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cs.AI, q-bio.NC updates on arXiv.org
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Language Ranker: A Lightweight Ranking framework for LLM Decoding
arXiv:2510.21883v1 Announce Type: cross Abstract: Conventional research on large language models (LLMs) has primarily focused on refining output distributions, while paying less attention to the decoding process that transforms these distributions into final responses. Recent advances, such as scaling the computation of inference time with reward models, have underscored the importance of decoding, but these methods often suffer from high computational costs and limited applicability. In this p
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
Nat Commun. 2025 Oct 17;16(1):9232. doi: 10.1038/s41467-025-64292-3.ABSTRACTRecent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. Here, we generate serial tissue sections from colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer samples for systematic evaluation. Using these uniformly processed samples, we generate spatial transcriptomics data across four high-throu
Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
Nat Commun. 2025 Oct 17;16(1):9232. doi: 10.1038/s41467-025-64292-3.
ABSTRACT
Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. Here, we generate serial tissue sections from colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer samples for systematic evaluation. Using these uniformly processed samples, we generate spatial transcriptomics data across four high-throughput platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, CosMx 6K, and Xenium 5K. To establish ground truth datasets, we profile proteins on tissue sections adjacent to all platforms using CODEX and perform single-cell RNA sequencing on the same samples. Leveraging manual nuclear segmentation and detailed annotations, we systematically assess each platform's performance across capture sensitivity, specificity, diffusion control, cell segmentation, cell annotation, spatial clustering, and concordance with adjacent CODEX. The uniformly generated and processed multi-omics dataset could advance computational method development and biological discoveries. The dataset is accessible via SPATCH, a user-friendly web server for visualization and download.
PMID:41107232 | PMC:PMC12534522 | DOI:10.1038/s41467-025-64292-3
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(Multiomics OR Omics) AND (Pancreatic)
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Tumor-derived exosomal CCT6A serves as a matchmaker introducing chemokines to tumor-associated macrophages in pancreatic ductal adenocarcinoma
Cell Death Dis. 2025 May 15;16(1):382. doi: 10.1038/s41419-025-07720-y.ABSTRACTM2-polarized tumor-associated macrophages (TAMs) are a key factor contributing to the poor prognosis of pancreatic ductal adenocarcinoma (PDAC). While various factors within the tumor microenvironment (TME) drive their formation, the role of PDAC-derived exosomes in this process remains unclear. We aim to clarify the regulatory impacts of tumor-derived exosomes to TAMs. After the intratumoral injection to subcutaneous
Tumor-derived exosomal CCT6A serves as a matchmaker introducing chemokines to tumor-associated macrophages in pancreatic ductal adenocarcinoma
Cell Death Dis. 2025 May 15;16(1):382. doi: 10.1038/s41419-025-07720-y.
ABSTRACT
M2-polarized tumor-associated macrophages (TAMs) are a key factor contributing to the poor prognosis of pancreatic ductal adenocarcinoma (PDAC). While various factors within the tumor microenvironment (TME) drive their formation, the role of PDAC-derived exosomes in this process remains unclear. We aim to clarify the regulatory impacts of tumor-derived exosomes to TAMs. After the intratumoral injection to subcutaneous tumor of C57BL/6 mice, we demonstrated PDAC-derived exosomes exacerbate PDAC progression, accompanied with upregulated M2 phenotype of TAMs and unaffected proliferation signatures. Through intratumoral injection model and multi-Omics analyses, we identified CCT6A as a novel tumor-derived exosomal protein, bridging TAMs M2 polarization and PDAC prognosis. Co-culture with exosomes derived from CCT6Ahigh PDAC leads to greater M2 phenotype of TAMs via PI3K-AKT signaling. According to proteomics data, chemokines' abundance reduces over tenfold once exosomal CCT6A absence, including CXCL1, CXCL3, CCL20 and CCL5, whose interaction with CCT6A in PDAC cells was confirmed by interactomics data. Moreover, we found silencing CCT6A abrogated the antagonism effects of CD47 antibody immunotherapy. Our findings implied that the subunit of the T-complex protein Ring Complex (TRiC) CCT6A serves as a matchmaker during exosome-mediated chemokines transfer from PDAC to TAMs. Silencing CCT6A effectively sensitized PDAC to CD47 antibody immunotherapy in vivo.
PMID:40374617 | PMC:PMC12081750 | DOI:10.1038/s41419-025-07720-y
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Nature Biotechnology - Issue - nature.com science feeds
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Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 13 July 2023; doi:10.1038/s41587-023-01884-8Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 13 July 2023; doi:10.1038/s41587-023-01884-8
Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination-
Nature Biotechnology - Issue - nature.com science feeds
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An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 25 May 2023; doi:10.1038/s41587-023-01796-7A cancer vaccine is delivered to the lung by an engineered attenuated influenza virus.
An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 25 May 2023; doi:10.1038/s41587-023-01796-7
A cancer vaccine is delivered to the lung by an engineered attenuated influenza virus.