CHD1 contributes to intestinal resistance against infection by P. aeruginosa in Drosophila melanogaster. by Johanna Sebald, Stefano Morettini, Valerie Podhraski, Cornelia Lass-Flörl, Alexandra Lusser

“…Evidence for a role as transcriptional regulator comes from its colocalization with elongating RNA polymerase II as well as from studies of fly Hsp70 transcription. Here we used microarray analysis to identify target genes of CHD1. …”
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Xirp proteins mark injured skeletal muscle in zebrafish. by Cécile Otten, Peter F van der Ven, Ilka Lewrenz, Sandeep Paul, Almut Steinhagen, Elisabeth Busch-Nentwich, Jenny Eichhorst, Burkhard Wiesner, Derek Stemple, Uwe Strähle, Dieter O Fürst, Salim Abdelilah-Seyfried

“…Through the use of Xirp1 and Xirp2a as markers, myocellular injury can now be detected, even though functional studies indicate that these proteins are not essential in this process. …”
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Parallel clustering algorithm for large-scale biological data sets. by Minchao Wang, Wu Zhang, Wang Ding, Dongbo Dai, Huiran Zhang, Hao Xie, Luonan Chen, Yike Guo, Jiang Xie

“…The runtime is reduced from serval hours to a few seconds, which indicates that parallel algorithm is capable of handling large-scale data sets effectively. The parallel affinity propagation also achieves a good performance when clustering large-scale gene data (microarray) and detecting families in large protein superfamilies.…”
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Transcription factor binding site analysis identifies FOXO transcription factors as regulators of the cutaneous wound healing process. by Karl Markus Roupé, Srinivas Veerla, Joshua Olson, Erica L Stone, Ole E Sørensen, Stephen M Hedrick, Victor Nizet

“…Conversely knockdown of FOXO3 in keratinocytes had the opposite effect and in an in vivo mouse model with FOXO3 knockout mice we detected significantly accelerated wound healing. …”
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A first large study of whole-exome sequencing (WES) in 489 patients with suspected rare genetic disorders at a tertiary centre in Malaysia by Lip Hen Moey, Go Hun Seo, Boon Eu Cheah, Wee Teik Keng, Hane Lee, Gaik Siew Ch’ng

“…Whole exome sequencing (WES) is a comprehensive test that can detect not only many of the same large deletions and duplications as CMA, but also detect other genetic variants that are detected by gene panels. …”
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The apoptotic and genomic studies on A549 cell line induced by silver nitrate by Ayse Kaplan, Gulsen Akalin Ciftci, Hatice Mehtap Kutlu

“…The influences of silver nitrate were studied via MTT assay, flow cytometry, immunocytochemical, confocal and transmission electron microscopy, and microarray assays. Silver nitrate showed inhibitory effects against A549 cells in a dose- and time-dependent manner for 24, 48, and 72 h and induced apoptosis. …”
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Pain-stimulated ultrasound vocalizations and their impact on pain response in mice. by Satoka Kasai, Saki Ukai, Junpei Kuroda, Tsugumi Yamauchi, Daisuke Yamada, Akiyoshi Saitoh, Satoshi Iriyama, Masashi Suzuki, Kazuki Arita, Yoshio Nakano, Satoru Miyazaki, Kazumi Yoshizawa

“…We also examined the effects of psychological stress caused by the ultrasound on an inflammatory pain model of mice. …”
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NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes by Michael Chang, Mohamed Sherief, Maria Ioannou, Viveka Chinnasamy, Lucy Chen, Michael Frost, Michelle Mattson-Hoss, Herb Sarnoff, David O. Kamson, Matthias Holdhoff, Debraj Mukherjee, Chetan Bettegowda, Jordina Rincon-Torroella, Victoria Croog, Peng Huang, Fausto J. Rodriguez, Calixto-Hope G. Lucas, Karisa C. Schreck

“…Methods We assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. …”
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Differential and directional estrogenic signaling pathways induced by enterolignans and their precursors. by Yun Zhu, Kayoko Kawaguchi, Ryoiti Kiyama

“…All the enterolignans/precursors examined showed activation of the Erk1/2 and PI3K/Akt pathways, indicating the involvement of rapid signaling through the non-genomic estrogen signaling pathway. However, when their effects on specific cell functions, cell cycle progression and chemokine (MCP-1) secretion were examined, positive effects were observed only for enterolactone, suggesting that signals are given in certain directions at a position closer to cell functions. …”
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Analysis of Gene Expression in Human Dermal Fibroblasts Treated with Senescence-Modulating COX Inhibitors by Jeong A. Han, Jong-Il Kim

“…To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. …”
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Genes that act downstream of sensory neurons to influence longevity, dauer formation, and pathogen responses in Caenorhabditis elegans. by Marta M Gaglia, Dae-Eun Jeong, Eun-A Ryu, Dongyeop Lee, Cynthia Kenyon, Seung-Jae Lee

“…However, the mechanisms underlying these effects are incompletely understood. Using whole-genome microarray analysis, we identified transcripts whose levels are altered by mutations in the intraflagellar transport protein daf-10, which result in impaired development and function of many sensory neurons in C. elegans. …”
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Constitutional Chromothripsis on Chromosome 2: A Rare Case with Severe Presentation by Afia Hasnain, Laura L. Thompson, Nicole L. Hoppman, Karine Hovanes, Jing Liu, Bita Hashemi

“…We concluded that the complexity of the genomic rearrangement and the combined dosage/structural effect of these copy number variants are likely explanations for the severe presentation in our patient.…”
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RRHGE: A Novel Approach to Classify the Estrogen Receptor Based Breast Cancer Subtypes by Ashish Saini, Jingyu Hou, Wanlei Zhou

“…We propose a novel method to measure and extract the reliable (biologically true or valid) interactions from gene interaction networks and incorporate the extracted reliable gene interactions into our proposed RRHGE algorithm to identify significant gene signatures from microarray gene expression data for classifying ER+ and ER− breast cancer samples. …”
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Integrated multiomics analysis identifies potential biomarkers and therapeutic targets for autophagy associated AKI to CKD transition by Yaojun Wang, Qiang Li

“…We performed weighted correlation network analysis (WGCNA) using two microarray datasets (GSE139061 and GSE66494) in the GEO database and identified autophagy signatures by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA enrichment analysis. …”
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Theory on the coupled stochastic dynamics of transcription and splice-site recognition. by Rajamanickam Murugan, Gabriel Kreiman

“…We evaluate these theoretical predictions by considering human and mouse exon microarray data as well as RNAseq data from multiple different tissues. …”
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Multiple Circulating Cytokines Are Coelevated in Chronic Obstructive Pulmonary Disease by Senthooran Selvarajah, Ian Todd, Patrick J. Tighe, Michelle John, Charlotte E. Bolton, Timothy Harrison, Lucy C. Fairclough

“…To investigate this, we developed a protein microarray system to detect multiple cytokines in small volumes of serum. …”
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Bioinformatics methods for identifying differentially expressed genes and signaling pathways in nano-silica stimulated macrophages by Lin Zhang, Changfu Hao, Juan Li, Yaqian Qu, Lei Bao, Yiping Li, Zhongzheng Yue, Miao Zhang, Xinghao Yu, Huiting Chen, Jianhui Zhang, Di Wang, Wu Yao

“…The incidence of disease relating to nanoparticle exposure has been rising rapidly in recent years, for which there is no effective treatment. Macrophage is suggested to play a crucial role in the development of pulmonary disease. …”
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CD155 blockade enhances allogeneic natural killer cell-mediated antitumor response against osteosarcoma by Lei Shi, Christian M Capitini, Amy K Erbe, Fernanda Szewc, Longzhen Song, Matthew H Forsberg, David P Turicek, Paul D Bates, Devin M Burpee, Aicha E Quamine, Johnathan D Ebben, Jillian M Kline, Emily O Lafeber, Madison F Phillips, Monica M Cho, Amanda S Ceas, John A Kink

“…Background Allogeneic bone marrow transplant (alloBMT) is curative for hematologic malignancies through the graft-versus-tumor (GVT) effect but has been ineffective for solid tumors like osteosarcoma (OS). …”
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A Synopsis of Serum Biomarkers in Cutaneous Melanoma Patients by Pierre Vereecken, Frank Cornelis, Nicolas Van Baren, Valérie Vandersleyen, Jean-François Baurain

“…The expression of biomarkers can be detected intracellularly or on the cell membrane of melanoma cells or noncancer cells in association with the melanoma. …”
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c-Myc-dependent LAMP3 regulates the proliferation, metastasis and metabolic reprogramming of tongue squamous cell carcinoma by Jing Feng, Wei He, Jin Fang

“…Differential expression of LAMP3 in TSCC from GEO microarray was analyzed, and pathway enrichment analysis of LAMP3 was performed utilizing GSEA. …”
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