Detection of Gene Interactions Based on Syntactic Relations

Interactions between proteins and genes are considered essential in the description of biomolecular phenomena, and networks of interactions are applied in a system's biology approach. Recently, many studies have sought to extract information from biomolecular text using natural language processing technology. Previous studies have asserted that linguistic information is useful for improving the detection of gene interactions. In particular, syntactic relations among linguistic information are good for detecting gene interactions. However, previous systems give a reasonably good precision but poor recall. To improve recall without sacrificing precision, this paper proposes a three-phase method for detecting gene interactions based on syntactic relations. In the first phase, we retrieve syntactic encapsulation categories for each candidate agent and target. In the second phase, we construct a verb list that indicates the nature of the interaction between pairs of genes. In the last phase, we determine direction rules to detect which of two genes is the agent or target. Even without biomolecular knowledge, our method performs reasonably well using a small training dataset. While the first phase contributes to improve recall, the second and third phases contribute to improve precision. In the experimental results using ICML 05 Workshop on Learning Language in Logic (LLL05) data, our proposed method gave an F-measure of 67.2% for the test data, significantly outperforming previous methods. We also describe the contribution of each phase to the performance

The Persistent Difficulty of Early Fraction Ideas in Early Secondary School Mathematics

This study explored the nature of difficulties of seventh and eighth grade students who struggled building their conceptual understanding of early fraction ideas, in particular ordering fractions. The participants engaged in a sequence of lessons that involved the use of fraction circles. The intervention of four weekly class sessions was adapted from the Rational Number Project (RNP) curriculum that has been created for and refined through teaching experiments in the RNP research since 1979. Pre and post group interviews were conducted with each student group for a sufficient identification of the nature of the students’ difficulties. This study identified the whole number dominance strategies used by the students for ordering fractions before and even after the intervention. The students also revealed minimal use of informal ordering strategies that involve more conceptual than procedural understanding of the concept of initial fraction ideas. Considering the short intervention, there was subtle (but meaningful) evidence for a positive influence of the fraction circle model developed within the RNP on students’ developing understanding of early fraction ideas. This study suggests the need of a remedial intervention for early secondary students showing the persistent difficulty with early fraction ideas. Students need to be given enough time with not only concrete models but also appropriate usage of language to support a complete understanding of how to use the models. Keywords: Rational Number Project (RNP), fraction circle model, initial fraction ideas, ordering fraction

Creating a Virtual World for Mathematics

A virtual world was created using the popular sandbox game Minecraft to support the development of preservice teachers’ knowledge for teaching mathematics. Preservice teachers explored the virtual world for a geometry activity involving area and volume problems. They then discussed how this integration of technology could support students’ effective learning of mathematics in a meaningful way. The findings of the study demonstrated that to a certain extent the Minecraft activity supported the transfer of knowledge from preservice teachers’ mathematics content knowledge to their mathematics pedagogical and instructional practice knowledge. Preservice teachers appreciated the usefulness and effectiveness of the Minecraft activity in enhancing the teaching and learning of mathematics by visualizing mathematical concepts in the virtual world. This integration of technology also gave them an opportunity for professional growth. Although this study focuses on preservice teachers’ perspectives on the Minecraft activity, the technology integration using Minecraft will also be beneficial for students because it engages them in active and discovery learning

Effective Teaching for Place Value Understanding: A Case Study of a Literacy-Integrated Math Curriculum Module

A lesson sequence for place value was developed as an early intervention for kindergarteners. The sequence begins with a children’s picture book involving language familiar to children and continues with hands-on activities for children to make connections between and within multiple representations of place value. Through engaging in the literacy-integrated math curriculum module, kindergartners deepened their understanding of place value and the base-ten number system, as they were consistently engaged in problem solving and mathematical discourse triggered by their own mathematical thinking, as well as purposeful questions prompted by the teacher

Final evaluation of the project for expanding the role of networks of people living with HIV/AIDS

In July 2006, the International HIV/AIDS Alliance launched a three-year project on Expanding the Role of Networks of People Living with HIV/AIDS in Uganda. The project, which is funded by the United States Agency for International Development (USAID)/Uganda, sought to increase the involvement of people living with HIV/AIDS (PHA) in the HIV/AIDS response and to improve access to and utilization of prevention, treatment, care, and support services for PHA households. USAID/Uganda commissioned an evaluation of the project’s design, strategies, and performance in order to improve its implementation and learn from its successes and challenges. The study was a cross-sectional descriptive and analytical process evaluation employing both rapid participatory assessment and appraisal techniques. It utilized mixed methodologies in data collection, including a desk review, 113 key informant interviews, and 16 focus group discussions. The evaluation was conducted in 11 project districts. This final evaluation report includes the main findings and recommendations

Enhanced terahertz conductivity in ultra-thin gold film deposited onto (3-mercaptopropyl) trimethoxysilane (MPTMS)-coated Si substrates

Various material properties change considerably when material is thinned down to nanometer thicknesses. Accordingly, researchers have been trying to obtain homogeneous thin films with nanometer thickness but depositing homogeneous few nanometers thick gold film is challenging as it tends to form islands rather than homogenous film. Recently, studies have revealed that treating the substrate with an organic buffer, (3-mercaptopropyl) trimethoxysilane (MPTMS) enables deposition of ultra-thin gold film having thickness as low as 5 nm. Different aspects of MPTMS treatment for ultrathin gold films like its effect on the structure and optical properties at visible wavelengths have been investigated. However, the effect of the MPTMS treatment on electrical conductivity of ultra-thin gold film at terahertz frequency remains unexplored. Here, we measure the complex conductivity of nanometer-thick gold films deposited onto an MPTMS-coated silicon substrate using terahertz time-domain spectroscopy. Following the MPTMS treatment of the substrate, the conductivity of the films was found to increase compared to those deposited onto uncoated substrate for gold films having the thickness less than 11 nm. We observed 5-fold enhancement in the conductivity for a 7 nm-thick gold film. We also demonstrate the fabrication of nanoslot-antenna arrays in 8.2-nm-thick gold films. The nanoslot-antenna with MPTMS coating has resonance at around 0.5 THz with an electric field enhancement of 44, whereas the nanoslot-antenna without MPTMS coating does not show resonant properties. Our results demonstrate that gold films deposited onto MPTMS-coated silicon substrates are promising advanced materials for fabricating ultra-thin terahertz plasmonic devices

Genotypic Characterization of Vibrio vulnificus Clinical Isolates in Korea

AbstractObjectivesVibrio vunificus is known to cause septicemia and severe wound infections in patients with chronic liver diseases or an immuno-compromised condition. We carried out the molecular characterization of V. vulnificus isolates from human Vibrio septicemia cases based on pulsed-field gel electrophoresis (PFGE) using NotI and SfiI.Methods and ResultsPFGE was used to characterize a total of 78 strains from clinical cases after NotI or SfiI digestion. The geographical distribution of PFGE patterns for the strains from the southern part of Korea, a high-risk region for Vibrio septicemia, indicated that the isolates from southeastern Korea showed a comparatively higher degree of homology than those from southwestern Korea.ConclusionsWe report the genetic distribution of V. vulnficus isolated from Vibrio septicemia cases during 2000–2004 in Korea. This method has potential use as a subspecies-typing tool for V. vulnificus strains isolated from distant geographic regions