• Title/Summary/Keyword: Vector Analysis

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Effect of Butyrate on Adenovirus-Mediated Herpes Simplex Virus Thymidine Kinase Gene Therapy (Butyrate가 Adenoviral Vector로 이입한 Herpes Simplex Virus Thymidine Kinase 유전자치료에 미치는 영향)

  • Park, Jae-Yong;Kim, Jeong-Ran;Chang, Hee-Jin;Kim, Chang-Ho;Park, Jae-Ho;Jung, Tae-Hoon
    • Tuberculosis and Respiratory Diseases
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    • v.45 no.3
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    • pp.587-595
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    • 1998
  • Background: Recombinant adenovirus hold promise as vectors to carry therapeutic genes for several reasons: 1) they can infect both dividing and non-dividing cells; 2) they have the ability to directly transduce tissues in vivo; 3) they can easily be produced in high titer; and 4) they have an established record of safety as vaccination material. However, one of the major limitation in the use of adenoviruses is that transgene expression is quite short because adenovirusees insert their DNA genome episomally rather than by chromosomal integration, and an immune response against the virus destroys cells expressing the therapeutic gene. Since sodium butyrate has been reported to induce adenovirus-mediated gene expression, we hypothesized that treatment of tumor cells, transduced with herpes simples virus thymidine kinase(HSVtk) gene using adenoviral vector, with butyrate could augment the effect of gene therapy. Methods: We transduced HSVtk gene, driven by the cytomegalovirus promoter, into REN cell line(human mesothelioma cell line). Before proceeding with the comparison of HSVtk/ganciclovir mediated bystander killing, we evaluated the effect of butyrate on the growth of tumor cells in order to rule out a potential antitumor effect of butyrate alone, and also on expression of HSVtk gene by Western blot analysis. Then we determined the effects of butyrate on bystander-mediated cell killing in vitro. Results: There was no inhibition of growth of cells exposed to butyrate for 24 hours at a concentration of 1.5mM/L. Toxic effects were seen when the concentration of butyrate was greater than 2.0mM/L. Gene expression was more stable and bystander effect was augmented by butyrate treatment of a concentration of 1.5mM/L. Conclusion: These results provide evidence that butyrate can augment the efficiency of cell killing with HSVtk/GCV system by inducing transgene expression and may thus by a promising new approach to improve responses in gene therapy using adenoviral vectors.

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The development of transgenic maize expressing Actinobacillus pleuropneumoniae ApxIIA gene using Agrobacterium (아그로박테리움을 이용한 Actinobacillus pleuropneumoniae ApxIIA (ApxII toxin) 유전자 발현 옥수수 형질전환체 개발)

  • Kim, Hyun-A;Yoo, Han-Sang;Yang, Moon-Sik;Kwon, Suk-Yoon;Kim, Jin-Seog;Choi, Pil-Son
    • Journal of Plant Biotechnology
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    • v.37 no.3
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    • pp.313-318
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    • 2010
  • To develop edible vaccines for swine, the embryogenic calli (type II) derived from HiII genotype were inoculated with A. tumefaciens strain C58C1 containing the binary vector pMYV611, 613, 616, and V621, 622 and 623 respectively. Six of those vectors carry nptII gene which confers resistance to paromomycin and apxIIA gene producing ApxII toxin which is generated in various serum types of A. pleuropneumoniae as a target gene. The 4,120 callus clones for pMYV611, 5,959 callus clones for pMYV613, 7,581 callus clones for pMYV616, 52,329 callus clones for V621, 48,948 callus clones for V622, and 56,188 callus clones for V623 were inoculated. The frequency of positive response clone was confirmed into range of 2.3% - 4.4% for each vectors by NPTII ELISA kit assay, and the selected callus clones of them were finally 3 callus clones from pMYV611 (0.07%), 4 callus clones from pMYV613 (0.07%), 2 callus clones from pMYV616 (0.03%), 51 callus clones from V621 (0.1%), 72 callus clones from V622 (0.15%), and 102 callus clones from V623 (0.18%) respectively. From the selected callus clones of each binary vector, the integration of the apxIIA gene into maize genome was detected from 2 plants of pMYV613 and 2 plants of V623 by Southern blot analysis.

Improving the Accuracy of Document Classification by Learning Heterogeneity (이질성 학습을 통한 문서 분류의 정확성 향상 기법)

  • Wong, William Xiu Shun;Hyun, Yoonjin;Kim, Namgyu
    • Journal of Intelligence and Information Systems
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    • v.24 no.3
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    • pp.21-44
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    • 2018
  • In recent years, the rapid development of internet technology and the popularization of smart devices have resulted in massive amounts of text data. Those text data were produced and distributed through various media platforms such as World Wide Web, Internet news feeds, microblog, and social media. However, this enormous amount of easily obtained information is lack of organization. Therefore, this problem has raised the interest of many researchers in order to manage this huge amount of information. Further, this problem also required professionals that are capable of classifying relevant information and hence text classification is introduced. Text classification is a challenging task in modern data analysis, which it needs to assign a text document into one or more predefined categories or classes. In text classification field, there are different kinds of techniques available such as K-Nearest Neighbor, Naïve Bayes Algorithm, Support Vector Machine, Decision Tree, and Artificial Neural Network. However, while dealing with huge amount of text data, model performance and accuracy becomes a challenge. According to the type of words used in the corpus and type of features created for classification, the performance of a text classification model can be varied. Most of the attempts are been made based on proposing a new algorithm or modifying an existing algorithm. This kind of research can be said already reached their certain limitations for further improvements. In this study, aside from proposing a new algorithm or modifying the algorithm, we focus on searching a way to modify the use of data. It is widely known that classifier performance is influenced by the quality of training data upon which this classifier is built. The real world datasets in most of the time contain noise, or in other words noisy data, these can actually affect the decision made by the classifiers built from these data. In this study, we consider that the data from different domains, which is heterogeneous data might have the characteristics of noise which can be utilized in the classification process. In order to build the classifier, machine learning algorithm is performed based on the assumption that the characteristics of training data and target data are the same or very similar to each other. However, in the case of unstructured data such as text, the features are determined according to the vocabularies included in the document. If the viewpoints of the learning data and target data are different, the features may be appearing different between these two data. In this study, we attempt to improve the classification accuracy by strengthening the robustness of the document classifier through artificially injecting the noise into the process of constructing the document classifier. With data coming from various kind of sources, these data are likely formatted differently. These cause difficulties for traditional machine learning algorithms because they are not developed to recognize different type of data representation at one time and to put them together in same generalization. Therefore, in order to utilize heterogeneous data in the learning process of document classifier, we apply semi-supervised learning in our study. However, unlabeled data might have the possibility to degrade the performance of the document classifier. Therefore, we further proposed a method called Rule Selection-Based Ensemble Semi-Supervised Learning Algorithm (RSESLA) to select only the documents that contributing to the accuracy improvement of the classifier. RSESLA creates multiple views by manipulating the features using different types of classification models and different types of heterogeneous data. The most confident classification rules will be selected and applied for the final decision making. In this paper, three different types of real-world data sources were used, which are news, twitter and blogs.

First Report of Soybean Dwarf Virus on Soybean(Glycine max) in Korea (콩(Glycine max)에서 콩위축바이러스(Soybean dwarf virus)의 최초 발생보고)

  • Kim, Sang-Mok;Lee, Jae-Bong;Lee, Yeong-Hoon;Choi, Se-Hoon;Choi, Hong-Soo;Park, Jin-Woo;Lee, Jun-Seong;Lee, Gwan-Seok;Moon, Jung-Kyung;Moon, Jae-Sun;Lee, Key-Woon;Lee, Su-Heon
    • Research in Plant Disease
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    • v.12 no.3
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    • pp.213-220
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    • 2006
  • In year 2003, a soybean(Glycine max) sample showing severe dwarfing symptom was collected from a farmers' field in Cheongsong in Korea. The results from the diagnosis of the sample by RT-PCR revealed that it was infected by Soybean dwarf virus(SbDV), SbDV-L81. This study could be the first report of the occurrence of the virus in Korea. To further characterize the virus, the partial nucleotide sequence of the genomic RNA of SbDV-L81 was determined by RT-PCR using species-specific primers. The sequences were analyzed and subsequently compared to previously characterized strains of SbDV based on the pattern of symptom expression and vector specificities. The intergenic region between ORF 2 and 3 and the coding regions of ORF 2, 3 and 4 were relatively similar to those of dwarfing strains(SbDV-DS and DP) rather than those of yellowing strains(SbDV-YS and YP). Likewise, the result from the analysis of 5'-half of the coding region of ORF5 indicated that SbDV-L81 was closely related to strains(SbDV-YP and DP) transmitted by Acyrthosiphon pisum. These data from the natural symptom and the comparisons of five regions of nucleotide sequences of SbDV suggested that SbDV-L81 might be closely related SbDV-DP.

Recombination and Expression of VP1 Gene of Infectious Pancreatic Necrosis Virus DRT Strain in a Baculovirus, Hyphantria cunea Nuclear Polyhedrosis Virus (전염성 췌장괴저바이러스 DRT Strain VP1유전자의 Baculovirus Hyphantria cunea Nuclear Polyhedrosis Virus에 재조합과 발현)

  • Lee, Hyung-Hoan;Chang, Jae-Hyeok;Chung, Hye-Kyung;Cha, Sung-Chul
    • The Journal of Korean Society of Virology
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    • v.27 no.2
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    • pp.239-255
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    • 1997
  • Expression of the cDNA of the VP1 gene on the genome RNA B segment of infectious pancreatic necrosis virus (IPNV) DRT strain in E. coli and a recombinant baculovirus were carried out. The VP1 gene in the pMal-pol clone (Lee et al. 1995) was cleaved with XbaI and transferred into baculovirus transfer vector, pBacPAK9 and it was named pBacVP1 clone. The VP1 gene in the pBacVP1 clone was double-digested with SacI and PstI and then inserted just behind T5 phage promoter and the $6{\times}His$ region of the pQE-3D expression vector, and it was called pQEVPl. Again, the $6{\times}$His-tagged VP1 DNA fragment in the pQEVP1 was cleaved with EcoRI and transferred into the VP1 site of the pBacVP1, resulting pBacHis-VP1 recombinant. The pBacHis-VP1 DNA was cotransfected with LacZ-Hyphantria cunea nuclear polyhedrosis virus (LacZ-HcNPV) DNA digested with Bsu361 onto S. frugiperda cells to make a recombinant virus. One VP1-gene inserted recombinant virus was selected by plaque assay. The recombinant virus was named VP1-HcNPV-1. The $6{\times}$His-tagged VP1 protein produced by the pQEVP1 was purified with Ni-NTA resin chromatography and analyzed by SDS-PAGE and Western blot analysis. The molecular weight of the VP1 protein was 94 kDa. The recombinant virus, VP1-HcNPV-1 did not form polyhedral inclusion bodies and expressed VP1 protein with 95 kDa in the infected S. frugiperda cells, which was detected by Western blot. The titer of the VP1-HcNPV-1 in the first infected cells was $2.0{\times}10^5\;pfu/ml$ at 7 days postinfection.

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Production of Transgenic Pigs with an Introduced Missense Mutation of the Bone Morphogenetic Protein Receptor Type IB Gene Related to Prolificacy

  • Zhao, Xueyan;Yang, Qiang;Zhao, Kewei;Jiang, Chao;Ren, Dongren;Xu, Pan;He, Xiaofang;Liao, Rongrong;Jiang, Kai;Ma, Junwu;Xiao, Shijun;Ren, Jun;Xing, Yuyun
    • Asian-Australasian Journal of Animal Sciences
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    • v.29 no.7
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    • pp.925-937
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    • 2016
  • In the last few decades, transgenic animal technology has witnessed an increasingly wide application in animal breeding. Reproductive traits are economically important to the pig industry. It has been shown that the bone morphogenetic protein receptor type IB (BMPR1B) A746G polymorphism is responsible for the fertility in sheep. However, this causal mutation exits exclusively in sheep and goat. In this study, we attempted to create transgenic pigs by introducing this mutation with the aim to improve reproductive traits in pigs. We successfully constructed a vector containing porcine BMPR1B coding sequence (CDS) with the mutant G allele of A746G mutation. In total, we obtained 24 cloned male piglets using handmade cloning (HMC) technique, and 12 individuals survived till maturation. A set of polymerase chain reactions indicated that 11 of 12 matured boars were transgene-positive individuals, and that the transgenic vector was most likely disrupted during cloning. Of 11 positive pigs, one (No. 11) lost a part of the terminator region but had the intact promoter and the CDS regions. cDNA sequencing showed that the introduced allele (746G) was expressed in multiple tissues of transgene-positive offspring of No.11. Western blot analysis revealed that BMPR1B protein expression in multiple tissues of transgene-positive $F_1$ piglets was 0.5 to 2-fold higher than that in the transgene-negative siblings. The No. 11 boar showed normal litter size performance as normal pigs from the same breed. Transgene-positive $F_1$ boars produced by No. 11 had higher semen volume, sperm concentration and total sperm per ejaculate than the negative siblings, although the differences did not reached statistical significance. Transgene-positive $F_1$ sows had similar litter size performance to the negative siblings, and more data are needed to adequately assess the litter size performance. In conclusion, we obtained 24 cloned transgenic pigs with the modified porcine BMPR1B CDS using HMC. cDNA sequencing and western blot indicated that the exogenous BMPR1B CDS was successfully expressed in host pigs. The transgenic pigs showed normal litter size performance. However, no significant differences in litter size were found between transgene-positive and negative sows. Our study provides new insight into producing cloned transgenic livestock related to reproductive traits.

Risk Assessment of Pine Tree Dieback in Sogwang-Ri, Uljin (울진 소광리 금강소나무 고사발생 특성 분석 및 위험지역 평가)

  • Kim, Eun-Sook;Lee, Bora;Kim, Jaebeom;Cho, Nanghyun;Lim, Jong-Hwan
    • Journal of Korean Society of Forest Science
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    • v.109 no.3
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    • pp.259-270
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    • 2020
  • Extreme weather events, such as heat and drought, have occurred frequently over the past two decades. This has led to continuous reports of cases of forest damage due to physiological stress, not pest damage. In 2014, pine trees were collectively damaged in the forest genetic resources reserve of Sogwang-ri, Uljin, South Korea. An investigation was launched to determine the causes of the dieback, so that a forest management plan could be prepared to deal with the current dieback, and to prevent future damage. This study aimedto 1) understand the topographic and structural characteristics of the area which experienced pine tree dieback, 2) identify the main causes of the dieback, and 3) predict future risk areas through the use of machine-learning techniques. A model for identifying risk areas was developed using 14 explanatory variables, including location, elevation, slope, and age class. When three machine-learning techniques-Decision Tree, Random Forest (RF), and Support Vector Machine (SVM) were applied to the model, RF and SVM showed higher predictability scores, with accuracies over 93%. Our analysis of the variable set showed that the topographical areas most vulnerable to pine dieback were those with high altitudes, high daily solar radiation, and limited water availability. We also found that, when it came to forest stand characteristics, pine trees with high vertical stand densities (5-15 m high) and higher age classes experienced a higher risk of dieback. The RF and SVM models predicted that 9.5% or 115 ha of the Geumgang Pine Forest are at high risk for pine dieback. Our study suggests the need for further investigation into the vulnerable areas of the Geumgang Pine Forest, and also for climate change adaptive forest management steps to protect those areas which remain undamaged.

The Role of MnSOD in the Mechanisms of Acquired Resistance to TNF (TNF에 대한 내성획득에서 MnSOD의 역할에 관한 연구)

  • Lee, Hyuk-Pyo;Yoo, Chul-Gyu;Kim, Young-Whan;Han, Sung-Koo;Shim, Young-Soo
    • Tuberculosis and Respiratory Diseases
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    • v.44 no.6
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    • pp.1353-1365
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    • 1997
  • Background : Tumor necrosis factor(TNF) has been considered as an important candidate for cancer gene therapy based on its potent anti-tumor activity. However, since the efficiency of current techniques of gene transfer is not satisfactory, the majority of current protocols is aiming the in vitro gene transfer to cancer cells and re-introducing genetically modified cancer cells to host. In the previous study, it was shown that TNF-sensitive cancer cells transfected with TNF-$\alpha$ cDNA would become highly resistant to TNF, and the probability was shown that the acquired resistance to TNF might be associated with synthesis of some protective protein. Understanding the mechanisms of TNF -resistance in TNF-$\alpha$ cDNA transfected cancer cells would be. an important step for improving the efficacy of cancer gene therapy as well as for better understandings of tumor biology. This study was designed to evaluate the role of MnSOD, an antioxidant enzyme, in the acquired resistance to TNF of TNF-$\alpha$ cDN A transfected cancer cells. Method : We transfected TNF-$\alpha$ c-DNA to WEHI164(murine fibrosarcoma cell line), NCI-H2058(human mesothelioma cell line), A549(human non-small cell lung cancer cell line), ME180(human cervix cancer cell line) cells using retroviral vector(pLT12SN(TNF)) and confirm the expression of TNF with PCR, ELISA, MIT assay. Then we determined the TNF resistance of TNF-$\alpha$ cDNA transfected cells(WEHI164-TNF, NCIH2058-TNF, A549-TNF, ME180-TNF) and the changes of MnSOD mRNA expressions with Northern blot analysis. Results : The MnSOD mRNA expressions of parental cells and genetically modified cells of WEHI164 and ME180 cells(both are naturally TNF sensitive) were not significantly different The MnSOD mRNA expressions of genetically modified cells of NCI-H2058 and A549(both are naturally TNF resistant) were higher than those of the parental cells, while those of parental cells with exogenous TNF were also elevated. Conclusion : The acquired resistance to TNF after TNF-$\alpha$ cDNA transfection may not be associated with the change in the MnSOD expression, but the difference in natural TNF sensitivity of each cell may be associated with the level of the MnSOD expression.

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Object Tracking Based on Exactly Reweighted Online Total-Error-Rate Minimization (정확히 재가중되는 온라인 전체 에러율 최소화 기반의 객체 추적)

  • JANG, Se-In;PARK, Choong-Shik
    • Journal of Intelligence and Information Systems
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    • v.25 no.4
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    • pp.53-65
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    • 2019
  • Object tracking is one of important steps to achieve video-based surveillance systems. Object tracking is considered as an essential task similar to object detection and recognition. In order to perform object tracking, various machine learning methods (e.g., least-squares, perceptron and support vector machine) can be applied for different designs of tracking systems. In general, generative methods (e.g., principal component analysis) were utilized due to its simplicity and effectiveness. However, the generative methods were only focused on modeling the target object. Due to this limitation, discriminative methods (e.g., binary classification) were adopted to distinguish the target object and the background. Among the machine learning methods for binary classification, total error rate minimization can be used as one of successful machine learning methods for binary classification. The total error rate minimization can achieve a global minimum due to a quadratic approximation to a step function while other methods (e.g., support vector machine) seek local minima using nonlinear functions (e.g., hinge loss function). Due to this quadratic approximation, the total error rate minimization could obtain appropriate properties in solving optimization problems for binary classification. However, this total error rate minimization was based on a batch mode setting. The batch mode setting can be limited to several applications under offline learning. Due to limited computing resources, offline learning could not handle large scale data sets. Compared to offline learning, online learning can update its solution without storing all training samples in learning process. Due to increment of large scale data sets, online learning becomes one of essential properties for various applications. Since object tracking needs to handle data samples in real time, online learning based total error rate minimization methods are necessary to efficiently address object tracking problems. Due to the need of the online learning, an online learning based total error rate minimization method was developed. However, an approximately reweighted technique was developed. Although the approximation technique is utilized, this online version of the total error rate minimization could achieve good performances in biometric applications. However, this method is assumed that the total error rate minimization can be asymptotically achieved when only the number of training samples is infinite. Although there is the assumption to achieve the total error rate minimization, the approximation issue can continuously accumulate learning errors according to increment of training samples. Due to this reason, the approximated online learning solution can then lead a wrong solution. The wrong solution can make significant errors when it is applied to surveillance systems. In this paper, we propose an exactly reweighted technique to recursively update the solution of the total error rate minimization in online learning manner. Compared to the approximately reweighted online total error rate minimization, an exactly reweighted online total error rate minimization is achieved. The proposed exact online learning method based on the total error rate minimization is then applied to object tracking problems. In our object tracking system, particle filtering is adopted. In particle filtering, our observation model is consisted of both generative and discriminative methods to leverage the advantages between generative and discriminative properties. In our experiments, our proposed object tracking system achieves promising performances on 8 public video sequences over competing object tracking systems. The paired t-test is also reported to evaluate its quality of the results. Our proposed online learning method can be extended under the deep learning architecture which can cover the shallow and deep networks. Moreover, online learning methods, that need the exact reweighting process, can use our proposed reweighting technique. In addition to object tracking, the proposed online learning method can be easily applied to object detection and recognition. Therefore, our proposed methods can contribute to online learning community and object tracking, detection and recognition communities.

Selective Word Embedding for Sentence Classification by Considering Information Gain and Word Similarity (문장 분류를 위한 정보 이득 및 유사도에 따른 단어 제거와 선택적 단어 임베딩 방안)

  • Lee, Min Seok;Yang, Seok Woo;Lee, Hong Joo
    • Journal of Intelligence and Information Systems
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    • v.25 no.4
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    • pp.105-122
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    • 2019
  • Dimensionality reduction is one of the methods to handle big data in text mining. For dimensionality reduction, we should consider the density of data, which has a significant influence on the performance of sentence classification. It requires lots of computations for data of higher dimensions. Eventually, it can cause lots of computational cost and overfitting in the model. Thus, the dimension reduction process is necessary to improve the performance of the model. Diverse methods have been proposed from only lessening the noise of data like misspelling or informal text to including semantic and syntactic information. On top of it, the expression and selection of the text features have impacts on the performance of the classifier for sentence classification, which is one of the fields of Natural Language Processing. The common goal of dimension reduction is to find latent space that is representative of raw data from observation space. Existing methods utilize various algorithms for dimensionality reduction, such as feature extraction and feature selection. In addition to these algorithms, word embeddings, learning low-dimensional vector space representations of words, that can capture semantic and syntactic information from data are also utilized. For improving performance, recent studies have suggested methods that the word dictionary is modified according to the positive and negative score of pre-defined words. The basic idea of this study is that similar words have similar vector representations. Once the feature selection algorithm selects the words that are not important, we thought the words that are similar to the selected words also have no impacts on sentence classification. This study proposes two ways to achieve more accurate classification that conduct selective word elimination under specific regulations and construct word embedding based on Word2Vec embedding. To select words having low importance from the text, we use information gain algorithm to measure the importance and cosine similarity to search for similar words. First, we eliminate words that have comparatively low information gain values from the raw text and form word embedding. Second, we select words additionally that are similar to the words that have a low level of information gain values and make word embedding. In the end, these filtered text and word embedding apply to the deep learning models; Convolutional Neural Network and Attention-Based Bidirectional LSTM. This study uses customer reviews on Kindle in Amazon.com, IMDB, and Yelp as datasets, and classify each data using the deep learning models. The reviews got more than five helpful votes, and the ratio of helpful votes was over 70% classified as helpful reviews. Also, Yelp only shows the number of helpful votes. We extracted 100,000 reviews which got more than five helpful votes using a random sampling method among 750,000 reviews. The minimal preprocessing was executed to each dataset, such as removing numbers and special characters from text data. To evaluate the proposed methods, we compared the performances of Word2Vec and GloVe word embeddings, which used all the words. We showed that one of the proposed methods is better than the embeddings with all the words. By removing unimportant words, we can get better performance. However, if we removed too many words, it showed that the performance was lowered. For future research, it is required to consider diverse ways of preprocessing and the in-depth analysis for the co-occurrence of words to measure similarity values among words. Also, we only applied the proposed method with Word2Vec. Other embedding methods such as GloVe, fastText, ELMo can be applied with the proposed methods, and it is possible to identify the possible combinations between word embedding methods and elimination methods.