Network Motif Detection： Algorithms, Parallel and Cloud Computing,and Related Tools

Network motif is defined as a frequent and unique subgraph pattern in a network, and the search involves counting all the possible instances or listing all patterns, testing isomorphism known as NP-hard and large amounts of repeated processes for statistical evaluation. Although many efficient algorithms have been introduced, exhaustive search methods are still infeasible and feasible approximation methods are yet implausible.Additionally, the fast and continual growth of biological networks makes the problem more challenging. As a consequence, parallel algorithms have been developed and distributed computing has been tested in the cloud computing environment as well. In this paper, we survey current algorithms for network motif detection and existing software tools. Then, we show that some methods have been utilized for parallel network motif search algorithms with static or dynamic load balancing techniques. With the advent of cloud computing services, network motif search has been implemented with MapReduce in Hadoop Distributed File System(HDFS), and with Storm, but without statistical testing. In this paper, we survey network motif search algorithms in general, including existing parallel methods as well as cloud computing based search, and show the promising potentials for the cloud computing based motif search methods.     

Fabrication and characterization of 3D scaffold using 3D plotting system

In this paper, we design and fabricate a 3D scaffold using rapid prototyping (RP) technology for tissue engineering. The scaffold should have a three-dimensional interconnected pore network. We fabricate a polycaprolactone (PCL) scaffold with interconnecting pores and uniform porosity for cell ingrowth using a 3D plotting system. In order to keep the three dimensional shape under mechanical loading while implanted, we design an oscillating nozzle system to increase elastic modulus and yield strength of PCL ...     

利用杀菌剂防治松萎蔫病

松萎蔫病是一种非常复杂的病害。据报道,松材线虫(Bursaphelenchus xylophilus)及其携带的细菌诱导了该病,但是对于细菌的的作用尚存争议。笔者筛选出杀细菌剂进行了温室和林间防治松萎蔫病的实验。利用每株3年生赤松(Pinus densiflora)注射3 mg的恶喹酸,松萎蔫病防效达到71 %。利用恶喹酸或阿维菌素及两者混合物对大约20年生赤松的试验表明,3种处理均显示了很高的防效。以上结果证明伴生细菌是诱导松萎蔫病的必要因素,对松萎蔫病可利用杀细菌剂或杀细菌剂与杀线剂混合物进行防控。     

An Approach to Share Architectural Drawing Information and Document Information for Automated Code Checking System

The purpose of this study is to suggest a way of optimized managing and sharing information between standard architectural drawings and construction documents in Korea architectural industry for automated code checking system by linked STEP and XML. To archive this purpose, the authors have analyzed current research and technical development for STEP and XML link and developed a prototype system for sharing information between model based drawings and XML based construction documents. Finally, the authors have suggested practical use scenario of sharing information through linked STEP and XML using test case of automatic code checking. In the paper, the possibility of constructing integrated architectural computing environment through exchange and sharing of drawing information and external data for the whole building life-cycle, from the conceptual design stage to the construction and maintenance stage has been examined. Automated code checking through linked STEP and XML could be enhanced through col-laboration business, more completed code, improved building performance, and reduced construction costs.     

A DNA sequence alignment algorithm using quality information and a fuzzy inference method

DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods. In this paper, we propose a DNA sequence alignment that uses quality information and a fuzzy inference method developed based on characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information. In conventional algorithms, DNA sequence alignment scores are calculated by the global sequence alignment algorithm proposed by Needleman-Wunsch, which is established by using quality information of each DNA fragment. However, there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low, because only overall DNA sequence quality information are used. In our proposed method, an exact DNA sequence alignment can be achieved in spite of low quality of DNA fragment tips by improvement of conventional algorithms using quality information. Mapping score parameters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments. From the experiments by applying real genome data of National Center for Biotechnology Information, we could see that the proposed method is more efficient than conventional algorithms.     

Seismic identification of along-axis hydrothermal flow on the East Pacific Rise

Hydrothermal circulation at the axis of mid-ocean ridges affects the chemistry of the lithosphere and overlying ocean, supports chemosynthetic biological communities and is responsible for significant heat transfer from the lithosphere to the ocean. It is commonly thought that flow in these systems is oriented across the ridge axis, with recharge occurring along off-axis faults, but the structure and scale of hydrothermal systems are usually inferred from thermal and geochemical models constrained by the geophysical setting, rather than direct observations. The presence of microearthquakes may shed light on hydrothermal pathways by revealing zones of thermal cracking where cold sea water extracts heat from hot crustal rocks, as well as regions where magmatic and tectonic stresses create fractures that increase porosity and permeability. Here we show that hypocentres beneath a well-studied hydrothermal vent field on the East Pacific Rise cluster in a vertical pipe-like zone near a small axial discontinuity, and in a band that lies directly above the axial magma chamber. The location of the shallow pipe-like cluster relative to the distribution and temperature of hydrothermal vents along this section of the ridge suggests that hydrothermal recharge may be concentrated there as a consequence of the permeability generated by tectonic fracturing. Furthermore, we interpret the band of seismicity above the magma chamber as a zone of hydrothermal cracking, which suggests that hydrothermal circulation may be strongly aligned along the ridge axis. We conclude that models that suggest that hydrothermal cells are oriented across-axis, with diffuse off-axis recharge zones, may not apply to the fast-spreading East Pacific Rise.     

Control of plant germline proliferation by SCF(FBL17) degradation of cell cycle inhibitors

Flowering plants possess a unique reproductive strategy, involving double fertilization by twin sperm cells. Unlike animal germ lines, the male germ cell lineage in plants only forms after meiosis and involves asymmetric division of haploid microspores, to produce a large, non-germline vegetative cell and a germ cell that undergoes one further division to produce the twin sperm cells. Although this switch in cell cycle control is critical for sperm cell production and delivery, the underlying molecular mechanisms are unknown. Here we identify a novel F-box protein of Arabidopsis thaliana, designated FBL17 (F-box-like 17), that enables this switch by targeting the degradation of cyclin-dependent kinase A;1 inhibitors specifically in male germ cells. We show that FBL17 is transiently expressed in the male germ line after asymmetric division and forms an SKP1-Cullin1-F-box protein (SCF) E3 ubiquitin ligase complex (SCF(FBL17)) that targets the cyclin-dependent kinase inhibitors KRP6 and KRP7 for proteasome-dependent degradation. Accordingly, the loss of FBL17 function leads to the stabilization of KRP6 and inhibition of germ cell cycle progression. Our results identify SCF(FBL17) as an essential male germ cell proliferation complex that promotes twin sperm cell production and double fertilization in flowering plants.     

Sojucktang induces apoptosis via loss of mitochondrial membrane potential and caspase-3 activation in KLE human endometrial cancer cells

Sojucktang （SJT） has long been used for the treatment of endometrial diseases in Korea. However, the mechanisms responsible for the SJT-induced apoptosis in endometrial cancer cells remain unclear. In the present study, SJT was demonstrated to show cytotoxic effect and induce apoptotic cell death via mitochondrial regulation in KLE endometrial cancer cells. Linderae Radix, Glycyrrhizae Radix, Zedoariae Rhizoma, Trogopterorum Faeces and Agelicae Gigantis Radix were found to be the potent constituent herbs of SJT to significantly decrease the viability of KLE cells by a tetra zolium salt （XTT） assay. Apoptotic bodies were observed in SJT-treated KLE cells by 4′-6-diamidino-2-phenylindole （DAPI） and TdT-mediated-dUTP nick-end labeling （TUNEL） assay. SJT also increased sub-G1 DNA contents of the cell cycle undergoing apoptosis in a dose-dependent manner. Furthermore, it was observed that SJT activated caspase-3 and cleaved poly （ADP-ribose） polymerase （PARP）, and decreased mitochondrial membrane potential in a dose-dependent manner. Taken together, this study shows that SJT exerts anti-tumor activity against KLE endometrial cancer cells via mitochondrial dependent apoptosis induction.     

AOP event manager in open service gateway 〖WT5"HZ〗Abstract:〖WT5"BZ〗 〖WT5”HZ〗Key words:〖WT5”BZ〗

The Open Service Gateway Initiative (OSGi) has played an important role in ubiquitous environments that support interoperability among embedded devices, such as home appliances and network devices. However, the OSGi does not have a common event mechanism yet, and it is difficult to communicate among services asynchronously. In the present work, a common event manager, AspectOriented Event Manager (AOEM), was designed on an OSGi framework. AOEM supports services to generate and provide notification of events. This paper presents the implementation of AOEM as an OSGi bundle with AspectJ. The experiment on transferring between device service and application service demonstrate that AOEM provides good abstraction of the services and convenience.     

A renormalization group approach to crowd psychology and inter-group coupling in social many-body systems

By adopting majority rule within a renormalization group approach, we can show that the strength of inter-group interaction in a social system either grows or shrinks monotonically with increasing group size, depending on the initial coupling strength of individuals in the group. This contrasts with the findings of previous studies in which the strength of the interaction grows with group size regardless of the initial strength. Our approach clearly demonstrates that the phenomena of crowd psychology, such as an extreme anti-reaction between different ethnic or ideological groups, could be a consequence of the many-particle nature of social systems when the initial strength of the interaction is larger than a critical value. The effect of neutral opinion holders is critically examined using the spin-one Ising model. The critical size of the population of neutral opinion holders, that can prevent crowd polarization, depends on the block spin rule.