• Title/Summary/Keyword: Log-Ratio Method

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Ecological Characteristics of Actinomycetes from Mercury and Chrome Polluted Soil (수은, 6가크롬 오염토양으로부터 분리된 방선균군의 생태학적 특성)

  • Cho Min-Hye;Han Sang-Mi;Baek Ha-Ju;Whang Kyung-Sook
    • Korean Journal of Environmental Biology
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    • v.24 no.1 s.61
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    • pp.38-45
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    • 2006
  • Ecological characteristics of microbial populations inhabiting heavy metal polluted soil were investigated. The samples were collected from 293 sites around an factory and industry at Gyeoungsangbuk-do. We measured the contents of seven heavy metal elements (Cd, Cu, As, Hg, Pb, $Cr^{6+}$, CN), seven sites have been seriously contaminated by mercury and chrome. A quantitative evaluation of microbial populations in mercury and chrome contaminated soil was examined by using plate count method. Bacterial numbers in polluted soil samples ranged from $7.4X10^5\;to\;9.3X10^7\;cfu\;g^{-1}$, about $10\sim100$ fold less than the count for the unpolluted soil. Moulds were not detected in chrome polluted soil. The log values of actinomycetes of each contaminated soil samples were log ranged from 6.18 to 7.52. The ratio of actinomycetes was similar to unpolluted soil. The investigation showed actinomycetes to be the major microbial population inhabiting the mercury and chrome polluted soil. Thirty-one isolates among the total isolates were examined for antibacterial activity. These isolates were identified based on a phylogenetic analysis using 16S rRNA gene nucleotide sequences, they were categorized in three major phylogenetic groups, belong to the Streptomyces (6 strains), Saccharopolyspora (3 strains), Nocardiodes (1 strain). On the phylogenetic tree, the clade consisting of five isolates were distantly related to all of the established Streptomycetes genera, indicating the possibility as members of new species.

Whey Protein Concentrate, Pullulan, and Trehalose as Thermal Protective Agents for Increasing Viability of Lactobacillus plantarum Starter by Spray Drying

  • Sun, Haiyue;Hua, Xiaoman;Zhang, Minghao;Wang, Yu;Chen, Yiying;Zhang, Jing;Wang, Chao;Wang, Yuhua
    • Food Science of Animal Resources
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    • v.40 no.1
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    • pp.118-131
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    • 2020
  • It is necessary to add protective agents for protecting the probiotic viability in the preparation process of probiotics starter. In this study, we used whey protein concentrate (WPC), pullulan, trehalose, and sodium glutamate as the protective agent and optimized the proportion of protective agent and spray-drying parameters to achieve the best protective effect on Lactobacillus plantarum. Moreover, the viable counts of L. plantarum in starter stored at different temperatures (-20℃, 4℃, and 25℃) for 360 days were determined. According to response surface method (RSM), the optimal proportion of protective agent was 24.6 g/L WPC, 18.8 g/L pullulan, 16.7 g/L trehalose and 39.3 g/L sodium glutamate. The optimum spray-drying parameters were the ratio of bacteria to protective agents 3:1 (v: v), the feed flow rate 240 mL/h, and the inlet air temperature 115℃ through orthogonal test. Based on the above results, the viable counts of L. plantarum was 12.22±0.27 Log CFU/g and the survival rate arrived at 85.12%. The viable counts of L. plantarum stored at -20℃ was more than 1010 CFU/g after 200 days.

A Study on Development of a Hearing Impairment Simulator considering Frequency Selectivity and Asymmetrical Auditory Filter of the Hearing Impaired (난청인의 주파수 선택도와 비대칭적 청각 필터를 고려한 난청 시뮬레이터 개발에 관한 연구)

  • Joo, Sang-Ick;Kang, Hyun-Deok;Song, Young-Rok;Lee, Sang-Min
    • The Transactions of The Korean Institute of Electrical Engineers
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    • v.59 no.4
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    • pp.831-840
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    • 2010
  • In this paper, we propose a hearing impairment simulator considering reduced frequency selectivity and asymmetrical auditory filter of the hearing impaired, and we verified the reduced frequency selectivity and asymmetrical auditory filter affected in speech perception through experiments. The reduced frequency selectivity has made embodied by spectral smearing using LPC(linear prediction coding). The shapes of auditory filter are asymmetrical different with each center frequency. Hearing impaired person which has hearing loss was differently changed with that of normal hearing people and it has different value for speech of quality through auditory filter. The experiments confirmed subjective test and objective test. The subjective experiments are composed of 4 kinds of tests: pure tone test, SRT(speech reception threshold) test, and WRS(word recognition score) test without spectral smearing, and WRS test with spectral smearing. The experiment of the hearing impairment simulator was performed from 9 subjects who have normal ears. The amount of spectral smearing was controlled by LPC order. The asymmetrical auditory filter of proposed hearing impairment simulator was simulated and then some tests to estimate the filter's performance objectively were performed. The objective experiment as simulated auditory filter's performance evaluation method used PESQ(perceptual evaluation of speech quality) and LLR(log likelihood ratio) for speech through auditory filter. The processed speech was evaluated objective speech quality and distortion using PESQ and LLR value. When hearing loss processed, PESQ and LLR value have big difference according to asymmetrical auditory filter in hearing impairment simulator.

LLR Based Generalization of Soft Decision Iterative Decoding Algorithms for Block Turbo Codes (LLR 기반 블록 터보 부호의 연판정 복호 알고리즘 일반화)

  • Im, Hyun-Ho;Kwon, Kyung-Hoon;Heo, Jun
    • Journal of Broadcast Engineering
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    • v.16 no.6
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    • pp.1026-1035
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    • 2011
  • This paper presents generalization and application for the conventional SISO decoding algorithm of Block Turbo Codes. R. M. Pyndiah suggested an iterative SISO decoding algorithm for Product Codes, two-dimensionally combined linear block codes, on AWGN channel. It wascalled Block Turbo Codes. Based on decision of Chase algorithm which is SIHO decoding method, SISO decoder for BTC computes soft decision information and transfers the information to next decoder for iterative decoding. Block Turbo Codes show Shannon limit approaching performance with a little iteration at high code rate on AWGN channel. In this paper we generalize the conventional decoding algorithm of Block Turbo Codes, under BPSK modulation and AWGN channel transmission assumption, to the LLR value based algorithm and suggest an application example such as concatenated structure of LDPC codes and Block Turbo Codes.

Discrimination of Local Microearthquakes and Artificial Underground Explosions on the Basis of Time-Frequency Domain (시간-주파수 영역에서의 국지 미소지진과 지하인공폭발의 구별)

  • 김소구;박용철
    • The Journal of Engineering Geology
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    • v.7 no.1
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    • pp.63-79
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    • 1997
  • In this study, our purpose is to develop a technique to discriminate artificial explosions from local microearthquakes on the basis of time-frequency domain. To obtain spectral features of artificial explosions and microearthquakes, we used 3-d spectrograms(frequency, time and amplitude) because this is a useful tool to study the frequency content of entire seismic waveforms observed at local and regional distances (e. g., Kim et al., 1994). P and S waves from quarry blasts show that frequency content of dominant amplitude appeared above 10 Hz and Rg phases that are observed at near distance ranges. But P and S waves from microearthquakes have more broad frequency content as well as below 10 Hz. And for discrimination, Pg/Lg spectral ratio is performed below 10 Hz. In order to select time windows we computed group velocity using multiple filter method(MFM) and removed free surface effects from all 3-components data for improving on data quality. Next step, we computed Fast-Fourier transform, and a log average spectral amplitude over seven frequency bands : 0.5 to 3, 2 to 4, 3 to 5, 4 to 6, 5 to 7, 6 to 8 and 8 to 10 Hz. The best separation is observed from 6 to 8 Hz.

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Lack of any Impact of Histopathology Type on Prognosis in Patients with Early-Stage Adenocarcinoma and Squamous Cell Carcinoma of the Uterine Cervix

  • Teke, Fatma;Yoney, Adnan;Teke, Memik;Inal, Ali;Urakci, Zuhat;Eren, Bekir;Zincircioglu, Seyit Burhanedtin;Buyukpolat, Muhammed Yakup;Ozer, Ali;Isikdogan, Abdurrahman;Unsal, Mustafa
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.6
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    • pp.2815-2819
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    • 2014
  • Background: The aim of this study was to evaluate the prognosis of patients with stage IA-IIB cervical carcinoma and to investigate a possible correlation of histology with prognosis. Materials and Methods: Two hundred fifty one patients with adenocarcinoma and squamous cell carcinoma (SCC) histology for FIGO (International Federation of Gynecology and Obstetrics) stage IA-IIB uterine cervical carcinomas at the Radiation Oncology Clinic of GH Okmeydan Training and Research Hospital between January 1996 and December 2006 were selected, analyzed retrospectively and evaluated in terms of general characteristics and survival. Disease-free survival (DFS) and overall survival (OS) was calculated using the Kaplan-Meier method and differences were compared with the log-rank test. Multivariate analysis using a Cox-proportional hazards model was used to adjust for prognostic factors and to estimate hazard ratio (HR) with 95% confidence interval (CI). Results: There was no differences between the two tumour types in age, stage, pelvic nodal metastasis, parametrial invasion, surgical margin status, DSI, LVSI, maximal tumor diameter, grade, and treatment modalities. 5-year OS and DFS were 73% and 77%, versus 64% and 69%, for SCC and adenocarcinoma, respectively (p> 0.05). Multivariate analysis revealed independent prognostic factors including pelvic nodal metastasis and resection margin status for OS (p=0.008, p=0.002, respectively). Conclusions: Prognosis of FIGO stage IA-IIB cervical cancer patients was found to be the same for those with adenocarcinoma and SCC.

Chemoradiotherapy in squamous cell carcinoma of the anal canal: a single institution experience

  • Kim, Kyung Hwan;Chang, Jee Suk;Keum, Ki Chang;Ahn, Joong Bae;Lee, Chang Geol;Koom, Woong Sub
    • Radiation Oncology Journal
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    • v.31 no.1
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    • pp.25-33
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    • 2013
  • Purpose: We reviewed the treatment outcomes and prognostic factors for patients with anal canal carcinoma who were treated with curative intent chemoradiotherapy (CRT) at Severance Hospital from 2005 to 2011. Materials and Methods: Data for 38 eligible patients treated during this period were reviewed. All patients were treated with curative intent using radiotherapy (RT) with (n = 35) or without concomitant chemotherapy (n = 3). Among 35 patients who received CRT, most of the chemotherapeutic regimens were either 5-fluorouracil (5-FU) plus mitomycin C (23 patients) or 5-FU plus cisplatin (10 patients). Recurrence-free survival (RFS), colostomy-free survival (CFS), overall survival (OS), and locoregional control (LRC) rates were calculated using the Kaplan-Meier method and survival between subgroups were compared using the log-rank test. Cox's proportional hazard model was used for multivariate analysis. Results: Over a median follow-up period of 44 months (range, 11 to 96 months), 3-year RFS, CFS, OS, and LRC were 80%, 79%, 85%, and 92%, respectively. In multivariate analysis, tumor size >4 cm was an independent predicting factor for poorer RFS (hazard ratio [HR], 6.35; 95% confidence interval [CI], 1.42 to 28.5; p = 0.006) and CFS (HR, 6.25; 95% CI, 1.39-28.0; p = 0.017), while the presence of external iliac lymph node metastasis was an independent prognosticator for poorer OS (HR, 9.32; 95% CI, 1.24 to 70.3; p = 0.030). No treatment-related colostomies or deaths occurred during or after treatment. Conclusion: Curative intent CRT resulted in excellent outcomes that were comparable to outcomes in previous randomized trials. No severe treatment-related toxicities were observed.

Combining Support Vector Machine Recursive Feature Elimination and Intensity-dependent Normalization for Gene Selection in RNAseq (RNAseq 빅데이터에서 유전자 선택을 위한 밀집도-의존 정규화 기반의 서포트-벡터 머신 병합법)

  • Kim, Chayoung
    • Journal of Internet Computing and Services
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    • v.18 no.5
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    • pp.47-53
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    • 2017
  • In past few years, high-throughput sequencing, big-data generation, cloud computing, and computational biology are revolutionary. RNA sequencing is emerging as an attractive alternative to DNA microarrays. And the methods for constructing Gene Regulatory Network (GRN) from RNA-Seq are extremely lacking and urgently required. Because GRN has obtained substantial observation from genomics and bioinformatics, an elementary requirement of the GRN has been to maximize distinguishable genes. Despite of RNA sequencing techniques to generate a big amount of data, there are few computational methods to exploit the huge amount of the big data. Therefore, we have suggested a novel gene selection algorithm combining Support Vector Machines and Intensity-dependent normalization, which uses log differential expression ratio in RNAseq. It is an extended variation of support vector machine recursive feature elimination (SVM-RFE) algorithm. This algorithm accomplishes minimum relevancy with subsets of Big-Data, such as NCBI-GEO. The proposed algorithm was compared to the existing one which uses gene expression profiling DNA microarrays. It finds that the proposed algorithm have provided as convenient and quick method than previous because it uses all functions in R package and have more improvement with regard to the classification accuracy based on gene ontology and time consuming in terms of Big-Data. The comparison was performed based on the number of genes selected in RNAseq Big-Data.

Analysis of Pumping Test Data and The Prediction of Drawdown for Daejong-Chun Area (대종천유역 충적대수층의 수리성 분석 및 수위강하예측에 관한 연구)

  • Choi, Jae-Jin;Sung, Won-Mo;Hahn, Jeong-Sang
    • Economic and Environmental Geology
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    • v.26 no.4
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    • pp.541-549
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    • 1993
  • The main goal of this paper is to determine hydraulic properties and to predict drawdown for the efficient and stable development of groundwater in the Daejong-Chun area, North of Kyungsang-Do. Based on geological survey and analysis of well logging data conducted in 1991, it is found that the type of aquifer of this area is considered to be an anisotropic unconfined aquifer with saturated thickness of 19.8 m. In order to characterize this aquifer pumping test was conducted, and the resulting drawdown data were utilized for the analysis by applying both type curve matching technique and semi-log straight line method. As a result, the average specific yield of this aquifer is estimated as 32.3%, and the average ratio of $K_H$ to $K_V$ is only 2.7, which means that gravitational effect is not significant factor for this type of aquifer. For the validation of the estimated hydraulic properties, the analytical model which was developed with Newton-Raphson iteration procedure in this study, was employed to generate the drawdown. And, the resulting drawdown was compared against actual drawdown data and it shows the excellent matches. The actual drawdown data for 9 hours of pumping were used for history matching purposes and relatively satisfactory matches were achieved in this match. Then, the model was run by using the tuned parameters that are obtained during history matching stage, and the drawdown was predicted for the next 30 years of pumping with $3,000m^3/day$ of constant pumping rate. Its result indicates that the drawdown was stabilized as 1.41 m from 20 days with $3,000m^3/day$ of constant pumping rate, which is the required amount of water to be safely supplied to this area.

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Design of a nonlinear ADC encoder to reduce the conversion errors in DBNS (DBNS 변환오차를 고려한 비선형 ADC 엔코더 설계)

  • Woo, Kyung-Haeng;Choi, Won-Ho;Kim, Jong-Soo;Choi, Jae-Ha
    • Journal of the Institute of Convergence Signal Processing
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    • v.14 no.4
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    • pp.249-254
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    • 2013
  • A fast multiplier and ADC are essential to process the analog signals in real time. The double-base number system(DBNS) is known as an efficient method for this purpose. The DBNS uses the numbers 2 and 3 as the base numbers simultaneously. The system has an advantage of fast multiplication, less chip area, and low power consumption compared to the binary multiplier. However, the inherent errors of the log number's intrinsic tolerance in DBNS are accumulated in a FIR digital filter, so the signal-to-noise ratio(SNR) has a tendency to be degraded. In this paper, the nonlinear encoder of ADC is designed to compensate the accumulated errors of DBNS by analysing the error distributions of various filter coefficients. The new ADC does not sacrifice its own advantages because the encoder circuits are modified only. The experiments were done with an FIR filters those were designed to have -70dB of SNR in stop band. The proposed nonlinear ADC encoder could drop the SNR to -45dB in stop band, in contrast to -35dB with the linear encoder.