Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types

Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer

Abstract Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings

Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues

Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types

Measurement of CP asymmetries in D(s)+→ηπ+ {D}_{(s)}^{+}\to \eta {\pi}^{+} and D(s)+→η′π+ {D}_{(s)}^{+}\to {\eta}^{\prime }{\pi}^{+} decays

Searches for CP violation in the decays ${D}_{(s)}^{+}\to \eta {\pi}^{+}$ and ${D}_{(s)}^{+}\to {\eta}^{\prime }{\pi}^{+}$ are performed using pp collision data corresponding to 6 fb$^{−1}$ of integrated luminosity collected by the LHCb experiment. The calibration channels ${D}_{(s)}^{+}\to \phi {\pi}^{+}$ are used to remove production and detection asymmetries. The resulting CP-violating asymmetries are${\displaystyle \begin{array}{l}{\mathcal{A}}^{CP}=\left({D}^{+}\to \eta {\pi}^{+}\right)=\left(0.34\pm 0.66\pm 0.16\pm 0.05\right)\%,\\ {}{\mathcal{A}}^{CP}=\left({D}_s^{+}\to \eta {\pi}^{+}\right)=\left(0.32\pm 0.51\pm 0.12\right)\%,\\ {}\begin{array}{l}{\mathcal{A}}^{CP}=\left({D}^{+}\to {\eta}^{\prime }{\pi}^{+}\right)=\left(0.49\pm 0.18\pm 0.06\pm 0.05\right)\%,\\ {}{\mathcal{A}}^{CP}=\left({D}_s^{+}\to {\eta}^{\prime }{\pi}^{+}\right)=\left(0.01\pm 0.12\pm 0.08\right)\%,\end{array}\end{array}}$where the first uncertainty is statistical, the second is systematic and the third, relevant for the D$^{+}$ channels, is due to the uncertainty on ${\mathcal{A}}^{CP}=\left({D}^{+}\to \phi {\pi}^{+}\right)$. These measurements, currently the most precise for three of the four channels considered, are consistent with the absence of CP violation. A combination of these results with previous LHCb measurements is presented.[graphic not available: see fulltext]Searches for $CP$ violation in the decays $D^+_{(s)}\rightarrow \eta \pi^+$ and $D^+_{(s)}\rightarrow \eta^{\prime} \pi^+$ are performed using $pp$ collision data corresponding to 6 fb$^{-1}$ of integrated luminosity collected by the LHCb experiment. The calibration channels $D^+_{(s)}\rightarrow \phi \pi^+$ are used to remove production and detection asymmetries. The resulting $CP$-violating asymmetries are $A^{CP}(D^+ \rightarrow \eta \pi^+) = (0.34 \pm 0.66 \pm 0.16 \pm 0.05)\%$, $A^{CP}(D^+_s \rightarrow \eta \pi^+) = (0.32 \pm 0.51 \pm 0.12)\%$, $A^{CP}(D^+ \rightarrow \eta^{\prime} \pi^+) = (0.49 \pm 0.18 \pm 0.06 \pm 0.05)\%$, $A^{CP}(D^+_s \rightarrow \eta^{\prime} \pi^+) = (0.01 \pm 0.12 \pm 0.08)\%$, where the first uncertainty is statistical, the second is systematic and the third, relevant for the $D^+$ channels, is due to the uncertainty on $A^{CP}(D^+ \to \phi \pi^+)$. These measurements, currently the most precise for three of the four channels considered, are consistent with the absence of $CP$ violation. A combination of these results with previous LHCb measurements is presented

Observation of the Bs0 ⁣→D∗+D∗−B^0_s\!\to D^{*+}D^{*-} decay

International audienceThe first observation of the ${B}_s^0$→ D$^{∗+}$D$^{∗−}$ decay and the measurement of its branching ratio relative to the B$^{0}$→ D$^{∗+}$D$^{∗−}$ decay are presented. The data sample used corresponds to an integrated luminosity of 9 fb$^{−1}$ of proton-proton collisions recorded by the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV between 2011 and 2018. The decay is observed with more than 10 standard deviations and the time-integrated ratio of branching fractions is determined to be$\frac{\mathcal{B}\left({B}_s^0\to {D}^{\ast +}{D}^{\ast -}\right)}{\mathcal{B}\left({B}^0\to {D}^{\ast +}{D}^{\ast -}\right)}=0.269\pm 0.032\pm 0.011\pm 0.008,$where the first uncertainty is statistical, the second systematic and the third due to the uncertainty of the fragmentation fraction ratio f$_{s}$/f$_{d}$. The ${B}_s^0$→ D$^{*+}$D$^{*−}$ branching fraction is calculated to be$\mathcal{B}\left({B}_s^0\to {D}^{\ast +}{D}^{\ast -}\right)=\left(2.15\pm 0.26\pm 0.09\pm 0.06\pm 0.16\right)\times {10}^{-4},$where the fourth uncertainty is due to the B$^{0}$→ D$^{*+}$D$^{*−}$ branching fraction. These results are calculated using the average ${B}_s^0$ meson lifetime in simulation. Correction factors are reported for scenarios where either a purely heavy or a purely light ${B}_s^0$ eigenstate is considered.[graphic not available: see fulltext

First observation and branching fraction measurement of the Λb0→Ds−p {\Lambda}_b^0\to {D}_s^{-}p decay

International audienceThe first observation of the ${\Lambda}_b^0\to {D}_s^{-}p$ decay is presented using proton-proton collision data collected by the LHCb experiment at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV, corresponding to a total integrated luminosity of 6 fb$^{−1}$. Using the ${\Lambda}_b^0\to {\Lambda}_c^{+}{\pi}^{-}$ decay as the normalisation mode, the branching fraction of the ${\Lambda}_b^0\to {D}_s^{-}p$ decay is measured to be $\mathcal{B}\left({\Lambda}_b^0\to {D}_s^{-}p\right)=\left(12.6\pm 0.5\pm 0.3\pm 1.2\right)\times {10}^{-6}$, where the first uncertainty is statistical, the second systematic and the third due to uncertainties in the branching fractions of the ${\Lambda}_b^0\to {\Lambda}_c^{+}{\pi}^{-}$, ${D}_s^{-}\to {K}^{-}{K}^{+}{\pi}^{-}$ and ${\Lambda}_c^{+}\to p{K}^{-}{\pi}^{+}$ decays.[graphic not available: see fulltext

Measurement of the CKM angle γγ with B±→D[K∓π±π±π∓]h± B^\pm \to D[K^\mp π^\pm π^\pm π^\mp] h^\pm decays using a binned phase-space approach

The CKM angle $\gamma$ is determined from $C\!P$-violating observables measured in ${B^\pm \to D[ K^\mp \pi^\pm\pi^\pm\pi^\mp] h^\pm}$, $(h = K,\pi)$ decays, where the measurements are performed in bins of the decay phase-space of the $D$ meson. Using proton-proton collision data collected by the LHCb experiment at centre-of-mass energies of $7, 8$ and $13\,\text{TeV}$, corresponding to a total integrated luminosity of $9\,\text{fb}^{-1}$, $\gamma$ is determined to be \begin{equation*} \gamma = \left( 54.8 \: ^{+\:6.0 }_{-\:5.8} \: ^{+\:0.6}_{-\:0.6} \: ^{+\:6.7}_{-\:4.3} \right)^\circ, \end{equation*} where the first uncertainty is statistical, the second systematic and the third from the external inputs on the coherence factors and strong phases of the $D$-meson decays.The CKM angle γ is determined from CP-violating observables measured in B$^{±}$ → D[K$^{∓}$π$^{±}$π$^{±}$π$^{∓}$]h$^{±}$, (h = K, π) decays, where the measurements are performed in bins of the decay phase-space of the D meson. Using proton-proton collision data collected by the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV, corresponding to a total integrated luminosity of 9 fb$^{−1}$, γ is determined to be$\gamma ={\left(54.8\begin{array}{c}+6.0\\ {}-5.8\end{array}\begin{array}{c}+0.6\\ {}-0.6\end{array}\begin{array}{c}+6.7\\ {}-4.3\end{array}\right)}^{\circ },$where the first uncertainty is statistical, the second systematic and the third from the external inputs on the coherence factors and strong phases of the D-meson decays.[graphic not available: see fulltext]The CKM angle $\gamma$ is determined from $C\!P$-violating observables measured in ${B^\pm \to D[ K^\mp \pi^\pm\pi^\pm\pi^\mp] h^\pm}$, $(h = K,\pi)$ decays, where the measurements are performed in bins of the decay phase-space of the $D$ meson. Using proton-proton collision data collected by the LHCb experiment at centre-of-mass energies of $7, 8$ and $13\,\text{TeV}$, corresponding to a total integrated luminosity of $9\,\text{fb}^{-1}$, $\gamma$ is determined to be \begin{equation*} \gamma = \left( 54.8 \: ^{+\:6.0 }_{-\:5.8} \: ^{+\:0.6}_{-\:0.6} \: ^{+\:6.7}_{-\:4.3} \right)^\circ, \end{equation*} where the first uncertainty is statistical, the second systematic and the third from the external inputs on the coherence factors and strong phases of the $D$-meson decays

Search for the lepton-flavour violating decays B0→K∗0μ±e∓B^0 \to K^{*0} \mu^\pm e^\mp and Bs0→ϕμ±e∓B_s^0 \to \phi \mu^\pm e^\mp

A search for the lepton-flavour violating decays $B^0 \to K^{*0} \mu^\pm e^\mp$ and $B_s^0 \to \phi \mu^\pm e^\mp$ is presented, using proton-proton collision data collected by the LHCb detector at the LHC, corresponding to an integrated luminosity of $9\,\text{fb}^{-1}$. No significant signals are observed and upper limits of \begin{align} {\cal B}( B^0 \to K^{*0} \mu^+ e^- ) &< \phantom{1}5.7\times 10^{-9}~(6.9\times 10^{-9}),\newline {\cal B}( B^0 \to K^{*0} \mu^- e^+ ) &< \phantom{1}6.8\times 10^{-9}~(7.9\times 10^{-9}),\newline {\cal B}( B^0 \to K^{*0} \mu^\pm e^\mp ) &< 10.1\times 10^{-9}~(11.7\times 10^{-9}),\newline {\cal B}( B_s^0 \to \phi \mu^\pm e^\mp ) &< 16.0\times 10^{-9}~(19.8\times 10^{-9}) \end{align} are set at $90\%~(95\%)$ confidence level. These results constitute the world's most stringent limits to date, with the limit on the decay $B_s^0 \to \phi \mu^\pm e^\mp$ the first being set. In addition, limits are reported for scalar and left-handed lepton-flavour violating New Physics scenarios.A search for the lepton-flavour violating decays B$^{0}$ → K$^{*0}$μ$^{±}$e$^{∓}$ and ${B}_s^0$→ ϕμ$^{±}$e$^{∓}$ is presented, using proton-proton collision data collected by the LHCb detector at the LHC, corresponding to an integrated luminosity of 9 fb$^{−1}$. No significant signals are observed and upper limits of${\displaystyle \begin{array}{c}\mathcal{B}\left({B}^0\to {K}^{\ast 0}{\mu}^{+}{e}^{-}\right)<5.7\times {10}^{-9}\left(6.9\times {10}^{-9}\right),\\ {}\mathcal{B}\left({B}^0\to {K}^{\ast 0}{\mu}^{-}{e}^{+}\right)<6.8\times {10}^{-9}\left(7.9\times {10}^{-9}\right),\\ {}\mathcal{B}\left({B}^0\to {K}^{\ast 0}{\mu}^{\pm }{e}^{\mp}\right)<10.1\times {10}^{-9}\left(11.7\times {10}^{-9}\right),\\ {}\mathcal{B}\left({B}_s^0\to \phi {\mu}^{\pm }{e}^{\mp}\right)<16.0\times {10}^{-9}\left(19.8\times {10}^{-9}\right)\end{array}}$are set at 90% (95%) confidence level. These results constitute the world’s most stringent limits to date, with the limit on the decay ${B}_s^0$→ ϕμ$^{±}$e$^{∓}$ the first being set. In addition, limits are reported for scalar and left-handed lepton-flavour violating New Physics scenarios.[graphic not available: see fulltext]A search for the lepton-flavour violating decays $B^0 \to K^{*0} \mu^\pm e^\mp$ and $B_s^0 \to \phi \mu^\pm e^\mp$ is presented, using proton-proton collision data collected by the LHCb detector at the LHC, corresponding to an integrated luminosity of $9\,\text{fb}^{-1}$. No significant signals are observed and upper limits of \begin{align} {\cal B}( B^0 \to K^{*0} \mu^+ e^- ) &< \phantom{1}5.7\times 10^{-9}~(6.9\times 10^{-9}),\newline {\cal B}( B^0 \to K^{*0} \mu^- e^+ ) &< \phantom{1}6.8\times 10^{-9}~(7.9\times 10^{-9}),\newline {\cal B}( B^0 \to K^{*0} \mu^\pm e^\mp ) &< 10.1\times 10^{-9}~(11.7\times 10^{-9}),\newline {\cal B}( B_s^0 \to \phi \mu^\pm e^\mp ) &< 16.0\times 10^{-9}~(19.8\times 10^{-9}) \end{align} are set at $90\%~(95\%)$ confidence level. These results constitute the world's most stringent limits to date, with the limit on the decay $B_s^0 \to \phi \mu^\pm e^\mp$ the first being set. In addition, limits are reported for scalar and left-handed lepton-flavour violating New Physics scenarios

Observation of sizeable ω\omega contribution to χc1(3872)→π+π−J/ψ\chi_{c1}(3872) \to \pi^+\pi^- J/\psi decays

Resonant structures in the dipion mass spectrum from $\chi_{c1}(3872)\to\pi^+\pi^- J/\psi$ decays, produced via $B^+\to K^+\chi_{c1}(3872)$ decays, are analyzed using proton-proton collision data collected by the LHCb experiment, corresponding to an integrated luminosity of 9 fb$^{-1}$. A sizeable contribution from the isospin conserving $\chi_{c1}(3872)\to\omega J/\psi$ decay is established for the first time, $(21.4\pm2.3\pm2.0)\%$, with a significance of more than $7.1\sigma$. The amplitude of isospin violating decay, $\chi_{c1}(3872)\to\rho^0 J/\psi$, relative to isospin conserving decay, $\chi_{c1}(3872)\to\omega J/\psi$, is properly determined, and it is a factor of six larger than expected for a pure charmonium state.Resonant structures in the dipion mass spectrum from χc1(3872)→π+π-J/ψ decays, produced via B+→K+χc1(3872) decays, are analyzed using proton-proton collision data collected by the LHCb experiment, corresponding to an integrated luminosity of 9  fb-1. A sizeable contribution from the isospin conserving χc1(3872)→ωJ/ψ decay is established for the first time, (21.4±2.3±2.0)%, with a significance of more than 7.1σ. The amplitude of isospin violating decay, χc1(3872)→ρ0J/ψ, relative to isospin conserving decay, χc1(3872)→ωJ/ψ, is properly determined, and it is a factor of 6 larger than expected for a pure charmonium state.Resonant structures in the dipion mass spectrum from $\chi_{c1}(3872)\to\pi^+\pi^- J/\psi$ decays, produced via $B^+\to K^+\chi_{c1}(3872)$ decays, are analyzed using proton-proton collision data collected by the LHCb experiment, corresponding to an integrated luminosity of 9 $fb^{-1}$. A sizeable contribution from the isospin conserving $\chi_{c1}(3872)\to\omega J/\psi$ decay is established for the first time, $(21.4\pm2.3\pm2.0)\%$, with a significance of more than $7.1\sigma$. The amplitude of isospin violating decay, $\chi_{c1}(3872)\to\rho^0 J/\psi$, relative to isospin conserving decay, $\chi_{c1}(3872)\to\omega J/\psi$, is properly determined, and it is a factor of six larger than expected for a pure charmonium state

Search for the rare hadronic decay Bs0→ppˉB_s^0\to p \bar{p}

A search for the rare hadronic decay Bs0→pp¯ is performed using proton-proton collision data recorded by the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 6  fb-1. No evidence of the decay is found and an upper limit on its branching fraction is set at B(Bs0→pp¯)&lt;4.4(5.1)×10-9 at 90% (95%) confidence level; this is currently the world’s best upper limit. The decay mode B0→pp¯ is measured with very large significance, confirming the first observation by the LHCb experiment in 2017. The branching fraction is determined to be B(B0→pp¯)=(1.27±0.15±0.05±0.04)×10-8, where the first uncertainty is statistical, the second is systematic and the third is due to the external branching fraction of the normalization channel B0→K+π-. The combination of the two LHCb measurements of the B0→pp¯ branching fraction yields B(B0→pp¯)=(1.27±0.13±0.05±0.03)×10-8.A search for the rare hadronic decay $B_s^0\to p \bar{p}$ is performed using proton-proton collision data recorded by the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 6 fb$^{-1}$. No evidence of the decay is found and an upper limit on its branching fraction is set at ${\cal B}(B_s^0\to p \bar{p}) < 4.4~(5.1) \times 10^{-9}$ at 90% (95%) confidence level; this is currently the world's best upper limit. The decay mode $B^0\to p \bar{p}$ is measured with very large significance, confirming the first observation by the LHCb experiment in 2017. The branching fraction is determined to be ${\cal B}(B^0\to p \bar{p}) = \rm (1.27 \pm 0.15 \pm 0.05 \pm 0.04) \times 10^{-8}$, where the first uncertainty is statistical, the second is systematic and the third is due to the external branching fraction of the normalization channel $B^0\to K^+\pi^-$. The combination of the two LHCb measurements of the $B^0\to p \bar{p}$ branching fraction yields ${\cal B}(B^0\to p \bar{p}) = \rm (1.27 \pm 0.13 \pm 0.05 \pm 0.03) \times 10^{-8}$