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1.	Klionsky, Daniel J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 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.
2.	Ablikim, M., et al. (author) Measurement of the $D\to K^-\pi^+$ strong phase difference in $\psi(3770)\to D^0\overline{D}{}^0$ 2014 In: PHYSICS LETTERS B. - : Elsevier BV. - 0370-2693. ; 734 Journal article (peer-reviewed)abstract We study $D^0\overline{D}{}^0$ pairs produced in $e^+e^-$ collisions at $\sqrt{s}=3.773$ GeV using a data sample of 2.92 fb$^{-1}$ collected with the BESIII detector. We measure the asymmetry $\mathcal{A}^{CP}_{K\pi}$ of the branching fractions of $D \to K^-\pi^+$ in $CP$-odd and $CP$-even eigenstates to be $(12.7\pm1.3\pm0.7)\times10^{-2}$. $\mathcal{A}^{CP}_{K\pi}$ can be used to extract the strong phase difference $\delta_{K\pi}$ between the doubly Cabibbo-suppressed process $\overline{D}{}^{0}\to K^-\pi^+$ and the Cabibbo-favored process $D^0\to K^- \pi^+$. Using world-average values of external parameters, we obtain $\cos\delta_{K\pi} = 1.02\pm0.11\pm0.06\pm0.01$. Here, the first and second uncertainties are statistical and systematic, respectively, while the third uncertainty arises from the external parameters. This is the most precise measurement of $\delta_{K\pi}$ to date.
3.	Ablikim, M., et al. (author) Observation of $e^+e^− → γX$(3872) at BESIII 2014 In: PHYSICAL REVIEW LETTERS. - 1079-7114. ; 112:9 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 $e^{+} e^{-} \to \gamma X(3872)$ is observed for the first time with a statistical significance of $6.3\sigma$. The measured mass of the $X(3872)$ is ($3871.9\pm 0.7_{\rm stat.}\pm 0.2_{\rm sys.}$) MeV/$c^2$, in agreement with previous measurements. Measurements of the product of the cross section $\sigma[e^{+} e^{-} \to \gamma X(3872)]$ and the branching fraction $\mathcal{B}[X(3872) \to \pi^{+} \pi^{-} J/\psi]$ 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 $Y(4260) \to \gamma X(3872)$.
4.	Ablikim, M., et al. (author) Observation of electromagnetic Dalitz decays J/\psi \to P e^+e^- 2014 In: PHYSICAL REVIEW D. - 2470-0010 .- 1550-7998 .- 1550-2368. ; 89:9 Journal article (peer-reviewed)abstract Based on a sample of (225.3\pm2.8)\times 10^{6} J/\psi events collected with the BESIII detector, the electromagnetic Dalitz decays of J/\psi \to P e^+e^-(P=\eta'/\eta/\pi^0) are studied. By reconstructing the pseudoscalar mesons in various decay modes, the decays J/\psi \to \eta' e^+e^-, J/\psi \to \eta e^+e^- and J/\psi \to \pi^0 e^+e^- are observed for the first time. The branching fractions are determined to be \mathcal{B}(J/\psi\to \eta' e^+e^-) = (5.81\pm0.16\pm0.31)\times10^{-5}, \mathcal{B}(J/\psi\to \eta e^+e^-) = (1.16\pm0.07\pm0.06)\times10^{-5}, and \mathcal{B}(J/\psi\to \pi^0 e^+e^-)=(7.56\pm1.32\pm0.50)\times10^{-7}, where the first errors are statistical and the second ones systematic.
5.	Ablikim, M., et al. (author) Precision measurements of $B(D^+ \rightarrow \mu^+ \nu_{\mu})$, the pseudoscalar decay constant $f_{D^+}$, and the quark mixing matrix element $\|V_{\rm cd}\|$ 2014 In: PHYSICAL REVIEW D. - 2470-0010 .- 1550-7998 .- 1550-2368. ; 89:5 Journal article (peer-reviewed)abstract We report a measurement of the branching fraction $B(D^+ \rightarrow \mu^+ \nu_{\mu}) = [3.71 \pm 0.19 (\rm stat) \pm 0.06 (\rm sys)]\times 10^{-4}$ based on 2.92 ${\rm fb^{-1}}$ of data accumulated at $\sqrt{s}=3.773$ GeV with the BESIII detector at the BEPCII collider. This measurement, in conjunction with the Cabibbo-Kobayashi-Maskawa matrix element $\|V_{\rm cd}\|$ determined from a global Standard Model fit, implies a value for the weak decay constant $f_{D^+}=(203.2 \pm 5.3 \pm 1.8)$ MeV. Additionally, using this branching fraction measurement together with a Lattice QCD prediction for $f_{D^+}$, we find $\|V_{\rm cd}\|=0.2210\pm 0.0058 \pm 0.0047$. In either case, these are the most precise results for these quantities to date.
6.	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.
7.	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.
8.	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.
9.	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.
10.	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.
11.	Ablikim, M., et al. (author) Amplitude analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot 2014 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:5, s. 052001- 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.
12.	Ablikim, M., et al. (author) Measurement of chi(cJ) decaying into eta ' K+K- 2014 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 074030- 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.
13.	Ablikim, M., et al. (author) Observation of e(+)e(-) -> gamma X(3872) at BESIII 2014 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:9, s. 092001- 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).
14.	Ablikim, M., et al. (author) Observation of eta' -> pi(+) pi(-) pi(+) pi(-) and eta' -> pi(+) pi(-) pi(0) pi(0) 2014 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:25, s. 251801- 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.
15.	Ablikim, M., et al. (author) Observation of the decay psi(3686) -> Lambda(Sigma)over-bar(+/-) pi(-/+) + c.c 2013 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112007- 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.
16.	Ablikim, M., et al. (author) Precision measurement of the mass of the tau lepton 2014 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:1 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.
17.	Ablikim, M., et al. (author) 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 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112001- 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.
18.	Ablikim, M., et al. (author) Search for the radiative transitions Psi(3770) -> gamma eta(c) and gamma eta(c) (2S) 2014 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112005- 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.
19.	Ablikim, M., et al. (author) Search for the rare decays J/y -> D-s(-) rho(+) and J/psi -> <(D)over bar(0)<(K)over bar(0) 2014 In:* Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 071101- 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.
20.	Ablikim, M., et al. (author) Study of e(+)e(-) -> p(p)over-bar in the vicinity of psi(3770) 2014 In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 735, s. 101-107 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.
21.	Ablikim, M., et al. (author) Study of e(+)e(-) -> p(p)over-bar pi(0) in the vicinity of the psi(3770) 2014 In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:3, s. 032007- 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.
22.	Wang, Zhaoming, et al. (author) Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33 2014 In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633 Journal article (peer-reviewed)abstract Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
23.	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.
24.	Cho, Yoon Shin, et al. (author) Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. 2012 In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:1 Journal article (peer-reviewed)abstract We conducted a three-stage genetic study to identify susceptibility loci for type 2 diabetes (T2D) in east Asian populations. We followed our stage 1 meta-analysis of eight T2D genome-wide association studies (6,952 cases with T2D and 11,865 controls) with a stage 2 in silico replication analysis (5,843 cases and 4,574 controls) and a stage 3 de novo replication analysis (12,284 cases and 13,172 controls). The combined analysis identified eight new T2D loci reaching genome-wide significance, which mapped in or near GLIS3, PEPD, FITM2-R3HDML-HNF4A, KCNK16, MAEA, GCC1-PAX4, PSMD6 and ZFAND3. GLIS3, which is involved in pancreatic beta cell development and insulin gene expression, is known for its association with fasting glucose levels. The evidence of an association with T2D for PEPD and HNF4A has been shown in previous studies. KCNK16 may regulate glucose-dependent insulin secretion in the pancreas. These findings, derived from an east Asian population, provide new perspectives on the etiology of T2D.
25.	Gu, Qiang, et al. (author) VKORC1-1639G>A, CYP2C9, EPHX1691A>G genotype, body weight, and age are important predictors for warfarin maintenance doses in patients with mechanical heart valve prostheses in southwest China 2010 In: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 66:12, s. 1217-1227 Journal article (peer-reviewed)abstract There were great interindividual differences in warfarin maintenance dosage (ranging from 0.6 to 8.4 mg/day) among the 127 patients with mechanical heart valve prostheses. VKORC1-1639G>A, CYP2C9, EPHX1691A>G polymorphism, body weight, and age were found to affect the dose demands. Multiple linear regression models incorporating genetic polymorphisms of VKORC1, CYP2C9, EPHX1691A>G, and the nongenetic factors of age and body weight were developed, and explained up to 76.8% of the total variation (adjusted R (2) of 0.743) in warfarin maintenance doses in southwest Chinese patients with mechanical heart valve prostheses.
26.	Li, Lili, et al. (author) Heparanase overexpression reduces carrageenan-induced mechanical and cold hypersensitivity in mice 2012 In: Neuroscience Letters. - : Elsevier BV. - 0304-3940 .- 1872-7972. ; 511:1, s. 4-7 Journal article (peer-reviewed)abstract Heparanase controls the structure and functions of extracellular matrix (ECM) by degrading heparan sulfate proteoglycans. Heparanase is involved in inflammatory process through modulating the functions of inflammatory cytokines. The present study aimed to find out whether overexpression of heparanase in mice affects carrageenan-induced localized inflammation and inflammatory hyperalgesia. Without challenge, the heparanase overexpression did not significantly affect the mice in response to mechanical, cold and heat stimulation. Unilateral subcutaneous administration of carrageenan produced hypersensitivity to mechanical and cold in both wildtype and the heparanase overexpression (Hpa-tg) mice 24h after treatment. In comparison to wildtype animals, the Hpa-tg mice showed significantly reduced mechanical and cold hypersensitivity. This may, at least partially, due to the reduced mast cell infiltration at the site of inflammation in Hpa-tg mice. These data support a role for heparanase that reduces localized inflammation and inflammatory hyperalgesia in mice.
27.	Yan, Xia, et al. (author) Heparanase Modulation of Early Growth Response Gene Expression 2011 In: Zoological Science. - : Zoological Society of Japan. - 0289-0003 .- 2212-3830. ; 28:3, s. 189-194 Journal article (peer-reviewed)abstract Heparan sulfate (HS), a polysaccharide ubiquitously expressed in animals, is essential for development and homeostasis. Degradation of HS by heparanase, an endoglucuronidase, may affect pathophysiological function. Expression of the heparanase gene has been found elevated in a number of pathological conditions. The goal of this work was to investigate the impact of heparanase on expression of other genes. DNA microarray analysis revealed that 1, 042 genes in the cortex and 1,039 genes in the thalamus are up-or down-regulated more than 2-fold in mouse brain over-expresssing human heparanase. Of these genes, two of the early growth response genes, Egr1 and Egr2, are substantially upregulated in the cortex, but essentially unchanged in the thalamus. RTPCR analysis demonstrated a significant increase of Egr2, but a minor increase of Egr1, in human embryonic kidney cells stably overexpressing heparanase. The upregulated expression of Egr genes is also observed in hepatoma cells with upregulated expression of heparanase. Earlier studies reported that Egr1 induced heparanase expression; our findings suggest a possible reciprocal regulation of Egr and heparanase expression. Furthermore, overexpression of heparanase influenced expression of most genes involved in heparan sulfate proteoglycan biosynthesis, albeit to a different degree in the cortex and thalamus of the transgenic mice.
28.	Zhang, Guojie, et al. (author) Comparative genomics reveals insights into avian genome evolution and adaptation 2014 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320 Journal article (peer-reviewed)abstract Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
29.	Zhang, Gan-lin, et al. (author) Towards Understanding the Roles of Heparan Sulfate Proteoglycans in Alzheimer's Disease 2014 In: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141. ; , s. 516028- Research review (peer-reviewed)abstract Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive loss of memory and cognitive dysfunctions. A central pathological event of AD is accumulation and deposition of cytotoxic amyloid-beta peptide (A beta) in the brain parenchyma. Heparan sulfate proteoglycans (HSPGs) and the side chains heparan sulfate (HS) are found associated with A beta deposits in the brains of AD patients and transgenic animal models of AD. A growing body of evidence from in vitro and in vivo studies suggests functional roles of HSPG/HS in A beta pathogenesis. Although the question of "how and why HSPG/HS is codeposited with A beta?" still remains, it is within reach to understand the mechanisms of the events. Recent progress by immunohistochemical examination with advanced antibodies shed light on molecular structures of HS codeposited with A beta Several recent reports have provided important new insights into the roles of HSPG in A beta pathogenesis. Particularly, experiments on mouse models revealed indispensible functions of HSPG in modulating A beta-associated neuroinflammation and clearance of A beta from the brain. Application of molecules to interfere with the interaction between HS and A beta peptides has demonstrated beneficial effects on AD mouse models. Elucidating the functions of HSPG/HS in A beta deposition and toxicity is leading to further understanding of the complex pathology of AD. The progress is encouraging development of new treatments for AD by targeting HS-A beta interactions.
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