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An integrative association method for omics data based on a modified Fisher's method with application to childhood asthma

Author: Yan Qi
Liu Nianjun
Forno E.
Canino G.
Celedón J.
Chen Wei
Publication venue
Publication date: 2020
Field of study

The development of high-throughput biotechnologies allows the collection of omics data to study the biological mechanisms underlying complex diseases at different levels, such as genomics, epigenomics, and transcriptomics. However, each technology is designed to collect a specific type of omics data. Thus, the association between a disease and one type of omics data is usually tested individually, but this strategy is suboptimal. To better articulate biological processes and increase the consistency of variant identification, omics data from various platforms need to be integrated. In this report, we introduce an approach that uses a modified Fisher’s method (denoted as Omnibus-Fisher) to combine separate p-values of association testing for a trait and SNPs, DNA methylation markers, and RNA sequencing, calculated by kernel machine regression into an overall gene-level p-value to account for correlation between omics data. To consider all possible disease models, we extend Omnibus-Fisher to an optimal test by using perturbations. In our simulations, a usual Fisher’s method has inflated type I error rates when directly applied to correlated omics data. In contrast, Omnibus-Fisher preserves the expected type I error rates. Moreover, Omnibus-Fisher has increased power compared to its optimal version when the true disease model involves all types of omics data. On the other hand, the optimal Omnibus-Fisher is more powerful than its regular version when only one type of data is causal. Finally, we illustrate our proposed method by analyzing whole-genome genotyping, DNA methylation data, and RNA sequencing data from a study of childhood asthma in Puerto Ricans

Long distance effects in inclusive rare $B$ decays and phenomenology of $\bar{B}\to X_d \ell^+\ell^-$

Author: Huber Tobias
Hurth Tobias
Jenkins Jack
Lunghi Enrico
Qin Qin
Vos K. Keri
Publication venue
Publication date: 2020
Field of study

Rare inclusive

B

decays such as

\bar{B}\to X_{s(d)} \ell^+\ell^-

are interesting probes for physics beyond the Standard Model. Due to the complementarity to their exclusive counterparts, they might shed light on the anomalies currently seen in exclusive

b \to s

transitions. Distinguishing new-physics effects from the Standard Model requires precise predictions and necessitates the control of long distance effects. In the present work we revisit and improve the description of various long distance effects in inclusive decays such as charmonium and light-quark resonances, nonfactorisable power corrections, and cascade decays. We then apply these results to a state-of-the-art phenomenological study of

\bar{B}\to X_{s(d)} \ell^+\ell^-

, including also logarithmically enhanced QED corrections and the recently calculated five-body contributions. To fully exploit the new-physics potential of inclusive flavour-changing neutral current decays, the

\bar{B}\to X_{s(d)} \ell^+\ell^-

observables should be measured in a dedicated Belle II analysis

A novel GPR55-mediated satiety signal in the oval Bed Nucleus of the Stria Terminalis

Author: Hawken E R
Normandeau C P
Gregory J Gardner
Cécyre B
Bouchard J F
Mackie Ken
Dumont É C
Publication venue
Publication date: 2020
Field of study

Nestled within feeding circuits, the oval (ov) region of the Bed Nucleus of the Stria Terminalis (BNST) may be critical for monitoring energy balance through changes in synaptic strength. Here we report that bidirectional plasticity at ovBNST GABA synapses was tightly linked to the caloric state of male rats, seesawing between long-term potentiation (iLTP, fed) and depression (iLTD, food restricted). L-α-lysophosphatidylinositol (LPI) acting on GPR55 receptors and 2-arachidonoylglycerol (2-AG) through CB1R were respectively responsible for fed (iLTP) and food restricted (iLTD) states. Thus, we have characterized a potential gating mechanism within the ovBNST that may signal metabolic state within the rat brain feeding circuitry

Drought legacies are dependent on water table depth, wood anatomy and drought timing across the eastern US

Author: Kannenberg Steve
Maxwell Justin Timothy
Pederson Neil
D'Orangeville Loic
Ficklin Darren
Phillips Richard P
Publication venue
Publication date: 2020
Field of study

Severe droughts can impart long‐lasting legacies on forest ecosystems through lagged effects that hinder tree recovery and suppress whole‐forest carbon uptake. However, the local climatic and edaphic factors that interact to affect drought legacies in temperate forests remain unknown. Here, we pair a dataset of 143 tree ring chronologies across the mesic forests of the eastern US with historical climate and local soil properties. We found legacy effects to be widespread, the magnitude of which increased markedly in diffuse porous species, sites with deep water tables, and in response to late‐season droughts (August–September). Using an ensemble of downscaled climate projections, we additionally show that our sites are projected to drastically increase in water deficit and drought frequency by the end of the century, potentially increasing the size of legacy effects by up to 65% and acting as a significant process shaping forest composition, carbon uptake and mortality

Measurement of branching fractions for $D$ meson decaying into $\phi$ meson and a pseudoscalar meson

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

The four decay modes

D^{0}\to\phi\pi^{0}

D^{0}\to\phi\eta

D^{+}\to\phi\pi^{+}

, and

D^{+}\to\phi K^{+}

are studied by using a data sample taken at the centre-of-mass energy

\sqrt{s}

=3.773 GeV with the BESIII detector, corresponding to an integrated luminosity of 2.93 fb

^{−1}

. The branching fractions of the first three decay modes are measured to be

{\cal B}(D^{0}\to\phi\pi^{0})=(1.168\pm0.028\pm0.028)\times10^{-3}

{\cal B}(D^{0}\to\phi\eta)=(1.81\pm0.46\pm0.06)\times10^{-4}

, and

{\cal B}(D^{+}\to\phi\pi^{+})=(5.70\pm0.05\pm0.13)\times10^{-3}

, respectively, where the first uncertainties are statistical and the second are systematic. No significant signal is observed of the decay

D^+\to\phi{K^+}

and the upper limit of its branching fraction is set for the first time, to be 2.1×10

^{−5}

at the 90% confidence level. The ratio of

{\cal B}(D^0\to\phi\pi^0)

\cal B(D^+\to\phi\pi^+)

is calculated to be (20.49±0.50±0.45)%, which is consistent with the theoretical prediction based on isospin symmetry between these two decay modes

Measurements of the absolute branching fractions and $CP$ asymmetries for $D^+\rightarrow K_{S,L}^0 K^+(\pi^0)$

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

Using

e^+e^−

collision data corresponding to an integrated luminosity of 2.93 fb

^{−1}

taken at a center-of-mass energy of 3.773 GeV with the BESIII detector, we determine the absolute branching fractions

\mathcal{B}(D^+\rightarrow K_S^0 K^+)

(3.02 \pm 0.09 \pm 0.08)\times10^{-3}

\mathcal{B}(D^+\rightarrow K_S^0 K^+ \pi^0)

(5.07 \pm 0.19 \pm 0.23)\times10^{-3}

\mathcal{B}(D^+\rightarrow K_L^0 K^+)

(3.21 \pm 0.11 \pm 0.11)\times10^{-3}

, and

\mathcal{B}(D^+\rightarrow K_L^0 K^+ \pi^0)

(5.24 \pm 0.22 \pm 0.22)\times10^{-3}

, where the first and second uncertainties are statistical and systematic, respectively. The branching fraction \wbrksk is consistent with the world average value and the other three branching fractions are measured for the first time. We also measure the

CP

asymmetries for the four decays and do not find a significant deviation from zero

Observation of $\psi(3686)\rightarrow\Xi(1530)^{-}\bar\Xi(1530)^{+}$ and $\Xi(1530)^{-}\bar\Xi^{+}$

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

Using

448.1 × 10^6

\psi(3686)

events collected with the BESIII detector at BEPCII, we employ a single-baryon tagging technique to make the first observation of

\psi(3686)\rightarrow\Xi(1530)^{-}\bar\Xi(1530)^{+}

and

\Xi(1530)^{-}\bar\Xi^{+}

decays with a statistical significance of more than 10

\sigma

and 5.0

\sigma

, respectively. The branching fractions are measured to be

\cal{B}

[\psi(3686)\rightarrow\Xi(1530)^{-}\bar\Xi(1530)^{+}]

=

(11.45 ± 0.40 ± 0.59) × 10^{−5}

and

\cal{B}

[\psi(3686)\rightarrow\Xi(1530)^{-}\bar\Xi^{+}]

=

(0.70 ± 0.11 ± 0.04) × 10^{−5}

. The angular distribution parameter for

\psi(3686)\rightarrow\Xi(1530)^{-}\bar\Xi(1530)^{+}

is determined to be

\alpha

= 0.40 ± 0.24 ± 0.06, which agrees with the theoretical predictions within 1

\sigma

. The first uncertainties are statistical, and the second systematic

Observation of $\psi(3686)\to p\bar{p}\phi$

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

Using a data sample of

4.48×10^8

\psi(3686)

events collected with the BESIII detector, we present a first observation of

\psi(3686)\to p\bar{p}\phi

, and we measure its branching fraction to be [6.06±0.38(stat.)±0.48(syst.)]×10

^{−6}

. In contrast to the earlier discovery of a threshold enhancement in the

p\bar{p}

-mass spectrum of the channel

J/\psi\to\gamma p\bar p

, denoted as

X(p\bar{p})

, we do not find a similar enhancement in

\psi(3686)\to p\bar{p}\phi

. An upper limit of 1.82×10

^{−7}

at the 90% confidence level on the branching fraction of

\psi(3686)\to X(p\bar{p})\phi\to p\bar{p}\phi

is obtained

Polarization and Entanglement in Baryon-Antibaryon Pair Production in Electron-Positron Annihilation

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

Using a sample of

1.31×10^9

J/\psi

events collected with the BESIII detector, we report the first observation of spin polarization of

\Lambda

and

\bar\Lambda

hyperons from the coherent production in the

J/\psi\to\Lambda\bar\Lambda

decay. We measure the phase between the hadronic form factors to be

\Delta\Phi=(42.4\pm0.6\pm0.5)^\circ

. The decay parameters for

\Lambda\to p\pi^-

(\alpha_-)

\bar\Lambda\to\bar p\pi^+

(\alpha_+)

and

\bar\Lambda\to\bar n\pi^0

(\bar\alpha_0)

are measured to be

\alpha_-=0.750\pm0.009\pm0.004

\alpha_+=-0.758\pm0.010\pm0.007

and

\bar\alpha_0=-0.692\pm0.016\pm0.006

, respectively. The obtained value of

\alpha_-

is higher by (17±3)% than the current world average. In addition, the

CP

asymmetry of −0.006±0.012±0.007 is extracted with substantially improved precision. The ratio

\bar{\alpha}_0/\alpha_{+} = 0.913\pm 0.028 \pm 0.012

is also measured

Search for a strangeonium-like structure $Z_s$ decaying into $\phi \pi$ and a measurement of the cross section $e^+e^-\rightarrow\phi\pi\pi$

Author: Ablikim M.
Mitchell R. E., et al.
Publication venue
Publication date: 2020
Field of study

Using a data sample of

e^+e^−

collision data corresponding to an integrated luminosity of 108 pb −1 collected with the BESIII detector at a center-of-mass energy of 2.125 GeV, we study the process

e^+e^-\rightarrow \phi\pi\pi

and search for a strangeonium-like structure

Z_s

decaying into

\phi\pi

. No signal is observed in the

\phi\pi

mass spectrum. Upper limits on the cross sections for

Z_s

production at the 90% confidence level are determined. In addition, the cross sections of

e^+e^-\rightarrow\phi\pi^{+}\pi^{-}

and

e^+e^-\rightarrow\phi\pi^{0}\pi^{0}

at 2.125 GeV are measured to be (436.2±6.4±30.1) pb and (237.0±8.6±15.4) pb, respectively, where the first uncertainties are statistical and the second systematic

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