Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Contribution of bacteria to the Artemia diet

The aim of this study was to determine the dietary role of bacteria in Artemia culture. In the first study, bacteria associated in Artemia culture were isolated and fed to germ-free Artemia nauplii under gnotobiotic cultutre condition (with a known flora) in 6 days experimental period. The results showed that among nines isolated (HT1-HT9), some bacteria could be a food source when offered as a sole food. Among nine isolates, HT3 and HT6 fed Artemia had higher survival and growth, for this reason HT3 and HT6 was included in the second study where mixed diets between bacteria and microalgae were fed to Artemia under gnotobiotic culture condition. In this study, 15N stable isotope was used to label on microalgae in the mixed diet. After 24 h feeding period, 15N accumulated in the Artemia tissue from microalgae were analyzed. The results show that, when bacteria were offered as food together with microalgae there may be enhanced assimilation of nitrogen from microalgae, as compared to the algal mono-diet. In the last study, heterotrophic bacteria were enhanced to grow by sucrose addition from day 2 after hatching (DAH2) onwards within the Artemia culture vials. The assimilation of bacteria by Artemia was evaluated with different depressive feeding regimes: standard feeding regime (SF), half of SF regime (SF1/2), one third of SF regime (SF1/3) and one fourth of SF regime (SF1/4). 15N stable isotope and fatty acids were used as study tools to follow the assimilation of bacteria by Artemia. The results at DAH15 showed that, Artemia biomass production increased in all sucrose addition treatments as compared to the control culture without sucrose addition. Particularly, the Artemia biomass production in the SF1/3 regime with carbon addition treatment was equal to that obtained in the SF regime treatment (without carbon addition). The results of fatty acids level and 15N accumulation in Artemia tissue showed that Artemia fed on bacteria, especially in the algae-limited conditions. Our results, however, still remain to be confirmed in pond culture conditions

Individualized Scaffolding of Scientific Reasoning Development – Complementing Teachers with an Auto-agent

Building on the success in a previous study in engaging the underserved middle-school population in the practice of science through individualized scaffolding, the current study sought to examine an automated-agent, Astro-world, developed to provide real-time guidance to students in order to increase the scalability of the intervention while maintaining the benefits of the individualized format. Through practices of argument and counterargument in advancing and challenging claims, the agent focused on coordination of multiple variables affecting an outcome, rather than only the foundational and more extensively studied strategy of controlled experimentation, in the context of a scenario in which students had to investigate multiple factors affecting the performance of potential astronauts in a space simulator. The intervention sought to help students see the purpose and value of scientific practices using social science content rather than traditional science topics. In addition to adapting the technology into a regular classroom setting in which the teacher is actively engaged (teacher-involved condition), the study included a second condition to determine if the technology could be used effectively without active teacher involvement (tech-only condition). Delayed far-transfer assessments showed that only students in the teacher-involved condition (but not the tech-only condition) outperformed those in a non-participating control group in recognizing the need for evidence and considering all contributing factors in making predictions. Furthermore, post-hoc analysis showed that these significant differences occurred predominantly among those who mastered the foundational control of variable skills. Possibilities are considered as to why teacher involvement was critical to effectiveness, and implications for classroom practice are addressed

The Impacts of an Entrepreneurial Course on Secondary Students\u27 Entrepreneurial Self-Efficacy and Entrepreneurial Intentions

There is considerable agreement that promoting entrepreneurship stimulates economic development and job creation, which helps maintain a country’s economic competitiveness. Entrepreneurship education is a key to increasing the likelihood of potential entrepreneurs. While substantial research has documented strategies for enhancing students\u27 entrepreneurial mindset and building entrepreneurial skills in higher education, entrepreneurship is rarely incorporated into or studied in secondary education. This mixed-method study examined the impact of an online ten-lesson entrepreneurship course on secondary students\u27 entrepreneurial self-efficacy and entrepreneurial intentions. Students took a pre-survey that measured their entrepreneurial self-efficacy and intentions before the course and a post-survey upon completing the course. Students\u27 artifacts (elevator pitch frameworks and business canvas models) from the capstone lesson were collected. A paired-sample t-test compared students’ entrepreneurial self-efficacy and intentions before and after the course, and artifacts were analyzed using a rubric. Survey results showed significant improvements in two dimensions of entrepreneurial intentions: Professional Attraction and Entrepreneurial Capacity. Students\u27 entrepreneurial self-efficacy subscales (Searching, Planning, Marshaling) did not yield a significant improvement. The analysis of students\u27 artifacts showed that students could identify problems and generate solutions to their problems. However, students did not clearly understand how to project revenue based on a target market

Spatial structure and prediction of Land use change considering development projects in urban promotion districts

n this paper, the actual conditions and the change structure of land use by using mesh data are studied in urban promotion area in a local hub city of Fukuoka, Japan. Firstly, all meshes are classified into 15 patterns based on distribution of land use. Then, transition probability models are made out based on the change of these 15 patterns. The Change structure of land use in an area depends on whether development projects are carried out or not. Therefore, all of the meshes are divided into two groups, and different transition probability models are proposed. Finally, a prediction method of land use is proposed under the consideration of the changing structure of meshes. Though our proposed approach is a macroscopic forecasting method of land use, it is useful to evaluate the effects of urban policies for development projects.

Evaluation of City Planning Road Development Measures by Microscopic Traffic Simulation

This study was made on the development plan of Kawahara Avenue, a road project authorized in city planning of Miyazaki City in Japan. The Kawahara Avenue development is planned along the Oyodo River. The land use of the area along the route comprises the tourist hotel zone, residential zone, and industrial zone. The Kawahara Avenue planning, unlike most other road development plans in Japan, requires much more than simply providing for the smooth flow of traffic. In the tourist hotel zone where the leading Miyazaki City hotels are located, the image and impression the tourists may have about the city is an important consideration. Therefore, the city government intends that this section of the road should not have excessive traffic. In the residential zone, the existing road network consists of narrow streets with no sidewalks. In addition to the sidewalks to be built, Kawahara Avenue is expected to handle a great deal of the traffic passing the residential district. This should help meet the goal in providing a safe environment for the pedestrians in other narrow streets without sidewalks. Under the circumstances as stated above, the planning has faced significant constraints in land purchasing involving forced move-out in the result of financial problems and coordination of the views between the city administration and the residents in the vicinity. The purpose of this research is to study under the given constraints what would be the most appropriate plan for the development of Kawahara Avenue. First, a traffic monitoring survey was conducted in the subject districts to compile Origin-Destination (OD) data of traffic flow in the districts. Then, the road network of the subject districts and traffic signal phase data were digitized to carry out microscopic traffic simulation and checked for reproduction accuracy of the current situation. The results confirmed that simulation reproduces the traffic conditions of the districts with sufficient precision. Furthermore, we prepared several hypothetical proposals for the road development and evaluated with the same simulation system as to how the traffic situations would be had those proposals been implemented. As a result it was demonstrated that the original goals can be achieved by developing the road within the given constraints.