Query: microarray*
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12399 records returned
Receptor-binding specificity of pandemic influenza A (H1N1) 2009 virus determined by carbohydrate microarray
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Matrosovich & Ten Feizi
Source: Nature Biotechnology - February 6, 2010 Category: Biotechnology Authors: Robert A ChildsAngelina S PalmaSteve WhartonTatyana MatrosovichYan LiuWengang ChaiMaria A Campanero-RhodesYibing ZhangMarkus EickmannMakoto KisoAlan HayMikhail MatrosovichTen Feizi Tags: Research Source Type: journals
Identification of growth insensitive to ABA3 (gia3), a Recessive Mutation Affecting ABA Signaling for the Control of Early Post-Germination Growth in Arabidopsis thalianaEmail this article to a colleague.
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The stress phytohormone ABA inhibits the developmental transition taking the mature embryo in the dry seed towards a young seedling. ABA also induces the accumulation of the basic leucine zipper (bZIP) transcription factor ABA-insensitive 5 (ABI5) which, apart from blocking endosperm rupture, also protects the embryo by stimulating the expression of late embryogenesis abundant (LEA) genes that conferred osmotolerance during seed maturation. It is unknown whether ABA recruits additional embryonic pathways to control early seedling growth and fitness. Here we identify gia3 (growth insensitive to ABA3), a recessive locus in A...
Source: Plant and Cell Physiology - February 6, 2010 Category: Cytology Authors: Kinoshita, N., Berr, A., Belin, C., Chappuis, R., Nishizawa, N. K., Lopez-Molina, L. Tags: Regular Papers Source Type: journals
Human T Cell Lymphotropic Virus 1 Manipulates Interferon Regulatory Signals by Controlling the TAK1-IRF3 and IRF4 Pathways [Molecular Bases Of Disease]Email this article to a colleague.
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We previously reported that human T cell lymphotropic virus 1 (HTLV-1) Tax oncoprotein constitutively activates transforming growth factor-β-activated kinase 1 (TAK1). Here, we established Tax-positive HuT-102 cells stably transfected with a short hairpin RNA vector (HuT-shTAK1 cells) and investigated the physiological function of TAK1. Microarray analysis demonstrated that several interferon (IFN)-inducible genes, including chemokines such as CXCL10 and CCL5, were significantly down-regulated in HuT-shTAK1 cells. In contrast, Tax-mediated constitutive activation of nuclear factor-B (NF-B) was intact in HuT-shTAK1 cel...
Source: Journal of Biological Chemistry - February 5, 2010 Category: Chemistry Authors: Suzuki, S., Zhou, Y., Refaat, A., Takasaki, I., Koizumi, K., Yamaoka, S., Tabuchi, Y., Saiki, I., Sakurai, H. Tags: Molecular Bases Of Disease Source Type: journals
Derepression of HMGA2 via Removal of ZBRK1/BRCA1/CtIP Complex Enhances Mammary Tumorigenesis [Gene Regulation]Email this article to a colleague.
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The high mobility group AT-hook 2 (HMGA2), a DNA architectural protein, is highly regulated during development and plays an important role in tumorigenesis. Indeed, HMGA2 was overexpressed in many different kinds of tumors. However, the mechanisms regulating HMGA2 expression remain elusive. Using microarray analysis, we found that HMGA2, along with a dozen of other genes, was co-repressed by ZBRK1, BRCA1, and CtIP. BRCA1 exerts its transcriptional repression activity through interaction with the transcriptional repressor ZBRK1 in the central domain, and with CtIP in the C-terminal BRCT domain. Here, we show that ZBRK1, BRC...
Source: Journal of Biological Chemistry - February 5, 2010 Category: Chemistry Authors: Ahmed, K. M., Tsai, C. Y., Lee, W.-H. Tags: Gene Regulation Source Type: journals
Staphylococcal Strains Vary Greatly in Their Ability to Induce an Inflammatory Response in Endothelial CellsEmail this article to a colleague.
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Conclusion. Given that agr‐defective strains are commonly recovered during colonization and infection, agr deficiency might represent a strategy of S. aureus to hide intracellularly without provoking the host immune system and causing relapsing infections.
Source: The Journal of Infectious Diseases Latest Issue - February 5, 2010 Category: Infectious Diseases Tags: article MAJOR ARTICLE Source Type: journals
Differential genome-wide gene expression profiling of bovine largest and second-largest follicles: identification of genes associated with growth of dominant folliclesEmail this article to a colleague.
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Conclusion:
We demonstrated that global gene expression profiling of F1 and F2 clearly reflected a difference in their follicular status. Expression of stage-specific genes in follicles may be closely associated with their growth or atresia. Several genes identified in this study will provide intriguing candidates for the determination of follicular growth.
Source: Reproductive Biology and Endocrinology - February 5, 2010 Category: Endocrinology Authors: Ken-Go HayashiKoichi UshizawaMisa HosoeToru Takahashi Source Type: journals
Clinicopathologic significance of cyclooxygenase-2 overexpression in colorectal adenocarcinomaEmail this article to a colleague.
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Conclusions: COX-2 overexpression was significantly associated with favorable clinicopathologic phenotype and an indicator of better survival in our cohort of colorectal cancer patients.
Source: Basic and Applied Pathology - February 5, 2010 Category: Pathology Authors: Se Min Jang, Young Jin Jun, Woong Na, Si-Hyong Jang, Kyueng Whan Min, Young Soo Song, Ki-Seok Jang, Hong Xiu Han, Kang Hong Lee, Seung Sam Paik Source Type: journals
Prognostic significance of pSTAT3 and Survivin expression in diffuse large B-cell lymphomaEmail this article to a colleague.
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Conclusions: pSTAT3 and Survivin expression appear to be important prognostic factors for DLBCL patients.
Source: Basic and Applied Pathology - February 5, 2010 Category: Pathology Authors: Ji-Youn Sung, Sung-Jig Lim, Youn Wha Kim, Juhie Lee Source Type: journals
Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturationEmail this article to a colleague.
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Conclusion:
This is the first report of long ncRNA expression in neuronal and glial cell differentiation and of the modulation of ncRNA expression by modification of chromatin architecture. These observations explicitly link ncRNA dynamics to neural stem cell fate decisions, specification and epigenetic reprogramming and may have important implications for understanding and treating neuropsychiatric diseases.
Source: BMC Neuroscience - Latest articles - February 5, 2010 Category: Neuroscience Authors: Timothy MercerIrfan QureshiSolen GokhanMarcel DingerGuangyu LiJohn MattickMark Mehler Source Type: journals
Onconase responsive genes in human mesothelioma cells: implications for an RNA damaging therapeutic agentEmail this article to a colleague.
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Conclusions:
These results provide a broad picture of gene activity after treatment with a drug that targets small non-coding RNAs and contribute to our overall understanding of MM cell response to Onconase as a therapeutic strategy. The findings provide insights regarding mechanisms that may contribute to the efficacy of this novel drug in clinical trials of MM patients who have failed first line chemotherapy or radiation treatment.
Source: BMC Cancer - February 5, 2010 Category: Cancer & Oncology Authors: Deborah AltomareSusanna RybakJianming PeiJacob MaizelMitchell CheungJoseph TestaKuslima Shogen Source Type: journals
Correlation-based Gene Selection and Classification Using Taguchi-BPSO.Email this article to a colleague.
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Conclusion: The introduced method outperformed five other methods from the literature in terms of classification error rate. It could thus constitute a valuable tool for gene expression analysis in future studies.
PMID: 20135079 [PubMed - as supplied by publisher]
Source: Methods of Information in Medicine - February 5, 2010 Category: Information Technology Authors: Chuang LY, Yang CS, Wu KC, Yang CH Tags: Methods Inf Med Source Type: journals
Overexpression of SUGT1 in human colorectal cancer and its clinicopathological significance.Email this article to a colleague.
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As recent technological innovations make it possible to clarify the concordant relationship between genomic alterations and aberrant gene expression during the progression of colorectal cancer (CRC), we aimed at identifying new overexpressing genes with genomic amplification on the responsible loci in CRC. The candidate gene was found using cDNA microarray and array-based comparative genomic hybridization (CGH) analysis after laser microdissection (LMD) in 132 Japanese CRC. We focused on SUGT1, which is associated with the assembling of kinetochore proteins at the metaphase of the cell cycle, with significant associati...
Source: International Journal of Oncology - February 4, 2010 Category: Cancer & Oncology Authors: Iwatsuki M, Mimori K, Sato T, Toh H, Yokobori T, Tanaka F, Ishikawa K, Baba H, Mori M Tags: Int J Oncol Source Type: journals
Role of the AKT pathway in microRNA expression of human U251 glioblastoma cells.Email this article to a colleague.
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Activation of the AKT (serine-threonine kinase) pathway is a common feature in glioblastoma cells. Downstream factors of the AKT pathway are involved in cell proliferation, apoptosis, cellular migration and angiogenesis. Micro-RNAs (miRNAs) are highly conserved small non-coding RNAs that block targeted mRNA expression at the post-transcriptional level. The aim of this study was to investigate the role of the AKT pathway in regulating miRNA. The changes of miRNA expression profile in human glioblastome U251 cells after AKT small interfering RNA transfection were examined by a microarray, and confirmed by Northern blotti...
Source: International Journal of Oncology - February 4, 2010 Category: Cancer & Oncology Authors: Zhou X, Ren Y, Han L, Mei M, Xu P, Zhang CZ, Wang GX, Jia ZF, Pu PY, Kang CS Tags: Int J Oncol Source Type: journals
Dynamism in gene expression across multiple studiesEmail this article to a colleague.
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In this study we develop methods of examining gene expression dynamics, how and when genes change expression, and demonstrate their application in a meta-analysis involving over 29,000 microarrays. By defining measures across many experimental conditions, we have a new way of characterizing dynamics, complementary to measures looking at changes in absolute variation or breadth of tissues showing expression. We show conservation in overall patterns of dynamism across three species (human, mouse, and rat) and show associations with known disease-related genes. We discuss the enriched functional properties of the sets of gene...
Source: Physiological Genomics - February 4, 2010 Category: Genetics & Stem Cells Authors: Morgan, A. A., Dudley, J. T., Deshpande, T., Butte, A. J. Tags: Call for Papers: Comparative Genomics Source Type: journals
Differential genomic responses in old vs. young humans despite similar levels of modest muscle damage after resistance loadingEmail this article to a colleague.
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Across numerous model systems, aging skeletal muscle demonstrates an impaired regenerative response when exposed to the same stimulus as young muscle. To better understand the impact of aging in a human model, we compared changes to the skeletal muscle transcriptome induced by unaccustomed high-intensity resistance loading (RL) sufficient to cause moderate muscle damage in young (37 yr) vs. older (73 yr) adults. Serum creatine kinase was elevated 46% 24 h after RL in all subjects with no age differences, indicating similar degrees of myofiber membrane wounding by age. Despite this similarity, from genomic microarrays 318 u...
Source: Physiological Genomics - February 4, 2010 Category: Genetics & Stem Cells Authors: Thalacker-Mercer, A. E., Dell'Italia, L. J., Cui, X., Cross, J. M., Bamman, M. M. Tags: Research Articles Source Type: journals
Epidermal growth factor receptor and vascular endothelial growth factor receptor 2 are specific biomarkers in triple-negative breast cancer. Results from a controlled randomized trial with long-term follow-upEmail this article to a colleague.
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Abstract Triple-negative breast cancer (TNB) has poor prognosis and moreover patients with TNB do not benefit from established targeted
drugs with endocrine therapy or trastuzumab. The aim of the study was to analyze the prevalence of candidate biomarkers in
tumors from patients with TNB. Tissue microarrays were prepared from primary tumors from premenopausal breast cancer patients
(500/564) randomized to adjuvant tamoxifen or no adjuvant treatment. Immunohistochemical (IHC) staining included ER, PR, HER2,
epidermal receptor growth factor (EGFR), vascular endothelial growth factor A (VEGF-A), and vascular en...
Source: Breast Cancer Research and Treatment - February 4, 2010 Category: Cancer & Oncology Tags: Breast Cancer Research and Treatment Source Type: journals
A Multisampling Reporter System for Monitoring MicroRNA Activity in the Same Population of CellsEmail this article to a colleague.
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In this study, we developed a multisampling reporter system in which two secretable bioluminescence-generating enzymes are employed, one as a reporter and the other as an internal control. The reporters consist of a pair of vectors containing the Metridia luciferase gene, one with and one without a duplicated miRNA targeting sequence at their 3′UTR, while the other vector coding for the secreted alkaline phosphatase gene is used as an internal control. This method allows miRNA activity to be monitored within the same population of cells over time by withdrawing aliquots of the culture medium. The practicability and ...
Source: Journal of Biomedicine and Biotechnology - February 4, 2010 Category: Biotechnology Source Type: journals
Tailored Electroactive and Quantitative Ligand Density Microarrays Applied to Stem Cell DifferentiationEmail this article to a colleague.
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Journal of the American Chemical Society, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable).
Source: Journal of the American Chemical Society - February 4, 2010 Category: Chemistry Tags: article Source Type: journals
Application of allele-specific primer extension-based microarray for simultaneous multi-gene mutation screening in patients with non-syndromic hearing loss.Email this article to a colleague.
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Congenital hearing loss (HL) is the most common sensory disorder in humans, affecting one in 1000 infants at birth. A high degree of genetic heterogeneity makes it difficult to screen for mutations in all known deafness genes in clinical applications. We have improved a genotyping microarray using the multiplex PCR-based allele-specific primer extension (ASPE) reaction and applied this method for the genetic diagnosis of congenital HL in Korea. Seven different mutations in the GJB2, SLC26A4 and mitochondrial 12S rRNA genes, which were identified on the basis of a previous study in a Korean population, were selected for...
Source: International Journal of Molecular Medicine - February 4, 2010 Category: Molecular Biology Authors: Choi SY, Lee KY, Kim YE, Bae JW, Oh SK, Kim SY, Hwang SJ, Kim UK, Lee SH Tags: Int J Mol Med Source Type: journals
Expression profile of significant immortalization genes in colon cancer.Email this article to a colleague.
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Cancer is a disease of genomic instability, a multistep process involving numerous mutations and chromosomal aberrations. Telomeres are highly specialized structures at the ends of chromosomes and function to stabilize and protect the ends of linear chromosomes, therefore determining cellular immortalization. Homeostasis of telomere length is a multifactor-dependent process. Since cellular immortalization is an early and essential step towards cancer, the aim of the present study was to determine immortalization genes that are significant in colon cancer and assess their usefulness in the early diagnosis of this tumor....
Source: International Journal of Molecular Medicine - February 4, 2010 Category: Molecular Biology Authors: Witkowska A, Gumprecht J, Glogowska-Ligus J, Wystrychowski G, Owczarek A, Stachowicz M, Bocianowska A, Nowakowska-Zajdel E, Mazurek U Tags: Int J Mol Med Source Type: journals
Specific microRNA expression during chondrogenesis of human mesenchymal stem cells.Email this article to a colleague.
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In this study, we cultured human MSCs and chondrogenic differentiation MSCs of 3 donors, and investigated the miRNA expression profiles of MSCs and chondrogenic differentiated MSCs from 2 donors by using miRNA microarrays. We found 5 miRNAs were significantly overexpressed in chondrogenic differentiated MSCs in each sample, and 4 were further confirmed by real-time RT-PCR assay in the sample from the third independent donor. We also predicted the confirmed miRNAs corresponding to putative target genes by online software. The results indicated that the overexpressed miRNAs in chondrogenic differentiated MSCs may play a role...
Source: International Journal of Molecular Medicine - February 4, 2010 Category: Molecular Biology Authors: Han J, Yang T, Gao J, Wu J, Qiu X, Fan Q, Ma B Tags: Int J Mol Med Source Type: journals
Altered Expression of E-cadherin by Hepatocyte Growth Factor and Effect on the Prognosis of Nasopharyngeal CarcinomaEmail this article to a colleague.
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Conclusion HGF may contribute to cell invasion in NPC by modulating E-cadherin-mediated cell–cell adhesion through downregulation and
internalization of E-cadherin. Altered expression of E-cadherin by HGF is a valuable predictor for prognostic evaluation of
NPC patients.
Content Type Journal ArticleCategory Translational Research and BiomarkersDOI 10.1245/s10434-010-0922-6Authors
Li-qiong Xie, Sun Yat-Sen University Department of Pathology, The First Affiliated Hospital Guangzhou ChinaLi-juan Bian, Sun Yat-Sen University Department of Pathology, The First Affiliated Hospital Guangzhou ChinaZhi Li, S...
Source: Annals of Surgical Oncology - February 4, 2010 Category: Cancer & Oncology Tags: Annals of Surgical Oncology Source Type: journals
Epigenetic Regulation of Milk Production in Dairy CowsEmail this article to a colleague.
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Abstract It is well established that milk production of the dairy cow is a function of mammary epithelial cell (MEC) number and activity
and that these factors can be influenced by diverse environmental influences and management practises (nutrition, milk frequency,
photoperiod, udder health, hormonal and local effectors). Thus, understanding how the mammary gland is able to respond to
these environmental cues provides a huge potential to enhance milk production of the dairy cow. In recent years our understanding
of molecular events within the MEC underlying bovine lactation has been advanced through mammary...
Source: Journal of Mammary Gland Biology and Neoplasia - February 4, 2010 Category: Cancer & Oncology Tags: Journal of Mammary Gland Biology and Neoplasia Source Type: journals
Hochuekkito, a Kampo (traditional Japanese herbal) Medicine, Enhances Mucosal IgA Antibody Response in Mice Immunized with Antigen-entrapped Biodegradable MicroparticlesEmail this article to a colleague.
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The effect of oral administration of Hochuekkito (HET; Bu-Zhong-Yi-Qi-Tang in Chinese), a traditional Japanese herbal medicine, on mucosal IgA immune response was investigated. To induce the antigen-specific antibodies in mucosal site, ovalbumin (OVA)-entrapped biodegradable microparticles (OVA-microparticles) were used as an antigen. Mice were orally immunized with OVA-microparticles for 3 successive days with intragastric gavage. From 7 days after the onset of immunization, the mice were boosted twice a week with the same antigen for 2 weeks. HET or water alone was orally administered to the mice via the intragastric rou...
Source: Evidence-based Complementary and Alternative Medicine - February 4, 2010 Category: Complementary Medicine Authors: Matsumoto, T., Noguchi, M., Hayashi, O., Makino, K., Yamada, H. Tags: Original Articles - Basic Science Source Type: journals
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-SeqEmail this article to a colleague.
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In this study, we used Illumina-based massively parallel sequencing to gain new insight into the transcriptome (RNA-Seq) of the human malaria parasite, Plasmodium falciparum. Using data collected at seven time points during the intraerythrocytic developmental cycle, we (i) detect novel gene transcripts; (ii) correct hundreds of gene models; (iii) propose alternative splicing events; and (iv) predict 5' and 3' untranslated regions. Approximately 70% of the unique sequencing reads map to previously annotated protein-coding genes. The RNA-Seq results greatly improve existing annotation of the P. falciparum genome with over 10...
Source: Molecular Microbiology - February 4, 2010 Category: Microbiology Authors: Thomas D. Otto, Daniel Wilinski, Sammy Assefa, Thomas M. Keane, Louis R. Sarry, Ulrike Böhme, Jacob Lemieux, Bart Barrell, Arnab Pain, Matthew Berriman, Chris Newbold, Manuel Llinás Source Type: journals
Tetraiodothyroacetic Acid (Tetrac) and Nanoparticulate Tetrac Arrest Growth of Medullary Carcinoma of the Thyroid.Email this article to a colleague.
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Conclusions: Acting via a cell surface receptor, tetrac and tetrac NP inhibit growth of h-MTC cells and associated angiogenesis in CAM and mouse xenograft models.
PMID: 20133461 [PubMed - as supplied by publisher]
Source: The Journal of Clinical Endocrinology and Metabolism - February 4, 2010 Category: Endocrinology Authors: Yalcin M, Dyskin E, Lansing L, Bharali DJ, Mousa SS, Bridoux A, Hercbergs AH, Lin HY, Davis FB, Glinsky GV, Glinskii A, Ma J, Davis PJ, Mousa SA Tags: J Clin Endocrinol Metab Source Type: journals
PIKing the right isoform: the emergent role of the p110β subunit in breast cancerEmail this article to a colleague.
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Abstract Class IA phosphoinositide-3’-kinases (PI3Ks) regulate many cellular processes. Despite a clear implication of PI3K in cancer,
the involvement of each of its isoforms namely p110α and p110β in the development of breast cancer remains elusive. Until
recently, the spotlight was given to the α subunit; however, the p110β isoform has now emerged as an interesting target as
well. In order to determine the importance of both these subunits in breast cancer, we aimed to study the expression of p110α
and p110β in a series of invasive breast carcinomas. We constructed tissue microarrays from 315 invas...
Source: Virchows Archiv - February 3, 2010 Category: Pathology Tags: Virchows Archiv Source Type: journals
Genetics of keloid scarringEmail this article to a colleague.
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Abstract Keloid scarring, also known as keloid disease (KD), is a common, abnormally raised fibroproliferative cutaneous lesion that
can occur following even minor skin trauma. The aetiopathogenesis of KD has remained an enigma todate compounded by an ill-defined
clinical management. There is strong evidence suggesting a genetic susceptibility in individuals affected by KD, including
familial heritability, common occurrence in twins and high prevalence in certain ethnic populations. This review aims to address
the genetic aspects of KD that have been described in present literature that include inheritance p...
Source: Archives of Dermatological Research - February 3, 2010 Category: Dermatology Tags: Archives of Dermatological Research Source Type: journals
A randomized phase III study of adjuvant platinum/docetaxel chemotherapy with or without radiation therapy in patients with gastric cancerEmail this article to a colleague.
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Abstract The optimal adjuvant treatment for gastric cancer remains controversial. We compared the efficacy of a docetaxel and platinum
adjuvant chemotherapy regimen, in patients with high-risk gastric cancer, with that of the same chemotherapy plus radiation
therapy (RT). In addition, we evaluated the prognostic and/or predictive value of a panel of molecular markers. Patients with
histologically proven, radically resected gastric cancer, stage ≥T3 and/or N+ were randomized to 6 cycles of docetaxel with
cisplatin, both at 75 mg/m2 every 3 weeks (arm A) or the same treatment with RT (arm...
Source: Cancer Chemotherapy and Pharmacology - February 3, 2010 Category: Cancer & Oncology Tags: Cancer Chemotherapy and Pharmacology Source Type: journals
Gene expression profiling of the proliferative effect of periplocin on mouse cardiac microvascular endothelial cellsEmail this article to a colleague.
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Conclusions The results demonstrated the proliferation action of periplocin on CMEC. Meanwhile, its lower cytotoxicity compared to ouabain
provides a new insight into the treatment of heart failure.
Content Type Journal ArticleCategory Experimental ResearchDOI 10.1007/s11655-010-0033-zAuthors
Xiao-ying Wang, Tianjin University of Traditional Chinese Medicine Institute of Traditional Chinese Medicine Research Tianjin ChinaXiu-mei Gao, Tianjin University of Traditional Chinese Medicine Institute of Traditional Chinese Medicine Research Tianjin ChinaHong Liu, Tianjin University of Traditional Chinese Medi...
Source: Chinese Journal of Integrative Medicine - February 3, 2010 Category: Internal Medicine Tags: Chinese Journal of Integrative Medicine Source Type: journals
Prokineticin-1 (PROK1) modulates interleukin (IL)-11 expression via prokineticin receptor 1 (PROKR1) and the calcineurin/NFAT signalling pathwayEmail this article to a colleague.
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Prokineticin-1 (PROK1) is a multifunctional secreted protein which signals via the G-protein coupled receptor, PROKR1. Previous data from our laboratory using a human genome survey microarray showed that PROK1–prokineticin receptor 1 (PROKR1) signalling regulates numerous genes important for establishment of early pregnancy, including the cytokine interleukin (IL)-11. Here, we have shown that PROK1–PROKR1 induces the expression of IL-11 in PROKR1 Ishikawa cells and first trimester decidua via the calcium–calcineurin signalling pathway in a guanine nucleotide-binding protein (Gq/11), extracellular signal-r...
Source: Molecular Human Reproduction - February 3, 2010 Category: Molecular Biology Authors: Cook, I. H., Evans, J., Maldonado-Perez, D., Critchley, H. O., Sales, K. J., Jabbour, H. N. Tags: Articles Source Type: journals
Endometrial gene expression analysis at the time of embryo implantation in women with unexplained infertilityEmail this article to a colleague.
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In conclusion, endometrial gene expression in women with unexplained infertility at the time of embryo implantation is markedly different from that in fertile women. These results provide new information on genes and pathways that may have functional significance as regards to endometrial receptivity and subsequent embryo implantation.
Source: Molecular Human Reproduction - February 3, 2010 Category: Molecular Biology Authors: Altmae, S., Martinez-Conejero, J.A., Salumets, A., Simon, C., Horcajadas, J.A., Stavreus-Evers, A. Tags: Articles Source Type: journals
microRNA 21: response to hormonal therapies and regulatory function in leiomyoma, transformed leiomyoma and leiomyosarcoma cellsEmail this article to a colleague.
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Aberrant expression of microRNAs (miRNAs), including miR-21, and alteration of their target genes stability have been associated with cellular transformation and tumorigenesis. We investigated the expression, regulation and function of miR-21 in leiomyomas which develop from myometrial cellular transformation. The results indicated that miR-21 is over-expressed in leiomyomas with specific elevation during the secretory phase of the menstrual cycle and in women who received Depo-Provera and oral contraceptives, but reduced due to GnRHa therapy (P < 0.05). Bioinformatic analysis of microarray gene expression profiles prev...
Source: Molecular Human Reproduction - February 3, 2010 Category: Molecular Biology Authors: Pan, Q., Luo, X., Chegini, N. Tags: Articles Source Type: journals
Initial study of microRNA expression profiles of colonic cancer without lymph node metastasisEmail this article to a colleague.
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CONCLUSION: The miRNAs are differentially expressed between colonic tumor tissues and para-cancerous tissues. Many of these miRNAs are expected to participate in the process of multiple tumorigenesis. These miRNAs could play an important role in the carcinogenesis of colon. These results provide new insights in human colorectal cancer genesis.
Source: Chinese Journal of Digestive Diseases - February 3, 2010 Category: Gastroenterology Authors: Ying Xin WANG, Xiao Yan ZHANG, Bao Feng ZHANG, Chang Qing YANG, Xi Mei CHEN, Heng Jun GAO Tags: Original Articles Source Type: journals
Defining the Canonical Form of T-Cell-Mediated Rejection in Human Kidney TransplantsEmail this article to a colleague.
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Banff defines T-cell-mediated rejection (TCMR) using nonspecific lesions and arbitrary cutoffs, with no external gold standard. We reexamined features of TCMR using exclusively molecular definition independent of histopathology. The definition was derived from mouse kidney transplants with fully developed TCMR, and is based on high expression of transcripts reflecting IFNG effects and alternative macrophage activation. In 234 human kidney transplant biopsies for cause phenotyped by microarrays, we identified 26 biopsies meeting these criteria. After excluding three biopsies with unrelated diseases, all 23 biopsies had typi...
Source: American Journal of Transplantation - February 3, 2010 Category: Transplant Surgery Authors: K. S. Famulski, G. Einecke, B. Sis, M. Mengel, L. G. Hidalgo, B. Kaplan, P. F. Halloran Source Type: journals
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasetsEmail this article to a colleague.
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Conclusions:
BABAR is an easy-to-use software tool, simplifying the simultaneous normalisation of heterogeneous two-colour common reference design cDNA microarray-based transcriptomic datasets. We show BABAR transforms real and simulated datasets to allow for the correct interpretation of these data, and is the ideal tool to facilitate the identification of differentially expressed genes or network inference analysis from transcriptomic datasets.
Source: BMC Bioinformatics - Latest articles - February 3, 2010 Category: Bioinformatics Authors: Mark AlstonJohn SeersJay HintonSacha Lucchini Source Type: journals
Constitutive Activation of Smoothened Leads to Female Infertility and Altered Uterine Differentiation in the Mouse.Email this article to a colleague.
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Previous work has identified Indian hedgehog (Ihh) as a major mediator of progesterone signaling during embryo implantation. Ihh acts through its downstream effector smoothened (Smo) to activate the GLI family of transcription factors. In order to gain a better understanding of Ihh action during embryo implantation, we expressed a Cre-recombinase-dependent constitutively activated SMO in the murine uterus using the Pgr(tm2(cre)Lyd) (PR(cre)) mouse model [Pgr(tm2(cre)Lyd+)Gt(ROSA)26Sor(tm1(Smo/EYFP)Amc+), (PR(cre/+)SmoM2(+))]. Female PR(cre/+)SmoM2(+) mice were infertile. They exhibited normal serum progesterone levels ...
Source: Biology of Reproduction - February 3, 2010 Category: Reproduction Medicine Authors: Franco HL, Lee KY, Rubel CA, Creighton CJ, White LD, Broaddus RR, Lewis MT, Lydon JP, Jeong JW, Demayo FJ Tags: Biol Reprod Source Type: journals
Roles of CYP2C29 and RXR{gamma} in vascular EET synthesis of female mice.Email this article to a colleague.
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In conclusion, our data provide the first evidence for a specific signaling cascade, by which estrogen activates CYP2C29 gene in the absence of NO, to synthesize EETs in response to shear stress, via an RXRgamma-related regulatory mechanism. Key words: estrogen, shear stress, endothelium, cytochrome P450.
PMID: 20130225 [PubMed - as supplied by publisher]
Source: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology - February 3, 2010 Category: Physiology Authors: Sun D, Yang YM, Jiang H, Wu H, Ojaimi C, Kaley G, Huang A Tags: Am J Physiol Regul Integr Comp Physiol Source Type: journals
LMNA Mutations, Skeletal Muscle Lipid Metabolism, and Insulin Resistance.Email this article to a colleague.
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Conclusions: Our study suggests imbalance between lipid oxidation and oxidative glucose metabolism in FPLD and LGMD1B patients. The observation suggests an intrinsic defect in skeletal muscle metabolism due to lamin A/C dysfunction. The metabolic FPLD phenotype likely results from this intrinsic defect combined with lipodystrophic "lipid pressure" due to decreased adipose tissue lipid storage capacity.
PMID: 20130076 [PubMed - as supplied by publisher]
Source: The Journal of Clinical Endocrinology and Metabolism - February 3, 2010 Category: Endocrinology Authors: Boschmann M, Engeli S, Moro C, Luedtke A, Adams F, Gorzelniak K, Rahn G, Mähler A, Dobberstein K, Krüger A, Schmidt S, Spuler S, Luft FC, Smith SR, Schmidt HH, Jordan J Tags: J Clin Endocrinol Metab Source Type: journals
PathGen: a transitive gene pathway generatorEmail this article to a colleague.
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Summary: Many online sources of gene interaction networks supply rich visual data regarding gene pathways that can aid in the study of biological processes, disease research and drug discovery. PathGen incorporates data from several sources to create transitive connections that span multiple gene interaction databases. Results are displayed in a comprehensible graphical format, showing gene interaction type and strength, database source and microarray expression data. These features make PathGen a valuable tool for in silico discovery of novel gene interaction pathways, which can be experimentally tested and verified. The ...
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Clement, K., Gustafson, N., Berbert, A., Carroll, H., Merris, C., Olsen, A., Clement, M., Snell, Q., Allen, J., Roper, R. J. Tags: SYSTEMS BIOLOGY Source Type: journals
Biomarker detection in the integration of multiple multi-class genomic studiesEmail this article to a colleague.
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Motivation: Systematic information integration of multiple-related microarray studies has become an important issue as the technology becomes mature and prevalent in the past decade. The aggregated information provides more robust and accurate biomarker detection. So far, published meta-analysis methods for this purpose mostly consider two-class comparison. Methods for combining multi-class studies and considering expression pattern concordance are rarely explored.
Results: In this article, we develop three integration methods for biomarker detection in multiple multi-class microarray studies: ANOVA-maxP, min-MCC and OW-mi...
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Lu, S., Li, J., Song, C., Shen, K., Tseng, G. C. Tags: GENE EXPRESSION Source Type: journals
Dynamically weighted clustering with noise setEmail this article to a colleague.
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Conclusion: Our method produces clusters with more consistent functional annotations and more coherent expression patterns than existing clustering techniques.
Contact: yshen@stat.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Shen, Y., Sun, W., Li, K.-C. Tags: GENE EXPRESSION Source Type: journals
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thalianaEmail this article to a colleague.
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Motivation: Identifying regulatory modules is an important task in the exploratory analysis of gene expression time series data. Clustering algorithms are often used for this purpose. However, gene regulatory events may induce complex temporal features in a gene expression profile, including time delays, inversions and transient correlations, which are not well accounted for by current clustering methods. As the cost of microarray experiments continues to fall, the temporal resolution of time course studies is increasing. This has led to a need to take account of detailed temporal features of this kind. Thus, while standar...
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Kiddle, S. J., Windram, O. P. F., McHattie, S., Mead, A., Beynon, J., Buchanan-Wollaston, V., Denby, K. J., Mukherjee, S. Tags: GENE EXPRESSION Source Type: journals
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effectsEmail this article to a colleague.
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Summary: Finite mixture models are routinely applied to time course microarray data. Due to the complexity and size of this type of data, the choice of good starting values plays an important role. So far initialization strategies have only been investigated for data from a mixture of multivariate normal distributions. In this work several initialization procedures are evaluated for mixtures of regression models with and without random effects in an extensive simulation study on different artificial datasets. Finally, these procedures are also applied to a real dataset from Escherichia coli.
Availability: The latest releas...
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Scharl, T., Gru, B., Leisch, F. Tags: GENE EXPRESSION Source Type: journals
Robust biomarker identification for cancer diagnosis with ensemble feature selection methodsEmail this article to a colleague.
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Motivation: Biomarker discovery is an important topic in biomedical applications of computational biology, including applications such as gene and SNP selection from high-dimensional data. Surprisingly, the stability with respect to sampling variation or robustness of such selection processes has received attention only recently. However, robustness of biomarkers is an important issue, as it may greatly influence subsequent biological validations. In addition, a more robust set of markers may strengthen the confidence of an expert in the results of a selection method.
Results: Our first contribution is a general framework ...
Source: Bioinformatics - February 2, 2010 Category: Bioinformatics Authors: Abeel, T., Helleputte, T., Van de Peer, Y., Dupont, P., Saeys, Y. Tags: DATA AND TEXT MINING Source Type: journals
Expression and Its Clinical Significance of SHP2 in Non-small Cell Lung CancerEmail this article to a colleague.
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Conclusion The expression rate of SHP2 is high and closely correlated to lymphnode metastasis in NSCLC, which implies the occurrence and development of lung cancer may be related to SHP2, and SHP2 may be a new marker and therapeutic targets for lung cancer.
Source: Chinese Journal of Lung Cancer - February 2, 2010 Category: Cancer & Oncology Source Type: journals
Detection of EGFR and COX-2 Expression by Immunohistochemical Method on a Tissue Microarray Section in Lung Cancer and Biological SignificanceEmail this article to a colleague.
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Conclusion Overexpression of EGFR and COX-2 may play an important role in the tumorgenesis, progression and malignancy of lung cancer. Detection of EGFR and COX-2 expression might be helpful to diagnosis and prognosis of lung cancer .
Source: Chinese Journal of Lung Cancer - February 2, 2010 Category: Cancer & Oncology Source Type: journals
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx moriEmail this article to a colleague.
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Conclusions:
In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that corresponding ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. These results should facilitate future functional analyses.
Source: BMC Genomics - Latest articles - February 2, 2010 Category: Genetics & Stem Cells Authors: Shiping LiuSong GaoDanyu ZhangJiyun YinZhonghuai XiangQingyou Xia Source Type: journals
A general co-expression network-based approach to gene expression analysis: comparison and applicationsEmail this article to a colleague.
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Conclusions:
We demonstrated that our novel approach is very effective in discovering the modular structures in microarray data, both for genes and for samples. As the method is essentially parameter-free, it may be applied to large data sets where the number of clusters is difficult to estimate. The method is also very general and can be applied to other types of data. A MATLAB implementation of our algorithm can be downloaded from http://cs.utsa.edu/~jruan/Software.html.
Source: BMC Systems Biology - Latest articles - February 2, 2010 Category: Molecular Biology Authors: Jianhua RuanAngela DeanWeixiong Zhang Source Type: journals
Ontological evaluation of transcriptional differences between sperm of infertile males and fertile donors using microarray analysisEmail this article to a colleague.
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Conclusions We found differences in Gene Ontology terms between the two groups. These differences could potentially be employed to establish
markers of fertility success and to identify cellular processes and complex systems related with male infertility.
Content Type Journal ArticleCategory Gamete BiologyDOI 10.1007/s10815-010-9388-5Authors
Sandra García-Herrero, Universidad de Valencia Instituto Universitario IVI Valencia Valencia SpainNicolás Garrido, Universidad de Valencia Instituto Universitario IVI Valencia Valencia SpainJosé Antonio Martínez-Conejero, Universidad de Valencia Instituto Unive...
Source: Journal of Assisted Reproduction and Genetics - February 1, 2010 Category: Reproduction Medicine Tags: Journal of Assisted Reproduction and Genetics Source Type: journals
