Harnessing Artificial Intelligence and Machine Learning for Identifying Quantitative Trait Loci (QTL) Associated with Seed Quality Traits in Crops by My Abdelmajid Kassem

“…I also explored AI-driven integration of multi-omics data—genomics, transcriptomics, metabolomics, and phenomics—to improve resolution in QTL mapping. …”
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Advancing breast cancer circulating tumour cell research at the Institute of Oncology Ljubljana by Tanja Jesenko, Cvetka Grašič Kuhar, Živa Pišljar, Simona Miceska, Veronika Kloboves-Prevodnik, Maja Čemažar

“…The first method is based on cell biological properties, such as the expression of the epithelial cell adhesion marker (EpCAM), while the second method is based on physical properties of CTCs, such as their larger size and deformability compared to other blood cells. …”
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Cell-in-cell associated lncRNA signature predicts prognosis and immunotherapy response in gastric cancer by Junzuo Lin, Liancheng Wu, Zhengfei Zhao

“…Drug sensitivity analysis revealed low-risk patients responded better to gefitinib/entinostat, while high-risk patients benefited from dasatinib/foretinib. …”
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Identification and expression analysis of myo-inositol oxygenase gene family in Brassica napus L. by CHEN Shubing, XU Zishu, HUANG Qian, ZHANG Hui, ZHANG Kangni, DUAN Yi, SUN Yue’e, ZHOU Weijun, XU Ling

“…Expression profiles under different stresses demonstrated that the expression of BnMIOX1 gene was obviously induced under drought and salt stresses, while BnMIOX1, BnMIOX2, and BnMIOX9 genes had significant responses to drought, salt, abscisic acid (ABA), and cold stresses. …”
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Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation. by Surbhi Kumawat, Askhan Shametov, Liia R Valeeva, Yoonha Ju, Irene Martinez, Dhenugen Logeswaran, Hongfei Chen, Jenn M Coughlan, Julian J-L Chen, Yao-Wu Yuan, James M Sobel, Dal-Hoe Koo, Eugene V Shakirov, Jae Young Choi

“…For instance, M. lewisii harbored two sequence-divergent TR paralogs while its sister species the paralog had pseudogenized. …”
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Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast. by Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský

“…Interestingly, Mga2 binding appears to be dependent on the presence of Cbf11 and Cbf11 likely acts as a tether to DNA, while Mga2 is needed to activate the target genes. …”
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Differential retinal ganglion cell resilience to optic nerve injury across vertebrate species by Julie D. De Schutter, Anyi Zhang, Pieter-Jan Serneels, Lieve Moons, Luca Masin, Steven Bergmans

“…In this study, we compare RGC densities and survival rates following optic nerve crush (ONC) in three vertebrate models—mice, zebrafish, and killifish—under standardized experimental conditions. Transcriptomic analysis confirmed that, similar to RBPMS in mice, Rbpms2 serves as a pan-RGC marker in zebrafish and killifish. …”
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Integrating Agronomic and Molecular Advancements to Enhance Nitrogen Use Efficiency (NUE) and Promote Sustainable Rice Production by Uttam Bahadur Kunwar, Nazer Manzoor, Jiancheng Wen, Naba Raj Pandit

“…This review highlights novel agronomic and molecular strategies to enhance NUE, rice yields, and profitability, while minimizing environmental impact. The agronomic strategies include the 4R Nutrient Stewardship framework, enhanced efficiency nitrogen fertilizers (EENFs), nano-fertilizers, biochar-based fertilizers, biological N fixation, and sensor-based fertilizer management in major rice-growing countries. …”
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Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a "giant virus". by Eric R Gann, P Jackson Gainer, Todd B Reynolds, Steven W Wilhelm

“…Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. …”
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Time-resolved oxidative signal convergence across the algae–embryophyte divide by Tim P. Rieseberg, Armin Dadras, Tatyana Darienko, Sina Post, Cornelia Herrfurth, Janine M. R. Fürst-Jansen, Nils Hohnhorst, Romy Petroll, Stefan A. Rensing, Thomas Pröschold, Sophie de Vries, Iker Irisarri, Ivo Feussner, Jan de Vries

“…Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood. …”
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Early assessment of IL8 and PD1+ Treg predicts response and guides treatment monitoring in cemiplimab-treated cutaneous squamous cell carcinoma by Teresa Troiani, Fabiana Napolitano, Luigi Formisano, Roberto Bianco, Daniela Russo, Daniela Esposito, Giuseppe Ercolano, Angela Ianaro, Alberto Servetto, Daniela Claudia Maresca, Marcella Scala, Annarita Amato, Stefania Belli, Claudia Maria Ascione, Angela Vallefuoco, Giovanna Attanasio, Fabio Somma, Silvia Varricchio, Massimo Mascolo, Claudia Costa, Alessia Villani, Massimiliano Scalvenzi, Gianfranco Orlandino

“…Finally, IL8 mirrored the tissue results, unlike IL1β, with early (T1) and then sustained (T3) downregulation of its levels in responder patients, while increased in non-responders.Conclusions Taken together, these findings shed light on the significance of early transcriptomic and immune cell modulation in predicting responses to cemiplimab therapy. …”
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Ability of SPP1 to Alleviate Post‐Intracerebral Hemorrhage Ferroptosis via Nrf2/HO1 Pathway by Pengpeng Li, Zhenxin Tao, Yangyang Gao, Zhengqian Mu, Jiajia Tian, YaTing Zhang, Wenhui Yang, Yilu Li, Xudong Zhao

“…In the ICH model, OPN administration improved neurological outcomes, elevated antioxidant markers, and reduced lipid peroxidation. OPN upregulated GPX4 while suppressing ACSL4, indicating anti‐ferroptotic effects. …”
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Comparative analysis of WC1.1+ and WC1.2+ γδ T cell subset responses from cattle naturally infected with Mycobacterium bovis to repeat stimulation with mycobacterial antigens. by Alia Parveen, Sajad A Bhat, Mahmoud Elnaggar, Kieran G Meade

“…Previous studies have identified a preferential transcriptomic response in WC1.1+ cells during natural bTB infection, suggesting a subset-specific response to mycobacterial antigens. …”
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Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut by Sergio Triana, Camila Metz‐Zumaran, Carlos Ramirez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, Daniel Schraivogel, Andreas R Gschwind, Ashwini K Sharma, Lars M Steinmetz, Carl Herrmann, Theodore Alexandrov, Steeve Boulant, Megan L Stanifer

“…To address this gap, we performed single‐cell transcriptomics of SARS‐CoV‐2‐infected intestinal organoids. …”
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Effects of Liquid Bio-Fertilizer on Plant Growth, Antioxidant Activity, and Soil Bacterial Community During Cultivation of Chinese Cabbage (<i>Brassica rapa</i> L. ssp. <i>pekinens... by Tran Yen Linh Le, Junkyung Lee, Su-Yeon Shim, Jiwon Jung, Soo-Ryang Kim, Sung-Ha Hong, Myung-Gyu Lee, Sun-Goo Hwang

“…These findings demonstrate that LBF enhances plant growth and soil fertility while influencing microbial dynamics and gene expression.…”
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Piceatannol Induces Mitochondrial Dysfunction in <i>Toxoplasma gondii</i> by Zhenhe Liu, Haolong Qiu, Yucong Jiang, Yuxi Mo, Linlin Lu, Yan Wang, Dandan Hu, Xingju Song

“…In this study, mechanistic analyses indicated that PIC disrupts mitochondrial integrity in tachyzoites, reducing mitochondrial membrane potential and ATP production while elevating ROS levels. Transcriptomic profiling identified significant suppression of oxidative phosphorylation-related genes, consistent with mitochondrial dysfunction. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…The presence of the HERV-K/HML-2 Gag antigen was confirmed by IHC in 20/40 (50%) ovarian cancers while no Gag expression was found in normal ovarian tissue samples. …”
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Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury by Fan Lu, Ting Huang, Ruichang Chen, Haiyan Yin

“…ABSTRACT The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota’s role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. …”
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TMEM132A: a novel susceptibility gene for lung adenocarcinoma combined with venous thromboembolism identified through comprehensive bioinformatic analysis by Pei Xie, Yingli Liu, Pingping Bai, Yue Ming, Qi Zheng, Li Zhu, Yong Qi

“…This study utilized public databases to identify crosstalk genes (CGs) between LUAD and VTE, applied machine learning methods to discover shared diagnostic biomarkers, and explored their underlying mechanisms.MethodsDisease-specific genes for VTE were extracted from comprehensive genomic databases (CTD, DisGeNET, GeneCards, OMIM), while transcriptomic profiles of LUAD and VTE cohorts were retrieved from GEO via GEOquery implementation. …”
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FAM111B knockdown attenuates tumorigenesis of ovarian cancer via the downregulation of MYC by Guoyu Yu, Fang Wei, Wanying Li, Qiuyun Guo, Lihong Zhang

“…Abstract Background Ovarian cancer, a prevalent malignancy with the highest fatality rate among gynecological cancers, continues to face challenges in the development of effectively targeted therapeutic approaches. While the FAM111B gene has been implicated in various cancer types, its specific role in ovarian cancer remains poorly understood. …”
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