Search results for: Kevin Chai Tshun Chuan

Authors: Hsuan-Chia Yang, Yan-Jhih Haung, Yu-Chuan Li

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Researchers of drug-drug interaction alert systems have often suggested that there were high overridden rate for alerts and also too false alerts. However, research about decreasing false alerts is scant. Therefore, the aim of this article attempts to proactive identification of false alert for drug-drug interaction and provide solution to decrease false alerts. This research involved retrospective analysis prescribing database and calculated false alert rate by using MYSQL and JAVA. Results of this study showed 17% of false alerts and the false alert rate in the hospitals (37%) was more than in the clinics. To conclude, this study described the importance that drug-drug interaction alert system should not only detect drug name but also detect frequency or route, as well as in providing solution to decrease false alerts.

Keywords: drug-drug interaction, proactive identification, false alert

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Authors: Jobby K. Chacko, Deepu Oommen, Kevin K. Mathew, Noble Sunny, N. Babu

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A new cost effective, eye controlled method was introduced to guide and control a wheel chair for disable people, based on Electrooculography (EOG). The guidance and control is effected by eye ball movements within the socket. The system consists of a standard electric wheelchair with an on-board microcontroller system attached. EOG is a new technology to sense the eye signals for eye movements and these signals are captured using electrodes, signal processed such as amplification, noise filtering, and then given to microcontroller which drives the motors attached with wheel chair for propulsion. This technique could be very useful in applications such as mobility for handicapped and paralyzed persons.

Keywords: Electrooculography, Microcontroller, Signal processing, Wheelchair.

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Authors: Shuen-Tai Wang, Ying-Chuan Chen, Hsi-Ya Chang

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The rapid improvement of the microprocessor and network has made it possible for the PC cluster to compete with conventional supercomputers. Lots of high throughput type of applications can be satisfied by using the current desktop PCs, especially for those in PC classrooms, and leave the supercomputers for the demands from large scale high performance parallel computations. This paper presents our development on enabling an automated deployment mechanism for cluster computing to utilize the computing power of PCs such as reside in PC classroom. After well deployment, these PCs can be transformed into a pre-configured cluster computing resource immediately without touching the existing education/training environment installed on these PCs. Thus, the training activities will not be affected by this additional activity to harvest idle computing cycles. The time and manpower required to build and manage a computing platform in geographically distributed PC classrooms also can be reduced by this development.

Keywords: PC cluster, automated deployment, cluster computing, PC classroom.

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Authors: Chang-Hsing Lee, Cheng-Chang Lien, Chin-Chuan Han

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In this paper, an edge-strength guided multiscale retinex (EGMSR) approach will be proposed for color image contrast enhancement. In EGMSR, the pixel-dependent weight associated with each pixel in the single scale retinex output image is computed according to the edge strength around this pixel in order to prevent from over-enhancing the noises contained in the smooth dark/bright regions. Further, by fusing together the enhanced results of EGMSR and adaptive multiscale retinex (AMSR), we can get a natural fused image having high contrast and proper tonal rendition. Experimental results on several low-contrast images have shown that our proposed approach can produce natural and appealing enhanced images.

Keywords: Image Enhancement, Multiscale Retinex, Image Fusion.

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Authors: Yi-Ting Mai, Chun-Chuan Yang, Cheng-Jung Wen

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IEEE 802.16 is a new wireless technology standard, it has some advantages, including wider coverage, higher bandwidth, and QoS support. As the new wireless technology for last mile solution, there are designed two models in IEEE 802.16 standard. One is PMP (point to multipoint) and the other is Mesh. In this paper we only focus on IEEE 802.16 Mesh model. According to the IEEE 802.16 standard description, Mesh model has two scheduling modes, centralized and distributed. Considering the pros and cons of the two scheduling, we present the combined scheduling QoS framework that the BS (Base Station) controls time frame scheduling and selects the shortest path from source to destination directly. On the other hand, we propose the Expedited Queue mechanism to cut down the transmission time. The EQ mechanism can reduce a lot of end-to-end delay in our QoS framework. Simulation study has shown that the average delay is smaller than contrasts. Furthermore, our proposed scheme can also achieve higher performance.

Keywords: IEEE 802.16 Mesh, Scheduling, Expedited Queue, QoS.

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Authors: Wan Chian Li, Justie Su-Tzu Juan, Yi-Chun Wang, Shu-Chuan Chen

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The evolutionary tree is an important topic in bioinformation. In 2006, Chen and Lindsay proposed a new method to build the mixture tree from DNA sequences. Mixture tree is a new type evolutionary tree, and it has two additional information besides the information of ordinary evolutionary tree. One of the information is time parameter, and the other is the set of mutated sites. In 2008, Lin and Juan proposed an algorithm to compute the distance between two mixture trees. Their algorithm computes the distance with only considering the time parameter between two mixture trees. In this paper, we proposes a method to measure the similarity of two mixture trees with considering the set of mutated sites and develops two algorithm to compute the distance between two mixture trees. The time complexity of these two proposed algorithms are O(n2 × max{h(T1), h(T2)}) and O(n2), respectively

Keywords: evolutionary tree, mixture tree, mutated site, distance.

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Authors: Chai Mingming, Li Lei, Lu Xiaoxia

Abstract:

In this paper, the mechanism of stratified liquids’ mixing in a cylinder is investigated. It is focused on the effects of Rayleigh-Taylor Instability (RTI) and rotation of the cylinder on liquid interface mixing. For miscible liquids, Planar Laser Induced Fluorescence (PLIF) technique is applied to record the concentration field for one liquid. Intensity of Segregation (IOS) is used to describe the mixing status. For immiscible liquids, High Speed Camera is adopted to record the development of the interface. The experiment of RTI indicates that it plays a great role in the mixing process, and meanwhile the large-scale mixing is triggered, and subsequently the span of the stripes decreases, showing that the mesoscale mixing is coming into being. The rotation experiments show that the spin-down process has a great role in liquid mixing, during which the upper liquid falls down rapidly along the wall and crashes into the lower liquid. During this process, a lot of interface instabilities are excited. Liquids mix rapidly in the spin-down process. It can be concluded that no matter what ways have been adopted to speed up liquid mixing, the fundamental reason is the interface instabilities which increase the area of the interface between liquids and increase the relative velocity of the two liquids.

Keywords: Interface instability, liquid mixing, Rayleigh-Taylor Instability, spin-down process, spin-up process.

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Authors: Chin-Hung Li, Te-Ming Chen, Ying-Chuan Chen, Shuen-Tai Wang

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This paper proposes a new approach to offer a private cloud service in HPC clusters. In particular, our approach relies on automatically scheduling users- customized environment request as a normal job in batch system. After finishing virtualization request jobs, those guest operating systems will dismiss so that compute nodes will be released again for computing. We present initial work on the innovative integration of HPC batch system and virtualization tools that aims at coexistence such that they suffice for meeting the minimizing interference required by a traditional HPC cluster. Given the design of initial infrastructure, the proposed effort has the potential to positively impact on synergy model. The results from the experiment concluded that goal for provisioning customized cluster environment indeed can be fulfilled by using virtual machines, and efficiency can be improved with proper setup and arrangements.

Keywords: Cloud Computing, HPC Cluster, Private Cloud, Virtualization

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Authors: Yung-Chuan Lee, Shahram Rahimi, Bidyut Gupta

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In this paper, we introduce an mobile agent framework with proactive load balancing for ambient intelligence (AmI) environments. One of the main obstacles of AmI is the scalability in which the openness of AmI environment introduces dynamic resource requirements on agencies. To mediate this scalability problem, our framework proposes a load balancing module to proactively analyze the resource consumption of network bandwidth and preferred agencies to suggest the optimal communication method to its user. The framework generally formulates an AmI environment that consists of three main components: (1) mobile devices, (2) hosts or agencies, and (3) directory service center (DSC). A preliminary implementation was conducted with NetLogo and the experimental results show that the proposed approach provides enhanced system performance by minimizing the network utilization to provide users with responsive services.

Keywords: Ambient intelligence, load balancing, multiagent systems, ubiquitous computing.

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Authors: Kevin Fong-Rey Liu, Ken Yeh, Cheng-Wu Chen, Han-Hsi Liang

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This paper proposes the use of Bayesian belief networks (BBN) as a higher level of health risk assessment for a dumping site of lead battery smelter factory. On the basis of the epidemiological studies, the actual hospital attendance records and expert experiences, the BBN is capable of capturing the probabilistic relationships between the hazardous substances and their adverse health effects, and accordingly inferring the morbidity of the adverse health effects. The provision of the morbidity rates of the related diseases is more informative and can alleviate the drawbacks of conventional methods.

Keywords: Bayesian belief networks, lead battery smelter factory, health risk assessment.

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Authors: Justice K. Owusu-Ansah, Kevin O'Connor

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This research explores the links between physical development and transportation infrastructure around Kumasi, Ghana. It utilizes census data as well as fieldwork and interviews carried out during July and December 2005. The results suggest that there is a weak association between transportation investments and physical development, and that recent housing has generally occurred in poorly accessible locations. Road investments have generally followed physical expansion rather than the reverse. Hence policies designed to manage the fast growth now occurring around Ghanaian cities should not focus exclusively on improving transportation infrastructure but also strengthening the underlying the traditional land management structures and the official land administrative institutions that operate within those structures.

Keywords: Housing, Kumasi, population, physical development, transportation, villages.

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Authors: Cheng-Hsien Chang, Jyi-Tsong Lin, Po-Hsieh Lin, Hung-Pei Hsu, Chan-Hsiang Chang, Ming-Tsung Shih, Shih-Chuan Tseng, Min-Yan Lin

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In this paper, we have proposed a novel FinFET with extended body under the poly gate, which is called EB-FinFET, and its characteristic is demonstrated by using three-dimensional (3-D) numerical simulation. We have analyzed and compared it with conventional FinFET. The extended body height dependence on the drain induced barrier lowering (DIBL) and subthreshold swing (S.S) have been also investigated. According to the 3-D numerical simulation, the proposed structure has a firm structure, an acceptable short channel effect (SCE), a reduced series resistance, an increased on state drain current (I on) and a large normalized I DS. Furthermore, the structure can also improve corner effect and reduce self-heating effect due to the extended body. Our results show that the EBFinFET is excellent for nanoscale device.

Keywords: SOI, FinFET, tri-gate, self-heating effect.

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Authors: Chien-Sheng Chen, Szu-Lin Su, Chuan-Der Lu

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Wireless location is to determine the mobile station (MS) location in a wireless cellular communications system. When fewer base stations (BSs) may be available for location purposes or the measurements with large errors in non-line-of-sight (NLOS) environments, it is necessary to integrate all available heterogeneous measurements to achieve high location accuracy. This paper illustrates a hybrid proposed schemes that combine time of arrival (TOA) at three BSs and angle of arrival (AOA) information at the serving BS to give a location estimate of the MS. The proposed schemes mitigate the NLOS effect simply by the weighted sum of the intersections between three TOA circles and the AOA line without requiring a priori information about the NLOS error. Simulation results show that the proposed methods can achieve better accuracy when compare with Taylor series algorithm (TSA) and the hybrid lines of position algorithm (HLOP).

Keywords: Time of arrival (TOA), angle of arrival (AOA), non-line-of-sight (NLOS).

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Authors: Ya-Hui Lee, Ching-Yi Lu, Hui-Chuan Wei

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The purpose of this research was to explore the relation between proactive coping and well-being of middle-aged adults. We conducted survey research that with t-test, one way ANOVA, Pearson correlation and stepwise multiple regression to analyze. This research drew on a sample of 395 participants from the senior learning centers of Taiwan. The results provided the following findings: 1.The participants from different residence areas associated significant difference with proactive coping, but not with well-being. 2. The participants’ perceived of financial level associated significant difference with both proactive coping and well-being. 3. There was significant difference between participants’ income and well-being. 4. The proactive coping was positively correlated with well-being. 5. From stepwise multiple regression analysis showed that two dimensions of proactive coping had positive predictability. Finally, these results of this study can be provided as references for designing older adult educational programs in Taiwan.

Keywords: Middle-age adults, learners, proactive coping, well-being.

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Authors: Chuan Li, Ming Liang, Qibing Yu

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To improve the dynamics response of the vehicle passive suspension, a two-terminal mass is suggested to connect in parallel with the suspension strut. Three performance criteria, tire grip, ride comfort and suspension deflection, are taken into consideration to optimize the suspension parameters. However, the three criteria are conflicting and non-commensurable. For this reason, the Chebyshev goal programming method is applied to find the best tradeoff among the three objectives. A simulation case is presented to describe the multi-objective optimization procedure. For comparison, the Chebyshev method is also employed to optimize the design of a conventional passive suspension. The effectiveness of the proposed design method has been clearly demonstrated by the result. It is also shown that the suspension with a two-terminal mass in parallel has better performance in terms of the three objectives.

Keywords: Vehicle, passive suspension, two-terminal mass, optimization, Chebyshev goal programming

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Authors: Souleymane Oumtanaga, Prosper Kimou, Kouadio Gaza Kevin

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The security of their network remains the priorities of almost all companies. Existing security systems have shown their limit; thus a new type of security systems was born: honeypots. Honeypots are defined as programs or intended servers which have to attract pirates to study theirs behaviours. It is in this context that the leurre.com project of gathering about twenty platforms was born. This article aims to specify a model of honeypots attack. Our model describes, on a given platform, the evolution of attacks according to theirs hours. Afterward, we show the most attacked services by the studies of attacks on the various ports. It is advisable to note that this article was elaborated within the framework of the research projects on honeyspots within the LABTIC (Laboratory of Information Technologies and Communication).

Keywords: Honeypot, networks, attack, leurrecom, computer network

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Authors: Jenn-Yih Chen, Bean-Yin Lee, Yuan-Chuan Hsu, Jui-Cheng Lin, Kuang-Chyi Lee

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In this paper, a sliding mode control method based on the passivity approach is proposed to control the position of surface-mounted permanent magnet synchronous motors (PMSMs). Firstly, the dynamics of a PMSM was proved to be strictly passive. The position controller with an adaptive law was used to estimate the load torque to eliminate the chattering effects associated with the conventional sliding mode controller. The stability analysis of the overall position control system was carried out by adopting the passivity theorem instead of Lyapunov-type arguments. Finally, experimental results were provided to show that the good position tracking can be obtained, and exhibit robustness in the variations of the motor parameters and load torque disturbances.

Keywords: Adaptive law, passivity theorem, permanent magnet synchronous motor, sliding mode control.

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Authors: Ying-Chuan Chen, Shuen-Tai Wang

Abstract:

Security is an interesting and significance issue for popular virtual platforms, such as virtualization cluster and cloud platforms. Virtualization is the powerful technology for cloud computing services, there are a lot of benefits by using virtual machine tools which be called hypervisors, such as it can quickly deploy all kinds of virtual Operating Systems in single platform, able to control all virtual system resources effectively, cost down for system platform deployment, ability of customization, high elasticity and high reliability. However, some important security problems need to take care and resolved in virtual platforms that include terrible viruses, evil programs, illegal operations and intrusion behavior. In this paper, we present useful Intrusion Detection Mechanism (IDM) software that not only can auto to analyze all system-s operations with the accounting journal database, but also is able to monitor the system-s state for virtual platforms.

Keywords: security, cluster, cloud, virtualization, virtual machine, virus, intrusion detection

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Authors: Shuen-Tai Wang, Chin-Hung Li, Ying-Chuan Chen

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In recent years there has been renewal of interest in the relation between Green IT and Cloud Computing. The growing use of computers in cloud platform has caused marked energy consumption, putting negative pressure on electricity cost of cloud data center. This paper proposes an effective mechanism to reduce energy utilization in cloud computing environments. We present initial work on the integration of resource and power management that aims at reducing power consumption. Our mechanism relies on recalling virtualization services dynamically according to user-s virtualization request and temporarily shutting down the physical machines after finish in order to conserve energy. Given the estimated energy consumption, this proposed effort has the potential to positively impact power consumption. The results from the experiment concluded that energy indeed can be saved by powering off the idling physical machines in cloud platforms.

Keywords: Green IT, Cloud Computing, virtualization, power consumption.

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Authors: Hung-Pei Hsu, Jyi-Tsong Lin, Po-Hsieh Lin, Cheng-Hsien Chang, Ming-Tsung Shih, Chan-Hsiang Chang, Shih-Chuan Tseng, Min-Yan Lin, Shih-Wen Hsu

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In this paper, we propose a novel metal oxide semiconductor field effect transistor with L-shaped channel structure (LMOS), and several type of L-shaped structures are also designed, studied and compared with the conventional MOSFET device for the same average gate length (Lavg). The proposed device electrical characteristics are analyzed and evaluated by three dimension (3-D) ISE-TCAD simulator. It can be confirmed that the LMOS devices have higher on-state drain current and both lower drain-induced barrier lowering (DIBL) and subthreshold swing (S.S.) than its conventional counterpart has. In addition, the transconductance and voltage gain properties of the LMOS are also improved.

Keywords: Average gate length (Lavg), drain-induced barrier lowering (DIBL), L-shaped channel MOSFET (LMOS), subthreshold swing (S.S.).

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Authors: Kevin McDaid, Simon P. Wilson

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Software developed for a specific customer under contract typically undergoes a period of testing by the customer before acceptance. This is known as user acceptance testing and the process can reveal both defects in the system and requests for changes to the product. This paper uses nonhomogeneous Poisson processes to model a real user acceptance data set from a recently developed system. In particular a split Poisson process is shown to provide an excellent fit to the data. The paper explains how this model can be used to aid the allocation of resources through the accurate prediction of occurrences both during the acceptance testing phase and before this activity begins.

Keywords: User acceptance testing. Software reliability growth modelling. Split Poisson process. Bayesian methods.

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Authors: Congmin Z. Xie, Terry Healy, Peter Robinson, Kevin Stewart

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An HPLC-UV analytical method was developed to determine ethylenediaminetetraacetic acid (EDTA) in dairy wastewater and surface water. The optimizing separation was achieved by reversed–phase ion-pair liquid chromatography on a C18 column using methanol as mobile phase solvent, tetrabutylammonium bromide as the ion-pair reagent in pH 3.3 formate buffer solution at a flow rate of 0.9 mL min-1 with a UV detector at 265 nm. No interference of Ca, Mg or NO3 - was detected. Method performance was evaluated in terms of linearity, repeatability and reproducibility. The method detection limit was 5 μg L-1. The contents of EDTA in dairy effluents were 72 ~ 261 μg L-1 at a large dairy site. A change of EDTA concentration was observed downstream of the dairy effluent discharge, but this was well under the predicted no effect concentration for aquatic ecosystem.

Keywords: Dairy wastewater, EDTA, HPLC, surface water.

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Authors: Mohammad Syuhaimi Ab-Rahman, Boon Chuan Ng, Norshilawati Mohamad Ibrahim, Sahbudin Shaari

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This paper describes the development of a 16-ports optical code division multiple access (OCDMA) encoder prototype based on Arrayed Waveguide Grating (AWG) and optical switches. It is potentially to provide a high security for data transmission due to all data will be transmitted in binary code form. The output signals from AWG are coded with a binary code that given to an optical switch before it signal modulate with the carrier and transmitted to the receiver. The 16-ports encoder used 16 double pole double throw (DPDT) toggle switches to control the polarization of voltage source from +5 V to -5 V for 16 optical switches. When +5 V is given, the optical switch will give code '1' and vice versa. The experimental results showed the insertion loss, crosstalk, uniformity, and optical signal-noise-ratio (OSNR) for the developed prototype are <12 dB, 9.77 dB, <1.63dB, and ≥20dB.

Keywords: AWG, encoder, OCDMA, optical switch.

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Authors: Jia-Chuan Lin, Meng-Kai Hsu, Hsi-Ting Hou, Sin-Hong Liu

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The electrolyte stirring method of anodization etching process for manufacturing porous silicon (PS) is reported in this work. Two experimental setups of nature air stirring (PS-ASM) and electrolyte stirring (PS-ESM) are employed to clarify the influence of stirring mechanisms on electrochemical etching process. Compared to traditional fabrication without any stirring apparatus (PS-TM), a large plateau region of PS surface structure is obtained from samples with both stirring methods by the 3D-profiler measurement. Moreover, the light emission response is also improved by both proposed electrolyte stirring methods due to the cycling force in electrolyte could effectively enhance etch-carrier distribution while the electrochemical etching process is made. According to the analysis of statistical calculation of photoluminescence (PL) intensity, lower standard deviations are obtained from PS-samples with studied stirring methods, i.e. the uniformity of PL-intensity is effectively improved. The calculated deviations of PL-intensity are 93.2, 74.5 and 64, respectively, for PS-TM, PS-ASM and PS-ESM.

Keywords: Porous Silicon, Photoluminescence, Uniformity Carrier Stirring Method

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Authors: Zane Turner, Kevin Labille, Susan Gauch

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Sentiment analysis is a broad and expanding field that aims to extract and classify opinions from textual data. Lexicon-based approaches are based on the use of a sentiment lexicon, i.e., a list of words each mapped to a sentiment score, to rate the sentiment of a text chunk. Our work focuses on predicting stock price change using a sentiment lexicon built from financial conference call logs. We present a method to generate a sentiment lexicon based upon an existing probabilistic approach. By using a domain-specific lexicon, we outperform traditional techniques and demonstrate that domain-specific sentiment lexicons provide higher accuracy than generic sentiment lexicons when predicting stock price change.

Keywords: Lexicon, sentiment analysis, stock movement prediction., computational finance.

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Authors: Zane Turner, Kevin Labille, Susan Gauch

Abstract:

Sentiment analysis is a broad and expanding field that aims to extract and classify opinions from textual data. Lexicon-based approaches are based on the use of a sentiment lexicon, i.e., a list of words each mapped to a sentiment score, to rate the sentiment of a text chunk. Our work focuses on predicting stock price change using a sentiment lexicon built from financial conference call logs. We introduce a method to generate a sentiment lexicon based upon an existing probabilistic approach. By using a domain-specific lexicon, we outperform traditional techniques and demonstrate that domain-specific sentiment lexicons provide higher accuracy than generic sentiment lexicons when predicting stock price change.

Keywords: Computational finance, sentiment analysis, sentiment lexicon, stock movement prediction.

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Authors: Ruwaida Abdul Rasid, Kevin J. Hughes, Peter J. Heggs, Mohamed Pourkashanian

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Heightened concerns over the amount of carbon emitted from coal-related processes are generating shifts to the application of biomass. In co-gasification, where coal is gasified along with biomass, the biomass may be fed together with coal (cofeeding) or an independent biomass gasifier needs to be integrated with the coal gasifier. The main aim of this work is to evaluate the biomass introduction methods in coal co-gasification. This includes the evaluation of biomass concentration input (B0 to B100) and its gasification performance. A process model is developed and simulated in Aspen HYSYS, where both coal and biomass are modelled according to its ultimate analysis. It was found that the syngas produced increased with increasing biomass content for both co-feeding and independent schemes. However, the heating values and heat duties decreases with biomass concentration as more CO2 are produced from complete combustion.

Keywords: Aspen HYSYS, biomass, coal, co-gasification modelling and simulation.

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Authors: Wei-Wen Liu, Feng-Chuan Pan, Pei-Chi Wen, Sen-Ji Chen, Su-Hui Lin

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Nurses in an Armed Force Hospital (AFH) expose to stronger stress than those in a civil hospital, especially in an emergency department (ED). Ironically, stresses of these nurses received few if any attention in academic research in the past. This study collects 227 samples from the emergency departments of four armed force hospitals in central and southern Taiwan. The research indicates that the top five stressors are a massive casualty event, delayed physician support, overloads of routine work, overloads of assignments, and annoying paper work. Excessive work loading was found to be the primary source of stress. Nurses who were perceived to have greater stress levels were more inclined to deploy emotion-oriented approaches and more likely to seek job rotations. Professional stressors and problem-oriented approaches were positively correlated. Unlike other local studies, this study concludes that the excessive work-loading is more stressful in an AFH.

Keywords: Emergency nurse, Job stressor, Coping behavior, Armed force hospital.

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Authors: Chuan Li, Ming Liang

Abstract:

Oil debris signal generated from the inductive oil debris monitor (ODM) is useful information for machine condition monitoring but is often spoiled by background noise. To improve the reliability in machine condition monitoring, the high-fidelity signal has to be recovered from the noisy raw data. Considering that the noise components with large amplitude often have higher frequency than that of the oil debris signal, the integral transform is proposed to enhance the detectability of the oil debris signal. To cancel out the baseline wander resulting from the integral transform, the empirical mode decomposition (EMD) method is employed to identify the trend components. An optimal reconstruction strategy including both de-trending and de-noising is presented to detect the oil debris signal with less distortion. The proposed approach is applied to detect the oil debris signal in the raw data collected from an experimental setup. The result demonstrates that this approach is able to detect the weak oil debris signal with acceptable distortion from noisy raw data.

Keywords: Integral transform, empirical mode decomposition, oil debris, signal processing, detection.

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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