piNET–An Automated Proliferation Index Calculator Framework for Ki67 Breast Cancer Images by Rokshana Stephny Geread, Abishika Sivanandarajah, Emily Rita Brouwer, Geoffrey A. Wood, Dimitrios Androutsos, Hala Faragalla, April Khademi

“…It is successfully tested on four datasets, from three scanners comprised of patches, tissue microarrays (TMAs) and whole slide images (WSI), representing a diverse multi-centre dataset for evaluating Ki67 quantification. …”
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G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions by Tiago Santos, Gilmar F. Salgado, Eurico J. Cabrita, Carla Cruz

“…The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. …”
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Monoamine Oxidase B Expression Correlates with a Poor Prognosis in Colorectal Cancer Patients and Is Significantly Associated with Epithelial-to-Mesenchymal Transition-Related Gene... by Yi-Chieh Yang, Ming-Hsien Chien, Tsung-Ching Lai, Chia-Yi Su, Yi-Hua Jan, Michael Hsiao, Chi-Long Chen

“…We therefore analyzed the importance of MAOs in CRC by an in silico analysis and tissue microarrays. Several independent cohorts indicated that high expression of MAOB, but not MAOA, was correlated with a worse disease stage and poorer survival. …”
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Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma by Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuss, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida

“…In this study, scanned histopathological tissue slides from tissue microarrays of PDAC patients (<i>n</i> = 201, image patches <i>n</i> = 81.165) were extracted and assigned to a training, validation, and test set. …”
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Efficacy of Immunohistochemistry for SDHB in the Screening of Hereditary Pheochromocytoma–Paraganglioma by Hye-Ryeon Choi, Ja-Seung Koo, Cho-Rok Lee, Jan-Dee Lee, Sang-Wook Kang, Young-Seok Jo, Woong-Youn Chung

“…In total, 52 patients who underwent surgery for PPGL treatment between 2006 and 2020 and underwent genetic analysis at diagnosis were included. Tissue microarrays (TMAs) were constructed with PPGL tissues and IHC for SDHB was performed on TMA sections. …”
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Single-Walled vs. Multi-Walled Carbon Nanotubes: Influence of Physico-Chemical Properties on Toxicogenomics Responses in Mouse Lungs by Silvia Aidee Solorio-Rodriguez, Andrew Williams, Sarah Søs Poulsen, Kristina Bram Knudsen, Keld Alstrup Jensen, Per Axel Clausen, Pernille Høgh Danielsen, Håkan Wallin, Ulla Vogel, Sabina Halappanavar

“…Neutrophil influx and DNA damage were assessed on days 1 and 28 post-exposure. Genome microarrays and various bioinformatics and statistical methods were used to identify the biological processes, pathways and functions altered post-exposure to CNTs. …”
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Analysis of A Disintegrin and Metalloprotease 17 (ADAM17) Expression as a Prognostic Marker in Ovarian Cancer Patients Undergoing First-Line Treatment Plus Bevacizumab by Marina Fabbi, Delfina Costa, Daniela Russo, Laura Arenare, Gabriele Gaggero, Simona Signoriello, Giovanni Scambia, Carmela Pisano, Nicoletta Colombo, Nunzia Simona Losito, Gilberto Filaci, Anna Spina, Daniela Califano, Giosuè Scognamiglio, Angiolo Gadducci, Delia Mezzanzanica, Marina Bagnoli, Silvano Ferrini, Vincenzo Canzonieri, Paolo Chiodini, Francesco Perrone, Sandro Pignata

“…ADAM17 has been involved in ovarian cancer development, progression and cell resistance to cisplatin. Tissue microarrays from 309 ovarian cancer patients enrolled in the MITO16A/MANGO-OV2 clinical trial were analyzed by immunohistochemistry for ADAM17 protein expression. …”
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Microneedle-Based Natural Polysaccharide for Drug Delivery Systems (DDS): Progress and Challenges by Fouad Damiri, Nagavendra Kommineni, Samuel Ogbeide Ebhodaghe, Raviteja Bulusu, Vaskuri G. S. Sainaga Jyothi, Amany A. Sayed, Aeshah A. Awaji, Mousa O. Germoush, Hamdan S. Al-malky, Mohammed Z. Nasrullah, Md. Habibur Rahman, Mohamed M. Abdel-Daim, Mohammed Berrada

“…As a result, carbohydrate-based microarrays have a high potential to achieve a future step in sensing, drug delivery, and biologics restitution. …”
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HTK vs. HTK-N for Coronary Endothelial Protection during Hypothermic, Oxygenated Perfusion of Hearts Donated after Circulatory Death by Lars Saemann, Kristin Wächter, Nitin Gharpure, Sabine Pohl, Fabio Hoorn, Sevil Korkmaz-Icöz, Matthias Karck, Gábor Veres, Andreas Simm, Gábor Szabó

“…We also determined the transcriptome of LAD samples using microarrays. The endothelial-dependent relaxation was significantly better after HOP with HTK-N. …”
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Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia by Andriana Valkama, Sandra Vorimo, Timo A. Kumpula, Hannele Räsänen, Eeva-Riitta Savolainen, Katri Pylkäs, Tuomo Mantere

“…For genome-wide analysis, FISH needs to be complemented with other cytogenetic methods, including karyotyping and/or chromosomal microarrays. However, this is often not feasible in a diagnostic setup. …”
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Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients by Hana Votavova, Zuzana Urbanova, David Kundrat, Michaela Dostalova Merkerova, Martin Vostry, Monika Hruba, Jaroslav Cermak, Monika Belickova

“…The gene expression profiles of bone marrow CD34⁺ cells were assessed by whole-genome microarrays. Initially, differentially expressed genes (DEGs) were determined between patients with normal ferritin levels and those with IO to address the effect of excessive iron on cellular pathways. …”
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Verification of molecular subtyping of bladder cancer in the GUSTO clinical trial by Jon Griffin, Jenny Down, Lewis A Quayle, Paul R Heath, Ewan A Gibb, Elai Davicioni, Yang Liu, Xin Zhao, Jayne Swain, Dennis Wang, Syed Hussain, Simon Crabb, James WF Catto, the GUSTO Trial Management Group

“…Formalin‐fixed paraffin‐embedded tissue blocks of MIBC were used for gene expression subtyping by gene expression microarrays. Intra‐ and inter‐laboratory technical reproducibilities, together with quality control of laboratory and bioinformatics processes, were assessed. …”
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Metabolic profiling reveals metabolic features of consolidation therapy in pediatric acute lymphoblastic leukemia by Jinqiu Fu, Aijun Zhang, Qinqin Liu, Dong Li, Xiaoming Wang, Libo Si

“…Orthogonal projections to latent structures discriminant analysis and significance analysis of microarrays were used to evaluate the metabolic changes. …”
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Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA by Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Francesco Tarantini, Cosimo Cumbo, Giuseppina Tota, Crescenzio Francesco Minervini, Angela Minervini, Maria Rosa Conserva, Immacolata Redavid, Elisa Parciante, Maria Giovanna Macchia, Giorgina Specchia, Pellegrino Musto, Francesco Albano

“…One of the most useful OGM applications is in hematological malignancies, where chromosomal rearrangements are frequent and conventional cytogenetic analysis alone is insufficient, necessitating further confirmation using ancillary techniques such as fluorescence in situ hybridization, chromosomal microarrays, or multiple ligation-dependent probe amplification. …”
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Dynamic interplay between sortilin and syndecan-1 contributes to prostate cancer progression by Joanna Lazniewska, Ka Lok Li, Ian R. D. Johnson, Alexandra Sorvina, Jessica M. Logan, Carmela Martini, Courtney Moore, Ben S.-Y. Ung, Litsa Karageorgos, Shane M. Hickey, Sarita Prabhakaran, Jessica K. Heatlie, Robert D. Brooks, Chelsea Huzzell, Nicholas I. Warnock, Mark P. Ward, Bashir Mohammed, Prerna Tewari, Cara Martin, Sharon O’Toole, Laura Bogue Edgerton, Mark Bates, Paul Moretti, Stuart M. Pitson, Stavros Selemidis, Lisa M. Butler, John J. O’Leary, Douglas A. Brooks

“…Here we show that there is a dynamic balance between sortilin and syndecan-1, that reports on different metabolic phenotypes. Using tissue microarrays, we demonstrated by immunohistochemistry that sortilin was highly expressed in low-grade cancer, while syndecan-1 was upregulated in high-grade disease. …”
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TOLLIP Protein Expression Predicts Unfavorable Outcome in Renal Cell Carcinoma by Adam Kowalewski, Damian Jaworski, Jędrzej Borowczak, Mateusz Maniewski, Krzysztof Szczerbowski, Paulina Antosik, Justyna Durślewicz, Marta Smolińska, Joanna Ligmanowska, Dariusz Grzanka, Łukasz Szylberg

“…We explored the relationship between primary and metastatic RCC tumor characteristics, patient survival, and TOLLIP expression. The tissue microarrays cohort contained 95 cores of the primary tumor, matched metastases, and matched adjacent tissues derived from 32 RCC patients. …”
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High-resolution analysis of long-term serum antibodies in humans following convalescence of SARS-CoV-2 infection by Antonio Facciuolo, Erin Scruten, Sean Lipsit, Amanda Lang, Zoë Parker Cates, Jocelyne M. Lew, Darryl Falzarano, Volker Gerdts, Anthony J. Kusalik, Scott Napper

“…In this study, we used high-density peptide microarrays representing the complete proteome of SARS-CoV-2 to identify binding sites (epitopes) targeted by antibodies present in the blood of COVID-19 resolved cases at 5 months post-diagnosis. …”
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A pan-cancer and single-cell sequencing analysis of CD161, a promising onco-immunological biomarker in tumor microenvironment and immunotherapy by He Li, Ke Zhou, Kaiyue Wang, Kaiyue Wang, Kaiyue Wang, Hui Cao, Hui Cao, Wantao Wu, Wantao Wu, Zeyu Wang, Zeyu Wang, Ziyu Dai, Ziyu Dai, Shi Chen, Yun Peng, Yun Peng, Yun Peng, Gelei Xiao, Gelei Xiao, Peng Luo, Jian Zhang, Zaoqu Liu, Quan Cheng, Quan Cheng, Hao Zhang

“…Multiplex immunofluorescence staining of tissue microarrays was used to detect the association between CD161 expression and macrophages and T cells.ResultsA high CD161 level was related to neoantigens expression, pathway enrichment, and drug sensitivity. …”
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Technologies for High-Throughput Identification of Antibiotic Mechanism of Action by Bernardo Ribeiro da Cunha, Paulo Zoio, Luís P. Fonseca, Cecília R. C. Calado

“…In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. …”
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Biomarker Candidates for Alzheimer’s Disease Unraveled through In Silico Differential Gene Expression Analysis by Maria-del-Carmen Silva-Lucero, Jared Rivera-Osorio, Laura Gómez-Virgilio, Gustavo Lopez-Toledo, José Luna-Muñoz, Francisco Montiel-Sosa, Luis O. Soto-Rojas, Mar Pacheco-Herrero, Maria-del-Carmen Cardenas-Aguayo

“…Open-access databases of RNA microarrays from the peripheral blood and brain of AD patients were analyzed after background correction and data normalization; the Limma package was used for differential expression analysis (DEA) through statistical R programming language. …”
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