PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. by Marialuisa Pellegrini-Calace, Tim Maiwald, Janet M Thornton

“…Therefore, computational methods which, given a set of 3D coordinates, can automatically identify and describe channels in transmembrane proteins are key tools to provide insights into how they function.Herein we present PoreWalker, a fully automated method, which detects and fully characterises channels in transmembrane proteins from their 3D structures. …”
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Identification of Keystone Plant Species for Avian Foraging and Nesting in Beijing’s Forest Ecosystems: Implications for Urban Forest Bird Conservation by Lele Lin, Yongjian Zhao, Chao Yuan, Yushu Zhang, Siyu Qiu, Jixin Cao

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Bioinformatics-driven exploration of key genes and mechanisms underlying oxidative stress in traumatic brain injury by Bin Ren, Jifang Liang, Leifang Yang, Xiaocong Wei, Min Guo, Hong Li

“…This study aims to elucidate the potential molecular interactions between key genes associated with oxidative stress and their influence on TBI pathogenesis.MethodsTBI dataset and oxidative stress-related genes sourced from Public databases. Differential expression analysis and machine learning models were executed to select key genes, which were further validated using receiver operating characteristic (ROC) curves. …”
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Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. by Franck Dedeine, Lucy A Weinert, Diane Bigot, Thibaut Josse, Marion Ballenghien, Vincent Cahais, Nicolas Galtier, Philippe Gayral

“…A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. …”
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Comparing soil microbial diversity in smallholder plantain backyard gardens and main farms in Western and Central Africa by Manoj Kaushal, Yao Adjiguita Kolombia, Amos Emitati Alakonya, Cargele Masso

“…Beneficial genera such as Bacillus, Streptomyces, Bradyrhizobium, and Paenibacillus were also detected. Functional predictions based on COG and KEGG databases indicated notable differences in microbial functional potential between the two settings. …”
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Positioning, navigation, and timing on the Moon and Mars with galactic cosmic rays by G. Leone, H.K.M. Tanaka, M. Holma, S. Krishnan, A.R. Duffy, T. Enqvist, P. Kuusiniemi, J. Joutsenvaara, G. Cerretto, E. Cantoni, M. Sellone, J. Marteau, D. Lo Presti, J.G. Szűcs, D. Varga

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Identification and Analysis of Phenolic Compounds in <i>Vaccinium uliginosum</i> L. and Its Lipid-Lowering Activity In Vitro by Ying Zhang, Wenjiang Dong, Manjun Zhao, Jiyue Zhang, Li Li, Yan Ma, Xianjun Meng, Yuehua Wang

“…(VU), rich in polyphenols, is an important wild berry resource primarily distributed in extremely cold regions. …”
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Exploring Autophagy-Related Gene Expression in Hepatocellular Carcinoma via TCGA, GEPIA2, and HPA Databases: Implications for Prognosis by Gu X, Chen Y, Hu X, Li Y, Zhu R, Li H, Yuan Z, Wang Y

“…RT-qPCR analysis further confirmed significant upregulation of mRNA expression levels of randomly selected BAG3, EIF2AK2, KIF5B, and RAB24 in HCC cell lines, consistent with the bioinformatics analysis findings.Conclusion: This study showed that the 41 obtained ARGs, such as ATG16L1, ATG4B, BAG3, KIF5B, MAPK1, RAB24, and SOGA1, these findings suggest that ARGs may serve as prognostic biomarkers for HCC, warranting further validation in clinical cohorts and functional studies.Keywords: hepatocellular carcinoma, bioinformatics, autophagy, prognostic markers, TCGA…”
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Exploring causal relationships between brain imaging-derived phenotypes and ovarian cancer risk: a bidirectional Mendelian randomization by Ting Liu, Xiaoqian Tuo, Huifang Zhao, Yan Wang, Yu Jiang, Jiaojiao Lu

“…Methods This study identified 587 brain IDPs using structural and diffusion magnetic resonance imaging (MRI) data from the UK Biobank and data were sourced from two independent Genome-Wide Association Studies (GWAS). …”
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Additive Manufacturing for Automotive Radar Sensors Using Copper Inks and Pastes by Nihesh Mohan, Fabian Steinberger, Sonja Wächter, Hüseyin Erdogan, Gordon Elger

“…It was revealed that low-cost conductive filaments with low resistivity and current carrying capacity are commercially still not available. The best option sourced was a copper–polyester-based filament with 6000 µΩcm after printing. …”
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Single-cell transcriptomics of vomeronasal neuroepithelium reveals a differential endoplasmic reticulum environment amongst neuronal subtypes by GVS Devakinandan, Mark Terasaki, Adish Dani

“…The AOS comprising the peripheral sensory vomeronasal organ has evolved elaborate molecular and cellular mechanisms to detect chemo signals. To gain insight into the cell types, developmental gene expression patterns, and functional differences amongst neurons, we performed single-cell transcriptomics of the mouse vomeronasal sensory epithelium. …”
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Assembly and comparative analysis of the complete mitochondrial of Spodiopogon sagittifolius, an endemic and protective species from Yunnan, China by Chao Xu, Wei Bi, Ren-yi Ma, Pin-rong Li, Feng Liu, Zhen-wen Liu

“…Abstract Background Spodiopogon sagittifolius, a C4 plant closely related to cultivated crops, is an edible resource and a Class II nationally protected species in China. …”
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Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons by Irika R. Sinha, Parker S. Sandal, Holly Spence, Grace D. Burns, Aswathy Peethambaran Mallika, Fatemeh Abbasinejad, Katherine E. Irwin, Anna Lourdes F. Cruz, Vania Wang, Shaelyn R. Marx, Josué Llamas Rodríguez, Ben Langmead, Jenna M. Gregory, Philip C. Wong, Jonathan P. Ling

“…We previously found that TDP-43 loss-of-function leads to transcriptome-wide inclusion of deleterious cryptic exons, a signature detected in presymptomatic biofluids and postmortem ALS-FTD brain tissue, but the upstream mechanisms that lead to TDP-43 dysregulation remain unclear. …”
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Effect of PM2.5 exposure on susceptibility to allergic asthma in elderly rats treated with allergens by Lianlian Zhao, Xiaolin Ding, Li Zhou, Chenchen Song, Taisheng Kang, Yanfeng Xu, Yunpeng Liu, Yunlin Han, Wenjie Zhao, Boxiang Zhang, Dan Xu, Jianguo Guo

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Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes. by Dave T Gerrard, Claudia Fricke, Dominic A Edward, Dylan R Edwards, Tracey Chapman

“…However, the subtle nature of those effects suggests substantial functional redundancy or parallelism in this gene network, which could buffer females against excessive responses. …”
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Incorporating Non-Coding Annotations into Rare Variant Analysis. by Tom G Richardson, Colin Campbell, Nicholas J Timpson, Tom R Gaunt

“…<h4>Methods & results</h4>We conducted a candidate gene analysis using the UK10K sequence and lipids data, filtering according to functional annotations using the resource CADD (Combined Annotation-Dependent Depletion) and contrasting results with 'nonsynonymous' and 'loss of function' consequence analyses. …”
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Joint analysis of single-cell RNA sequencing and bulk transcriptome reveals the heterogeneity of the urea cycle of astrocytes in glioblastoma by Minfeng Tong, Qi Tu, Lude Wang, Huahui Chen, Xing Wan, Zhijian Xu

“…GB-mRNA expression data, clinical data, and SNV mutation data were sourced from the Cancer Genome Atlas (TCGA). GB-mRNA expression data and clinical data were downloaded from the Chinese Glioma Genome Atlas (CGGA). …”
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From ancient practices to contemporary green building: Analyzing organic additives in Pitalkhora earthen plasters for sustainable construction by Bhushan Dighe, Manager Rajdeo Singh

“…The findings underscore the resource-efficient approach of early builders in material selection. …”
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Near telomere-to-telomere genome assembly of the blackspot tuskfish (Choerodon schoenleinii) by Zhongdian Dong, Jiahao Gao, Yanfei Zhao, Jin Gao, Yusong Guo, Zhongduo Wang, Ning Zhang

“…Notably, telomeres were identified at both ends of 23 chromosomes, with 14 being completely gapless and only 12 gaps detected across the remaining nine. A total of 24,524 protein-coding genes were annotated, with 96.25% assigned functional annotations. …”
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The cardiac phospho-proteome during pressure overload in mice by Rhys Wardman, Steve Grein, Jennifer Schwartz, Frank Stein, Joerg Heineke

“…Our analysis highlights significant changes in hypertrophic signalling, metabolic remodelling, contractile function, and the stress response pathways. We present proteomic data from the main cardiac cell types (endothelial cells, fibroblasts and cardiomyocytes) to reveal the cellular localisation of the detected phospho-proteins, offering insights into temporal and site-specific phosphorylation events, facilitating the potential discovery of novel therapeutic targets and biomarkers. …”
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