Automated cell annotation and classification on histopathology for spatial biomarker discovery by Zhe Li, Seyed Hossein Mirjahanmardi, Rasoul Sali, Feyisope Eweje, Matthew Gopaulchan, Leon Kloker, Xiaoming Zhang, Guoxin Li, Yuming Jiang, Ruijiang Li

“…By co-registering H&E images with mIF of the same tissue section at the single-cell level, we create a dataset of 1,127,252 cells with high-quality annotations on tissue microarray cores. A deep learning model combining self-supervised learning with domain adaptation is trained to classify four cell types on H&E images with an overall accuracy of 86%-89%, and the cell classification model is applicable to whole slide images. …”
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Interaction between expression of CD23 on B-lymphocytes and level of specific IgE against molecular components of NPC2 family, lipocalins, uteroglobins, and molecular components of... by Jarmila Čelakovská, Petra Boudkova, Eva Cermakova, Ctirad Andrys

“…Serum levels of specific IgE were measured using the component-resolved diagnostic microarray ALEX2 Allergy Xplorer, and the expression of the CD23 molecule on B-cells was evaluated using flow cytometry. …”
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Assessment of Human Epididymis Protein 4 Expression in Breast Ductal Carcinoma In Situ by Nah Ihm Kim, Min Ho Park, Ji Shin Lee

“…An additional independent tissue microarray of 41 DCIS cases was also analyzed for HE4 expression in tumor tissue only. …”
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Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes by Kithmee K. de Silva, Jim M. Dunwell, Anushka M. Wickramasuriya

“…A total of 17,059 genes were filtered from a microarray dataset comprising four stages of SE, i.e., stage I (zygotic embryos), stage II (proliferating tissues at 7 days of induction), stage III (proliferating tissues at 14 days of induction), and stage IV (mature somatic embryos). …”
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The Role of Chromosomal Instability and Epigenetics in Colorectal Cancers Lacking β-Catenin/TCF Regulated Transcription by Wael M. Abdel-Rahman, Johanna E. Lotsari-Salomaa, Sippy Kaur, Anni Niskakoski, Sakari Knuutila, Heikki Järvinen, Jukka-Pekka Mecklin, Päivi Peltomäki

“…MFISH and CGH revealed distinct instability of chromosome structure in RKO. Gene expression microarray of RKO versus 7 colon cancer lines (with active Wnt signaling) and 3 normal specimens revealed 611 differentially expressed genes. …”
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Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. by Owen H Donohoe, Kathy Henshilwood, Keith Way, Roya Hakimjavadi, David M Stone, Dermot Walls

“…Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA-offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. …”
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Anti-Obesity Properties of <i>Boesenbergia rotunda</i> Rhizome Extract: Regulation of Inflammation, Lipid Metabolism, and Insulin Signaling in <i>ob/ob</i> Mice by Muhammad Hermawan Widyananda, Dinia Rizqi Dwijayanti, Airi Fujii, Keita Minamisaka, Yuto Nishidono, Mikio Nishizawa, Nashi Widodo

“…In addition, this treatment reduced triglyceride levels in both the serum and liver and decreased lipid accumulation in hepatocytes. Microarray analysis revealed that hepatic mRNA affected the expression of genes involved in inflammation, lipid metabolism, lipid synthesis, and insulin signaling, leading to improvements in obesity. …”
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R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. by Takeshi Kawakami, Meghan K Jensen, Andrea Slavney, Petra E Deane, Ausra Milano, Vandana Raghavan, Brett Ford, Erin T Chu, Aaron J Sams, Adam R Boyko

“…We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835-11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. …”
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Gut Akkermansia muciniphila, Prevotellaceae, and Enterobacteriaceae spp. as Possible Markers in Women-Related Nutritional and Clinical Trials: Familial Mediterranean Fever Disease by Astghik Pepoyan

“…Materials and Methods: The bacterial response to placebo was fully evaluated on a previous PhyloChip™ DNA microarray-based assay (GEO Series; accession number GSE111835). …”
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Specific binding of human P[28] rotavirus VP8* protein to blood group ABH antigens on type 1 chains. by Yi Zheng, Xiaoman Sun, Yuting Li, Beibei Huang, Yang Chen, Han Zhou, Cuiyan Cao, Wengang Chai, Zhaojun Duan, Dandi Li, Jingyu Yan, Xinmiao Liang

“…In the present study, using a multiphasic approach, including X-ray crystallography, glycan microarray with a dedicated probe library, bio-layer interferometry, site-specific mutagenesis, and molecular docking and dynamics simulations, we found that P[28]-VP8* can bind to all blood group A, B and H(O) antigens but on type 1 chain only, without the capability to bind to any Lewis epitopes or mucin O-glycan cores. …”
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Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk. by Cathy Slack, Christian Werz, Daniela Wieser, Nazif Alic, Andrea Foley, Hugo Stocker, Dominic J Withers, Janet M Thornton, Ernst Hafen, Linda Partridge

“…Biochemical and genetic data suggest that Lnk functions in both the IIS and Ras/Mitogen activated protein Kinase (MapK) signaling pathways. Microarray studies support this model, showing transcriptional feedback onto genes in both pathways as well as indicating global changes in both lipid and carbohydrate metabolism. …”
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Myo‐inositol oxygenase (MIOX) accelerated inflammation in the model of infection‐induced cardiac dysfunction by NLRP3 inflammasome by Wenjun Zhou, Congyi Yu, Yiwen Long

“…Quantitative analysis of messenger RNAs (mRNAs) and gene microarray hybridization was used to analyze the mRNA expression levels. …”
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The impact of MITF expression on tumor-infiltrating lymphocytes in melanoma: Insights into immune microenvironment dynamics by Damir Vučinić, Matea Lekić, Gordana Žauhar, Gordana Zamolo

“…Archival formalin-fixed, paraffin-embedded tissue samples from 81 primary melanoma patients were analyzed via tissue microarray immunohistochemistry to assess MITF protein levels. …”
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The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. by Nhu Thi Khanh Nguyen, Vinh Ha, Nga Vu Thieu Tran, Richard Stabler, Duy Thanh Pham, Thi Minh Vien Le, H Rogier van Doorn, Ana Cerdeño-Tárraga, Nicholas Thomson, James Campbell, Van Minh Hoang Nguyen, Thi Thu Nga Tran, Minh Van Pham, Thuy Thu Cao, Brendan Wren, Jeremy Farrar, Stephen Baker

“…These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla(CTX-M) encoding plasmid.…”
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Uncovering endothelial to mesenchymal transition drivers in atherosclerosis via multi-omics analysis by Qingyan Huang, Yuhong Gan, Xiaoqi Zheng, Zhikang Yu, Qionghui Huang, Mingfeng Huang

“…Methods The single-cell RNA sequencing (scRNA-seq) dataset GSE159677, bulk RNA-seq dataset GSE118446 and microarray dataset GSE56309 were obtained from the Gene Expression Omnibus (GEO) database. …”
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Human umbilical vein endothelial cell miRNA secretome highlights endothelial origin of serum miRNAs by Nora J. Doleschall, Zoltán F. Doleschall, Flóra Demeter, Márta L. Debreczeni, Erika Kajdácsi, László Cervenak, Katalin Keltai

“…Our results also demonstrate that the microarray technology has great use in precision microRNA biomarker discovery using simple models, which should be utilised for further mapping of cell-type specific healthy signatures to further refine blood-based diagnostics.…”
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The Olive Oil Monophenolic Secoiridoid Ligstroside Aglycone Suppresses Melanoma Progression by Targeting the BRAF Signaling Pathway by Md Ashiq Mahmud, Abu Bakar Siddique, Afsana Tajmim, Judy Ann King, Khalid A. El Sayed

“…Daily oral 10 mg/kg LA exhibited potent in vivo antitumor effects against Malme-3M cells xenograft in a nude mouse model by targeting the BRAF signaling pathway. A human Clariom S microarray analysis of the collected Malme- 3M tumors identified 571 dysregulated genes, with the downregulation of pathways critical for melanoma cells growth and survival. …”
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Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. by Zeinab Chaharlashkar, Yousof Saeedi Honar, Meghdad Abdollahpour-Alitappeh, Sepideh Parvizpour, Abolfazl Barzegar, Effat Alizadeh

“…We conducted an integrated analysis to identify critical regulators associated with the prognosis, pathogenesis, and targeted therapies of metastatic-melanoma. A microarray dataset, GSE15605, including 12 metastatic-melanoma and sixteen normal skin (NS) samples, were obtained from the GEO database. …”
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Implications of CYP1B1 in the treatment and prognosis of breast cancer by Maria Carolina Stipp, Jeanine Marie Nardin, José Claudio Casali-da-Rocha, Sérgio Ioshii, Alexandra Acco

“…The aim of the present study was to identify the expression and role of this enzyme in progression, prognosis, and clinical features of breast cancer patients. Methods Microarray paraffin-embedded tumor samples from 166 women with breast cancer were analyzed by immunohistochemical for CYP1B1. …”
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Interaction of Wnt Signaling with BMP/Smad Signaling during the Transition from Cell Proliferation to Myogenic Differentiation in Mouse Myoblast-Derived Cells by Kumiko Terada, Satomi Misao, Naoki Katase, Shin-ichiro Nishimatsu, Tsutomu Nohno

“…Among several extrinsic signaling molecules examined in a microarray analysis of C2C12 cells during the transition from cell proliferation to differentiation after mitogen deprivation, bone morphogenetic protein 4 (BMP4) expression was prominently increased. …”
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