Genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep using parametric models and artificial neural networks.

This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inês sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genotyped animals was 551 (PCV), 548 (FEC), and 565 (FAM), and 41,676 SNP. The average prediction accuracy (ACC) calculated by Pearson correlation between observed and predicted values and mean squared errors (MSE) were obtained using genomic best unbiased linear predictor (GBLUP), BayesA, BayesB, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayesian regularized artificial neural network (three and four hidden neurons, BRANN_3 and BRANN_4, respectively) in a 5-fold cross-validation technique. The average ACC varied from moderate to high according to the trait and models, ranging between 0.418 and 0.546 (PCV), between 0.646 and 0.793 (FEC), and between 0.414 and 0.519 (FAM). Parametric models presented nearly the same ACC and MSE for the studied traits and provided better accuracies than BRANN. The GBLUP, BayesA, BayesB and BLASSO models provided better accuracies than the BRANN_3 method, increasing by around 23% for PCV, and 18.5% for FEC. In conclusion, parametric models are suitable for genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep. Due to the small differences in accuracy found between them, the use of the GBLUP model is recommended due to its lower computational costs.

Observation of high-energy neutrinos from the Galactic plane.

The origin of high-energy cosmic rays, atomic nuclei that continuously impact Earth's atmosphere, is unknown. Because of deflection by interstellar magnetic fields, cosmic rays produced within the Milky Way arrive at Earth from random directions. However, cosmic rays interact with matter near their sources and during propagation, which produces high-energy neutrinos. We searched for neutrino emission using machine learning techniques applied to 10 years of data from the IceCube Neutrino Observatory. By comparing diffuse emission models to a background-only hypothesis, we identified neutrino emission from the Galactic plane at the 4.5σ level of significance. The signal is consistent with diffuse emission of neutrinos from the Milky Way but could also arise from a population of unresolved point sources.

Evidence for neutrino emission from the nearby active galaxy NGC 1068.

A supermassive black hole, obscured by cosmic dust, powers the nearby active galaxy NGC 1068. Neutrinos, which rarely interact with matter, could provide information on the galaxy's active core. We searched for neutrino emission from astrophysical objects using data recorded with the IceCube neutrino detector between 2011 and 2020. The positions of 110 known gamma-ray sources were individually searched for neutrino detections above atmospheric and cosmic backgrounds. We found that NGC 1068 has an excess of [Formula: see text] neutrinos at tera-electron volt energies, with a global significance of 4.2σ, which we interpret as associated with the active galaxy. The flux of high-energy neutrinos that we measured from NGC 1068 is more than an order of magnitude higher than the upper limit on emissions of tera-electron volt gamma rays from this source.

Search for Unstable Sterile Neutrinos with the IceCube Neutrino Observatory.

We present a search for an unstable sterile neutrino by looking for a resonant signal in eight years of atmospheric ν_{µ} data collected from 2011 to 2019 at the IceCube Neutrino Observatory. Both the (stable) three-neutrino and the 3+1 sterile neutrino models are disfavored relative to the unstable sterile neutrino model, though with p values of 2.8% and 0.81%, respectively, we do not observe evidence for 3+1 neutrinos with neutrino decay. The best-fit parameters for the sterile neutrino with decay model from this study are Δm_{41}^{2}=6.7_{-2.5}^{+3.9} eV^{2}, sin^{2}2θ_{24}=0.33_{-0.17}^{+0.20}, and g^{2}=2.5π±1.5π, where g is the decay-mediating coupling. The preferred regions of the 3+1+decay model from short-baseline oscillation searches are excluded at 90% C.L.

Strong Constraints on Neutrino Nonstandard Interactions from TeV-Scale ν_{µ} Disappearance at IceCube.

We report a search for nonstandard neutrino interactions (NSI) using eight years of TeV-scale atmospheric muon neutrino data from the IceCube Neutrino Observatory. By reconstructing incident energies and zenith angles for atmospheric neutrino events, this analysis presents unified confidence intervals for the NSI parameter ε_{µτ}. The best-fit value is consistent with no NSI at a p value of 25.2%. With a 90% confidence interval of -0.0041≤ε_{µτ}≤0.0031 along the real axis and similar strength in the complex plane, this result is the strongest constraint on any NSI parameter from any oscillation channel to date.

Angular Analysis of D

The first full angular analysis and an updated measurement of the decay-rate CP asymmetry of the D^{0}→π^{+}π^{-}µ^{+}µ^{-} and D^{0}→K^{+}K^{-}µ^{+}µ^{-} decays are reported. The analysis uses proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. The dataset corresponds to an integrated luminosity of 9 fb^{-1}. The full set of CP -averaged angular observables and their CP asymmetries are measured as a function of the dimuon invariant mass. The results are consistent with expectations from the standard model and with CP symmetry.

Search for Relativistic Magnetic Monopoles with Eight Years of IceCube Data.

We present an all-sky 90% confidence level upper limit on the cosmic flux of relativistic magnetic monopoles using 2886 days of IceCube data. The analysis was optimized for monopole speeds between 0.750c and 0.995c, without any explicit restriction on the monopole mass. We constrain the flux of relativistic cosmic magnetic monopoles to a level below 2.0×10^{-19} cm^{-2} s^{-1} sr^{-1} over the majority of the targeted speed range. This result constitutes the most strict upper limit to date for magnetic monopoles with ß≳0.8 and up to ß∼0.995 and fills the gap between existing limits on the cosmic flux of nonrelativistic and ultrarelativistic magnetic monopoles.

Dynamics of the orphan myosin MyoF over Trypanosoma cruzi life cycle and along the endocytic pathway.

Trypanosoma cruzi proliferative forms perform endocytosis through a specialized structure named the cytostome-cytopharynx complex (SPC). The SPC is a specialized invagination of the cell membrane that extends through the cell body towards the posterior regions, with its aperture close to the flagellar pocket. Recently, diverse proteins were found along the cytopharynx, including two myosin motors. One of these is the orphan myosin MyoF, that was proved to be essential for endocytosis in epimastigotes. However, the dynamics of MyoF localization along the endocytic pathway and through the T. cruzi life cycle remain unclear. Using CRISPR-Cas9 genome editing, we generated epimastigotes expressing MyoF fused to mNeonGreen from its endogenous locus. Using these cells, we observed that during the epimastigote cell cycle MyoF signal disappeared during G2, reappearing at early cytokinesis. Additionally, we show that MyoF localization during metacyclogenesis is compatible with the progressive disappearance of the SPC, being absent in metacyclic trypomastigotes. Detergent fractionation showed that MyoF was predominantly present in the insoluble fraction and immunolocalized at the SPC microtubules in whole-mount cytoskeleton preparations. Moreover, during tracer uptake through the SPC, MyoF followed the tracer along the endocytic pathway and was found in posterior compartments after 30 min. Taken together, the data suggest that MyoF may play a role not only at the cargo entry site but also along the endocytic pathway.

Genome-enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods.

This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and 319 619 (STAY) and 3356 and 319 108 (EP). Predictive ability of support vector regression (SVR), Bayesian regularized artificial neural network (BRANN) and random forest (RF) were compared with results obtained using parametric models (genomic best linear unbiased predictor, GBLUP, and Bayesian least absolute shrinkage and selection operator, BLASSO). A 5-fold cross-validation strategy was performed and the average prediction accuracy (ACC) and mean squared errors (MSE) were computed. The ACC was defined as the linear correlation between predicted and observed breeding values for categorical traits (EP and STAY) and as the correlation between predicted and observed adjusted phenotypes divided by the square root of the estimated heritability for continuous traits (AFC and SC). The average ACC varied from low to moderate depending on the trait and model under consideration, ranging between 0.56 and 0.63 (AFC), 0.27 and 0.36 (SC), 0.57 and 0.67 (EP), and 0.52 and 0.62 (STAY). SVR provided slightly better accuracies than the parametric models for all traits, increasing the prediction accuracy for AFC to around 6.3 and 4.8% compared with GBLUP and BLASSO respectively. Likewise, there was an increase of 8.3% for SC, 4.5% for EP and 4.8% for STAY, comparing SVR with both GBLUP and BLASSO. In contrast, the RF and BRANN did not present competitive predictive ability compared with the parametric models. The results indicate that SVR is a suitable method for genome-enabled prediction of reproductive traits in Nellore cattle. Further, the optimal kernel bandwidth parameter in the SVR model was trait-dependent, thus, a fine-tuning for this hyper-parameter in the training phase is crucial.

Constraints on the K_{S}

A search for the decay K_{S}^{0}→µ^{+}µ^{-} is performed using proton-proton collision data, corresponding to an integrated luminosity of 5.6 fb^{-1} and collected with the LHCb experiment during 2016, 2017, and 2018 at a center-of-mass energy of 13 TeV. The observed signal yield is consistent with zero, yielding an upper limit of B(K_{S}^{0}→µ^{+}µ^{-})<2.2×10^{-10} at 90% C.L.. The limit reduces to B(K_{S}^{0}→µ^{+}µ^{-})<2.1×10^{-10} at 90% C.L. once combined with the result from data taken in 2011 and 2012.

Observation of Enhanced Double Parton Scattering in Proton-Lead Collisions at sqrt[s_{NN}]=8.16 TeV.

A study of prompt charm-hadron pair production in proton-lead collisions at sqrt[s_{NN}]=8.16 TeV is performed using data corresponding to an integrated luminosity of about 30 nb^{-1}, collected with the LHCb experiment. Production cross sections for different pairs of charm hadrons are measured and kinematic correlations between the two charm hadrons are investigated. This is the first measurement of associated production of two charm hadrons in proton-lead collisions. The results confirm the predicted enhancement of double parton scattering production in proton-lead collisions compared to the single parton scattering production.

Measurement of CP-Averaged Observables in the B

An angular analysis of the B^{0}→K^{*0}(→K^{+}π^{-})µ^{+}µ^{-} decay is presented using a dataset corresponding to an integrated luminosity of 4.7 fb^{-1} of pp collision data collected with the LHCb experiment. The full set of CP-averaged observables are determined in bins of the invariant mass squared of the dimuon system. Contamination from decays with the K^{+}π^{-} system in an S-wave configuration is taken into account. The tension seen between the previous LHCb results and the standard model predictions persists with the new data. The precise value of the significance of this tension depends on the choice of theory nuisance parameters.

Search for the Rare Decays B_{s}

A search for the decays B_{s}^{0}→e^{+}e^{-} and B^{0}→e^{+}e^{-} is performed using data collected with the LHCb experiment in proton-proton collisions at center-of-mass energies of 7, 8, and 13 TeV, corresponding to integrated luminosities of 1, 2, and 2 fb^{-1}, respectively. No signal is observed. Assuming no contribution from B^{0}→e^{+}e^{-} decays, an upper limit on the branching fraction B(B_{s}^{0}→e^{+}e^{-})<9.4(11.2)×10^{-9} is obtained at 90(95)% confidence level. If no B_{s}^{0}→e^{+}e^{-} contribution is assumed, a limit of B(B^{0}→e^{+}e^{-})<2.5(3.0)×10^{-9} is determined at 90(95)% confidence level. These upper limits are more than one order of magnitude lower than the previous values.

Observation of New Ξ_{c}

The Λ_{c}^{+}K^{-} mass spectrum is studied with a data sample of pp collisions at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 5.6 fb^{-1} collected by the LHCb experiment. Three Ξ_{c}^{0} states are observed with a large significance and their masses and natural widths are measured to be m[Ξ_{c}(2923)^{0}]=2923.04±0.25±0.20±0.14 MeV, Γ[Ξ_{c}(2923)^{0}]=7.1±0.8±1.8 MeV, m[Ξ_{c}(2939)^{0}]=2938.55±0.21±0.17±0.14 MeV, Γ[Ξ_{c}(2939)^{0}]=10.2±0.8±1.1 MeV, m[Ξ_{c}(2965)^{0}]=2964.88±0.26±0.14±0.14 MeV, Γ[Ξ_{c}(2965)^{0}]=14.1±0.9±1.3 MeV, where the uncertainties are statistical, systematic, and due to the limited knowledge of the Λ_{c}^{+} mass. The Ξ_{c}(2923)^{0} and Ξ_{c}(2939)^{0} baryons are new states. The Ξ_{c}(2965)^{0} state is in the vicinity of the known Ξ_{c}(2970)^{0} baryon; however, their masses and natural widths differ significantly.

Measurement of f_{s}/f_{u} Variation with Proton-Proton Collision Energy and B-Meson Kinematics.

The ratio of the B_{s}^{0} and B^{+} fragmentation fractions f_{s} and f_{u} is studied with B_{s}^{0}→J/ψϕ and B^{+}→J/ψK^{+} decays using data collected by the LHCb experiment in proton-proton collisions at 7, 8, and 13 TeV center-of-mass energies. The analysis is performed in bins of B-meson momentum, longitudinal momentum, transverse momentum, pseudorapidity, and rapidity. The fragmentation-fraction ratio f_{s}/f_{u} is observed to depend on the B-meson transverse momentum with a significance of 6.0σ. This dependency is driven by the 13 TeV sample (8.7σ), while the results for the other collision energies are not significant when considered separately. Furthermore, the results show a 4.8σ evidence for an increase of f_{s}/f_{u} as a function of collision energy.

Isospin Amplitudes in Λ_{b}

Ratios of isospin amplitudes in hadron decays are a useful probe of the interplay between weak and strong interactions and allow searches for physics beyond the standard model. We present the first results on isospin amplitudes in b-baryon decays, using data corresponding to an integrated luminosity of 8.5 fb^{-1}, collected with the LHCb detector in pp collisions at center of mass energies of 7, 8, and 13 TeV. The isospin amplitude ratio |A_{1}(Λ_{b}^{0}→J/ψΣ^{0})/A_{0}(Λ_{b}^{0}→J/ψΛ)|, where the subscript on A indicates the final-state isospin, is measured to be less than 1/21.8 at 95% confidence level. The Cabibbo suppressed Ξ_{b}^{0}→J/ψΛ decay is observed for the first time, allowing for the measurement |A_{0}(Ξ_{b}^{0}→J/ψΛ)/A_{1/2}(Ξ_{b}^{0}→J/ψΞ^{0})|=0.37±0.06±0.02, where the uncertainties are statistical and systematic, respectively.

First Observation of Excited Ω_{b}

We report four narrow peaks in the Ξ_{b}^{0}K^{-} mass spectrum obtained using pp collisions at center-of-mass energies of 7, 8, and 13 TeV, corresponding to a total integrated luminosity of 9 fb^{-1} recorded by the LHCb experiment. Referring to these states by their mass, the mass values are m[Ω_{b}(6316)^{-}]=6315.64±0.31±0.07±0.50 MeV, m[Ω_{b}(6330)^{-}]=6330.30±0.28±0.07±0.50 MeV, m[Ω_{b}(6340)^{-}]=6339.71±0.26±0.05±0.50 MeV, m[Ω_{b}(6350)^{-}]=6349.88±0.35±0.05±0.50 MeV, where the uncertainties are statistical, systematic, and the last is due to the knowledge of the Ξ_{b}^{0} mass. The natural widths of the three lower mass states are consistent with zero, and the 90% confidence-level upper limits are determined to be Γ[Ω_{b}(6316)^{-}]<2.8 MeV, Γ[Ω_{b}(6330)^{-}]<3.1 MeV and Γ[Ω_{b}(6340)^{-}]<1.5 MeV. The natural width of the Ω_{b}(6350)^{-} peak is 1.4_{-0.8}^{+1.0}±0.1 MeV, which is 2.5σ from zero and corresponds to an upper limit of 2.8 MeV. The peaks have local significances ranging from 3.6σ to 7.2σ. After accounting for the look-elsewhere effect, the significances of the Ω_{b}(6316)^{-} and Ω_{b}(6330)^{-} peaks are reduced to 2.1σ and 2.6σ, respectively, while the two higher mass peaks exceed 5σ. The observed peaks are consistent with expectations for excited Ω_{b}^{-} resonances.

Search for A

Searches are performed for both promptlike and long-lived dark photons, A^{'}, produced in proton-proton collisions at a center-of-mass energy of 13 TeV. These searches look for A^{'}→µ^{+}µ^{-} decays using a data sample corresponding to an integrated luminosity of 5.5 fb^{-1} collected with the LHCb detector. Neither search finds evidence for a signal, and 90% confidence-level exclusion limits are placed on the γ-A^{'} kinetic mixing strength. The promptlike A^{'} search explores the mass region from near the dimuon threshold up to 70 GeV and places the most stringent constraints to date on dark photons with 214

Observation of Several Sources of CP Violation in B

Observations are reported of different sources of CP violation from an amplitude analysis of B^{+}→π^{+}π^{+}π^{-} decays, based on a data sample corresponding to an integrated luminosity of 3 fb^{-1} of pp collisions recorded with the LHCb detector. A large CP asymmetry is observed in the decay amplitude involving the tensor f_{2}(1270) resonance, and in addition significant CP violation is found in the π^{+}π^{-}S wave at low invariant mass. The presence of CP violation related to interference between the π^{+}π^{-}S wave and the P wave B^{+}→ρ(770)^{0}π^{+} amplitude is also established; this causes large local asymmetries but cancels when integrated over the phase space of the decay. The results provide both qualitative and quantitative new insights into CP -violation effects in hadronic B decays.

Amplitude Analysis of B

The first amplitude analysis of the B^{±}→π^{±}K^{+}K^{-} decay is reported based on a data sample corresponding to an integrated luminosity of 3.0 fb^{-1} of pp collisions recorded in 2011 and 2012 with the LHCb detector. The data are found to be best described by a coherent sum of five resonant structures plus a nonresonant component and a contribution from ππ↔KK S-wave rescattering. The dominant contributions in the π^{±} K^{∓} and K^{+} K^{-} systems are the nonresonant and the B^{±}→ρ(1450)^{0}π^{±} amplitudes, respectively, with fit fractions around 30%. For the rescattering contribution, a sizable fit fraction is observed. This component has the largest CP asymmetry reported to date for a single amplitude of (-66±4±2)%, where the first uncertainty is statistical and the second systematic. No significant CP violation is observed in the other contributions.