| 1. |
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| 2. |
- 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
-
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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| 3. |
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- 2019
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Journal article (peer-reviewed)
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| 4. |
- 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
-
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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| 5. |
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| 6. |
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| 7. |
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| 8. |
- Haycock, Philip C., et al.
(author)
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Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
-
In: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
-
Journal article (peer-reviewed)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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| 9. |
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| 10. |
- Weinstein, John N., et al.
(author)
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The cancer genome atlas pan-cancer analysis project
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Research review (peer-reviewed)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 11. |
- Ablikim, M., et al.
(author)
-
Amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:5
-
Journal article (peer-reviewed)abstract
- An amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays is presented. In particular, a piecewise function that describes the dynamics of the pi(0)pi(0) system is determined as a function of M pi(0)pi(0) from an analysis of the (1.311 +/- 0.011) x 10(9) J/psi decays collected by the BESIII detector. The goal of this analysis is to provide a description of the scalar and tensor components of the pi(0)pi(0) system while making minimal assumptions about the properties or number of poles in the amplitude. Such a model-independent description allows one to integrate these results with other related results from complementary reactions in the development of phenomenological models, which can then be used to directly fit experimental data to obtain parameters of interest. The branching fraction of J/psi -> pi(0)pi(0) is determined to be (1.15 +/- 0.05) x 10(-3), where the uncertainty is systematic only and the statistical uncertainty is negligible.
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| 12. |
- Ablikim, M., et al.
(author)
-
An improved limit for Gamma(ee) of X(3872) and Gamma(ee) measurement of psi(3686)
- 2015
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 749, s. 414-420
-
Journal article (peer-reviewed)abstract
- Using the data sets taken at center-of-mass energies above 4 GeV by the BESIII detector at the BEPCII storage ring, we search for the reaction e(+)e(-) -> gamma(ISR) X(3872) -> gamma(ISR)pi(+)pi(-) J/psi via the Initial State Radiation technique. The production of a resonance with quantum numbers J(PC) = 1(++) such as the X(3872) via single photon e(+)e(-) annihilation is forbidden, but is allowed by a next-to-leading order box diagram. We do not observe a significant signal of X(3872), and therefore give an upper limit for the electronic width times the branching fraction Gamma B-X(3872)(ee)(X(3872) -> pi(+)pi(-) J/psi) < 0.13 eVat the 90% confidence level. This measurement improves upon existing limits by a factor of 46. Using the same final state, we also measure the electronic width of the psi(3686) to be Gamma(psi)(ee)(3686) ee = 2213 +/- 18(stat) +/- 99(sys) eV.
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| 13. |
- Ablikim, M., et al.
(author)
-
Dark photon search in the mass range between 1.5 and 3.4 GeV/c
- 2017
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 252-257
-
Journal article (peer-reviewed)abstract
- Using a data set of 2.93 fb taken at a center-of-mass energy root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we perform a search for an extra U(1) gauge boson, also denoted as a dark photon. We examine the initial state radiation reactions e(+)e(-) -> e(+)e(-) gamma(ISR) and e(+)e(-) -> mu(+)mu(-) gamma(ISR) for this search, where the dark photon would appear as an enhancement in the invariant mass distribution of the leptonic pairs. We observe no obvious enhancement in the mass range between 1.5 and 3.4 GeV/c(2) and set a 90% confidence level upper limit on the mixing strength of the dark photon and the Standard Model photon. We obtain a competitive limit in the tested mass range.
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| 14. |
- Ablikim, M., et al.
(author)
-
Evidence for e(+)e(-)->gamma chi c1,2 at center-of-mass energies from 4.009 to 4.360 GeV
- 2015
-
In: Chinese Physics C. - : IOP Publishing. - 1674-1137 .- 2058-6132. ; 39:4
-
Journal article (peer-reviewed)abstract
- Using data samples collected at center-of-mass energies of root s=4.009, 4.230, 4.260, and 4.360 GeV with the BESIII detector operating at the BEPCII collider, we perform a search for the process e(+)e(-)->gamma chi(cJ) (J=0, 1, 2) and find evidence for e(+)e(-)->gamma chi(c1) and e(+)e(-)->gamma chi(c2) with statistical significances of 3.0 sigma and 3.4 sigma, respectively. The Born cross sections sigma(B)(e(+)e(-)->gamma chi(cJ)), as well as their upper limits at the 90% confidence level (C.L.) are determined at each center-of-mass energy.
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| 15. |
- Ablikim, M., et al.
(author)
-
Measurement of B(psi(3770) -> gamma chi(c1)) and search for psi(3770) -> gamma chi(c2)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:9
-
Journal article (peer-reviewed)abstract
- We report a measurement of the branching fraction for psi(3770) -> gamma chi(c1) and search for the transition psi(3770) -> gamma chi(c2) based on 2.92 fb(-1) of e(+)e(-) data accumulated at root s = 3.773 GeV with the BESIII detector at the BEPCII collider. We measure B(psi(3770) -> gamma chi(c1)) = (2.48 +/- 0.15 +/- 0.23) x 10(-3), which is the most precise measurement to date. The upper limit on the branching fraction of psi(3770) -> gamma chi(c2) at a 90% confidence level is B(psi(3770) -> gamma chi(c2)) < 0.64 x 10(-3). The corresponding partial widths are Gamma(psi(3770) -> gamma chi(c1)) = (67.5 +/- 4.1 +/- 6.7)keV and Gamma(psi(3770) -> gamma chi(c2)) < 17.4 keV.
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| 16. |
- Ablikim, M., et al.
(author)
-
Measurement of the branching fraction for psi(3686) -> omega K+K-
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112006-
-
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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| 17. |
- Ablikim, M., et al.
(author)
-
Measurement of the branching fractions of D-s(+) -> eta ' X and D-s(+) -> eta 'rho(+) in e(+)e(-) -> Ds+Ds-
- 2015
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 750, s. 466-474
-
Journal article (peer-reviewed)abstract
- We study D-s(+) decays to final states involving the eta' with a 482 pb(-1) data sample collected at root s = 4.009 GeV with the BESIII detector at the BEPCII collider. We measure the branching fractions B(D-s(+) -> eta'X) = (8.8 +/- 1.8 +/- 0.5)% and B(D-s(+) > eta'rho(+)) = (5.8 +/- 1.4 +/- 0.4)% where the first uncertainty is statistical and the second is systematic. In addition, we estimate an upper limit on the non-resonant branching ratio B(D-s(+) -> eta'pi(+)pi(0)) < 5.1% at the 90% confidence level. Our results are consistent with CLEO's recent measurements and help to resolve the disagreement between the theoretical prediction and CLEO's previous measurement of B(D-s(+) -> eta'rho(+)).
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| 18. |
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| 19. |
- Ablikim, M., et al.
(author)
-
Measurement of the leptonic decay width of J/psi using initial state radiation
- 2016
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 761, s. 98-103
-
Journal article (peer-reviewed)abstract
- Using a data set of 2.93 fb(-1) taken at a center-of-mass energy of root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we measure the process e(+) e(-) -> J/psi gamma -> mu(+)mu(-)gamma and determine the product of the branching fraction and the electronic width B-mu mu . Gamma(ee) = (333.4 +/- 2.5(stat) +/- 4.4(sys)) eV. Using the earlier-published BESIII result for B-mu mu = (5.973 +/- 0.007(stat) +/- 0.037(sys))%, we derive the J/psi electronic width Gamma(ee) = (5.58 +/- 0.05(stat) +/- 0.08(sys)) keV. (C) 2016 The Author(s). Published by Elsevier B.V.
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| 20. |
- Ablikim, M., et al.
(author)
-
Measurement of the matrix elements for the decays eta -> pi(+)pi(-)pi(0) and eta/eta ' -> pi(0)pi(0)pi(0)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:1
-
Journal article (peer-reviewed)abstract
- Based on a sample of 1.31 x 10(9) J/psi events collected with the BESIII detector at the BEPCII collider, Dalitz plot analyses of selected 79,625 eta -> pi(+)pi(-)pi(0) events, 33,908 eta -> pi(0)pi(0)pi(0) events, and 1,888 eta' -> pi(0)pi(0)pi(0) events are performed. The measured matrix elements of eta -> pi(+)pi(-)pi(0) are in reasonable agreement with previous measurements. The Dalitz plot slope parameters of eta -> pi(0)pi(0)pi(0) and eta' -> pi(0)pi(0)pi(0) are determined to be -0.055 +/- 0.014 +/- 0.004 and -0.640 +/- 0.046 +/- 0.047, respectively, where the first uncertainties are statistical and the second systematic. Both values are consistent with previous measurements, while the precision of the latter one is improved by a factor of 3. Final state interactions are found to have an important role in those decays.
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| 21. |
- Ablikim, M., et al.
(author)
-
Measurement of the proton form factor by studying e(+)e(-) -> p(p)over-tilde
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:11
-
Journal article (peer-reviewed)abstract
- Using data samples collected with the BESIII detector at the BEPCII collider, we measure the Born cross section of e(+)e(-) -> p (p) over tilde at 12 center-of-mass energies from 2232.4 to 3671.0 MeV. The corresponding effective electromagnetic form factor of the proton is deduced under the assumption that the electric and magnetic form factors are equal (vertical bar G(E)vertical bar = vertical bar G(M)vertical bar). In addition, the ratio of electric to magnetic form factors, vertical bar G(E)/G(M)vertical bar, and vertical bar G(M)vertical bar are extracted by fitting the polar angle distribution of the proton for the data samples with larger statistics, namely at root s = 2232.4 and 2400.0 MeV and a combined sample at root s = 3050.0, 3060.0 and 3080.0 MeV, respectively. The measured cross sections are in agreement with recent results from BABAR, improving the overall uncertainty by about 30%. The vertical bar G(E)/G(M)vertical bar ratios are close to unity and consistent with BABAR results in the same q(2) region, which indicates the data are consistent with the assumption that vertical bar G(E)vertical bar = vertical bar G(M)vertical bar within uncertainties.
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| 22. |
- Ablikim, M., et al.
(author)
-
Measurement of y(CP) in D-0-(D)over-bar(0) oscillation using quantum correlations in e(+)e(-) -> D-0(D)over-bar(0) at root s=3.773 GeV
- 2015
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 744, s. 339-346
-
Journal article (peer-reviewed)abstract
- We report a measurement of the parameter y(CP) in D-0-(D) over bar (0) oscillations performed by taking advantage of quantum coherence between pairs of D-0(D) over bar (0) mesons produced in e(+)e(-) annihilations near threshold. In this work, doubly-tagged D-0(D) over bar (0) events, where one D decays to a CP eigenstate and the other D decays in a semileptonic mode, are reconstructed using a data sample of 2.92 fb(-1) collected with the BESIII detector at the center-of-mass energy of root s = 3.773 GeV. We obtain y(CP) = (-2.0 +/- 1.3 +/- 0.7)%, where the first uncertainty is statistical and the second is systematic. This result is compatible with the current world average.
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| 23. |
- Ablikim, M., et al.
(author)
-
Measurements of psi(3686) -> K-Lambda(Xi)over-bar(+) + c.c. and psi(3686) -> gamma K-Lambda(Xi)over-bar(+) + c.c.
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:9
-
Journal article (peer-reviewed)abstract
- Using a sample of 1.06 x 10(8) psi(3686) events produced in e(+)e(-) collisions at root s = 3.686 GeV and collected with the BESIII detector at the BEPCII collider, we present studies of the decays psi(3686) -> K-Lambda(Xi) over bar (+) + c.c. and psi(3686) -> gamma K-Lambda(Xi) over bar (+) + c.c. We observe two hyperons, Xi(1690)(-) and Xi(1820)(-), in the K-Lambda invariant mass distribution in the decay psi(3686) -> K-Lambda(Xi) over bar (+) + c.c. with significances of 4.9 sigma and 6.2 sigma, respectively. The branching fractions of psi(3686) -> K-Lambda(Xi) over bar (+) + c.c., psi(3686) -> K-Sigma(0)(Xi) over bar (+) + c.c, psi(3686) -> gamma chi cJ -> gamma K-Lambda(Xi) over bar (+) + c.c (J = 0, 1, 2), and psi(3686) -> Xi(1690/1820)(-)(Xi) over bar (+) + c.c with sub-sequent decay Xi(1690/1820)(-) -> K-Lambda are measured for the first time.
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| 24. |
- Ablikim, M., et al.
(author)
-
Observation and Spin-Parity Determination of the X(1835) in J/psi -> gamma(KSKS0)-K-0 eta
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 115:9
-
Journal article (peer-reviewed)abstract
- We report an observation of the process J/psi -> gamma X(1835) -> gamma(KSKS0)-K-0 eta at low (KSKS0)-K-0 mass with a statistical significance larger than 12.9s using a data sample of 1.31 x 109 J/psi events collected with the BESIII detector. In this region of phase space the (KSKS0)-K-0 system is dominantly produced through the f (0)(980). By performing a partial wave analysis, we determine the spin parity of the Xd1835_ to be J(PC) = 0(-+). The mass and width of the observed X(1835) are 1844 +/- 9(stat)(-25)(+16)(syst) MeV/c(2) and 192(-17)(+20)(sta)(-43)(+62)(syst) MeV, respectively, which are consistent with the results obtained by BESIII in the channel J/psi -> gamma pi(+)pi(-)eta'.
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| 25. |
- Ablikim, M., et al.
(author)
-
Observation of a Neutral Charmoniumlike State Z(c)(4025)(0) in e(+)e(-) -> (D*(D)over-bar*)(0)pi(0)
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 115:18
-
Journal article (peer-reviewed)abstract
- We report a study of the process e(+)e(-) -> (D*(D) over bar*)(0)pi(0) using e(+)e(-) collision data samples with integrated luminosities of 1092 pb(-1) at root s = 4.23 GeV and 826 pb(-1) at root s = 4.26 GeV collected with the BESIII detector at the BEPCII storage ring. We observe a new neutral structure near the (D*(D) over bar*)(0) mass threshold in the pi(0) recoil mass spectrum, which we denote as Z(c)(4025)(0). Assuming a Breit-Wigner line shape, its pole mass and pole width are determined to be (4025.5(-4.7)(+2.0) +/- 3.1) MeV/c(2) and (23.0 +/- 6.0 +/- 1.0) MeV, respectively. The Born cross sections of e(+)e(-) -> Z(c)(4025)(0)pi(0) -> (D*(D) over bar*)(0)pi(0) are measured to be (61.6 +/- 8.2 +/- 9.0) pb at root s = 4.23 GeV and (43.4 +/- 8.0 +/- 5.4) pb at root s = 4.26 GeV. The first uncertainties are statistical and the second are systematic.
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| 26. |
- Ablikim, M., et al.
(author)
-
Observation of e(+)e(-) -> pi(0)pi(0)h(c) and a Neutral Charmoniumlike Structure Z(c)(4020)(0)
- 2014
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 113:21, s. 212002-
-
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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| 27. |
- Ablikim, M., et al.
(author)
-
Observation of J/psi -> p(p)over-bara(0)(980) at BESIII
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:5, s. 052009-
-
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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| 28. |
- Ablikim, M., et al.
(author)
-
Observation of the Dalitz decay eta ' -> gamma e(+)e(-)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:1
-
Journal article (peer-reviewed)abstract
- We report the first observation of the Dalitz decay eta' -> gamma e(+)e(-), based on a data sample of 1.31 billion J/psi events collected with the BESIII detector. The eta' mesons are produced via the J/psi -> gamma eta' decay process. The ratio (eta' -> gamma e(+)e(-))/Gamma (eta' -> gamma gamma) is measured to be (2.13 +/- 0.09(stat) +/- 0.07(sys)) x 10(-2). This corresponds to a branching fraction B(eta' -> gamma e(+)e(-)) = (4.69 +/- 0.20(stat) +/- 0.23(sys)) x 10(-4). The transition form factor is extracted and different expressions are compared to the measured dependence on the e(+)e(-) invariant mass. The results are consistent with the prediction of the vector meson dominance model.
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| 29. |
- Ablikim, M., et al.
(author)
-
Observation of the electromagnetic doubly OZI-suppressed decay J/psi -> phi pi(0)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:11
-
Journal article (peer-reviewed)abstract
- Using a sample of 1.31 billion J/psi events accumulated with the BESIII detector at the BEPCII collider, we report the observation of the decay J/psi -> phi pi(0), which is the first evidence for a doubly Okubo-Zweig-Iizuka suppressed electromagnetic J/psi decay. A clear structure is observed in the K+K- mass spectrum around 1.02 GeV/c(2), which can be attributed to interference between J/psi -> phi pi(0) and J/psi -> K+K- pi(0) decays. Due to this interference, two possible solutions are found. The corresponding measured values of the branching fraction of J/psi -> phi pi(0) are [2.94 +/- 0.16(stat) +/- 0.16(syst)] x 10(-6) and [1.24 +/- 0.33(stat) +/- 0.30(syst)] x 10(-7).
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| 30. |
- Ablikim, M., et al.
(author)
-
Observation of the isospin-violating decay J/psi -> phi pi(0)f(0) (980)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:1
-
Journal article (peer-reviewed)abstract
- Using a sample of 1.31 x 10(9) J/psi events collected with the BESIII detector at the BEPCII collider, the decays J/psi -> phi pi(+)pi(-)pi(0) and J/psi -> phi pi(0)pi(0)pi(0) are investigated. The isospin- violating decay J/psi -> phi pi(0)f(0)(980) with f(0)(980)-> pi pi is observed for the first time. The width of the f(0)(980) obtained from the dipion mass spectrum is found to be much smaller than the world average value. In the pi(0)f(0)(980) mass spectrum, there is evidence of f(1)(1285) production. By studying the decay J/psi ->eta', the branching fractions of eta' -> pi(+)pi(-)pi(0) and eta' -> pi(0)pi(0)pi(0), as well as their ratio, are also measured.
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| 31. |
- Ablikim, M., et al.
(author)
-
Observation of the Psi(1(3)D(2)) State in e(+)e(-) -> pi(+)pi(-)gamma chi(c1) at BESIII
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 115:1
-
Journal article (peer-reviewed)abstract
- We report the observation of the X(3823) state in the process e(+)e(-) -> pi(+)pi(-) X(3823) pi(+)pi(-)gamma chi(c1) with a statistical significance of 6.2 sigma, in data samples at center-of-mass energies root s = 4.230, 4.260, 4.360, 4.420, and 4.600 GeV collected with the BESIII detector at the BEPCII electron positron collider. The measured mass of the X(3823) state is (3821.7 +/- 1.3 +/- 0.7) MeV/c(2), where the first error is statistical and the second systematic, and the width is less than 16 MeV at the 90% confidence level. The products of the Born cross sections for e(+)e(-) -> pi(+)pi(-) X(3823) and the branching ratio B [X(3823) -> gamma X-c1c2] are also measured. These measurements are in good agreement with the assignment of the X(3823) state as the Psi(1(3)D(2)) charmonium state.
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| 32. |
- Ablikim, M., et al.
(author)
-
Observation of Z(c)(3900)(0) in e(+)e(-) -> pi(0)pi(0) J/Psi
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 115:11
-
Journal article (peer-reviewed)abstract
- Using a data sample collected with the BESIII detector operating at the BEPCII storage ring, we observe a new neutral state Z(c)(3900)(0) with a significance of 10.4 sigma. The mass and width are measured to be 3894.8 +/- 2.3 +/- 3.2 MeV/c(2) and 29.6 +/- 8.2 +/- 8.2 MeV, respectively, where the first error is statistical and the second systematic. The Born cross section for e(+)e(-) -> pi(0)pi(0) J/Psi and the fraction of it attributable to pi(0)Z(c)(3900)(0) -> pi(0)pi(0) J/Psi in the range E-c.m. = 4.19-4.42 GeV are also determined. We interpret this state as the neutral partner of the four-quark candidate Z(c)(3900)(+/-).
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| 33. |
- Ablikim, M., et al.
(author)
-
Precision measurement of the D*(0) decay branching fractions
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368 .- 2470-0010. ; 91:3
-
Journal article (peer-reviewed)abstract
- Using 482 pb(-1) of data taken at root s = 4.009 GeV, we measure the branching fractions of the decays of D*(0) into D-0 pi(0) and D-0 gamma to be B(D*(0) -> D-0 pi(0)) = (65.5 +/- 0.8 +/- 0.5)% and B(D*(0) -> D0 gamma) = (34.5 +/- 0.8 +/- 0.5)%, respectively, by assuming that the D*(0) decays only into these two modes. The ratio of the two branching fractions is B(D*(0) -> D-0 pi(0))/B(D*(0) -> D-0 gamma) = 1.90 +/- 0.07 +/- 0.05, which is independent of the assumption made above. The first uncertainties are statistical and the second ones systematic. The precision is improved by a factor of 3 compared to the present world average values.
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| 34. |
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| 35. |
- Ablikim, M., et al.
(author)
-
Search for C-parity violation in J/psi -> gamma gamma and gamma phi
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:9, s. 092002-
-
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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| 36. |
- Ablikim, M., et al.
(author)
-
Search for D-0 -> gamma gamma and improved measurement of the branching fraction for D-0 -> pi(0)pi(0)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:11
-
Journal article (peer-reviewed)abstract
- Using 2.92 fb(-1) of electron-positron annihilation data collected at root s = 3.773 GeV with the BESIII detector, we report the results of a search for the flavor-changing neutral current process D-0 -> gamma gamma using a double-tag technique. We find no signal and set an upper limit at 90% confidence level for the branching fraction of B(D-0 -> gamma gamma < 3.8 x 10(-6). We also investigate D-0-meson decay into two neutral pions, obtaining a branching fraction of B(D-0 -> pi(0)pi(0)) = (8.24 +/- 0.21(stat) +/- 0.30(syst)) x 10(-4), the most precise measurement to date and consistent with the current world average.
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| 37. |
- Ablikim, M., et al.
(author)
-
Search for the isospin violating decay Y(4260)-> J/psi eta pi(0)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:1
-
Journal article (peer-reviewed)abstract
- Using data samples collected at center-of-mass energies of root s = 4.009, 4.226, 4.257, 4.358, 4.416, and 4.599 GeV with the BESIII detector operating at the BEPCII storage ring, we search for the isospin violating decay Y(4260)-> J/psi eta pi(0). No signal is observed, and upper limits on the cross section sigma(e(+)e(-) -> J/psi eta pi(0)) at the 90% confidence level are determined to be 3.6, 1.7, 2.4, 1.4, 0.9, and 1.9 pb, respectively.
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| 38. |
- Ablikim, M., et al.
(author)
-
Search for the weak decays J/psi -> D-s(()*()-) e(+)nu(e) + c.c.
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:11, s. 112014-
-
Journal article (peer-reviewed)abstract
- Using a sample of 2.25 x 10(8) J/psi events collected with the BESIII detector at the BEPCII collider, we search for the J/psi semileptonic weak decay J/psi -> D-s(-) e(+)nu(e) +c.c. with a much higher sensitivity than previous searches. We also perform the first search for J/psi -> D-s(*-) e(+) nu(e) + c.c. No significant excess of a signal above background is observed in either channel. At the 90% confidence level, the upper limits are determined to be B(J/psi -> D-s(-) e(+) nu(e) + c.c.) < 1.3 x 10(-6) and B(J/psi -> D-s*(-) e(+) nu(e) + c.c.) < 1.8 x 10(-6), respectively. Both are consistent with Standard Model predictions.
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| 39. |
- Ablikim, M., et al.
(author)
-
Search for the Y(4140) via e(+)e(-) -> gamma phi J/psi at root s=4.23, 4.26 and 4.36 GeV
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:3
-
Journal article (peer-reviewed)abstract
- Using data samples collected at center-of-mass energies root s = 4.23, 4.26, and 4.36 GeV with the BESIII detector operating at the BEPCII storage ring, we search for the production of the charmoniumlike state Y(4140) through a radiative transition followed by its decay to phi J/psi. No significant signal is observed and upper limits on sigma[e(+)e(-) -> gamma Y(4140)] . B(Y(4140) -> phi J/psi at the 90% confidence level are estimated as 0.35, 0.28, and 0.33 pb at root s = 4.23, 4.26, and 4.36 GeV, respectively.
|
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| 40. |
- Ablikim, M., et al.
(author)
-
Search for Z(c)(3900)(+/-) -> omega pi(+/-)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:3
-
Journal article (peer-reviewed)abstract
- The decay Z(c)(3900)(+/-) -> omega pi(+/-) is searched for using data samples collected with the BESIII detector operating at the BEPCII storage ring at center-of-mass energies root s = 4.23 and 4.26 GeV. No significant signal for the Z(c)(3900)(+/-) is found, and upper limits at the 90% confidence level on the Born cross section for the process e(+)e(-) -> Z(c)(3900)(+/-) pi(-/+) -> omega pi(+)pi(-) are determined to be 0.26 and 0.18 pb at root s = 4.23 and 4.26 GeV, respectively.
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| 41. |
- Ablikim, M., et al.
(author)
-
Searches for isospin-violating transitions chi(c0,2) -> pi(0)eta(c)
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:11
-
Journal article (peer-reviewed)abstract
- We present the first upper-limit measurement of the branching fractions of the isospin-violating transitions chi(c0,2) -> pi(0)eta(c). The measurements are performed using 106 x 10(6) psi(3686) events accumulated with the BESIII detector at the BEPCII e(+)e(-) collider at a center-of-mass energy corresponding to the psi(3686) mass. We obtained upper limits on the branching fractions at a 90% confidence level of B(chi(c0) -> pi(0)eta(c)) < 1.6 x 10(-3) and B(chi(c2) -> pi(0)eta(c)) < 3.2 x 10(-3).
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| 42. |
- Ablikim, M., et al.
(author)
-
Study of chi(cJ) decaying into phi K*(892)(K)over-bar
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:11
-
Journal article (peer-reviewed)abstract
- Using a data sample of 106 million psi(3686) events collected with the BESIII detector operated at the BEPCII storage ring, we study for the first time the decays chi(cJ) -> phi(KSK +/-)-K-0 pi(-/+) and chi(cJ) -> phi K+K-pi(0) in the E1 radiative transition psi(3686) -> gamma chi(cJ). The decays are dominated by the three-body decay chi(cJ) -> phi K*(892)(K) over bar. We measure branching fractions for this reaction via the neutral and charged K*(892) and find them consistent with each other within the expectation of isospin symmetry. In the K (K) over bar pi invariant mass distribution, a structure near the K*(892)(K) over bar mass threshold is observed, and the corresponding mass and width are measured to be 1412 +/- 4(stat) +/- 8(sys) MeV/c(2) and Gamma = 84 +/- 12(stat) +/- 40(sys) MeV, respectively. The observed state favors an assignment to the h(1)(1380), considering its possible J(PC) and comparing its mass, width and decay mode to those reported in the Particle Data Group.
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| 43. |
- Ablikim, M., et al.
(author)
-
Study of e(+)e(-) -> omega chi(cJ) at Center of Mass Energies from 4.21 to 4.42 GeV
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 114:9
-
Journal article (peer-reviewed)abstract
- Based on data samples collected with the BESIII detector at the BEPCII collider at nine center of mass energies from 4.21 to 4.42 GeV, we search for the production of e(+)e(-) -> omega chi(cJ) (J = 0, 1, 2). The process e(+)e(-) -> omega chi(c0) is observed for the first time, and the Born cross sections at root s = 4.23 and 4.26 GeV are measured to be (55.4 +/- 6.0 +/- 5.9) and (23.7 +/- 5.3 +/- 3.5) pb, respectively, where the first uncertainties are statistical and the second are systematic. The omega chi(c0) signals at the other seven energies and the e(+)e(-) -> omega chi(c1) and omega chi(c2) signals are not significant, and the upper limits on the cross sections are determined. By examining the omega chi(c0) cross section as a function of center of mass energy, we find that it is inconsistent with the line shape of the Y(4260) observed in e(+)e(-) -> pi(+)pi(-) J/psi Assuming the omega chi(c0) signals come from a single resonance, we extract the mass and width of the resonance to be (4230 +/- 8 +/- 6) MeV/c(2) and (38 +/- 12 +/- 2) MeV, respectively, and the statistical significance is more than 9 sigma.
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| 44. |
- Ablikim, M., et al.
(author)
-
Study of J/psi -> eta phi pi(+)pi(-) at BESIII
- 2015
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 91:5
-
Journal article (peer-reviewed)abstract
- invariant mass spectrum of phi f(0)(980) with a statistical significance of greater than 10 sigma. The corresponding mass and width are determined to be M = 2200 +/- 6(stat) +/- 5(syst) MeV/c(2) and Gamma = 104 +/- 15(stat) +/- 15(syst) MeV, respectively, and the product branching fraction is measured to be B(J/psi ->eta Y(2175), Y(2175)->phi f(0)(980), f(0)(980)->pi(+)pi(-)) = (1.20 +/- 0.14(stat)+/- 0.37(syst))x10(-4). The results are consistent within errors with those of previous experiments. We also measure the branching fraction of J/psi ->phi f(1)(1285) with f(1)(1285)->eta pi(+)pi(-) and set upper limits on the branching fractions for J/psi ->phi eta(1405)/phi X(1835)/phi X(1870) with eta(1405)/X(1835)/X(1870)->eta pi(+)pi(-) at the 90% confidence level.
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| 45. |
- 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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| 46. |
- Campbell, PJ, et al.
(author)
-
Pan-cancer analysis of whole genomes
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
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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| 47. |
- Hyde, K. D., et al.
(author)
-
Global consortium for the classification of fungi and fungus-like taxa
- 2023
-
In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
-
Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 48. |
- Kattge, Jens, et al.
(author)
-
TRY plant trait database - enhanced coverage and open access
- 2020
-
In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
-
Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 49. |
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| 50. |
- Pettersson, Mats, et al.
(author)
-
A chromosome-level assembly of the Atlantic herring : detection of a supergene and other signals of selection
- 2019
-
In: Genome Research. - : Cold Spring Harbor Laboratory Press (CSHL). - 1088-9051 .- 1549-5469. ; 29:11, s. 1919-1928
-
Journal article (peer-reviewed)abstract
- The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
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