Abstract
Summary
An R package that can implement multiple linear learners, including penalized regression and regression with spike and slab priors, in a single model has been developed. Solutions ...are obtained with fast minorize-maximization algorithms in the framework of variational Bayesian inference. This package helps to incorporate multimodal and high-dimensional explanatory variables in a single regression model.
Availability and implementation
The R package VIGoR (Variational Bayesian Inference for Genome-wide Regression) is available at the Comprehensive R Archive Network (CRAN) (https://cran.r-project.org/) and at GitHub (https://github.com/Onogi/VIGoR).
Supplementary information
Supplementary data are available at Bioinformatics online.
This study investigates the quality of the Japanese 55-year Reanalysis (JRA-55), which is the second global reanalysis constructed by the Japan Meteorological Agency (JMA), by comparing it with other ...reanalyses and observational datasets. Improvements were found in the representation of atmospheric circulation on an isentropic surface and in the consistency of momentum budget based on the mass-weighted isentropic zonal mean method. The representation of climate variability in several regions was also examined. In the tropics, the frequencies of high spatial correlations with precipitation, which were estimated using the Tropical Rainfall Measuring Mission Multisatellite Precipitation Analysis, are clearly higher in JRA-55 than in JRA-25. The results indicate that JRA-55 generally improved the representations of phenomena on a wide range of space-time scales, such as equatorial waves, and transient eddies in the storm track regions, compared with JRA-25 during the satellite era. Moreover, JRA-55 improved the temporal consistency compared with the older reanalyses throughout the reanalysis period. In the stratosphere, we found larger discrepancies between reanalyses for the extra-tropical stratosphere during the Southern Hemisphere (SH) winter. Comparisons with radiosonde temperature revealed that JRA-55 has a smaller bias in temperature than the other reanalyses in the extra-tropical SH winter before 1979. Some issues in JRA-55 were also identified. The amplitude of equatorial waves and Madden-Julian oscillation in JRA-55 are weaker than in the other reanalyses. JRA-55 shows unrealistic strong cooling in South America and Australia, although the spatial distribution of the long-term temperature trends in JRA-55 is the closest to an observational dataset of global historical surface temperature.
Abstract
Motivation
Genomic prediction is now an essential technique in breeding and medicine, and it is interesting to see how omics data can be used to improve prediction accuracy. Precedent work ...proposed a metabolic network-based method in biomass prediction of Arabidopsis; however, the method consists of multiple steps that possibly degrade prediction accuracy.
Results
We proposed a Bayesian model that integrates all steps and jointly infers all fluxes of reactions related to biomass production. The proposed model showed higher accuracies than methods compared both in simulated and real data. The findings support the previous excellent idea that metabolic network information can be used for prediction.
Availability and implementation
All R and stan scripts to reproduce the results of this study are available at https://github.com/Onogi/MetabolicModeling.
We review lattice results related to pion, kaon, D- and B-meson physics with the aim of making them easily accessible to the particle-physics community. More specifically, we report on the ...determination of the light-quark masses, the form factor \f_+(0)\, arising in the semileptonic \K \rightarrow \pi \ transition at zero momentum transfer, as well as the decay constant ratio \f_K/f_\pi \ and its consequences for the CKM matrix elements \V_{us}\ and \V_{ud}\. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of \SU(2)_L\times SU(2)_R\ and \SU(3)_L\times SU(3)_R\ Chiral Perturbation Theory. We review the determination of the \B_K\ parameter of neutral kaon mixing as well as the additional four B parameters that arise in theories of physics beyond the Standard Model. The latter quantities are an addition compared to the previous review. For the heavy-quark sector, we provide results for \m_c\ and \m_b\ (also new compared to the previous review), as well as those for D- and B-meson-decay constants, form factors, and mixing parameters. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. Finally, we review the status of lattice determinations of the strong coupling constant \\alpha _s\.
The inheritance of racing performance in Thoroughbreds is of interest to breeders and geneticists. Therefore, the genetic parameters of racing performance have been investigated in various ...populations of Thoroughbreds. However, the predictability of the racing performance of a racehorse has not been assessed well. In this study, we built mixed‐effects models for Japanese Thoroughbreds and assessed their predictability of racing performance. We used the average velocity as an index of racing performance and treated each category of racecourse and distance as different traits. Model selection using the deviance information criterion showed that explanatory variables, such as race, age and jockey effects are important for racing performance. Using the selected models, the phenotypic values of horses born after 2009, adjusted using the entire dataset, were predicted with the breeding values estimated from a partial dataset until 2010. The correlation coefficients ranged from 0.000 to 0.235 (average of 0.084 ± 0.066) and were higher for longer distances. When predicting the graded race winners born after 2009 from the partial dataset until 2010, the area under the curve values ranged from 0.516 to 0.776 (average of 0.613 ± 0.073) and were also higher for longer distances. Although these results indicate the predictability of racing performance, further efforts, including exploring more suitable racing performance indices and refining statistical modelling, are required for improvement.
The Atiyah-Patodi-Singer (APS) index theorem attracts attention for understanding physics on the surface of materials in topological phases. The mathematical setup for this theorem is, however, not ...directly related to the physical fermion system, as it imposes on the fermion fields a nonlocal boundary condition known as the “APS boundary condition” by hand, which is unlikely to be realized in the materials. In this work, we attempt to reformulate the APS index in a “physicist-friendly” way for a simple setup with U(1) or SU(N) gauge group on a flat four-dimensional Euclidean space. We find that the same index as APS is obtained from the domain-wall fermion Dirac operator with a local boundary condition, which is naturally given by the kink structure in the mass term. As the boundary condition does not depend on the gauge fields, our new definition of the index is easy to compute with the standard Fujikawa method.
We review lattice results related to pion, kaon,
D
- and
B
-meson physics with the aim of making them easily accessible to the particle-physics community. More specifically, we report on the ...determination of the light-quark masses, the form factor
f
+
(
0
)
, arising in semileptonic
K
→
π
transition at zero momentum transfer, as well as the decay-constant ratio
f
K
/
f
π
of decay constants and its consequences for the CKM matrix elements
V
u
s
and
V
u
d
. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of
SU
(
2
)
L
×
SU
(
2
)
R
and
SU
(
3
)
L
×
SU
(
3
)
R
Chiral Perturbation Theory and review the determination of the
B
K
parameter of neutral kaon mixing. The inclusion of heavy-quark quantities significantly expands the FLAG scope with respect to the previous review. Therefore, we focus here on
D
- and
B
-meson decay constants, form factors, and mixing parameters, since these are most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. In addition we review the status of lattice determinations of the strong coupling constant
α
s
.
The Japan Meteorological Agency (JMA) conducted the second Japanese global atmospheric reanalysis, called the Japanese 55-year Reanalysis or JRA-55. It covers the period from 1958, when regular ...radiosonde observations began on a global basis. JRA-55 is the first comprehensive reanalysis that has covered the last half-century since the European Centre for Medium-Range Weather Forecasts 45-year Reanalysis (ERA-40), and is the first one to apply four-dimensional variational analysis to this period. The main objectives of JRA-55 were to address issues found in previous reanalyses and to produce a comprehensive atmospheric dataset suitable for studying multidecadal variability and climate change. This paper describes the observations, data assimilation system, and forecast model used to produce JRA-55 as well as the basic characteristics of the JRA-55 product. JRA-55 has been produced with the TL319 version of JMA’s operational data assimilation system as of December 2009, which was extensively improved since the Japanese 25-year Reanalysis (JRA-25). It also uses several newly available and improved past observations. The resulting reanalysis products are considerably better than the JRA-25 product. Two major problems of JRA-25 were a cold bias in the lower stratosphere, which has been diminished, and a dry bias in the Amazon basin, which has been mitigated. The temporal consistency of temperature analysis has also been considerably improved compared to previous reanalysis products. Our initial quality evaluation revealed problems such as a warm bias in the upper troposphere, large upward imbalance in the global mean net energy fluxes at the top of the atmosphere and at the surface, excessive precipitation over the tropics, and unrealistic trends in analyzed tropical cyclone strength. This paper also assesses the impacts of model biases and changes in the observing system, and mentions efforts to further investigate the representation of low-frequency variability and trends in JRA-55.
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