Arukikata Travelogue Dataset with Geographic Entity Mention, Coreference, and Link Annotation

Geoparsing is a fundamental technique for analyzing geo-entity information in text. We focus on document-level geoparsing, which considers geographic relatedness among geo-entity mentions, and presents a Japanese travelogue dataset designed for evaluating document-level geoparsing systems. Our dataset comprises 200 travelogue documents with rich geo-entity information: 12,171 mentions, 6,339 coreference clusters, and 2,551 geo-entities linked to geo-database entries

Systems Analysis of ATF3 in Stress Response and Cancer Reveals Opposing Effects on Pro-Apoptotic Genes in p53 Pathway

Stress-inducible transcription factors play a pivotal role in cellular adaptation to environment to maintain homeostasis and integrity of the genome. Activating transcription factor 3 (ATF3) is induced by a variety of stress and inflammatory conditions and is over-expressed in many kinds of cancer cells. However, molecular mechanisms underlying pleiotropic functions of ATF3 have remained elusive. Here we employed systems analysis to identify genome-wide targets of ATF3 that is either induced by an alkylating agent methyl methanesulfonate (MMS) or over-expressed in a prostate tumour cell line LNCaP. We show that stress-induced and cancer-associated ATF3 is recruited to 5,984 and 1,423 targets, respectively, in the human genome, 89% of which are common. Notably, ATF3 targets are highly enriched for not only ATF/CRE motifs but also binding sites of several other stress-inducible transcription factors indicating an extensive network of stress response factors in transcriptional regulation of target genes. Further analysis of effects of ATF3 knockdown on these targets revealed that stress-induced ATF3 regulates genes in metabolic pathways, cell cycle, apoptosis, cell adhesion, and signalling including insulin, p53, Wnt, and VEGF pathways. Cancer-associated ATF3 is involved in regulation of distinct sets of genes in processes such as calcium signalling, Wnt, p53 and diabetes pathways. Notably, stress-induced ATF3 binds to 40% of p53 targets and activates pro-apoptotic genes such as TNFRSF10B/DR5 and BBC3/PUMA. Cancer-associated ATF3, by contrast, represses these pro-apoptotic genes in addition to CDKN1A/p21. Taken together, our data reveal an extensive network of stress-inducible transcription factors and demonstrate that ATF3 has opposing, cell context-dependent effects on p53 target genes in DNA damage response and cancer development

Assessment of chemical compositions in coral skeletons (Acropora digitifera and Porites australiensis) as temperature proxies

Although biogenic carbonates, such as foraminifera and coccolithophorids, are valuable tools for reconstructing past environments, scleractinian corals also offer environmental data from tropical to subtropical regions with a higher time resolution. For example, oxygen isotopes (δ18O) and strontium-calcium (Sr/Ca) ratios have been utilized to reconstruct sea surface temperatures and salinity, primarily through the use of massive-type Porites sp. from the Pacific, as well as corals like Diploria and Montastrea from the Atlantic. While a few types of corals other than Porites have been utilized in paleoclimate studies, comprehensive evaluations of their geochemical tracers as temperature proxies have not been thoroughly conducted. Therefore, in this study, we focused on branching-type Acropora, which are found worldwide and are often present in fossil corals. We conducted a comparison of the chemical compositions (δ18O, δ13C, Sr/Ca, U/Ca, Mg/Ca, and Ba/Ca) of Acropora digitifera and Porites australiensis through temperature-controlled culture experiments. The validity of using the chemical components of A. digitifera as temperature proxies was then evaluated. Three colonies of A. digitifera and P. australiensis were collected for culture experiments on Sesoko Island, Okinawa, Japan. We reared coral samples in seawater with five different temperature settings (18, 21, 24, 27, 30°). The calcification rate and photosynthesis efficiency (Fv/Fm) of each nubbin were measured during the experimental period. After the culture experiment for 77 days, chemical components in skeletal parts grown during the experiment were then measured. Consequently, the mean growth rates and Fv/Fm throughout the experiment were higher for A. digitifera (0.22%/d and 0.63 for growth rate and Fv/Fm) compared to those for P. australiensis (0.11%/d and 0.38 for growth rate and Fv/Fm). This suggests that the higher efficiency of photosynthesis in A. digitifera would promote greater calcification compared to P. australiensis. Regarding the potential use as temperature proxies, A. digitifera exhibited a strong negative correlation, on average, between δ18O and the water temperature (r = 0.95, p< 0.001). The temperature dependency was found to be comparable to that reported in Porites corals (-0.11 and -0.17 ‰/°C for P. australiensis and A. digitifera, respectively). Thus, the δ18O of A. digitifera appeared to be a useful temperature proxy, although it was also slightly influenced by skeletal growth rate at the same temperature. A strong negative correlation was also observed between the mean Sr/Ca ratio and temperature in A. digitifera (r = 0.61, p< 0.001) as well as P. australiensis (r = 0.56, p< 0.001), without a clear influence from the skeletal growth rate. Therefore, the skeletal Sr/Ca ratio in corals may have been primarily influenced by water temperature, although large deviations in Sr/Ca were observed in A. digitifera, even at the same temperature settings. This deviation can be reduced by subsampling an apical part of a polyp including the axis of skeletal growth. The U/Ca ratio of A. digitifera appeared to be affected by internal pH variation within the corals, especially at 30°C. Similar to U/Ca ratios, metabolic and kinetic effects on corals were observed in δ13C of A. digitifera at 18 and 30°C. In addition, considering the variation pattern of both U/Ca and δ13C of A. digitifera at 30°C, it has been suggested that respirations may overwhelm photosynthesis for coral samples at 30°C. Therefore, the U/Ca and δ13C of A. digitifera could potentially be used as proxies of biomineralization processes, whereas the δ18O and Sr/Ca displayed a high possibility of acting as temperature proxies

Single ingestion of soy β-conglycinin induces increased postprandial circulating FGF21 levels exerting beneficial health effects

Soy protein β-conglycinin has serum lipid-lowering and anti-obesity effects. We showed that single ingestion of β-conglycinin after fasting alters gene expression in mouse liver. A sharp increase in fibroblast growth factor 21 (FGF21) gene expression, which is depressed by normal feeding, resulted in increased postprandial circulating FGF21 levels along with a significant decrease in adipose tissue weights. Most increases in gene expressions, including FGF21, were targets for the activating transcription factor 4 (ATF4), but not for peroxisome proliferator-activated receptor α. Overexpression of a dominant-negative form of ATF4 significantly reduced β-conglycinin-induced increases in hepatic FGF21 gene expression. In FGF21-deficient mice, β-conglycinin effects were partially abolished. Methionine supplementation to the diet or primary hepatocyte culture medium demonstrated its importance for activating liver or hepatocyte ATF4-FGF21 signaling. Thus, dietary β-conglycinin intake can impact hepatic and systemic metabolism by increasing the postprandial circulating FGF21 levels.UTokyo Research掲載「大豆のタンパク質1回摂取で代謝を改善する因子が急増」 URI: http://www.u-tokyo.ac.jp/ja/utokyo-research/research-news/single-ingestion-of-soy-protein-improves-metabolism.htmlUTokyo Research "Single ingestion of soy protein improves metabolism" URI: http://www.u-tokyo.ac.jp/en/utokyo-research/research-news/single-ingestion-of-soy-protein-improves-metabolism.htm

A coherent Ising machine for 2000-node optimization problems

The analysis and optimization of complex systems can be reduced to mathematical problems collectively known as combinatorial optimization. Many such problems can be mapped onto ground-state search problems of the Ising model, and various artificial spin systems are now emerging as promising approaches. However, physical Ising machines have suffered from limited numbers of spin-spin couplings because of implementations based on localized spins, resulting in severe scalability problems. We report a 2000-spin network with all-to-all spin-spin couplings. Using a measurement and feedback scheme, we coupled time-multiplexed degenerate optical parametric oscillators to implement maximum cut problems on arbitrary graph topologies with up to 2000 nodes. Our coherent Ising machine outperformed simulated annealing in terms of accuracy and computation time for a 2000-node complete graph