scale multi-ethnic epigenome-wide association study combined with epigenetic (cis-QTL and eQTM) data, and identify CpG-lipid traits associations that are specific to or common across racial/ethnic groups.
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21.
  • Karoly, Janik, et al. (author)
  • The JCMT BISTRO Survey: Studying the Complex Magnetic Field of L43
  • 2023
  • In: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 952:1
  • 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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22.
  • Kwon, Woojin, et al. (author)
  • B-fields in Star-forming Region Observations (BISTRO): Magnetic Fields in the Filamentary Structures of Serpens Main
  • 2022
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 926:2
  • Journal article (peer-reviewed)abstract
    • We present 850 mu m polarimetric observations toward the Serpens Main molecular cloud obtained using the POL-2 polarimeter on the James Clerk Maxwell Telescope as part of the B-fields In STar-forming Region Observations survey. These observations probe the magnetic field morphology of the Serpens Main molecular cloud on about 6000 au scales, which consists of cores and six filaments with different physical properties such as density and star formation activity. Using the histogram of relative orientation (HRO) technique, we find that magnetic fields are parallel to filaments in less-dense filamentary structures where NH2 < 0.93 x 10(22) cm(-2) (magnetic fields perpendicular to density gradients), while they are perpendicular to filaments (magnetic fields parallel to density gradients) in dense filamentary structures with star formation activity. Moreover, applying the HRO technique to denser core regions, we find that magnetic field orientations change to become perpendicular to density gradients again at NH2 approximate to 4.6 x 10(22) NH2 approximate to 16 x 10(22) cm(-2), magnetic fields change back to being parallel to density gradients once again, which can be understood to be due to magnetic fields being dragged in by infalling material. In addition, we estimate the magnetic field strengths of the filaments (B-POS = 60-300 mu G)) using the Davis-Chandrasekhar-Fermi method and discuss whether the filaments are gravitationally unstable based on magnetic field and turbulence energy densities.
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23.
  • Li, Wei, et al. (author)
  • Heat transfer to aviation kerosene flowing upward in smooth tubes at supercritical pressures
  • 2015
  • In: International Journal of Heat and Mass Transfer. - : Elsevier BV. - 0017-9310. ; 85, s. 1084-1094
  • Journal article (peer-reviewed)abstract
    • This study experimentally investigated convective heat transfer performances of China RP-3 kerosene flowing in a vertical upward tube under supercritical pressures. Effects of mass flux, heat flux, pressure and inlet temperature on the heat transfer performance were given in detail. The influences of buoyancy and flow acceleration under different flow conditions were discussed as well. It was found that the inner wall temperature varies non-linearly at different mass fluxes. Heat transfer is improved when the fuel temperature is around the critical temperature. The heat transfer coefficient increases as heat flux or inlet temperature increases, while increase in inlet pressure reduces heat transfer coefficient. Besides, as nanofluids generally have higher thermal conductivity compared to their corresponding base fluids (i.e. kerosene), the heat transfer characteristics of Fe3O4-kerosene nanofluid was also investigated. It was found that the addition of nanoparticles tends to deteriorate the heat transfer performance of nanofluids flowing in a vertical tube under supercritical pressure. As the particle content increases, the heat transfer coefficient decreases due to the modification of the inner wall surface by the nanoparticles. (C) 2015 Elsevier Ltd. All rights reserved.
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24.
  • Luo, Yifei, et al. (author)
  • Technology Roadmap for Flexible Sensors
  • 2023
  • In: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
  • Research review (peer-reviewed)abstract
    • Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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25.
  • Lyo, A-Ran, et al. (author)
  • The JCMT BISTRO Survey: An 850/450 mu m Polarization Study of NGC 2071IR in Orion B
  • 2021
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 918:2
  • Journal article (peer-reviewed)abstract
    • We present the results of simultaneous 450 mu m and 850 mu m polarization observations toward the massive star-forming region NGC 2071IR, a target of the BISTRO (B-fields in STar-forming Region Observations) Survey, using the POL-2 polarimeter and SCUBA-2 camera mounted on the James Clerk Maxwell Telescope. We find a pinched magnetic field morphology in the central dense core region, which could be due to a rotating toroidal disklike structure and a bipolar outflow originating from the central young stellar object IRS 3. Using the modified Davis-Chandrasekhar-Fermi method, we obtain a plane-of-sky magnetic field strength of 563 +/- 421 mu G in the central similar to 0.12 pc region from 850 mu m polarization data. The corresponding magnetic energy density of 2.04 x 10(-8) erg cm(-3) is comparable to the turbulent and gravitational energy densities in the region. We find that the magnetic field direction is very well aligned with the whole of the IRS 3 bipolar outflow structure. We find that the median value of polarization fractions is 3.0% at 450 mu m in the central 3 ' region, which is larger than the median value of 1.2% at 850 mu m. The trend could be due to the better alignment of warmer dust in the strong radiation environment. We also find that polarization fractions decrease with intensity at both wavelengths, with slopes, determined by fitting a Rician noise model of 0.59 +/- 0.03 at 450 mu m and 0.36 +/- 0.04 at 850 mu m, respectively. We think that the shallow slope at 850 mu m is due to grain alignment at the center being assisted by strong radiation from the central young stellar objects.
  •  
26.
  • Ma, Ruijie, et al. (author)
  • Adding a Third Component with Reduced Miscibility and Higher LUMO Level Enables Efficient Ternary Organic Solar Cells
  • 2020
  • In: ACS Energy Letters. - : American Chemical Society (ACS). - 2380-8195. ; 5:8, s. 2711-2720
  • Journal article (peer-reviewed)abstract
    • It is widely known that the miscibility between donor and acceptor is a crucial factor that affects the morphology and thus device performance of nonfullerene organic solar cells (OSCs). In this Letter, we show that incorporating a third component with lower miscibility and higher lowest unoccupied molecular orbital (LUMO) level into the state-of-the-art PM6:Y6 system can significantly enhance the performance of devices. The best results of the ternary devices are achieved by adding a small molecular acceptor named ITCPTC (similar to 5% w/w), which significantly improves the power conversion efficiency (PCE) of the host system from 16.44% to 17.42%. The higher LUMO of the third component increases the open-circuit voltage (V-oc), while the low miscibility enlarges the domains and leads to improved short-circuit current density (J(sc)) and fill factor (FF). The efficacy of this strategy is supported by using other nonfullerene third components including an asymmetric small molecule (N7IT) and a polymer acceptor (PF2-DTC), which play the same role as ITCPTC and boost the PCEs to 16.96% and 17.04%, respectively. Our approach can be potentially applied to a wide range of OSC material systems and should facilitate the development of the OSC field.
  •  
27.
  • Ngoc, Nguyen Bich, et al. (author)
  • Observations of Magnetic Fields Surrounding LkH alpha 101 Taken by the BISTRO Survey with JCMT-POL-2
  • 2021
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 908:1
  • Journal article (peer-reviewed)abstract
    • We report the first high spatial resolution measurement of magnetic fields surrounding LkH alpha 101, part of the Auriga-California molecular cloud. The observations were taken with the POL-2 polarimeter on the James Clerk Maxwell Telescope within the framework of the B-fields In Star-forming Region Observations (BISTRO) survey. Observed polarization of thermal dust emission at 850 mu m is found to be mostly associated with the redshifted gas component of the cloud. The magnetic field displays a relatively complex morphology. Two variants of the Davis-Chandrasekhar-Fermi method, unsharp masking and structure function, are used to calculate the strength of magnetic fields in the plane of the sky, yielding a similar result of B-POS similar to 115 mu G. The mass-to-magnetic-flux ratio in critical value units, lambda similar to 0.3, is the smallest among the values obtained for other regions surveyed by POL-2. This implies that the LkH alpha 101 region is subcritical, and the magnetic field is strong enough to prevent gravitational collapse. The inferred delta B/B-0 similar to 0.3 implies that the large-scale component of the magnetic field dominates the turbulent one. The variation of the polarization fraction with total emission intensity can be fitted by a power law with an index of alpha = 0.82 0.03, which lies in the range previously reported for molecular clouds. We find that the polarization fraction decreases rapidly with proximity to the only early B star (LkH alpha 101) in the region. Magnetic field tangling and the joint effect of grain alignment and rotational disruption by radiative torques can potentially explain such a decreasing trend.
  •  
28.
  • Nie, Shuai, et al. (author)
  • Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
  • 2023
  • In: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
  • Journal article (peer-reviewed)abstract
    • The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
  •  
29.
  • Qi, Qibin, et al. (author)
  • FTO genetic variants, dietary intake and body mass index : insights from 177 330 individuals
  • 2014
  • In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:25, s. 6961-6972
  • Journal article (peer-reviewed)abstract
    • FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177 330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m(2), P = 1.9 × 10(-105)), and all participants (0.30 [0.30, 0.35] kg/m(2), P = 3.6 × 10(-107)). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10(-16)), and relative weak associations with lower total energy intake (-6.4 [-10.1, -2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (-0.07 [-0.11, -0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10(-9)) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposity.
  •  
30.
  • Rothfels, Carl J., et al. (author)
  • The evolutionary history of ferns inferred from 25 low-copy nuclear genes
  • 2015
  • In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 102:7, s. 1089-1107
  • Journal article (peer-reviewed)abstract
    • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to similar to 200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
  •  
31.
  • Shi, Tian-Le, et al. (author)
  • High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
  • 2024
  • In: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
  • Journal article (peer-reviewed)abstract
    • Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
  •  
32.
  • Sun, Tao, et al. (author)
  • Empirical evidence that manganese enrichment accelerates decomposition
  • 2021
  • In: Agriculture, Ecosystems & Environment. Applied Soil Ecology. - : Elsevier. - 0929-1393 .- 1873-0272. ; 168
  • Journal article (peer-reviewed)abstract
    • Our understanding of the controls regulating the rate of litter decomposition is important for improving confidence in the parameterization of carbon cycle–climate feedbacks. Traditional conceptual models rely primarily on climate and lignin/N ratios as the main regulators of decomposition. Here we studied the effects of manganese (Mn) addition on long-term decomposition across 18 substrates in a laboratory incubation. Mn addition remarkably promoted later stage of decomposition, resulting into a smaller fraction of slowly decomposing litter. This dynamic is closely associated with the changes of activities of manganese peroxidase, an important enzyme with greater capacity for lignin degradation. Our findings suggest the necessity of incorporating the interaction of Mn and decomposition into biogeochemical models.
  •  
33.
  • Suo, Tao, et al. (author)
  • Oral traditional Chinese medication for adhesive small bowel obstruction
  • 2012
  • In: Cochrane Database of Systematic Reviews. - 1469-493X. ; :5
  • Research review (peer-reviewed)abstract
    • Background Small bowel obstruction (SBO) is one of the most common emergent complications of general surgery. Intra-abdominal adhesions are the leading cause of SBO. Because surgery can induce new adhesions, non-operative management is preferred in the absence of signs of peritonitis or strangulation. Oral traditional Chinese herbal medicine has long been used as a non-operative therapy to treat adhesive SBO in China. Many controlled trials have been conducted to investigate its therapeutic value in resolving adhesive SBO. Objectives The aim of this review was to assess the efficacy and safety of oral traditional Chinese medicine (TCM) for adhesive small bowel obstruction. Search methods We searched the following databases, without regard to language or publishing restrictions: the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Chinese Biomedical Database (CBM), China National Knowledge Infrastructure/Chinese Academic Journals full-text Database (CNKI), and VIP (a full-text database of Chinese journals). The searches were conducted in November 2011. Selection criteria Randomised controlled trials and quasi-randomised controlled trials comparing Chinese medicines administered orally, via the gastric canal, or both with a placebo or conventional therapy in participants diagnosed with adhesive SBO were considered. We also considered trials of TCM (oral administration, gastric tube perfusion, or both) plus conventional therapy compared with conventional therapy alone for patients with adhesive SBO. Studies addressing the safety and efficacy of oral traditional Chinese medicinal agents in the treatment of adhesive SBO were also considered. Data collection and analysis Two authors collected the data independently. We assessed the risk of bias according to the following methodological criteria: random sequence generation, allocation concealment, blinding, incomplete outcome data, selective outcome reporting and other sources of bias. Dichotomous data are presented as risk ratios (OR) and 95% confidence intervals (CI); continuous outcomes are presented as mean differences (MD) and 95% CIs. The data analyses were carried out using Review Manager 5.1. For cases in which necessary information was not reported in the paper, we contacted the primary authors for additional information. Main results Five randomised trials involving 664 participants were analysed. Five different herbal medicines were tested in these trials, including Huo-Xue-Tong-Fu decoction, Xiao-Cheng-Qi-Tang decoction, a combination of Xiao-Cheng-Qi-Tang and Si-Jun-Zi-Tang decoctions, Chang-Nian-Lian-Song-Jie-Tang decoction, and Fufang-Da-Cheng-Qi-Tang decoction. There were variations in the tested herbal compositions and methods of medicine administration. The main outcomes reported in the trials were effects on abdominal pain, abdominal distension, constipation defection, time of first defecation after treatment, and reoperation rate during the course of the disease. Secondary outcomes selected for this review were not available, including complications such as small bowel perfusion (bowel resection, system complications, and other possible complications), length of hospital stay, cost of hospitalisation, and time from admission to surgical intervention. The results of five trials showed that patients receiving TCM combined with conventional therapy seemed to have improved outcomes compared with patients receiving conventional treatment alone (OR 4.24, 95% CI 2.83 to 6.36). However, we cannot conclusively determine the efficacy of TCM in this review due to inadequate reporting, low methodological quality, and the prevalence of various biases in the reviewed studies. Furthermore, because none of the reviewed trials discussed adverse events, we could not evaluate the safety of TCM for adhesive SBO patients. All trials were conducted and published in China. Authors' conclusions Although many studies have assessed the use of TCM products for adhesive SBO, most were excluded from this review due to their methodological limitations. This systematic review did not find sufficient evidence to support the objective efficacy and safety of TCM for patients with adhesive SBO. The positive evidence should be interpreted with caution given the insufficient number of studies with large sample sizes, the absence of well-designed, high-quality trials, and the lack of safety information. Therefore, further studies with larger sample sizes and high-quality, randomised, and controlled trials are necessary to produce more accurate and meaningful data on the efficacy of Chinese herbal medicines for adhesive SBO.
  •  
34.
  • Tahani, Mehrnoosh, et al. (author)
  • JCMT BISTRO Observations: Magnetic Field Morphology of Bubbles Associated with NGC 6334
  • 2023
  • In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 944:2
  • Journal article (peer-reviewed)abstract
    • We study the Hii regions associated with the NGC 6334 molecular cloud observed in the submillimeter and taken as part of the B-fields In STar-forming Region Observations Survey. In particular, we investigate the polarization patterns and magnetic field morphologies associated with these Hii regions. Through polarization pattern and pressure calculation analyses, several of these bubbles indicate that the gas and magnetic field lines have been pushed away from the bubble, toward an almost tangential (to the bubble) magnetic field morphology. In the densest part of NGC 6334, where the magnetic field morphology is similar to an hourglass, the polarization observations do not exhibit observable impact from Hii regions. We detect two nested radial polarization patterns in a bubble to the south of NGC 6334 that correspond to the previously observed bipolar structure in this bubble. Finally, using the results of this study, we present steps (incorporating computer vision; circular Hough transform) that can be used in future studies to identify bubbles that have physically impacted magnetic field lines.
  •  
35.
  • Wei, Yanfei, et al. (author)
  • Stalled oligodendrocyte differentiation in IDH-mutant gliomas.
  • 2023
  • In: Genome medicine. - 1756-994X. ; 15:1
  • Journal article (peer-reviewed)abstract
    • Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized.Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers.Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas.Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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36.
  •  
37.
  • Yang, Tao, et al. (author)
  • Mullite-derivative Bi2MnxAl7-xO14 (x similar to 1) : structure determination by powder X-ray diffraction from a multi-phase sample
  • 2012
  • In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 41:10, s. 2884-2889
  • Journal article (peer-reviewed)abstract
    • As a supplementary method to single crystal X-ray diffraction (XRD), nowadays crystal structure determination by powder XRD has become popular, especially for those areas with difficulties getting high quality single crystals. Here we observed an intermediate phase Bi2MnxAl7-xO14 (x similar to 1) during the decomposition of mullite-Bi2MnxAl4-xO9+delta (solid solution of Bi2Mn4O10-Bi2Al4O9). As a metastable phase, it started to decompose while forming, thus no single-phase sample can be obtained. We successfully determined its structure by powder XRD from a multi-phase sample. A modified Le Bail fitting using the atomic structure information of known impurities showed a more reliable intensity extraction from a multi-phase powder XRD than that without using atomic structures for the known impurities. The charge-flipping algorithm and Monte-Carlo based simulated annealing technique were then applied to obtain the full structural model. In principle, this strategy is applicable to more complex problems, and not limited to the oxide materials. Bi2MnxAl7-xO14 possesses a mullite-related structure. There are one tetrahedral and two octahedral sites for Mn and Al, where disordering with substantial site preferences is observed. Specifically, M1O(6) and M3O(6) octahedra share edges along the c-direction with the periodicity of 1 : 2. These octahedral chains are further connected into a 3D structure through M2O(4) dimmers and Bi.
  •  
38.
  • Zhang, Qi, et al. (author)
  • Muscle-like Artificial Molecular Actuators for Nanoparticles
  • 2018
  • In: Chem. - : Cell Press. - 2451-9308 .- 2451-9294. ; 4:11, s. 2670-2684
  • Journal article (peer-reviewed)abstract
    • Muscle tissue performs crucial contraction/extension motions that generate mechanical force and work by consuming chemical energy. Inspired by this naturally created biomolecular machine, artificial molecular muscles are designed and synthesized to undertake linear actuation functions. However, most of these muscle-like actuators are performed at large ensembles, while to realize the nanoscale actuation at the single-to few-molecule level remains challenging. Herein, we developed an artificial muscle-like molecular actuator that can reversibly control the proximity of the attached nano-objects, gold nanoparticles, within the single-molecule length level by its stimuli-responsive muscle-like linear contraction/extension motion. The molecular actuation motion is accompanied by an optical signal output resulting from the plasmonic resonance properties of gold nanoparticles. Meanwhile, the thermal noise of the muscle-like molecular actuator can be overcome by integrating the optical signal over a sufficiently long period.
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39.
  • Zhao, Shi-Wei, et al. (author)
  • Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub
  • 2023
  • In: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
  • Journal article (peer-reviewed)abstract
    • Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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40.
  • Zhu, Youjian, et al. (author)
  • Effect of sodium carboxymethyl cellulose addition on particulate matter emissions during biomass pellet combustion
  • 2018
  • In: Applied Energy. - : Elsevier BV. - 0306-2619 .- 1872-9118. ; 230, s. 925-934
  • Journal article (peer-reviewed)abstract
    • Sodium carboxymethyl cellulose (CMC) can be used as a cost-effective and environmentally friendly binder in the pelletizing process for production of biomass pellets with good quality. However, the effect of its addition on the emission of particulate matters (PM) during the combustion process, are still not clear. In this study, four typical biomass fuels, cotton stalk, cornstalk, camphorwood and rice husk, were used to investigate the effect of the addition of 5 wt% CMC in the biomass pellets on PM emissions during the combustion process. In the case of pure CMC combustion, a large amount of PM mainly with PM2.5 were generated, which was associated to the evaporation and condensation of NaOH and Na2CO3. The PM10 emission from the combustion of the four biomass fuels varied from 9.72 mg/Nm3 to 23.12 mg/Nm3 with mainly PM1. The addition of 5 wt% CMC in cotton stalk, corn stalk and camphorwood significantly increased the PM emissions due to the evaporation and subsequent condensation of Na-containing species, e.g. NaCl, Na2SO4, NaOH and Na2CO3. For rice husk, the addition of CMC hardly affected PM1 emission due to the dominated SiO2 component in rice husk ash, which reacted with the Na-containing species from the combustion of CMC and facilitated the formation of coarse ash particles and the reduction of PM1 emission. Although the addition of CMC in biomass fuels can greatly enhance the pellets qualities, its addition increases the PM emissions to varying degree. Therefore, in the industrial application of CMC to biomass densification, countermeasures such as mixing of high Si-containing rice husk or SiO2-rich minerals with biomass fuels should be taken to alleviate the PM issues resulting from the introduction of CMC. 
  •  
41.
  • Ai, Jin Wei, et al. (author)
  • Clinical Characteristics of COVID-19 Patients With Gastrointestinal Symptoms : An Analysis of Seven Patients in China
  • 2020
  • In: Frontiers in Medicine. - : Frontiers Media SA. - 2296-858X. ; 7
  • Journal article (peer-reviewed)abstract
    • Objectives: Patients with novel coronavirus disease 2019 (COVID-19) can present with gastrointestinal symptoms as their initial symptoms or as the main manifestations during disease progression, but the clinical characteristics of these patients are still unknown. Methods: We identified COVID-19 patients who admitted to Xiangyang No. 1 People's Hospital and presented with gastrointestinal symptoms as their initial or main symptoms. Their medical records were reviewed by two independent clinical scientists. The epidemiological and clinical characteristics as well as the clinical outcomes were analyzed. Results: Among 142 confirmed COVID-19 cases, 7 (4.9%) of them presented with gastrointestinal symptoms. Three patients had gastrointestinal symptoms as the initial symptoms and chief complaints, and 4 patients as the main symptoms during disease progression. Six patients had symptoms of diarrhea (3–16 days), 7 with anorexia (7–22 days), 6 with upper abdominal discomfort (1–7 days), and 4 with nausea (1–7 days), 1 with heartburn lasting 2 days, and 2 with vomiting symptoms (1 day). The chest CT scan showed typical COVID-19 imaging features, and associated with the progression of the disease. During treatment, 2 patients died due to organ failure. Discussion: COVID-19 patients with gastrointestinal symptoms are relatively rare and might be misdiagnosed. The clinical features include watery stools, anorexia, and upper abdominal discomfort. These patients may have severe disease and be associated with a poor prognosis. The underlying mechanisms of SARS-CoV-2 related gastrointestinal symptoms need to clarify in future studies.
  •  
42.
  • Almquist, Ben, et al. (author)
  • Outstanding Reviewers for Materials Horizons in 2019
  • 2020
  • In: Materials Horizons. - : ROYAL SOC CHEMISTRY. - 2051-6347 .- 2051-6355. ; 7:5, s. 1207-1207
  • Journal article (other academic/artistic)abstract
    • We would like to take this opportunity to highlight the Outstanding Reviewers for Materials Horizons in 2019, as selected by the editorial team for their significant contribution to the journal.
  •  
43.
  • Alström, Per, et al. (author)
  • Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes)
  • 2008
  • In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 47:3, s. 960-973
  • Journal article (peer-reviewed)abstract
    • The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophertax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6-7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.
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44.
  • Bell, David, et al. (author)
  • Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution
  • 2020
  • In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 107:1, s. 91-115
  • Journal article (peer-reviewed)abstract
    • Premise Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. Methods We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. Results Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. Conclusions A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
  •  
45.
  • Bentham, James, et al. (author)
  • A century of trends in adult human height
  • 2016
  • In: eLIFE. - 2050-084X. ; 5
  • Journal article (peer-reviewed)abstract
    • Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
  •  
46.
  • Bentham, James, et al. (author)
  • A century of trends in adult human height
  • 2016
  • In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
  • Journal article (peer-reviewed)abstract
    • Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
  •  
47.
  • Bixby, H., et al. (author)
  • Rising rural body-mass index is the main driver of the global obesity epidemic in adults
  • 2019
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 569:7755, s. 260-4
  • Journal article (peer-reviewed)abstract
    • Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities(.)(1,2) This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity(3-6). Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017-and more than 80% in some low- and middle-income regions-was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing-and in some countries reversal-of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.
  •  
48.
  • Charalambous, Themistoklis, et al. (author)
  • Decentralised Minimum-Time Average Consensus in Digraphs
  • 2013
  • In: 2013 IEEE 52nd Annual Conference on Decision and Control (CDC). - : IEEE conference proceedings. - 9781467357142 ; , s. 2617-2622
  • Conference paper (peer-reviewed)abstract
    • Distributed algorithms for average consensus in directed graphs are typically asymptotic in the literature. In this work, we propose a protocol to distributively reach average consensus in a finite number of steps on interconnection topologies that form strongly connected directed graphs (digraphs). The average consensus value can be computed, based exclusively on local observations at each component, by running a protocol that requires each component to observe and store its own value over a finite and minimal number of steps, and to have knowledge of the number of its out-going links (i.e., the number of components to which it sends information). The proposed algorithm is demonstrated via illustrative examples.
  •  
49.
  • Charalambous, Themistoklis, et al. (author)
  • Distributed Finite-Time Average Consensus in Digraphs in the Presence of Time Delays
  • 2015
  • In: IEEE Transactions on Control of Network Systems. - : IEEE. - 2325-5870. ; 2:4, s. 370-381
  • Journal article (peer-reviewed)abstract
    • Most algorithms for distributed averaging only guarantee asymptotic convergence. This paper introduces a distributed protocol that allows nodes to find the exact average of the initial values in a finite and minimum number of steps on interconnection topologies described by strongly connected directed graphs (digraphs). More specifically, under the assumption that each component has knowledge of the number of its outgoing links (i.e., the number of components to which it sends information), we show that the average value can be computed based on local observations over a finite time interval. The average can be obtained in a finite number of steps even when the information exchange is subject to delays. The proposed algorithm is the first in the literature that allows for distributed computation of the exact average in digraphs in finite time, with and without delays.
  •  
50.
  • Chen, Tao, et al. (author)
  • SinoPedia—A Linked Data Services platform for decentralized knowledge base
  • 2019
  • In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14:8
  • Journal article (peer-reviewed)abstract
    • Knowledge bases are largely developed and utilized in academic and industrial fields, such as DBPedia, VIAF, LoC, Getty, and which are published in the Linked Data format. However, if you want to view different resources on these knowledge bases, you have to switch between different web pages from these resources. Therefore, we proposed a decentralized data hub named SinoPedia, which consists of several linked data services and can re-publish these RDF data in one platform. Firstly, these different Linked Data services include: Linked Data Transformation Service (LDTS), Linked Data Query Service (LDQS), Linked Data Publishing Service (LDPS) and Linked Data Knowledge Service (LDKS). The resource URI is the basis and core of the linked data, thus we will focus on the resource forwarding mechanism in LDPS service which can rewrite resource URI using a global and standard format among knowledge bases. Some knowledge bases were configured in SinoPedia platform in this paper. In addition to the above services, Linked Data Reasoning Service (LDRS) and Linked Data Intelligence Service (LDIS) will be added to the platform in the future. In short, all of these Linked Data Services will form the core framework in order to providing a good linked data application ecosystem.
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