GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.Comment: 23 pages, 5 figure

Impact of Information Sharing in Supply Chain Management

It has been pointed out that a vital element of SCM systems is the sharing of information such as sales figures and delivery plans between multiple companies or between different divisions of a company. However, the potential benefits of SCM for individual companies that actually share information has yet to be properly investigated. In view of this, the present study modeled company activities in a way that considered decision-making not just over the execution-level, but also over the tactics- and strategy-level. Simulation was then used to investigate the impact of information sharing on company gross profits. In this study on supply chains in the electronics industry, we confirmed that sharing information such as product plan and procurement plan between a component manufacturer and assembly manufacturer can lead to improved gross profits for all companies involved. We demonstrated that the benefit of sharing strategy-level plans is greater than in the case of sharing execution- and tactics-level information. The increase in gross profit was seen to be particularly large in the case of declining demand. In addition, while earlier studies evaluated the impact of information sharing by looking at inventory levels, this study confirms that reducing inventory does not necessarily lead to improved gross profits, thereby highlighting the importance of gross profits as a measure for assessing the impact of information sharing

Consistent map building in petrochemical complexes for firefighter robots using SLAM based on GPS and LIDAR

The objective of this study was to achieve simultaneous localization and mapping (SLAM) of firefighter robots for petrochemical complexes. Consistency of the SLAM map is important because human operators compare the map with aerial images and identify target positions on the map. The global positioning system (GPS) enables increased consistency. Therefore, this paper describes two Rao-Blackwellized particle filters (RBPFs) based on GPS and light detection and ranging (LIDAR) as SLAM solutions. Fast-SLAM 1.0 and Fast-SLAM 2.0 were used in grid maps for RBPFs in this study. We herein propose the use of Fast-SLAM to combine GPS and LIDAR. The difference between the original Fast-SLAM and the proposed method is the use of the log-likelihood function of GPS; the proposed combination method is implemented using a probabilistic mathematics formulation. The proposed methods were evaluated using sensor data measured in a real petrochemical complex in Japan ranging in size from 550–380 m. RTK-GPS data was used for the GPS measurement and had an availability of 56%. Our results showed that Fast-SLAM 2.0 based on GPS and LIDAR in a dense grid map produced the best results. There was significant improvement in alignment to aerial data, and the mean square root error was 0.65 m. To evaluate the mapping consistency, accurate 3D point cloud data measured by Faro Focus 3D (± 3 mm) was used as the ground truth. Building sizes were compared; the minimum mean errors were 0.17 and 0.08 m for the oil refinery and management building area and the area of a sparse building layout with large oil tanks, respectively. Consequently, a consistent map, which was also consistent with an aerial map (from Google Maps), was built by Fast-SLAM 1.0 and 2.0 based on GPS and LIDAR. Our method reproduced map consistency results for ten runs with a variance of ± 0.3 m. Our method reproduced map consistency results with a global accuracy of 0.52 m in a low RTK-Fix-GPS environment, which was a factory with a building layout similar to petrochemical complexes with 20.9% of RTK-Fix-GPS data availability

12Epi -9deacetoxyxenicin, new cytotoxic diterpenoid from a Bornean soft coral Xenia sp

One new compound, 12-epi-9-deacetoxyxenicin (1) along with a hydroperoxide product, 12-epi-9-deacetoxy-8-hydroperoxyxenicin (2) and two known sesquiterpenoids (3–4) were isolated from a population of Bornean soft coral Xenia sp. The structures of these secondary metabolites were elucidated based on their spectroscopic data. Compounds 1 and 2 showed cytotoxic activity against ATL cell line, S1T. In addition, compound 3 exhibited hyphal inhibition of Lagenidium thermophilum

Explicitly Multi-Modal Benchmarks for Multi-Objective Optimization

In multi-objective optimization, designing good benchmark problems is an important issue for improving solvers. Although many benchmark problems have been proposed and some of them became de facto standards, designing multimodal problems that have a controllable landscape is still an open problem especially for high-dimensional cases. We thus propose the Benchmark with Explicit Multimodality (BEM), which lets the benchmark designer specify the basins of attraction using a graph structure known as the reachability graph. In this article, we focus on the mathematical formulation of the BEM. We will see that the BEM has preferable characteristics such as (i) realizing user-specified local Pareto set, (ii) allowing high-dimensional design spaces and (iii) possessing nonseparability

Effects of Olopatadine Hydrochloride, a Histamine H1 Receptor Antagonist, on Histamine-Induced Skin Responses

Effects of olopatadine hydrochloride, a histamine H1 receptor antagonist, on histamine-induced skin responses were evaluated in 10 healthy subjects in comparison with placebo, fexofenadine hydrochloride, and bepotastine besilate. Olopatadine significantly suppressed histamine-induced wheal, flare, and itch, starting 30 minutes after oral administration. Olopatadine was more effective than fexofenadine and bepotastine. None of the drugs studied impaired performance of word processing tasks. These results suggest that olopatadine can suppress skin symptoms caused by histamine soon after administration

NIMA-related kinases 6, 4, and 5 interact with each other to regulate microtubule organization during epidermal cell expansion in Arabidopsis thaliana

NimA-related kinase 6 (NEK6) has been implicated in microtubule regulation to suppress the ectopic outgrowth of epidermal cells; however, its molecular functions remain to be elucidated. Here, we analyze the function of NEK6 and other members of the NEK family with regard to epidermal cell expansion and cortical microtubule organization. The functional NEK6-green fluorescent protein fusion localizes to cortical microtubules, predominantly in particles that exhibit dynamic movement along microtubules. The kinase-dead mutant of NEK6 (ibo1-1) exhibits a disturbance of the cortical microtubule array at the site of ectopic protrusions in epidermal cells. Pharmacological studies with microtubule inhibitors and quantitative analysis of microtubule dynamics indicate excessive stabilization of cortical microtubules in ibo1/nek6 mutants. In addition, NEK6 directly binds to microtubules in vitro and phosphorylates beta-tubulin. NEK6 interacts and co-localizes with NEK4 and NEK5 in a transient expression assay. The ibo1-3 mutation markedly reduces the interaction between NEK6 and NEK4 and increases the interaction between NEK6 and NEK5. NEK4 and NEK5 are required for the ibo1/nek6 ectopic outgrowth phenotype in epidermal cells. These results demonstrate that NEK6 homodimerizes and forms heterodimers with NEK4 and NEK5 to regulate cortical microtubule organization possibly through the phosphorylation of beta-tubulins

Analysis of Delayed Bleeding after Endoscopic Submucosal Dissection for Gastric Epithelial Neoplasms

Aim. Delayed bleeding after endoscopic submucosal dissection (ESD) for gastric epithelial neoplasms is a major complication. We investigated factors related to post-ESD bleeding to identify preventive measures. Methods. The study included 161 gastric epithelial neoplasms in 142 patients from June 2007 to September 2010. Post-ESD bleeding was defined as an ulcer with active bleeding or apparent exposed vessels diagnosed by an emergency endoscopy or a planned follow-up endoscopy. We analyzed associations between bleeding and the following factors: age, sex, morphology, pathology, tumor depth, ulcer presence/absence, location, size of the resected lesion, duration of the procedure, the number of times bleeding occurred during ESD, and the use of anticoagulants and/or antiplatelet drugs. Subsequently, we examined characteristics of bleeding cases. Results. Post-ESD bleeding occurred in 21 lesions. Univariate analysis of these cases showed that ulcer presence/absence (P < 0.001), middle or lower third lesions (P = 0.036), circumference (P = 0.014), and a post-ESD ulcer with an extended lesser curve (P = 0.009) were significant predictors of bleeding. Multivariate analysis showed that ulcer presence/absence (OR 9.73, 95% CI 2.28–41.53) was the only significant predictor. Conclusion. Ulcer presence/absence was considered the most significant predictor of post-ESD bleeding