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- 2019
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Journal article (peer-reviewed)
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| 7. |
- 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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| 8. |
- Ablikim, M., et al.
(author)
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Observation of e(+)e(-) -> pi(0)pi(0)h(c) and a Neutral Charmoniumlike Structure Z(c)(4020)(0)
- 2014
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 113:21, s. 212002-
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Journal article (peer-reviewed)abstract
- Using data collected with the BESIII detector operating at the Beijing Electron Positron Collider at center-of-mass energies of root s = 4.23, 4.26, and 4.36 GeV, we observe e(+)e(-) -> pi(0)pi(0)h(c) for the first time. The Born cross sections are measured and found to be about half of those of e(+)e(-) -> pi(+)pi(-)h(c) within less than 2 sigma. In the pi(0)h(c) mass spectrum, a structure at 4.02 GeV/c(2) is found. It is most likely to be the neutral isospin partner of the Z(c)(4020)(+/-) observed in the process of e(+)e(-) -> pi(+)pi(-)h(c) being found. A fit to the pi(0)h(c) invariant mass spectrum, with the width of the Z(c)(4020)(0) fixed to that of its charged isospin partner and possible interferences with non-Z(c)(4020)(0) amplitudes neglected, gives a mass of (4023.9 +/- 2.2 +/- 3.8) MeV/c(2) for the Z(c)(4020)(0), where the first error is statistical and the second systematic.
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| 9. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:5, s. 052001-
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Journal article (peer-reviewed)abstract
- We perform an analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot using a data set of 2.92 fb(-1) of e(+) e(-) collisions at the (3770) mass accumulated by the BESIII experiment, in which 166694 candidate events are selected with a background of 15.1%. The Dalitz plot is found to be well represented by a combination of six quasitwo- body decay channels [k(SP)(0)(+) (1450)(+,) ] plus a small nonresonant component. Using the fit fractions from this analysis, partial branching ratios are updated with higher precision than previous measurements.
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| 10. |
- Ablikim, M., et al.
(author)
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Measurement of chi(cJ) decaying into eta ' K+K-
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 074030-
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Journal article (peer-reviewed)abstract
- Using (106.41 +/- 0.86) x 10(6) Psi(3686) events collected with the BESIII detector at BEPCII, we study for the first time the decay chi(cJ) -> eta'K+K- (J = 1, 2), where eta' -> gamma rho(0) and eta' -> eta pi(+)pi(-). A partial wave analysis in the covariant tensor amplitude formalism is performed for the decay chi(c1) -> eta'K+K-. Intermediate processes chi(c1) -> eta'f(2)'(1525) chi(c1) -> K-0*(1430)K-+/-(-/+) (K-0*(1430)(+/-) -> eta'K-+/-) are observed with statistical significances larger than 5 sigma, and their branching fractions are measured.
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| 11. |
- Ablikim, M., et al.
(author)
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Measurement of the branching fraction for psi(3686) -> omega K+K-
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112006-
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Journal article (peer-reviewed)abstract
- With 1.06 x 10(8) psi(3686) events collected with the BESIII detector, the branching fraction of psi(3686) -> omega K+K- is measured to be (1.54 +/- 0.04 +/- 0.11) x 10(-4). This is the most precise result to date, due to the largest psi(3686) sample, improved signal reconstruction efficiency, good simulation of the detector performance, and a more accurate knowledge of the continuum contribution. Using the branching fraction of J/psi -> omega K+K-, the ratio B(psi(3868) -> K+K-)/B(J/psi -> K+K-) is determined to be (18.4 +/- 3.7)%. This constitutes a significantly improved test of the 12% rule, with the uncertainty now dominated by the J/psi branching fraction.
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| 12. |
- Ablikim, M., et al.
(author)
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Observation of e(+)e(-) -> gamma X(3872) at BESIII
- 2014
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:9, s. 092001-
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Journal article (peer-reviewed)abstract
- With data samples collected with the BESIII detector operating at the BEPCII storage ring at center-of-mass energies from 4.009 to 4.420 GeV, the process e(+)e(-) -> gamma X(3872) is observed for the first time with a statistical significance of 6.3 sigma. The measured mass of the X(3872) is (3871.9 +/- 0.7(stat) +/- 0.2(syst)) MeV/c(2), in agreement with previous measurements. Measurements of the product of the cross section sigma[e(+)e(-) -> gamma X(3872)] and the branching fraction B [X(3872) -> pi(+)pi(-)J/psi] at center-of-mass energies 4.009, 4.229, 4.260, and 4.360 GeV are reported. Our measurements are consistent with expectations for the radiative transition process Y(4260) -> gamma X(3872).
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| 13. |
- Ablikim, M., et al.
(author)
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Observation of eta' -> pi(+) pi(-) pi(+) pi(-) and eta' -> pi(+) pi(-) pi(0) pi(0)
- 2014
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:25, s. 251801-
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Journal article (peer-reviewed)abstract
- Using a sample of 1.3 x 10(9) J/psi events collected with the BESIII detector, we report the first observation of eta' -> pi(+) pi(-) pi(+) pi(-) and eta' -> pi(+) pi(-) pi(0) pi(0). The measured branching fractions are B(eta' -> pi(+) pi(-) pi(+) pi(-)) = [8.53 +/- 0.69(stat.) +/- 0.64(syst.)] x 10(-5) and B(eta' -> pi(+) pi(-) pi(0) pi(0)) = [1.82 +/- 0.35(stat.) +/- 0.18(syst.)] x 10(-4), which are consistent with theoretical predictions based on a combination of chiral perturbation theory and vector-meson dominance.
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| 14. |
- Ablikim, M., et al.
(author)
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Observation of J/psi -> p(p)over-bara(0)(980) at BESIII
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:5, s. 052009-
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Journal article (peer-reviewed)abstract
- Using 2.25 x 10(8) J/psi events collected with the BESIII detector at the BEPCII storage rings, we observe for the first time the process J/psi -> p (p) over bara(0)(980) -> pi(0)eta with a significance of 6.5 sigma (3.2 sigma including systematic uncertainties). The product branching fraction of J/psi -> p (p) over bara(0)(980) -> p (p) over bara(0)pi(0)eta is measured to be (6.8 +/- 1.2 +/- 1.3) x 10(-5), where the first error is statistical and the second is systematic. This measurement provides information on the a(0) production near threshold coupling to p (p) over bar and improves the understanding of the dynamics of J/psi decays to four-body processes.
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| 15. |
- Ablikim, M., et al.
(author)
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Observation of the decay psi(3686) -> Lambda(Sigma)over-bar(+/-) pi(-/+) + c.c
- 2013
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112007-
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Journal article (peer-reviewed)abstract
- Using a sample of 1:06 X 10(8) psi(3686) events collected with the BESIII detector, we present the first observation of the decays of psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c. and psi(3686) -> Lambda(Sigma) over bar (-) pi(+) + c.c. The branching fractions are measured to be B(psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c.) = (1.40 +/- 0.03 +/- 0.13) X 10(-4) and B(psi(3686) -> Lambda (Sigma) over bar (-) pi(+) + c.c.) = (1.54 +/- 0.04 +/- 0.13) X 10(-4) where the first errors are statistical and the second ones systematic.
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| 16. |
- Ablikim, M., et al.
(author)
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Precision measurement of the mass of the tau lepton
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:1
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Journal article (peer-reviewed)abstract
- An energy scan near the tau pair production threshold has been performed using the BESIII detector. About 24 pb(-1) of data, distributed over four scan points, were collected. This analysis is based on t pair decays to ee, e mu, eh, h, hh, e.,. and p. final states, where h denotes a charged p or K. The mass of the t lepton is measured from a maximum likelihood fit to the t pair production cross- section data to be m(tau) = 1776.91 +/- 0.12_0.10 - 0.13 _ MeV/c(2), which is currently the most precise value in a single measurement.
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| 17. |
- Ablikim, M., et al.
(author)
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Search for C-parity violation in J/psi -> gamma gamma and gamma phi
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:9, s. 092002-
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Journal article (peer-reviewed)abstract
- Using 1.06 x 10(8) psi(3686) events recorded in e(+)e(-) collisions at root s = 3.686 GeV with the BESIII at the BEPCII collider, we present searches for C-parity violation in J/psi -> gamma gamma and gamma phi decays via psi(3686) -> J/psi pi(+)pi(-). No significant signals are observed in either channel. Upper limits on the branching fractions are set to be B(J/psi -> gamma gamma) < 2.7 x 10(-7) and B(J/psi -> gamma phi) < 1.4 x 10(-6) at the 90% confidence level. The former is one order of magnitude more stringent than the previous upper limit, and the latter represents the first limit on this decay channel.
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| 18. |
- Ablikim, M., et al.
(author)
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Search for eta(c)(2S)h(c) -> p(p)over-bar decays and measurements of the chi(cJ) -> p(p)over-bar branching fractions
- 2013
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112001-
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Journal article (peer-reviewed)abstract
- Using a sample of 1.06 x 10(8)psi(3686) events collected with the BESIII detector at BEPCII, the decays eta(c)(2S) -> p (p) over bar and h(c) -> p (p) over bar are searched for, where eta(c)(2S) and h(c) are reconstructed in the decay chains psi(3686) -> gamma eta(c)(2S), eta(c)(2S) -> p (p) over bar and psi(3686) -> pi(0)h(c), h(c) -> p (p) over bar, respectively. No significant signals are observed. The upper limits of the product branching fractions are determined to be B(psi(3686) -> gamma eta(c)(2S)) x B(eta(c)(2S) -> p (p) over bar) < 1.4 x 10(-6) and B(psi(3686) -> pi(0)h(c)) x B(h(c) -> p<(p)over bar>) < 1.3 x 10(-7) at the 90% C.L.. The branching fractions for chi(cJ) -> p<(p)over bar> (J = 0, 1, 2) are also measured to be (24.5 +/- 0.8 +/- 1.3, 8.6 +/- 0.5 +/- 0.5, 8.4 +/- 0.5 +/- 0.5) x 10(-5), which are the world's most precise measurements.
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| 19. |
- Ablikim, M., et al.
(author)
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Search for the radiative transitions Psi(3770) -> gamma eta(c) and gamma eta(c) (2S)
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112005-
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Journal article (peer-reviewed)abstract
- By using a 2.92 fb-1 data sample taken at pffisffiffi 3.773 GeV with the BESIII detector operating at the BEPCII collider, we search for the radiative transitions.d3770c and cd2S through the hadronic decays cdcd2S. K0 SK p. No significant excess of signal events above background is observed. We set upper limits at a 90% confidence level for the product branching fractions to be Bdd3770cxBd.c. K0 SK k p < 1.6x10-5 and Bd.d3770cd2SxBd.cd2S. K0 SK p<5.6x10-6. Combining our result with world-average values of Bd.cd.cd2S. K0 SK p, we find the branching fractions Bd.d3770c< 6.8 x 10-4 and Bd.d3770cd2S< 2.0 x 10-3 at a 90% confidence level.
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| 20. |
- Ablikim, M., et al.
(author)
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Search for the rare decays J/y -> D-s(-) rho(+) and J/psi -> <(D)over bar(0)<(K)over bar*(0)
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 071101-
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Journal article (peer-reviewed)abstract
- A search for the rare decays of J/psi -> D-S(-) rho(+) + c.c. and J/psi -> <(D)over bar(0)<(K)over bar*(0) + c.c. is performed with a data sample of 225.3-million J/psi events collected with the Beijing Spectrometer III detector. No evident signal is observed. Upper limits on the branching fractions are determined to be beta(J/psi -> D-S(-)rho(+) + c.c.) < 1.3 x 10(-5) and beta(J/psi -> <(D)over bar(0)<(K)over bar*(0) + c.c.) < 2.5 x 10(-6) at the 90% confidence level.
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| 21. |
- Ablikim, M., et al.
(author)
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Study of e(+)e(-) -> p(p)over-bar in the vicinity of psi(3770)
- 2014
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 735, s. 101-107
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Journal article (peer-reviewed)abstract
- Using 2917 pb(-1) of data accumulated at 3.773 GeV, 44.5 pb(-1) of data accumulated at 3.65 GeV and data accumulated during a psi(3770) line-shape scan with the BESIII detector, the reaction e(+)e(-) -> p (p) over bar is studied considering a possible interference between resonant and continuum amplitudes. The cross section of e(+)e(-) -> psi(3770) -> p (p) over bar, sigma(e(+)e(-)-> psi(3770) -> p (p) over bar), is found to have two solutions, determined to be (0.059(-0.020)(+0.070) +/- 0.012) pb with the phase angle phi = (255.8(-26.6)(+39.0) +/- 4.8). (< 0.166 pb at the 90% confidence level), or sigma(e(+)e(-) -> psi(3770) -> p<(p)over bar>) = (2.57(-0.13)(+0.12) +/- 0.12) pb with phi = (266.9(-6.3)(+6.1) +/- 0.9)degrees both of which agree with a destructive interference. Using the obtained cross section of psi(3770) -> p (p) over bar, the cross section of p (p) over bar -> psi(3770), which is useful information for the future PANDA experiment, is estimated to be either (9.8(-3.9)(+11.8)) nb (< 27.5 nb at 90% C.L.) or (425.6(-43.7)(+42.9)) nb. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.
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| 22. |
- Ablikim, M., et al.
(author)
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Study of e(+)e(-) -> p(p)over-bar pi(0) in the vicinity of the psi(3770)
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:3, s. 032007-
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Journal article (peer-reviewed)abstract
- The process e(+)e(-) -> p (p) over bar pi(0) has been studied by analyzing data collected at root s = 3.773 GeV, root s = 3.650 GeV, and during a psi(3770) line shape scan with the BESIII detector at the BEPCII collider. The Born cross section of p (p) over bar pi(0) in the vicinity of the psi(3770) is measured, and the Born cross section of psi(3770) -> p (p) over bar pi(0) is extracted considering interference between resonant and continuum production amplitudes. Two solutions with the same probability and a significance of 1.5 sigma are found. The solutions for the Born cross section of psi(3770) -> p (p) over bar pi(0) are 33.8 +/- 1.8 +/- 2.1 pb and 0.06(-0.04-0.01)(+0.10+0.01) pb (< 0.22 pb at a 90% confidence level). Using the estimated cross section and a constant decay amplitude approximation, the cross section sigma(p<(p)over bar> -> psi(3770)pi(0)) is calculated for the kinematic situation of the planned (p) over bar ANDA experiment. The maximum cross section corresponding to the two solutions is expected to be less than 0.79 nb at 90% confidence level and 122 +/- 10 nb at a center-of-mass energy of 5.26 GeV.
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| 23. |
- 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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| 24. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 25. |
- Kristan, Matej, et al.
(author)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 26. |
- Jin, Ying-Hui, et al.
(author)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Journal article (peer-reviewed)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 27. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Journal article (peer-reviewed)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 28. |
- Ma, Jiang-Jiang, et al.
(author)
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High-Temperature Mechanical and Dynamical Properties of gamma-(U,Zr) Alloys
- 2023
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In: Materials. - : MDPI. - 1996-1944. ; 16:7
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Journal article (peer-reviewed)abstract
- High-temperature body-centered cubic (BCC) gamma-U is effectively stablized by gamma-(U,Zr) alloys that also make it feasible to use it as a nuclear fuel. However, relatively little research has focused on gamma-(U,Zr) alloys due to their instability at room temperature. The effect of Zr composition on its mechanical properties is not clear yet. Herein, we perform molecular dynamics simulations to investigate the mechanical and dynamical stabilities of gamma-(U,Zr) alloys under high temperatures, and we calculate the corresponding lattice constants, various elastic moduli, Vickers hardness, Debye temperature, and dynamical structure factor. The results showed that gamma-U, beta-Zr, and gamma-(U,Zr) are all mechanically and dynamically stable at 1200 K, which is in good agreement with the previously reported high-temperature phase diagram of U-Zr alloys. We found that the alloying treatment on ?-U with Zr can effectively improve its mechanical strength and melting points, such as Vickers hardness and Debye temperature, making it more suitable for nuclear reactors. Furthermore, the Zr concentrations in gamma-(U,Zr) alloys have an excellent effect on these properties. In addition, the dynamical structure factor reveals that gamma-U shows different structural features after alloying with Zr. The present simulation data and insights could be significant for understanding the structures and properties of UZr alloy under high temperatures.
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| 29. |
- Shi, Tian-Le, et al.
(author)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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In: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
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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.
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| 30. |
- Wang, Xue Jing, et al.
(author)
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Autonomic ganglionic injection of α-synuclein fibrils as a model of pure autonomic failure α-synucleinopathy
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- α-Synucleinopathies are characterized by autonomic dysfunction and motor impairments. In the pure autonomic failure (PAF), α-synuclein (α-Syn) pathology is confined within the autonomic nervous system with no motor features, but mouse models recapitulating PAF without motor dysfunction are lacking. Here, we show that in TgM83+/− mice, inoculation of α-Syn preformed fibrils (PFFs) into the stellate and celiac ganglia induces spreading of α-Syn pathology only through the autonomic pathway to both the central nervous system (CNS) and the autonomic innervation of peripheral organs bidirectionally. In parallel, the mice develop autonomic dysfunction, featured by orthostatic hypotension, constipation, hypohidrosis and hyposmia, without motor dysfunction. Thus, we have generated a mouse model of pure autonomic dysfunction caused by α-Syn pathology. This model may help define the mechanistic link between transmission of pathological α-Syn and the cardinal features of autonomic dysfunction in α-synucleinopathy.
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| 31. |
- Berglund, Carolina, et al.
(author)
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Genetic diversity of methicillin-resistant Staphylococcus aureus carrying type IV SCCmec in Orebro County and the western region of Sweden
- 2009
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In: Journal of Antimicrobial Chemotherapy. - Oxford : Oxford University Press. - 0305-7453 .- 1460-2091. ; 63:1, s. 32-41
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Journal article (peer-reviewed)abstract
- BACKGROUND: Recent studies have shown a predominance of type IV SCCmec among the methicillin-resistant Staphylococcus aureus (MRSA) isolated in the low endemic areas of Orebro County and the western region of Sweden. However, many of these isolates were not possible to classify as existing subtypes IVa, IVb, IVc or IVd. METHODS: We analysed 16 such MRSA isolates by multilocus sequence typing, spa typing, staphylocoagulase (SC) typing and detection of type IVg and IVh SCCmec. MRSA that remained as unknown type IV SCCmec were investigated by long-range PCR covering the J1 region; however, only two isolates were possible to amplify by PCR. The nucleotide sequences of the entire SCCmec of these two MRSA were determined. In addition, isolates that had unknown SC types were investigated by nucleotide sequencing of the coa genes. RESULTS: Five of 16 isolates were classified as type IVg SCCmec, and four isolates had type IVh SCCmec. Two subtypes of type IV SCCmec shared J1 regions previously identified in other types of SCCmec, types I.2 and II.2. The novel elements were designated as type IVi and IVj SCCmec. In addition, the genetic backgrounds of these Swedish MRSA were diverse and constituted at least nine sequence types and eight SC types, including four new types of SC. CONCLUSIONS: Type IV SCCmec is occurring in heterogeneous clones of MRSA in Sweden, and the majority of the type IV SCCmec were identified in community-acquired MRSA. We describe two novel subtypes of type IV SCCmec with common J1 regions shared by other types of SCCmec, which indicate that J1 regions occurred as primordial SCC.
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| 32. |
- Berglund, Carolina, et al.
(author)
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Novel type of staphylococcal cassette chromosome mec in a methicillin-resistant Staphylococcus aureus strain isolated in Sweden
- 2008
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In: Antimicrobial Agents and Chemotherapy. - 0066-4804 .- 1098-6596. ; 52:10, s. 3512-3516
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Journal article (peer-reviewed)abstract
- We identified a novel type of staphylococcal cassette chromosome mec (SCCmec) element carried by methicillin-resistant Staphylococcus aureus (MRSA) strain JCSC6082 isolated in Sweden. The SCCmec element was demarcated by characteristic nucleotide sequences at both ends and was integrated at the 3' end of orfX. The element carried a novel combination of a type 5 ccr gene complex and class C1 mec gene complex. The J regions of the element were homologous to those of the SCCmercury element of S. aureus strain 85/2082, with nucleotide identity greater than 99%. However, the novel SCCmec element from JCSC6082 did not carry the mer operon nor Tn554, suggesting that evolution to SCCmec could have been from a common ancestor by acquisition of the class C1 mec gene complex. The novel SCCmec element from JCSC6082 was flanked by a novel SCC-like chromosome cassette (CC6082), which was demarcated by two direct repeats and could be excised from the chromosome independently of the SCCmec element. Our data suggest that novel SCCmec elements can be generated on the staphylococcal chromosome through the recombination between extant SCC elements and mec gene complexes.
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| 33. |
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| 34. |
- He, YQ, et al.
(author)
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A polygenic risk score for nasopharyngeal carcinoma shows potential for risk stratification and personalized screening
- 2022
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 1966-
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Journal article (peer-reviewed)abstract
- Polygenic risk scores (PRS) have the potential to identify individuals at risk of diseases, optimizing treatment, and predicting survival outcomes. Here, we construct and validate a genome-wide association study (GWAS) derived PRS for nasopharyngeal carcinoma (NPC), using a multi-center study of six populations (6 059 NPC cases and 7 582 controls), and evaluate its utility in a nested case-control study. We show that the PRS enables effective identification of NPC high-risk individuals (AUC = 0.65) and improves the risk prediction with the PRS incremental deciles in each population (Ptrend ranging from 2.79 × 10−7 to 4.79 × 10−44). By incorporating the PRS into EBV-serology-based NPC screening, the test’s positive predictive value (PPV) is increased from an average of 4.84% to 8.38% and 11.91% in the top 10% and 5% PRS, respectively. In summary, the GWAS-derived PRS, together with the EBV test, significantly improves NPC risk stratification and informs personalized screening.
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| 35. |
- Kristanl, Matej, et al.
(author)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 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 as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. 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(1).
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| 36. |
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| 37. |
- Ma, Zhaoying, et al.
(author)
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Mineralogical and magnetic variations of periglacial loess in SE Tibet reveal mid-Pleistocene expansion of Tibetan glacial activity
- 2024
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In: Quaternary Science Reviews. - : Elsevier. - 0277-3791 .- 1873-457X. ; 330
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Journal article (peer-reviewed)abstract
- The formation and evolution of the cryosphere on the Tibetan Plateau is of great significance in understanding the Earth's carbon and climatic system. Periglacial loess deposits in southeastern Tibet offer a means to constrain this history as they contain critical information on glacial grinding and frost shattering processes in high-altitude mountain regions through time, which yield lithogenic fractions of largely loess silts and sands. Based on combined analyses of lithogenic magnetic properties and mineralogical composition, here we find that increasing high mountain production and supply of fresh detrital components since the mid-Pleistocene climate transition (MPT, 1.2–0.7 Ma) led to a substantial increase of the lithogenic susceptibility and decrease in chemical weathering intensity of periglacial loess in southeastern Tibet. The agreement of these findings with similar results from eolian loess on the northern margins of the Tibetan Plateau suggests a plateau-wide glacier expansion during the MPT. Enhanced glacial erosion and freeze-thaw activities occurred in the high-altitude mountain regions of the plateau during the MPT, thereby providing vast amounts of fresh detritus for the formation of loess deposits. High and constant values of lithogenic magnetic parameters in the loess deposits after 0.7–0.6 Ma further indicate that the Middle Pleistocene is a critical period for the establishment of modern-like glacial and periglacial landforms on the Tibetan Plateau. Our results further suggest that enhanced Quaternary glaciation in SE Tibet occurred earlier than in the north, which we attribute to climate cooling combined with regional seasonal snowline lowering. As such, a close relationship exists between global climate changes, development of pan-Tibetan glaciations, and large-scale dust emission.
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| 38. |
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