PATHOMICS – A NOVEL OMICS APPROACH FOR HISTOPATHOLOGY

“…., an approach in which the model learns all the steps between the initial input and the final output, providing qualitative or semiquantitative (class) data. …”
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Genome-wide identification and molecular characterization of the MAPK family members in sand pear (Pyrus pyrifolia) by Yue Xu, Huiying Wang, Haiyan Shi

“…These findings indicate that the integrated analysis of transcriptomic and genomic data provides critical genetic insights into the MAPK genes in sand pear, culminating in the identification of a total of 25 PpMAPK genes in this species. …”
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Versatile physiological functions of the Nudix hydrolase family in berry development and stress response in grapevine by Pei-pei WANG, Zhao-ke WANG, Le GUAN, Muhammad Salman HAIDER, Maazullah NASIM, Yong-bing YUAN, Geng-sen LIU, Xiang-peng LENG

“…Nudix hydrolases are widely distributed across all classes of organisms and provide the potential capacity to hydrolyze a wide range of organic pyrophosphates. …”
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Shengyu decoction ameliorates knee osteoarthritis by inhibiting endoplasmic reticulum stress via Piezo1 channels by Xuyu Song, Ying Liu, Xianhui Shen, Lei Zhang, Hongwei Kong, Siyi Chen, Lisong Sheng, Lisong Sheng, Rong Sun, Rong Sun, Rong Sun

“…Overall, our work emphasizes the pivotal role of TCM in addressing medical challenges and provides new ideas for the treatment of KOA.…”
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Response of different cotton genotypes to salt stress and re-watering by Kang Zhao, Tao Yang, Bo Pang, Honggang Wang, Zhining Yang, Weiwei Liang, Cun Rui, Wengwei Gao

“…This study provides a theoretical basis for further exploration of the molecular mechanism of cotton salt tolerance and genetic resources for breeding salt-tolerant cotton.…”
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Integrative analysis of epigenetic subtypes in acute myeloid Leukemia: A multi-center study combining machine learning for prognostic and therapeutic insights. by Jincan Li, Shengyue Wang

“…The BEAT (n = 649), TARGET (n = 156), GSE12417 (n = 79), and GSE37642 (n = 136) cohorts contributed transcriptome data. Molecular subtypes were identified using empirical Bayes-based clustering on the TCGA cohort. …”
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Ethyl β-carboline-3-carboxylate targets PRDX5/c-Jun axis for novel therapeutic strategy against cervical cancer by Wan-Qiu Xiao, Dong-Hun Lee, Hakjin Kim, Hui-Na Zhang, Yao-Yuan Feng, Ying-Hua Jin, Mei-Hua Jin, Ying-Hao Han, Taeho Kwon, Hu-Nan Sun

“…Notably, β-CCE treatment promotes apoptosis through c-Jun up-regulation, with PRDX5 knockdown enhancing this effect while its overexpression provides protection. In xenograft mouse models, β-CCE treatment significantly suppressed tumor growth and enhanced anti-tumor immune responses, particularly in PRDX5-depleted conditions, without apparent systemic toxicity. …”
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Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties by Choy Yuen Khew, Jennifer Ann Harikrishna, Wei Yee Wee, Ee Tiing Lau, Siaw San Hwang

“…Comparison of flower and fruit transcriptome data from the three different black pepper varieties revealed a large number of DEGs between flower and fruit of the SA variety. …”
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Identification and Validation of Key Genes Involved in the Coupling of Mitochondria-Associated Endoplasmic Reticulum Membrane in Hemorrhoidal Disease by Mao L, Rao Z, Wang Y, Yang J, He J, Zheng Z, Chen L

“…This study aims to identify key genes linked to MAM in HD and to provide novel therapeutic targets.Methods: Transcriptome data and MAM-related genes (MAM-RGs) were obtained from the Gene Expression Omnibus (GEO) database and relevant literature. …”
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Genome-Wide Identification and Characterization of <i>TaCRY</i> Gene Family and Its Expression in Seed Aging Process of Wheat by Guoqing Cui, Xiuyan Cui, Junjie Wang, Menglin Lei, Xia Liu, Yanzhen Wang, Haigang Wang, Longlong Liu, Zhixin Mu, Xia Xin

“…This study expands our understanding of <i>TaCRY</i> diversity and provides valuable molecular information for marker-assisted selection in wheat improvement.…”
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Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks by Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara C Klett, Sabrina J Kugler, Jose M Muino, Vladimir B Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe

“…Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.…”
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Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution by John F. Fullard, Prashant NM, Donghoon Lee, Deepika Mathur, Karen Therrien, Aram Hong, Clara Casey, Zhiping Shao, Marcela Alvia, Stathis Argyriou, Tereza Clarence, David Burstein, Sanan Venkatesh, Pavan K. Auluck, Lisa L. Barnes, David A. Bennett, Stefano Marenco, PsychAD Consortium, Kiran Girdhar, Vahram Haroutunian, Gabriel E. Hoffman, Georgios Voloudakis, Jaroslav Bendl, Panos Roussos

“…As a commitment to fostering collaborative research, we provide this valuable resource as an online repository, enabling widespread analyses across the scientific community.…”
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A RACK1 family protein regulates pathogenicity of Peronophythora litchii by acting as a scaffold for MAPK signal modules by Guanghui Kong, Rui Li, Weixiong Huang, Yaowen Yang, Tianfang Guan, Jinghan Liu, Wen Li, Tom Hsiang, Pinggen Xi, Minhui Li, Zide Jiang

“…As well, PlMKP1 also interacted with PlMAPK1 and PlMAPK2. These results provide insights into the direct interactions between RACK1, MAPKs, and MKP, and their functions in growth, development, and pathogenesis in a plant pathogenic oomycete.…”
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microRNA‐122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma by Julja Burchard, Chunsheng Zhang, Angela M Liu, Ronnie T P Poon, Nikki P Y Lee, Kwong‐Fai Wong, Pak C Sham, Brian Y Lam, Mark D Ferguson, George Tokiwa, Ryan Smith, Brendan Leeson, Rebecca Beard, John R Lamb, Lee Lim, Mao Mao, Hongyue Dai, John M Luk

“…In vitro miR‐122 data further provided a direct link between induction of miR‐122‐controlled genes and impairment of mitochondrial metabolism. …”
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Pericytes Promote More Vascularization than Stromal Cells via an Interleukin‐6‐Dependent Mechanism in Microfluidic Chips by Julian Gonzalez‐Rubio, Hannah Kubiza, Yong Xu, Hiltrud Koenigs‐Werner, Mona Sophie Schmitz, Michaela Schedel, Christian Apel, Stefan Jockenhoevel, Christian G. Cornelissen, Anja Lena Thiebes

“…Pericytes can wrap around endothelial vessels acting as mural cells, while stromal cells remain separated. Whole‐transcriptome sequencing confirms an upregulation of pro‐vascularization genes in endothelial cell‐pericyte co‐cultures, while metabolism increases and inflammation decreases in stromal cell co‐cultures. …”
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ARF4 acting upstream of LBD16 promotes adventitious root formation in peach by Jingjing Liu, Lingling Gao, Ruoxi Zhang, Anqi Gao, Zamith Kerubo Oginga, Beibei Zheng, Yuepeng Han

“…The results not only provide novel insights into the functions of ARFs in regulating plant growth and development, but will also be useful for fulfilling asexual propagation by stem cuttings in peach.…”
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A library of lineage-specific driver lines connects developing neuronal circuits to behavior in the Drosophila ventral nerve cord by Jelly HM Soffers, Erin Beck, Daniel J Sytkowski, Marianne E Maughan, Devasri Devarakonda, Yi Zhu, Beth A Wilson, Yu-Chieh David Chen, Ted Erclik, James W Truman, James B Skeath, Haluk Lacin

“…Looking forward, this lineage-specific split-GAL4 driver library will provide the genetic tools needed to address the questions emerging from the analysis of the recent VNC connectome and transcriptome datasets.…”
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Lipophilic Resazurin in Bioelectrochemical Systems: Role in Regulating Carbon Metabolic Pathways by Siyu Tan, Xiao Zhu, Xinxin Wang, Huangsheng Su, Zongqiang Zhu, Xiaobo Luo, John R. Reinfelder, Yundang Wu, Fangbai Li

“…This mechanism enhances TCA cycle activity and overall lactate metabolic efficiency. The findings provide insights into microbial carbon metabolic regulation and offer strategies for optimizing bioelectrochemical systems for bioremediation.…”
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ABA-activated subclass III SnRK2s control kernel maturation in maize by Yayun Wang, Tiandan Long, Aying Qin, Qiang Liao, Hao Wang, Junjie Zhang, Hanmei Liu, Yinghong Liu, Yufeng Hu, Yubi Huang, Yangping Li

“…Overall, our findings establish ABA-activated SnRK2s as central regulators of kernel maturation in maize and provide valuable genetic resources for breeding maize varieties with low moisture content at harvest.…”
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The Root Development Genes (RDGs) Network in <i>Brassica napus</i> and the Role of <i>BnaSHR-6</i> in Response to Low Nitrogen by Xingying Chen, Sining Zhou, Shuang Ye, Zhuo Chen, Zexuan Wu, Shiying Liu, Liping Hu, Xiwen Yang, Xiaoya Yang, Peiji He, Xingzhi Qian, Huafang Wan, Ti Zhang, Nengwen Ying, Huiyan Zhao, Jiana Li, Cunmin Qu, Hai Du

“…These findings advance our understanding of RDGs in <i>B. napus</i> and provide valuable gene resources for subsequent molecular breeding.…”
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