Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Abstracts from the 20th International Symposium on Signal Transduction at the Blood-Brain Barriers

https://deepblue.lib.umich.edu/bitstream/2027.42/138963/1/12987_2017_Article_71.pd

Two model analyses of the urban structure of minimal transportation energy consumption

The transportation sector needs to reduce fuel consumption to deal with global warming because it depends on fossil fuels strongly and it seems to be difficult to substitute other fuels. This study aims at investigating an optimal land use in urban areas from the viewpoint of reducing energy consumption for transportation. For this purpose, the authors developed two kinds of models. One minimizes the total trip length under the condition of constant congestion. The other minimizes the fuel consumption directly where congestion is taken into account endogenously. The optimal structures calculated numerically illustrate that business areas are located around the center of a city while residential areas are on the suburbs, which is similar to the actual land use observed generally. These results are compared with the land use of the central business district (CBD) in Tokyo.Urban land use Transportation Energy consumption Congestion

Distant metastasis in patients with myxofibrosarcoma

Purpose: A clinical feature of myxofibrosarcoma is local recurrence, but knowledge about distant metastasis is sparse. We evaluated the tendency of clinical and histological features of metastasis in myxofibrosarcoma patients. Methods: Fifty-eight patients with myxofibrosarcoma were treated in our hospitals, and a total of 16 consecutive patients with distant metastases were included in this retrospective study (9 males and 7 females, with a mean age of 77 years). Because there was no patient complicated by both lung and lymph node metastases, we compared the age, sex, tumor size and location, French Federation of Cancer Centers Sarcoma Group (FNCLCC) grade, American Joint Committee on Cancer (AJCC) stage, and times of the first metastasis from the initial examination between the lung and lymph node groups. In addition, we examined factors affecting the prognosis. Results: The median follow-up period was 42.9 months (range 8–142). Eleven of 16 patients developed pulmonary metastases. The sites of extra pulmonary metastases were the lymph nodes in 5 patients, bone in 1, subcutaneous in 1, intramuscular in 1, and peritoneum in 1. The median time for patients to develop distant metastases was 17.4 months (range 0–59). The time until the onset of the first metastasis in the lung metastasis group was significantly shorter than in the lymph node group (p < 0.05). Also, the survival rate in the lymph node metastasis group was better than in the lung metastasis group (p < 0.05). Conclusions: Not only lung metastasis but also lymph node metastasis occurs frequently in myxofibrosarcoma patients. Myxofibrosarcoma with lung metastasis is more aggressive than the type with lymph node metastasis