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Search algorithms for the bandit problems are applicable in materials discovery. However, the objectives of the conventional bandit problem are different from those of materials discovery. The conventional bandit problem aims to maximize the total rewards, whereas materials discovery aims to achieve breakthroughs in material properties. The max K-armed bandit (MKB) problem, which aims to acquire the single best reward, matches with the discovery tasks better than the conventional bandit. Thus, here, we propose a search algorithm for materials discovery based on the MKB problem using a pseudo-value of the upper confidence bound of expected improvement of the best reward. This approach is pseudo-guaranteed to be asymptotic oracles that do not depends on the time horizon. In addition, compared with other MKB algorithms, the proposed algorithm has only one hyperparameter, which is advantageous in materials discovery. We applied the proposed algorithm to synthetic problems and molecular-design demonstrations using a Monte Carlo tree search. According to the results, the proposed algorithm stably outperformed other bandit algorithms in the late stage of the search process when the optimal arm of the MKB could not be determined based on its expectation reward.

Reducing antibiotic usage in livestock animals has become an urgent issue worldwide to prevent antimicrobial resistance. Here, abuse of chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentration in calves was investigated. Japanese Black calves were fed milk replacer containing CTC at 10 g/kg (CON) or 0 g/kg (EXP). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected according to certain rules the population of various types of fecal bacteria. It is particularly interesting that the population of several methane-producing bacteria was high in the CON, and that of Lachnospiraceae, a butyrate-producing bacteria, was high in the EXP at 60 d of age. Furthermore, statistical causal inference based on machine learning data estimated that CTC treatment affects the entire intestinal environment, inhibiting butyrate production for growth and biological defense, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on intestinal health and the potential production of greenhouse gas in the calves.

Seagrass meadows play an essential role in blue carbon and aquatic ecosystem services. However, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the seagrass symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture., Comment: 54 pages, 3 figures, 16 supporting information

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, red color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that L-2-aminoadipate, phenylalanine, flavonoids and / or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus, L-2-aminoadipate and nicotinamide, and S-methyl L-cysteine were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen., Comment: 6 figures, 1 Table, and support information

Natural decomposition of organic matter is essential in food systems, and compost is used worldwide as an organic fermented fertilizer. However, as a feature of the ecosystem, its effects on the animals are poorly understood. Here we show that oral administration of compost and/or its derived thermophilic Bacillaceae, i.e., Caldibacillus hisashii and Weizmannia coagulans, can modulate the prophylactic activities of various industrial animals. The fecal omics analyses in the modulatory process showed an improving trend dependent upon animal species, environmental conditions, and administration. However, structural equation modeling (SEM) estimated the grouping candidates of bacteria and metabolites as standard key components beyond the animal species. In particular, the SEM model implied a strong relationship among partly digesting fecal amino acids, increasing genus Lactobacillus as inhabitant beneficial bacteria and 2-aminoisobutyric acid involved in lantibiotics. These results highlight the potential role of compost for sustainable protective control in agriculture, fishery, and livestock industries.

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive mechanism are expected to speculate a novel rule in wood biomass processing. Here, the relationships of inhabitant bacteria involved in carbon and nitrogen metabolism in the intestine of beetle larvae, an insect model, are investigated. Bacterial analysis of larval feces showed enrichment of members of which could include candidates for plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The abundances of these bacteria were not necessarily positively correlated with the abundance in the habitat, suggesting that they might be selectively enriched in the intestines of larvae. Further association analysis predicted that carbon and nitrogen metabolism in the intestine was affected by the presence of the other common bacteria, the populations of which were not remarkably altered in the habitat and feces. Based on hypotheses targeting these selected bacterial groups, structural estimation modeling analyses statistically suggested that their metabolism of carbon and nitrogen and their stable isotopes, {\delta}13C and {\delta}15N, may be associated with fecal enriched bacteria and other common bacteria. In addition, other causal inference analyses, such as causal mediation analysis, linear non-Gaussian acyclic model (LiNGAM), and BayesLiNGAM, did not necessarily affirm the existence of prominent bacteria involved in metabolism, implying its importance as the bacterial groups for metabolism rather than a remarkable bacterium. Thus, these observations highlight a multifaceted view of symbiotic bacterial groups utilizing carbon and nitrogen from wood biomass in insect larvae as a cultivator of potentially environmentally beneficial bacteria.

We present continuum extrapolated results of charmonium and bottomonium correlators in the vector channel at several temperatures below and above $T_c$. The continuum extrapolation jointly performed with the interpolations to have physical values of $J/\psi$ and $\Upsilon$ masses in the confined phase is based on calculations on several large quenched isotropic lattices using clover-improved Wilson valence fermions carrying different quark masses. The extrapolated lattice correlators are confronted with perturbation theory results incorporating resummed thermal effects around the threshold from pNRQCD and vacuum asymptotics above the threshold. An additional transport peak is modelled below the threshold allowing for an estimate of the diffusion coefficients for charm and bottom quarks. We find that charmonium correlators in the vector channel can be well reproduced by perturbative spectral functions above $T_c$ where no resonance peaks for $J/\psi$ are needed at and above 1.1 $T_c$, while for bottomonium correlators a resonance peak for $\Upsilon$ is still needed up to 1.5 $T_c$. By analyzing the transport contribution to the correlators we find that the drag coefficient of a charm quark is larger than that of a bottom quark., Comment: published version

We investigate the in-medium modifications of heavy quarkonia in the vector channel and the heavy quark diffusion coefficient by comparing Euclidean correlators from the lattice to a perturbative spectral function. On the lattice side, we work with continuum extrapolated data from four different large and fine lattices with Clover-improved Wilson fermions in the quenched approximation at five temperatures (0.75, 1.1, 1.3, 1.5 and 2.25$T_c$). On the perturbative side, we use a combination of pNRQCD and vacuum asymptotics to describe the spectral function. After accounting for systematic errors, we obtain a spectral function that is suited to describe the bound state region. This spectral function describes charmonium well without a resonance peak at any of our analyzed temperatures above $T_c$, while we observe a thermally broadened resonance peak for bottomonium that is only melted at our largest temperature, $2.25T_c$. For the transport contribution we assume a Breit-Wigner shaped peak and find that the drag coefficient of charm quarks is larger than that of bottom quarks.

We study the nature of the finite temperature phase transition for three-flavor QCD. In particular we investigate the location of the critical endpoint along the three flavor symmetric line in the light quark mass region of the Columbia plot. In the study, the Iwasaki gauge action and the nonperturvatively O($a$) improved Wilson-Clover fermion action are employed. We newly generate data at $N_{\rm t}=12$ and set an upper bound of the critical pseudoscalar meson mass in the continuum limit $m_{\rm PS,E}\lesssim 110$MeV., Comment: 14 pages, 11 figures

We investigate the critical endpoints of the finite temperature phase transition of QCD at zero chemical potential. We employ the renormalization-group improved Iwasaki gauge action and non-perturbatively O(a)-improved Wilson-clover fermion action. The critical endpoints are determined by using the intersection point of kurtosis, employing the multi-parameter, multi-ensemble reweighting method. We present results for the critical endline at $N_{\rm T}$ = 6 and the continuum extrapolation for the critical endpoint of the SU(3)-flavor symmetric point., Comment: Typos corrected, references added. 8 pages, 5 figures, talk presented at 37th International Symposium on Lattice Field Theory - Lattice2019, 16 - 22 June 2019, Wuhan, China

We present lattice QCD results for mesonic screening masses in the temperature range 140 MeV $\lesssim T \lesssim$ 2500 MeV. Our calculations were carried out using (2+1)-flavors of the Highly Improved Staggered Quark (HISQ) action, with a physical value for the strange quark mass and two values of the light quark mass corresponding to pion masses of 160 MeV and 140 MeV. Continuum-extrapolated results were obtained using calculations with a variety of lattice spacings corresponding to temporal lattice extents $N_\tau = 6 - 16$. We discuss the implications of these results for the effective restoration of various symmetries in the high temperature phase of QCD, as well as the approach toward the perturbative limit., Comment: Corrected some errors pertaining to the discussion on emergent SU(2)CS and SU(4) symmetries

We report our study on the critical endpoint of the finite temperature phase transition in 4-flavor QCD with Wilson-Clover fermions. Using the kurtosis intersection method, we determined the critical endpoint on lattices with $N_t$ = 4, 6 and 8. Our continuum extrapolated results show that the pseudo-scalar meson mass at the critical endpoint, $m_\mathrm{PS,E}$, for 4-flavor is clearly larger than that for 3-flavor. We also compared our results to those with staggered fermions and found that $m_\mathrm{PS,E}/T_E$ for 4-flavor with Wilson fermions might remain finite even in the continuum limit in contrast to that with staggered fermions, where $m_\mathrm{PS,E}/T_E$ is very close to zero, which suggests that the difference between Wilson and staggered fermions is at least not due to the rooting., Comment: 7 pages, 6 figures, talk presented in the 36th International Symposium on Lattice Field Theory (Lattice 2018), 22-28 July, 2018, Michigan State University, East Lansing, Michigan, USA