Identifying therapeutic target genes for diabetic retinopathy using systematic druggable genome-wide Mendelian randomization by Long Xie, Yu Qin Peng, Xiang Shen

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Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft by Mikhail G. Dozmorov, Maggie A. Marshall, Narmeen S. Rashid, Jacqueline M. Grible, Aaron Valentine, Amy L. Olex, Kavita Murthy, Abhijit Chakraborty, Joaquin Reyna, Daniela Salgado Figueroa, Laura Hinojosa-Gonzalez, Erika Da-Inn Lee, Brittany A. Baur, Sushmita Roy, Ferhat Ay, J. Chuck Harrell

“…However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. …”
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Jinxinkang granule alleviates chronic heart failure by enhancing GPER/AMPK/PCG-1α-mediated fatty acid oxidation by Haixiang Zhong, Liu He, Wanru Zhong, Lili Wang, Jianmin Luo, Qi Chen, Rong Li, Rong Zhang, Zhongqiu Liu, Yuanyuan Cheng

“…Jinxinkang granule (JXK) is an integrated traditional Chinese medicine formula for treating CHF. …”
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PEAK1 maintains tight junctions in intestinal epithelial cells and resists colitis by inhibiting autophagy-mediated ZO-1 degradation by Zaikuan Zhang, Yajun Xie, Qiying Yi, Jianing Liu, Lin Yang, Runzhi Wang, Jing Cai, Xinyi Li, Xiaosong Feng, Shixiang Yao, Zheng Pan, Magdalena Paolino, Qin Zhou

“…Additionally, PEAK1 binds to CSK to positively regulate Src activity. …”
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AIBP Protects Müller Glial Cells Against Oxidative Stress-Induced Mitochondrial Dysfunction and Reduces Retinal Neuroinflammation by Seunghwan Choi, Soo-Ho Choi, Tonking Bastola, Keun-Young Kim, Sungsik Park, Robert N. Weinreb, Yury I. Miller, Won-Kyu Ju

“…It has previously been shown that apolipoprotein A-I binding protein (APOA1BP or AIBP) has an anti-inflammatory function. …”
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Single‐Cell Analysis of Alternative Splicing and Gene Regulatory Network Reveals Remarkable Expression and Regulation Dynamics During Human Early Embryonic Development by Jiwei Chen, Gaigai Wei, Fangge Sun, Yunjin Li, Shuang Tang, Geng Chen

“…Additionally, we identified functionally important specific gene regulatory modules for each stage and revealed dynamic usage of transcription factor binding motifs (TFBMs). In conclusion, this study provides informative insights into gene dynamic characteristics of human early embryonic development by integrating gene expression level with alternative splicing, isoform switching, and gene regulatory networks. …”
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Omega-3 Fatty Acids and Neuroinflammation in Depression: Targeting Damage-Associated Molecular Patterns and Neural Biomarkers by Ikbal Andrian Malau, Jane Pei-Chen Chang, Yi-Wen Lin, Cheng-Chen Chang, Wei-Che Chiu, Kuan-Pin Su

“…We explore the intricate roles of microglia and astrocytes in propagating inflammatory cascades and discuss how these processes affect neuronal integrity at the cellular level. Central to our analysis are three key molecules: High Mobility Group Box 1 (HMGB1) and S100 Calcium Binding Protein β (S100β) as alarmins, and Neuron-Specific Enolase (NSE) as an indicator of neuronal stress. …”
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Identification and bioinformatics analysis of cilia-associated gene families in Euplotes amieti (Ciliophora, Hypotrichia) by Liheng Shen, Xiaobing Xiong, Zixiang Xu, Yingli Liu, Yan Sheng, Xin Sheng

“…GO terms were enriched in tubulin binding, cilia assembly, and microtubule-based movement. …”
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Advances in Structural Biology for Anesthetic Drug Mechanisms: Insights into General and Local Anesthesia by Hanxiang Liu, Zheng Liu, Huixian Zhou, Rongkai Yan, Yuzhen Li, Xiaofeng Zhang, Lingyu Bao, Yixin Yang, Jinming Zhang, Siyuan Song

“…Structural studies have elucidated anesthetic binding sites and gating mechanisms, providing a foundation for drug optimization. …”
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Genome-Wide Identification and Expression Analysis of the <i>SPL</i> Gene Family in <i>Solanum melongena</i> (Eggplant) by Hefen Cheng, Zhiliang Li, Baojuan Sun, Wei Zhao, Songyuan Zhang, Tao Li, Qian You, Dinggang Zhou

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Role of DEAD/DEAH-box helicases in immunity, infection and cancers by Rex Devasahayam Arokia Balaya, Saptami Kanekar, Shreya Kumar, Richard K. Kandasamy

“…Abstract DEAD/DEAH-box helicases (DDX) are integral RNA-binding proteins within the RNA helicase superfamily 2 (SF2), characterized by distinct DEAD (Asp-Glu-Ala-Asp) and DEAH (Asp-Glu-Ala-His) motifs. …”
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A novel mechanism and model of hydrogen isotope exchange in vacancy considering nuclear quantum effects by Qihang Liu, Fei Sun, Jipeng Zhu, Hai-Shan Zhou, Hongxiang Zong, Zhangcan Yang, Hong-Bo Zhou, Yasuhisa Oya, Yucheng Wu

“…For the first time, this work employs path integral molecular dynamics to account for the nuclear quantum effects of HIs and explore the microscopic mechanisms of HI exchange in tungsten (W) vacancies. …”
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Metabolomics and network analysis reveal the mechanism of Salvia miltiorrhiza bunge extract in ameliorating cognitive dysfunction in sleep-deprived rats by Meiya Zhang, Xirui Huang, Mengxiang Dai, Shunbo Zhang, Chao Yin, Qiuyun You

“…Validation experiments revealed that all eight components of DS extracts had a higher binding ability with PIK3CA, and DS restored the SD-induced abnormal expression of PIK3CA. …”
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UC-MSCs Secretome Induces Proliferation of CD4+ T Cells, CD8+ T Cells, NK Cells, and Increases sPD-1 Levels in Severe COVID-19’s Whole Blood by Winna Soleha, Heri Wibowo, Murdani Abdullah, Saraswati Pradipta, Lucky Novita Syari, Isabella Kurnia Liem, Arleni Bustami, Anna Rozaliyan

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Aberrant fragmentomic features of circulating cell-free mitochondrial DNA as novel biomarkers for multi-cancer detection by Yang Liu, Fan Peng, Siyuan Wang, Huanmin Jiao, Miao Dang, Kaixiang Zhou, Wenjie Guo, Shanshan Guo, Huanqin Zhang, Wenjie Song, Jinliang Xing

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Quantum chemical modeling, molecular docking, and ADMET evaluation of imidazole phenothiazine hybrids by Deepanjali Shukla, Iqbal Azad, Sabahat Yasmeen Sheikh, Saud Nusrat Ali, Naseem Ahmad, Azhar Kamal, Mohd Faiyyaz, Abdul Rahman Khan, Varish Ahmad, Anwar A. Alghamdi, Malik Nasibullah, Firoj Hassan

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Project quality, regulation quality by Elena Mussinelli

“…The scenario is even more complex, if we broaden the scope to include, in addition to prescriptive and binding rules, the vast universe of guiding principles, voluntary standards, guidelines, best practices, etc. …”
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Research progress of CRISPR/Cas systems in nucleic acid detection of infectious diseases by Jinying Dong, Yuguang Du, Lei Zhou

“…The CRISPR/Cas system, consisting of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR‐associated (Cas), is an adaptive immune system that specifically recognizes, binds and cleaves exogenous invasive nucleic acids. …”
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Structure-threshold relationship in food aroma molecules: Insights from S-curve method, molecular docking, and dynamics simulations by Jingtao Wang, Chenglei Zhang, Jiancai Qian, Shan Wang, Wu Fan, Qingzhao Shi, Jian Mao, Jianping Xie, Qidong Zhang, Guobi Chai

“…This study investigates structure-odor threshold relationships of aroma compounds using integrated S-curve analysis, molecular docking, and dynamics simulations. …”
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Unveiling the structural spectrum of SARS-CoV-2 fusion by in situ cryo-ET by Caner Akıl, Jialu Xu, Juan Shen, Peijun Zhang

“…S2’ cleavage is indispensable for advancing fusion intermediates to the fully folded postfusion state, culminating in membrane integration. Subtomogram averaging reveals that the WS6 S2 antibody binds to the spike’s stem-helix, crosslinks and clusters prefusion spikes, as well as inhibits refolding of fusion intermediates. …”
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