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

TIMP-1 Induces α-Smooth Muscle Actin in Fibroblasts to Promote Urethral Scar Formation

Background/Aims: Tissue inhibitor of metalloproteinases-1 (TIMP-1) has been reported to upregulate in urethral scar. However, the underlying molecular mechanisms remain undefined. Methods: Here, we studied levels of TIMP-1 and α-smooth muscle actin (α-SMA) in the fibroblasts isolated from urethral scar tissues, compared to the fibroblasts isolated from normal urethra. Then we either overexpressed TIMP-1, or inhibited TIMP-1 by lentiviruses carrying a transgene or a short hairpin small interfering RNA for TIMP-1 in human fibroblasts. We examined the effects of modulation of TIMP-1 on α-SMA, and on epithelial-mesenchymal transition (EMT)-related genes. We also studied the underlying mechanisms. Results: We detected significantly higher levels of TIMP-1 and α-smooth muscle actin (α-SMA) in the fibroblasts isolated from urethral scar tissues, compared to the fibroblasts isolated from normal urethra. Moreover, the levels of TIMP-1 and α-SMA strongly correlated. Moreover, we found that TIMP-1 significantly increased levels of α-SMA, transforming growth factor β 1 (TGFβ1), Collagen I and some other key factors related to an enhanced EMT, suggesting that TIMP-1 may induce transformation of fibroblasts into myofibroblasts to promote tissue EMT to enhance the formation of urethral scar. Moreover, increases in TIMP-1 also induced an increase in fibroblast cell growth and cell invasion, in an ERK/MAPK-signaling-dependent manner. Conclusion: Our study thus highlights a pivotal role of TIMP-1 in urethral scar formation

Dynamic Modeling and Experimental Validation of a Water Hydraulic Soft Manipulator Based on an Improved Newton—Euler Iterative Method

Compared with rigid robots, soft robots have better adaptability to the environment because of their pliability. However, due to the lower structural stiffness of the soft manipulator, the posture of the manipulator is usually decided by the weight and the external load under operating conditions. Therefore, it is necessary to conduct dynamics modeling and movement analysis of the soft manipulator. In this paper, a fabric reinforced soft manipulator driven by a water hydraulic system is firstly proposed, and the dynamics of both the soft manipulator and hydraulic system are considered. Specifically, a dynamic model of the soft manipulator is established based on an improved Newton–Euler iterative method, which comprehensively considers the influence of inertial force, elastic force, damping force, as well as combined bending and torsion moments. The dynamics of the water hydraulic system consider the effects of cylinder inertia, friction, and water response. Finally, the accuracy of the proposed dynamic model is verified by comparing the simulation results with the experimental data about the steady and dynamic characteristics of the soft manipulator under various conditions. The results show that the maximum sectional error is about 0.0245 m and that the maximum cumulative error is 0.042 m, which validate the effectiveness of the proposed model

Interagency discrepancies in tropical cyclone intensity estimates over the western North Pacific in recent years

Abstract This study investigates interagency discrepancies among best‐track estimates of tropical cyclone (TC) intensity in the western North Pacific, provided by the Joint Typhoon Warning Center (JTWC), the China Meteorological Administration (CMA), and the Regional Specialized Meteorological Center (RSMC) Tokyo during 2013 to 2019. The results reveal evident differences in maximum wind speed (MSW) estimates, where linear systematic differences are significant. However, the Dvorak parameter (CI) numbers derived from the MSWs reported by the three agencies are internally consistent. Further analysis suggests that the remained CI discrepancies are related to differences in the estimation of intensity trends, initial intensities, and TC positions among these datasets. In addition, the CI estimates provided by the JTWC for TCs over the open ocean are generally higher than those reported by the CMA and RSMC. However, the estimates from CMA and RSMC tend to give higher TC intensities for the TCs in the mainland and coastal areas of China and Japan, respectively, than those over the open ocean with the same intensity in JTWC dataset. This pattern potentially reflects the extensive use of surface observations by these two agencies for landfalling and offshore TCs. These results may help the research community to get more accurate details about the TCs in WNP from the best track datasets of different agencies

A metamorphic testing approach for event sequences.

Test oracles are commonly used in software testing to determine the correctness of the execution results of test cases. However, the testing of many software systems faces the test oracle problem: a test oracle may not always be available, or it may be available but too expensive to apply. One such software system is a system involving abundant business processes. This paper focuses on the testing of business-process-based software systems and proposes a metamorphic testing approach for event sequences, called MTES, to alleviate the oracle problem. We utilized event sequences to represent business processes and then applied the technique of metamorphic testing to test the system without using test oracles. To apply metamorphic testing, we studied the general rules for identifying metamorphic relations for business processes and further demonstrated specific metamorphic relations for individual case studies. Three case studies were conducted to evaluate the effectiveness of our approach. The experimental results show that our approach is feasible and effective in testing the applications with rich business processes. In addition, this paper summarizes the experimental findings and proposes guidelines for selecting good metamorphic relations for business processes

Spatiotemporal Change of Urban Ecologic Environment Quality Based on RSEI—Taking Meizhou City, China as an Example

An ecological index that is constructed based on remote sensing images can enable a rapid evaluation of the quality of the urban ecological environment and can provide a scientific basis for the construction of urban ecological civilization. Taking Meizhou City, in Guangdong in China, as a study area, based on the Landsat TM/OLI and MODIS remote sensing data, this paper extracts the total primary productivity (GPP), land surface temperature (LST), humidity component (Wetness), and bare soil index (SI), which represent the remote sensing ecological index (RSEI) evaluation indicators. The greenness, heat, humidity, and dryness in the indicators are used to characterize the quality of the regional ecological environment and its change characteristics. The results show that: (1) the high-quality areas of ecological environment in the study area are increasing, and the proportion of high-grade RSEI areas has increased from 61.7% to 66.2%. (2) About 26.3% of the area in the study area has an optimized ecological environment quality. (3) The correlation between POI and each index is significant, among which GPP and LST have a high correlation with RSEI, while POI and RSEI have a moderately negative correlation. (4) MODIS data are suitable for regional ecological environmental quality assessments. In the future, research on RSEI data sources and processing efficiency and the spatiotemporal changes of ecological quality and environmental factors can be strengthened, and the sustainable development of ecological protection and urban construction planning can be explored