• Title/Summary/Keyword: Expression analysis

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A Study on Creation and Development of Folksonomy Tags on LibraryThing (폭소노미 태그의 생성과 성장에 관한 연구 - LibraryThing을 중심으로 -)

  • Kim, Dong-Suk;Chung, Yeon-Kyoung
    • Journal of the Korean Society for Library and Information Science
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    • v.44 no.4
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    • pp.203-230
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    • 2010
  • This study analyzed the development and growth of folksonomy by examining tags associated with 40 bestsellers on LibraryThing.com in 6-month intervals. It was found that tag values do not decrease but grow in terms of quantity and quality. Accordingly, we examined the major significances of the tags and their potential utilization as an expression of subjects. Our findings were as follows. First, the motivations for tagging can be categorized into personal information for search purposes, self-fulfillment such as sense of achievement, display of emotion and sharing of one's experience with others, or an altruistic objective that emphasizes sociality with a desire that one's actions might provide social benefits. According to our analysis, 74.12% of tags had a social motivation. Second, the total number of tags and the frequency of usage increased with time. Third, the categories that showed a high increase in tag usage were dates of publication and reading, key words, main characters, and book reviews. Tags related to subjects had the highest ratio. Fourth, among Library of Congress Subject Headings (LCSH), multiple genres, key words and main characters were assigned to books, and specific key words and other properties were added as time progressed. There was also a slight increase in the number of tags consistent with LCSH. Fifth, we found that key tags could serve as a compilation of terms that reflects the knowledge base of the corresponding era. Thus, folksonomy should be continuously monitored for its quantitative and qualitative development of the tags to make improvements on its formative disadvantages, and identify internal semantic significance, be actively utilized in conjunction with taxonomy as a flexible compilation of terms that incorporate the history of a specific era.

Effects of Genistein on Cell Proliferation and Adipogenesis in Mouse 3T3-L1 Preadipocytes (이소플라본 genistein이 전지방세포 성장 및 지방세포형성과정에 미치는 영향)

  • Lim, Seung-Hyun;Kim, Hyo-Rim;Kim, Min-Jeong;Kim, Jong-Sik
    • Journal of Life Science
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    • v.22 no.1
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    • pp.49-54
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    • 2012
  • The effects of genistein on cell proliferation and adipogenesis were examined in mouse 3T3-L1 preadipocyte cells. Genistein decreased viability of 3T3-L1 pre-adipocytes in a dose-dependent manner. Oil Red O staining of these cells also indicated that adipogenesis was inhibited by 50 ${\mu}M$ genistein treatment. We investigated the molecular mechanisms involved in the decrease in cell viability in genistein-treated 3T3-L1 cells by conducting an oligo DNA microarray analysis. We selected the sirtuin-1 gene, one of the upregulated genes, for further experimentation because sirtuin-1 belongs to the sirtuin family, which is associated with anti-obesity and anti-inflammation activities. We found that four phytochemicals (resveratrol, capsaicin, daidzein, and genistein) could increase sirtuin-1 expression. Genistein was the strongest inducer of sirtuin-1 among the tested phytochemicals. The inhibition of adipogenesis by genistein was recovered by surtuin-1 siRNA transfection. Overall, these results may further our understanding of the molecular mechanisms underlying the inhibition of proliferation and adipogenesis by genistein in mouse 3T3-L1 cells.

The View on Childrearing of University Women (여대생의 자녀 양육관)

  • Kim, Young-Hee;Kim, Shin-Jeong
    • Women's Health Nursing
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    • v.6 no.2
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    • pp.269-290
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    • 2000
  • This study was conducted to inquire about the view on childrearing of university women for the purpose of building up the positive parent- child relationship and setting up preliminary parenting education program. The subjects were 137 university women who were freshmen to junior in one women's university in Seoul. Using the self-report questionnaire, data were collected from December in 1998 to March in 1999 and the contents which subjects wrote down were categorized by content analysis method. The results were as followed: 1. The age range of subjects were 20-22 years and main rearer was her mother(71.5%) 2. The view of subjects were revealed by 374 statements and then tied together 34 themes: 'exemplary parent model as a guider'(8.6%), 'determination for oneself' (8.0%), 'expression of love'(6.2%), 'humanity education'(4.8%), 'carrot and stick'(4.5%), 'respect of personality'(4.3%), 'sound living habit'(4.1%), 'conversation'(3.7%), 'regulation of greediness' (3.7%), 'supply of live experience'(3.7%), 'supply of broad and substantial vision'(3.5%), 'free choice'(3.5%), 'broad-mindedness'(3.5%), 'consideration'(3.0%), 'doing together'(3.0%), 'propriety education' (2.4%), 'pursuit of naturalness'(2.4%), 'looking for one's life'(2.4%), 'confidence'(2.1%), 'rearing by oneself'(2.1%), 'encouragement'(2.1%), 'cultivation of right sexual senses'(2.1%), 'desirable home environment'(1.9%), 'doing one's best'(1.9%), 'understanding'(1.6%), 'psychological intimacy'(1.6%), 'treat fair'(1.6%), 'pursuit of physical, psychological health' (1.6%), 'concerning'(1.3%), 'religious life'(1.3%), 'respect of individuality'(1.3%), 'cooperation' (1.1%), 'often-minded family'(0.8%), 'positive attitude'(0.8%). 34 themes were categorized by 12 categories once more: 'mature parenthood'(15.5%), 'acceptance' (11.5%), 'autonomy'(11.5%), 'pursuit of healthy life style'(9.4%), 'eagerness'(9.1%), 'making efforts'(8.8%), 'education'(8.8%), 'emotional bonding' (7.8%), 'respect'(7.2%), 'corporal punishment' (4.5%), 'supporting'(3.2%), 'composition of environment'(2.7%). In conclusion, we could expect that university women had a democratic view on childrearing with love and autonomy for a base. So we need to offer them nursing implementations such as preliminary parenting programs and parenting consulting in order to promote positive and interactional parent-child relationship by strengthening their desirable view on childrearing.

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Identification of Functional and In silico Positional Differentially Expressed Genes in the Livers of High- and Low-marbled Hanwoo Steers

  • Lee, Seung-Hwan;Park, Eung-Woo;Cho, Yong-Min;Yoon, Duhak;Park, Jun-Hyung;Hong, Seong-Koo;Im, Seok-Ki;Thompson, J.M.;Oh, Sung-Jong
    • Asian-Australasian Journal of Animal Sciences
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    • v.20 no.9
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    • pp.1334-1341
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    • 2007
  • This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.

Prognostic Significance of Hes-1, a Downstream Target of Notch Signaling in Hepatocellular Carcinoma

  • Zou, Jing-Huai;Xue, Tong-Chun;Sun, Chun;Li, Yan;Liu, Bin-Bin;Sun, Rui-Xia;Chen, Jie;Ren, Zheng-Gang;Ye, Sheng-Long
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.9
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    • pp.3811-3816
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    • 2015
  • Background: Hairy and enhancer of split 1 (Hes-1) protein is a downstream target of Notch signaling and is a basic helix-loop-helix transcriptional repressor. However, definitive evidence for a role in hepatocellular carcinoma (HCC) cells has not been reported. Here, Hes-1 was revealed to an important component of the Notch signaling cascade in HCC cell lines possessing different potential for lung metastasis. Materials and Methods: RNAi mediated by plasmid constructs was used to analyze the role of Hes-1 in MHCC-97L HCC cells by assessing proliferation, apoptosis, cell migration and matrigel invasion following transfection. Hes-1 protein expression analysis in HCC tissue was also conducted by immunohistochemistry. Results: Our studies revealed that Hes-1 was decreased in HCC cell lines with higher lung metastasis potential at both the mRNA and protein levels. Down-regulation of the Hes-1 gene in MHCC-97L cells resulted in increased cell proliferation, reduced apoptosis and increased migration and invasion. Conclusions: Hes-1 has potential prognostic value in post-surgical HCC patients and may be an independent prognostic indicator for overall survival and tumor recurrence. These findings have important implications for understanding the mechanisms by which Hes-1 participates in tumor proliferation and invasion.

PU.1 Is Identified as a Novel Metastasis Suppressor in Hepatocellular Carcinoma Regulating the miR-615-5p/IGF2 Axis

  • Song, Li-Jie;Zhang, Wei-Jie;Chang, Zhi-Wei;Pan, Yan-Feng;Zong, Hong;Fan, Qing-Xia;Wang, Liu-Xing
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.9
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    • pp.3667-3671
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    • 2015
  • Invasion and metastasis is the major cause of tumor recurrence, difficulty for cure and low survival rate. Excavating key transcription factors, which can regulate tumor invasion and metastasis, are crucial to the development of therapeutic strategies for cancers. PU.1 is a master hematopoietic transcription factor and a vital regulator in life. Here, we report that, compared to adjacent non-cancerous tissues, expression of PU.1 mRNA in metastatic hepatocellular carcinoma (HCC), but not primary HCC, was significantly down-regulated. In addition, levels of PU.1 mRNA in metastatic hepatoma cell lines MHCC97L and MHCC97H were much lower than in non-metastatic Hep3B cells. Transwell invasion assays after PU.1 siRNA transfection showed that the invasion of hepatoma cell lines was increased markedly by PU.1 knockdown. Oppositely, overexpression of PU.1 suppressed the invasion of these cells. However, knockdown and overexpression of PU.1 did not influence proliferation. Finally, we tried to explore the potential mechanism of PU.1 suppressing hepatoma cell invasion. ChIP-qPCR analysis showed that PU.1 exhibited a high binding capacity with miR-615-5p promoter sequence. Overexpression of PU.1 caused a dramatic increase of pri-, pre- and mature miR-615-5p, as well as a marked decrease of miR-615-5p target gene IGF2. These data indicate that PU.1 inhibits invasion of human HCC through promoting miR-615-5p and suppressing IGF2. These findings improve our understanding of PU.1 regulatory roles and provided a potential target for metastatic HCC diagnosis and therapy.

Male Breast Cancer: 20 Years Experience of a Tertiary Hospital from the Middle Black Sea Region of Turkey

  • Serarslan, Alparslan;Gursel, Bilge;Okumus, Nilgun Ozbek;Meydan, Deniz;Sullu, Yurdanur;Gonullu, Guzin
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.15
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    • pp.6673-6679
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    • 2015
  • Background: Male breast cancer is a rare neoplasm, and its treatments are based on those of female breast cancer. This study aimed to analyze 20 years of male breast cancer clinical characteristics and treatment results from the Middle Black Sea Region of Turkey. Materials and Methods: A retrospective analysis of 16 male breast cancer patients treated in our tertiary hospital between 1994 and 2014 was performed. Epidemiologic data, tumor characteristics, and treatments were recorded and compared with 466 female breast cancer ((premenopausal; n = 230) + (postmenopausal n = 236)) patients. The 5-year disease-free and overall survival rates were calculated. Results: Male breast cancer constituted 0.1% of all malignant neoplasms in both sexes, 0.2% of all malignant neoplasms in males, and 0.7% of all breast cancers. The mean patient age in this study was $59.8{\pm}9.5$ (39-74) years. The mean time between first symptom and diagnosis was $32.4{\pm}5.3$ (3-60) months. Histology revealed infiltrative ductal carcinoma in 81.3% of patients. The most common detected molecular subtype was luminal A, in 12 (75%) patients. Estrogen receptor rate (93.8%) in male breast cancer patients was significantly higher than that in female breast cancer (70.8% in all females, p = 0.003; 68.2% in postmenopausal females, p = 0.002) patients. Most of the tumors (56.3%) were grade 2. Tumor stage was T4 in 50% of males. The majority (56.3%) of the patients were stage III at diagnosis. Surgery, chemotherapy, radiotherapy and endocrine-therapy were applied to 62.5%, 62.5%, 81.2% and 73.3%, respectively. Loco-regional failure did not occur in any of the cases. All recurrences were metastastic. The 5-year disease-free and overall survival rates in male breast cancer patients were 58% and 68%, respectively. Conclusions: Tumors found in male breast cancer patients were similar in size to tumors found in females, but they advanced to T4 stage more rapidly because of the lack of breast parenchymal tissues. The rate of estrogen receptor expression tended to be higher in male breast cancer patients than in female breast cancer patients. Metastasis is the most important problem in initially non-metastatic male breast cancer patients.

Retrospective Analysis of Neoadjuvant Chemotherapy for Breast Cancer in Turkish Patients

  • Duman, Berna Bozkurt;Afsar, Cigdem Usul;Gunaldi, Meral;Sahin, Berksoy;Kara, I. Oguz;Erkisi, Melek;Ercolak, Vehbi
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.8
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    • pp.4119-4123
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    • 2012
  • Background: Neoadjuvant systemic chemotherapy is the accepted approach for women with locally advanced breast cancer. Anthracycline- and taxane-based regimens have been extensively studied in clinical trials and consequently are widely used. In this study aimed to research the complete response (pCR) rates in different regimens for neoadjuvant setting and determine associated clinical and biological factors. Methods: This study included 63 patients diagnosed with breast carcinoma among 95 patients that had been treated with neoadjuvant chemotherapy between 2007 and 2010. TNM staging system was used for staging. The histologic response to neoadjuvant chemotherapy was characterized as a pCR when there was no evidence of residual invasive tumor in the breast or axillary lymph nodes. Biologic subclassification using estrogen receptor (ER), progesterone receptor (PR), HER2 were performed. Luminal A was defined as ER+, PR+, HER2-; Luminal B tumor was defined as ER+, PR-, HER2-; ER+, PR-, HER2+; ER-, PR+, HER2-; ER+, PR+, HER2+; HER2 like tumor ER-, PR+, HER2+; and triple negative tumor ER, PR, HER2 negative. Results: Patients median age was 54.14 (min-max: 30-75). Thirty-two patients (50.8%) were premenapousal and 31 (49.2%) were postmenapousal. Staging was performed postoperatively based on the pathology report and appropriated imaging modalities The TNM (tumor, lymph node, metastasis) system was used for clinical and pathological staging. Fifty-seven (90.5%) were invasive ductal carcinomas, 6 (9.5%) were other subtypes. Thirty nine (61.9%) were grade II and 24 (38.1%) were grade III. Seven (11.1%) patients were stage II and 56 (88.9) patients were stage III. The patients were classified for ER, PR receptor and HER2 positivity. Seventeen patients had complete response to chemotherapy. Forty patients (63.5%) were treated with dose dense regimen (cyclophosphamide 600 mg/m2 and doxorubicine 60 mg/m every two weeks than paclitaxel 175 mg/m2 every two weeks with filgrastim support) 40 patients (48%) were treated anthracycline and taxane containing regimens. Thirteen patients (76%) from 17 patients with pCR were treated with the dose dense regimen but without statistical significance (p=0.06). pCR was higher in HER2(-), ER(-), grade III, premenopausal patients. Conclusion: pCR rate was higher in the group that treated with dose dense regimen, which should thus be the selected regimen in neoadjuvant setting. Some other factors can predict pCR in Turkish patients, like grade, menopausal status, triple negativity, percentage of ER positivity, and HER2 expression.

Fatty Acid Synthesis Pathway Genetic Variants and Clinical Outcome of Non-Small Cell Lung Cancer Patients after Surgery

  • Jin, Xin;Zhang, Ke-Jin;Guo, Xu;Myers, Ronald;Ye, Zhong;Zhang, Zhi-Pei;Li, Xiao-Fei;Yang, Hu-Shan;Xing, Jin-Liang
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.17
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    • pp.7097-7103
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    • 2014
  • Over-expression of de novo lipogenesis (DNL) genes is associated with the prognosis of various types of cancers. However, the effects of single nucleotide polymorphisms (SNPs) in these genes on recurrence and survival of non-small cell lung cancer (NSCLC) patients after surgery are still unknown. In this study, a total of 500 NSCLC patients who underwent surgery treatment were included. Eight SNPs in 3 genes (ACACA, FASN and ACLY) of the DNL pathway were examined using the Sequenom iPLEX genotyping system. Multivariate Cox proportional hazards regression and Kaplan-Meier curves were used to analyze the association of SNPs with patient survival and tumour recurrence. We found that two SNPs in the FASN gene were significantly associated with the recurrence of NSCLC. SNP rs4246444 had a significant association with lung cancer recurrence under additive model (hazard ratio [HR], 0.82; 95% confidence interval [95%CI], 0.67-1.00; p=0.05). Under the dominant model, rs4485435 exhibited a significant association with recurrence (HR, 0.75; 95%CI, 0.56-1.01; p=0.05). Additionally, SNP rs9912300 in ACLY gene was significantly associated with overall survival in lung cancer patients (HR, 1.41; 95%CI, 1.02-1.94, p=0.04) under the dominant model. Further cumulative effect analysis showed moderate dose-dependent effects of unfavorable SNPs on both survival and recurrence. Our data suggest that the SNPs in DNL genes may serve as independent prognostic markers for NSCLC patients after surgery.

Cloning and Expression of an Insecticidal Crystal Protein CryIIA Gene from Bacillus thuringiensis subsp. kurstaki HD-1 (Bacillus thuringiensis subsp. kurstaki HD-1 CryIIA의 내독소 단백질 유전자의 클로닝 및 발현)

  • 김호산;김상현;제연호;유용만;서숙재;강석권;조용섭
    • Korean journal of applied entomology
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    • v.32 no.3
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    • pp.300-306
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    • 1993
  • The CryIIA gene encoding the insecticidal crystal protein of Bacillus thuringiens!s subsp. kurstalri HD-l has been cloned in Escherichia col!, and its nucleotide sequences were determined completely. 5kb Hindlli fragment harboring CryIIA gene was screened in the large ca. 225kb plasmid DNA by southern blot. HindlIT digested 5kb fragment was ligated into pUC19 and transformed in E. coli. The 4kb BamHI-HindlIT fragment containing the CryIIA gene was subcloned and named pSKIIA. DNA sequence analysis demonstrates that pSKIIA is the gene of an operon which is comprised of Lhree open reading frames (designated orn, orf2 and or£3). The CrylIA gene is composed of 3,952bp-long BamHI-Hindill DNA restriction fragment. The orf3 code for a polypeptide of 633 amino acid residues. The protoxin protein has a predicted molecular weight of 70,780. The E. coli derived protoxin gene product is biologICally active against three species of Lepidopteran (Plu.lelia maculipennis, He/iolhis assulta, Spodoptera litura) and a species of Dip Leran( Culex pipines) larvae in bioassay.

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